MCAT Review

Biology

Molecular Biology

y

Phospholipids o Membranes

y

Triglycerols o Store metabolic energy o Padding and insulation

y

Steroids o Regulate metabolic activity o Hormones

y y

Lipoproteins o Transport lipids Carbohydrates o 5 and 6 carbon are most common      Pentoses and Hexoses

o Glucose Six carbon, Alpha linkage y y y Nucleotides o Contain:       A five-carbon sugar A nitrogenous base A phosphate group Only animals eat

Beta linkage Bacteria eat

Double bonded carbon to oxygen connects to ±OH of carbon 5

o Most common: Adenine Guanine Cytosine

  y Enzymes

Thymine Uracil

o Typically globular proteins o Act as catalysts       y Usually end in ±ase Contains N Subject to denaturation

o Cofactor Non-protein component Either Coenzyme (vitamins) Or metal ions (minerals)

Enzyme inhibition o Irreversible inhibitors     Bind covalently to enzymes and disrupt their function

o Competitive inhibitors Compete with substrate and bind reversibly

o Non-competitive inhibitors AKA allosteric inhibitors Bind to sport other than active site and change the conformation of the enzyme. y Anabolic o Build up o Requires energy y Catabolic o Breakdown o Gives off energy y 3 Basic stages of Metabolism o Macromolecules broken down   Polysaccharides, proteins, and lipids Releases little energy

o Parts are oxidized to acetyl CoA and Pyruvate     y Glycolysis o First stage of respiration (both in anaerobic and aerobic)      Occurs in the cytosol 6-carbon glucose converted into pyruvate 2 ATP spent and 4 remain Reduces NAD+ to NADH 2 stages: y y Fermentation o Anaerobic o Starts with glycolysis then oxidizes NADH to NAD+   y Yeast produce methanol Humans make lactic acid 6-carbon and 3-carbon Some ATP produced NADH formed

o Oxygen present Citric acid cycle y Produces large amounts of ATP

Otherwise NAD+ is recycled

Aerobic respiration o Pyruvate and NADH move into mitochondria  Acetyl CoA is the enzyme that transfers 2 carbons from pyruvate to ³oxo-acid´ in order to begin the Krebs cycle.

y

Krebs Cycle o Forms 1 ATP, 3 NADH, and 1 FADH2 o Carbon dioxide is lost o ³oxo-acid´ is reproduced

y y

Substrate level phosphorylation o ATP produced in glycolysis and Krebs Oxidative phosphorylation

o ATP created with Electron transport chain y Overall: o 36 ATP¶s produced o 1 NADH= 2-3 ATPs o 1 FADH2 = 2 ATPs

Genes

y y

DNA RNA Proteins DNA o Phosphodiester bonds o Sugar phosphate backbones o 3¶ to 5¶ directionality o Double stranded o Produced by replication o Starts at the primer

y

Purines o Adenine o Guanine

y

Pyrimides o Thymine o Cytosine o Uracil

y

Bonding o Adenine bonds to Thymine and Uracil which has 2 Hydrogen bonds o Guanine bonds to Cytosol which has 3 Hydrogen bonds

y

DNA replication o Semiconservative because there is one parent strand and 1 new strand o Bidirectional process

y

DNA Polymerase o Builds DNA strands o Requires RNA primer to start o Reads upstream (3¶-5¶) o Creates downstream (5¶-3¶)

y y

Leading strand o Continuous Lagging strand

o Interupted and restarted with primer o Made from Okazaki fragments o DNA ligase connects the fragments y RNA o Single stranded o Contains Uracil instead of Thymine o Can move through nuclear pores o Ribose o Produced by transcription o Starts at its promoter y mRNA o ³messenger´ o Takes DNA code to cytosol to produce proteins y rRNA o ³ribosomal´ o Combines with proteins to form ribosomes o Made in the nucleus y tRNA o ³Transfer´ o Takes amino acids in cytosol to ribosomes to form proteins y Transcription o Creation of RNA o Takes place only in the nucleus and mitochondria o Stages:  Initiation y y  y y Requires promoter (spot on DNA that tells DNA polymerase where to begin) For RNA- RNA polymerase binds to promoter

Elongation One strand of DNA transcribed Called template strand



Termination y Uses termination sequence

o mRNA first primary transcript is processed in 3 ways:      y Translation o 5¶-3¶ o mRNA comes from nucleus (codons) o tRNA carries anticodon o rRNA + protein creates the ribosome where translation takes place. o Initiation        y y mRNA leaves nucleus 5¶ end attaches to small subunit of the ribosome Large ribosome subunit joins to form ³initiation complex´ Addition of nucleotides (Poly A tail) Deletion of nucleotides (Excision of Introns) Modification of nitrogenous bases (5¶ cap is the attachment site)

o Start codon AUG

o Stop codon UAA, UAG, UGA

o Elongation tRNA attaches at A-site Translocation occurs (shift)

o Termination Stop codon Polypeptide freed from mRNA and ribosome.

46 double stranded DNA molecules o Each chromosome has a homologous partner Cell Life Cycle o Interphase  G1: y Cell has just split

y  S: y y  o M:  G2: y

Gets bigger

Replicates DNA Now cell has sister chromatids

Prepares for division

Prophase y y Chromatin to chromosomes Centrioles move to opposite ends of the cell

  

Metaphase y y y Chromosomes line up

Anaphase Splitting

Telophase Membrane reforms

o Meiosis   Prophase I Metaphase I (tetrads split) (23 replicated chromosomes) Meiosis II occurs and 23 chromosomes are formed in haploid gametes. Anaphase I Telophase I

Microbiology

y

Viruses o Much smaller than bacteria o Contain capsid   Head made of protein 1-100¶s of DNA or RNA

o Some have a lipid rich envelope (mostly animal) o Don¶t metabolize or reproduce y y Viruses attach to specific chemical receptor o Usually glycoprotein Attachment o Landing o Attachment o Tail contraction o Penetration and injection y Lytic infection o Virus infects cells o Viruses made inside cell o Viruses leave the cell killing it o Virulent viruses y Lysogenic infection o Called a temperate virus o DNA incorporated into the cells genome o Provirus y y Retrovirus o Contains RNA Prokaryotes o No membrane-bound nucleus o No nucleus o Single and circular strand of DNA called a nucleoid

o Have DNA and RNA o No nuclear bound organelles o Have phospholipids bilayer called a plasma membrane o 2 groups  Archae y y y  y o Autotrophs       y y Capable of fixing Carbon dioxide solely Extreme environments Similar to eukaryotes No PGL

Bacteria Have PGL

o Heterotrophs use pre-formed organic molecules as source of carbon

o Phototrophs use light as energy

o Chemotrophs Organic and inorganic matter is their energy. Can perform nitrogen fixation or ³Nitrification´ N2 Ammonia

Integral Proteins o Transverse on inside and outside of cell Peripheral proteins o Entirely on surface o Bonded to integral proteins

y y

Size and polarity of a compound affect how it can cross a membrane Bacteria o plasma membrane o Cell wall (envelope)   Stops bacteria from bursting because they are hypertonic Hydrostatic pressure = osmotic pressure

o Gram Positive      Thick PGL (Purple) have endospores

o Gram Negative Thin PGL (pink) Some have fimbriae Outer membrane

o Have flagella that rotate o Cannot undergo mitosis meiosis, or reproduce sexually o Undergo genetic recombination  Conjugation y y y  y y  Bacteria has to have plasmid (small circular DNA) that contains special gene for sex pilus. F-plasmid: fertility or F-factor, F+ has it and F- doesn¶t R-plasmid: resistance

Transformation Bacteria take DNA from environment and put into their genome Example: heat killed virulent bacteria DNA can be take by harmless living bacteria and become virulent Transduction y Viruses mistake DNA for bacteria and transport it in place of their own genomes

o Binary fission  y Endospores o Gram positive o Very resistant o Inactive until heat or germination y Fungi o All are Eukaryotic heterotrophs Asexual reproduction

o Most have cell walls made of chitin o Alternate between haploid and diploid o Almost always haploid though o Spores are asexual o Sexual reproduction     Between 2 hyphae of different mycelia of different types (+ and -) Two hyphae connect and form a zygospore It leaves and goes dormant until the right conditions It will undergo meiosis to produce haploid cells (reproduce asexually) o Asexual reproduction takes place when conditions are good o Sexual reproduction takes place when conditions are bad o Fungi are Saprophytes  o Yeast  Facultative anaerobes Break down dead organisms

Eukaryotic Cell

y

Nucleus o Liquid is neoplasm o Nuclear envelope/membrane o Nuclear pores

y

Nucleolus o rRNA is transcribed and ribosomes assembled o NOT separate from the nucleus

y

Endocytosis o Phagocytosis   Engulf particles

o Pinocytosis Engulf liquid

y

Granular/ Rough ER o Near nucleus o Has many ribosomes o Makes proteins for the outside of the cell and these go into the golgi complex

y

Golgi complex o Flat, membrane sacs o Ship out proteins o Proteins either leave cell in secretory vesicles or o They are released into lysosomes

y

Secretory vesicles o Release through exocytosis o Maintain membrane

y y

Lysosomes o Can break down any molecule in cell Smooth ER

o Lack ribosomes o Tubular o Deals with glucose o Makes phospholipids for the membrane o Deals with internal environment y y Adipocytes o Cells that are mostly fat Peroxisomes o Vesicles in cytosol o Break down substances with H2O2 (peroxide) o Inactivate alcohol o Regulate O2 y Cytoskeleton o Structure and motility o Anchors membrane o Moves cell with two structures:   Microtubules y y y Flagella and cilia o Made form microtubules o Major part is the axoneme    y Cell Junctions o 3 types:  Tight junctions 9 pairs around 2 microtubules in a 9+2 formation Dyenin connects them Centrosome is at negative (-) end and it grows at the positive (+) end (outside) Rigid hollow tubes made of protein (tubulin)

Microfilaments Smaller, squeeze membrane in phagocytosis and cytokinesis (separating of cytoplasm during replication)

y y y  y y y  y y y y Mitochondria o Powerhouse

Forms water tight seal around cell Fluid barrier Found in brain (brain blood barrier)

Desmosomes Join two cells at single point at cytoskeleton Found in cell with a lot of stress, like skin or the intestines Strongest

Gap Junctions Small tunnels that connect cells Allow molecules or ions to pass Allow the atria in the heart to contract in unison.

o Only have circular DNA and have distinct RNA and ribosomes  y This supports the endosymbionic theory

o Mitochondrial DNA is passed only through mothers (maternally) Cell communication via: o Neurotransmitters        In the nervous system Fast acting and used for short distances (synapses)

o Local mediators Paracrine system Act directly in interstitial fluid to neighbor cells

o Hormones Endocrine system Long lasting Travel throughout the body

Nervous System y y y Dendrites o Receive signal Axon hillock o End of the cell body (soma) where Action Potential begins Axon o Carries action potential to synapse o Which passes to another cell by releasing neurotransmitters to the synapse o Bundle together to increase signal speed  y Neurons o Do not depend on insulin to obtain glucose o Overall cell in nervous system y Action Potential o Disturbance in electrical field across the membrane o Slightly depolarizing are called EPSP¶s o Slightly hyperpolarizing are called IPSP¶s o Steps for Action Potential     Membrane is at resting potential and only the sodium and potassium leak channels are open. Sodium ion voltage-gated channels open and the cell depolarizes Potassium ion voltage-gated channels open and cell starts to repolarize Potassium ion voltage-gated channels close and the membrane goes back to equilibrium. o Stimulus must be greater than threshold stimulus to depolarize the cell (-50mV) y Resting Potential o Measured at -70mV o Established equilibrium using Na+/K+ pump Called Tracts in Central Nervous System and Nerves in Peripheral Nervous System

 y

Sodium potassium pump that actively pumps 3 Sodium ions out and takes 2 Potassium ions in

Voltage gated channels o Can be either Potassium or Sodium o Voltage-gated sodium channels     Integral membrane proteins Protein changes conformation and lets sodium ions inside the cells Positive feedback occurs and all adjacent voltage-gated channels start to change. Absolute Refractory period occurs when these channels are inactivated, so no stimulus can cause them to open o Voltage-gated Potassium channels   Take longer to open By this time potassium ions flow out of the cell to repolarize the cell.

y

Depolarization o When voltage-gated sodium channels open o Membrane potential switches to positive inside the cell

y

Hyperpolarization o Potassium channels are slow moving so the inside of the cell becomes too negative.

y

Electrical synapses o Uncommon o Composed of gap junction o Fast o Goes in 2 directions

y

Chemical Synapses o Unidirectional (refractory periods) o Neurotransmitters in presynaptic membrane o Calcium ion voltage-gated channels open and calcium ions bind to vesicles to release the neurotransmitters into the synaptic cleft

o Neurotransmitters diffuse by Brownian Motion o Postsynaptic terminal has neurotransmitter receptors, which are ligand gated channels o Membrane becomes more permeable to ions o Neurotransmitter only in receptor for fraction of a second, then it goes back into the cleft for degradation or reuptake. y Second Messenger System o Neurotransmitters activate other process in cell y Myelin o Is produced by Schwann Cells o White matter o Allows the action potential to move down the axon via saltatory conduction by having the action potential jump from Node of Ranvier to Node of Ranvier. y Neuron Functions o Sensory neurons         y o CNS o Brain and Spinal Cord o Lower Brain:  Medulla Afferent Links environment to receptor Enters the spinal cord via the Dorsal root (back)

o Interneurons Connect neuron to neuron Usually in the central nervous system

o Motor Neurons Efferent Signals to muscle or gland Leaves the spinal cord via the Ventral root (front)

Central Nervous System

     y o PNS

Hypothalamus Thalamus Cerebellum

o Higher Brain Cerebrum Cerebral Cortex

Peripheral Nervous System

o Everything besides the brain and spinal cord o Two divisions:  Somatic Nervous System y y  y Respond to external environment Voluntary control

Autonomic Nervous System Sympathetic and parasympathetic nervous system o Parasympathetic releases Acetylcholine on target cell  Secondary messenger system

o Sympathetic releases Epinephrine/ Norepinephrine on target cell.

Eye

y

Background o Light first hits at the cornea, then it hits the lens (which is a converging lens)

y

Ciliary Muscle o Used for focusing o Surrounds Lens o Flattening is relaxing and this increases the focal point

y

Retina o Inside o Has rods and cones o Rods detect black and white o Cones detect color

y

Iris o Color of the eye

Ear

y

Structure o Outer ear o Middle Ear  Has 3 bones: y y y  y o Inner Ear     Cochlea Detects Sound Movement detected by hair cells of the organ of Corti Semicircular Canals y Responsible for balance Malleus Incas Stapes

Tympanic membrane Eardrum

Terms y y Sense of Smell o Olfactory Sense of Taste o Gustatory

Endocrine System

y

Hormones exist as: o Peptides o Steroids o Amines known as Tyrosine derivatives

y

Peptide Hormones o Bind to receptors on the cell o Includes:  FSH, LH, ACTH, hGH, TSH, Prolactin, ADH, Oxytocin, PTH, Glucagon, and Insulin

y

Steroid Hormones o Released from the adrenal cortex, gonads, and the placenta o Includes:  Cortisol, Aldosterone, estrogen, progesterone, testosterone

y

Tyrosine Derivatives o Released from the adrenal medulla o Includes:  T3, T4, epinephrine, norepinephrine, Dopamine.

y y

Negative Feedback in Endocrine Glands: o Control point is the conduct of the effector, not the concentration Anterior Pituitary o Governed by the Hypothalamus o Releases Tropic Hormones, which stimulate other hormones    FSH y LH y ACTH y Peptide, stimulates adrenal cortex to release glucocorticoids (stress hormones) Peptide, Lutenizing Hormone Peptide, Follicle stimulating hormone



TSH y Peptide, stimulates thyroid to release T3 and T4

o Releases Non-tropic hormones:    Prolactin y hGH y y y Posterior Pituitary o Release hormones, don¶t actually make them.  Oxytocin y  ADH y y Adrenal Glands o Located on top of the kidneys o Made of two components  Adrenal Cortex y y Outside portion Secretes two types of steroids o Mineralcorticoids      Adrenal Medulla y Inside portion Affect electrolyte balance Aldosterone Peptide, makes kidneys permeable to water and retain water in the body. Peptide, increases uterine contractions during pregnancy and ejects milk Peptide, stimulates growth Peptide, stimulates lactation

Endorphins Block pain

o Glucocorticoids Increase blood glucose levels Cortisol

y

Produces Catecholamines, which are Tyrosine derivatives o Epinephrine and norepinephrine, which constrict the blood vessels.

y

Steroids o Aldosterone    Increases blood pressure In kidney: Sodium reabsorption and Potassium secretion

o Cortisol Increase glucose levels

y

Tyrosine Derivatives o Epinephrine and norepinephrine    Made in adrenal medulla

o T3 and T4 Lipid soluble Made in the Thyroid

y

Other Hormones o Calcitonin    o Insulin      Peptide, released when carbohydrate and protein levels are high Lowers blood glucose levels by promoting storage (glycogen) Made in Pancreas Large peptide Decreases blood calcium Made in the Thyroid

o Glucagon Peptide, raises blood glucose levels. Made in Pancreas

y

Blood Glucose o Cortisol  o Insulin Increases blood glucose levels

  y Thyroid

Decreases Blood glucose levels

o Glucagon Increases blood glucose levels

o Calcitonin   y Parathyroid o PTH     Increases blood calcium Breaks down bones Released by four small gland in the Parathyroid Peptide Decreases blood calcium Builds bones

Reproduction y Male o Seminiferous Tubules   o Semen  y Female o FSH at puberty starts forming Zona Pellucida, which is the viscous substance around eggs. o LH cause a secretion of estradiol o Just before ovulation      Estradiol rises Spike in LH called the luteal surge Egg goes into fallopian tube. Composed of fluid from seminal vesicles, prostate, and bulbourethral glands Produce sperm in the testes and is stored in the epididymus Sperm then travels to the vas deferens and then to the Urethra.

o Menstrual cycle phases Follicular phase y y  Flow y y o Ovulation      FSH stimulates follicle to mature Follicle secretes estrogen LH spike stimulates ovulation Estrogen and progesterone rise and inhibit LH Estrogen and progesterone levels fall of if the egg isn¶t fertilized. Shedding of uterine lining Takes 5 days Development of follicle

Luteal phase Begins with ovulation and ends with degeneration of corpus luteum

Fertilization and Embryology

y

Fertilization o Occurs in the fallopian tubes o Sperms enters, then oocyte undergoes meiosis, then fertilization

y y y

Cleavage occurs while the fertilized egg is still in fallopian tubes o 32 cells as a morula, then it turns into a blastocyst Blastocyst goes in uterus o Implantation Egg secretes hcG o Maintains the corpus luteum, which maintains estrogen and progesterone secretion

y y y

Determination o Cell early on are pre-determined to form tissues Differentiation o End of development of specialized tissue Gastrulation o Takes two weeks o Cells move about embryo to form shape o Three primary germ layers formed:  Ectoderm y y   y y y Out covering Skin, nails, nose, mouth, eyes, nervous system

Endoderm Digestive tract, liver, and respiratory

Mesoderm Stuff in between Muscle, bone, notochord, kidneys

y

Neurulation o Happens in the 3rd week o Notochord induces ectoderm to thicken

o Occurs when differentiation happens y Apoptosis o Programmed cell death of the embryo.

Digestion

y

Path o Mouth Esophagus anus Stomach small intestine large intestine rectum

y y

Digestion¶s major reaction o Hydrolysis Mouth o Alpha-amylase is contained in saliva o Peristaltic action, which is food moved down esophagus

y

Stomach o Both mixes and stores o Reduces food to semi-fluid mass called chyme o 4 major types of cells     Mucous Cells y y y G-cells y Secrete gastrin, which stimulates parietal cells to secrete HCl. Secrete Mucous

Chief (peptic) cells Secrete pepsinogen, which digests proteins

Parietal (oxyntic) cells Secrete HCl

y

Small Intestine o 90% of digestion takes place here o Wall same as stomach except has villi, which help absorb more nutrients   Lymph vessel, called a lacteal, and capillary network are in each villus Microvilli on surface of each villus, ³brush border´ contains enzymes o Goblet cells

 y Pancreas

Secrete mucus to lubricate intestine.

o Food moves through as chyme by peristalsis

o Major Enzymes released    All as zymogens Trypsin and Chymotrypsin y y  Lipase y y Liver Functions o Blood storage    Liver can expand to create a blood reservoir Degrades fat (triglycerides) Degrade proteins to polypeptides

Pancreatic Amylase Hydrolyzes polysaccharides to disaccharides (carbohydrates)

o Blood Filtration Phagocytize bacteria from intestines

o Fat Metabolism Synthesizes Bile y y y    Converts Carbohydrates and proteins to fat Adds to lipase to decrease surface area of fat because it clumps together. Stored in the gall bladder.

o Carbohydrate Metabolism Maintains normal blood glucose level through glucogenesis

o Protein Metabolism Forms urea from amino acids and ammonia When liver metabolizes fat and protein for energy the blood pH drops o Detoxification  Chemicals excreted by liver

o Erythrocyte destruction   Dying red blood cells

o Vitamin Storage A,D, and Iron

Excretory

y

Functions o Excrete waste products, o Maintain homeostasis (fluid and pH)

y

Composed of: o The out cortex o Inner Medulla

y

Path o Emptied into the renal pelvis o Then through ureter and o Then into the bladder

y

Nephron o Blood into first capillary bed called glomerulus o Bowman¶s capsule + Glomerulus = Renal Corpuscle           Non-selective Filtration. Amount of filtrate is related to hydrostatic pressure of glomerulus.

o Fenestrations Screen out blood cells and large proteins from entering Bowman¶s capsule Primary Filtrate

o Proximal Tubule Where filtrate goes Reabsorption occurs here for proteins, glucose, etc. Toxins are secreted here

o Loop of Henle Increase solute concentration and/or osmotic pressure of medulla. Descending loop is permeable to water Ascending loop is permeable to Sodium ions

o Distal Tubule

       o Renin 

Reabsorbs Sodium ions and Calcium ions while secreting potassium, hydrogen, and bicarbonate ions. Lowers filtrate osmolarity Empties into the Collecting Duct

o Collecting Duct Carries filtrate to highly osmotic medulla Concentrates Urine

o Juxtaglomerular Monitors filtrate pressure in distal tubule Secretes Renin

Stimulates adrenal cortex to release aldosterone, which acts on the distal tubule to absorb Sodium ions and water, while secreting Potassium ions.



Increases reabsorption of water/Na+

Cardiovascular System

y

Components o Heart, Blood, Blood vessels

y

Blood travels through the heart o Systemic Circuit            Left ventricle Aorta To arteries, to arterioles, than to capillaries Capillaries to venules, to veins Blood returns to the heart via the Superior and Inferior Vena Cava. Right atrium Right ventricle

o Pulmonary Circuit Blood sent to the lungs by pulmonary artery Sent back by the pulmonary veins Into Left atrium Into left ventricle.

y y y

Systole o Ventricular contraction Diastole o Ventricular relaxation, then contraction of Atria SA node o In right atrium o Specialized cells that keep the hearts ³pace´

y

Vagus Nerve o Parasympathetic o Slows Contractions

y

AV node o Slower to contract than the SA node. o Allows blood to enter ventricle before it contracts

y

Blood Pressure o Very high at Aorta and large arteries o Low at capillaries, veins, and the pulmonary circuit.

Respiratory System

y

Components o Diaphragm        o Larynx        Voicebox Sits behind the epiglottis Relaxed= Dome shaped Contracted= flat

o Nasal Cavity Filters, moistens, and warms air Hair traps large particles Mucus traps small particles

o Pharynx Passageway for food and air Throat

o Epiglottis Prevents food from entering the trachea

o Trachea Lies in front of esophagus Splits into Right and Light Bronchi

o Bronchi Branch into Bronchioles This goes to the lungs, which contain alveoli

y

Air o 79% Nitrogen and 21% Oxygen   This is inhaled

o 79% Nitrogen, 16% oxygen, 5% Carbon Dioxide This is exhaled

y

Oxygen

o In blood, 98% of it combines with a protein called hemoglobin, which contains iron   Each hemoglobin contains 4 iron molecules Each iron molecule attaches to an Oxygen

o When oxygen Pressure increases the hemoglobin has oxygen saturation o When there is an increase in Carbon Dioxide, Hydrogen ions, or temperature, there is a decrease in Oxygen saturation y Carbon Dioxide o In blood, it is acidic, so bicarbonate acts as a buffer to maintain blood pH.  H2CO3 H+ + HCO3-

Lymphatic System

y

Background o Open System  blood. Enters at one end and leaves at the other.

o Collects excess interstitial fluid and particles and returns them to the

y

Blood o Connective tissue o Contains cells and a matrix o Composed of:  Plasma y y Matrix, water, ions, proteins. Important proteins are albumin, which transport fatty acids and steroids. The other protein is immunoglobulins, which are antibodies.   Buffy Coat Red Blood Cells y y y  y y Erythrocytes Bags of Hemoglobin No nucleus

Granulocytes General white blood cells that live for short periods of time. Neutrophil, basophils. etc.

y

2 Types of Acquired Immunity: o Humoral Immunity     B-cell B-lymphocytes produce specific antibodies that attack a antigen With helper T-cell activation, they begin to produce antibodies.

o Cell Mediated Immunity T-Cell

   y Blood Type

T-cells reside and mature in the thymus Cytotoxic T-cells destroy invaders Non-destroying T-cells differentiate into helper, memory, and suppressor T-cells.

o Codominant genes.

Muscle

y

3 Types of Muscle o Skeletal, Smooth, and Cardiac

y

4 Functions of Muscles o Movement o Stabilization of body position o Movement of substances through body o Generating heat

y

Skeletal Muscle o Voluntary muscle o Can be controlled o Striated o Attaches to Tendon, which is a muscle to bone connection o Multinucleated. o may aid in circulation of blood and lymph o Contraction produces large amounts of heat o Agonist contracts and Antagonist stretches

y y

Synergistic Muscles o Stabilize origin of bone. Sarcomere o Thick filament   Myosin

o Thin Filament Actin

o H and I bands get smaller with contraction o A band doesn¶t get smaller. y Action Potential o Moves through T-tubules, which allows for uniform contraction o Transferred to Sarcoplasmic reticulum, which contains many Calcium ions, and the Action potential makes the SR permeable to Calcium ions.

y y

Myoglobin o Oxygen storing protein found in muscles Skeletal Muscle Contraction: o Tropomyosin covers active site on actin, which prevents myosin head from binding  Myosin head is in high energy position, because it hydrolyzed an ATP molecule into a phosphate and ADP. o Calcium ions attach to troponin molecules, which cause the tropomyosin to move off of actin¶s active sites.        Myosin head then bind to actin

o Myosin head expels its phosphate and ADP Binds into low energy position Drags actin with it, which is the muscle contraction.

o ATP binds to myosin head Releases myosin head from the active site Active site of actin is then covered by tropomyosin immediately

o ATP is hydrolyzed into a phosphate and ADP Myosin is an ATPase, This process causes myosin head to cock back into high energy position. y Cardiac Muscle o Striated, meaning it has sarcomeres o Only one nucleus o Separated by neighbors via gap junctions called intercalated discs o Involuntary y Smooth Muscle o Mainly involuntary, meaning its controlled by the autonomic nervous system o One Nucleus o No sarcomeres o Contain intermediate filaments that attach to dense bodies

Bones

y

Function o Support, protection, movement, mineral storage, blood cell production, and energy

y

Contains o Osteoblasts      Secrete collagen to form bone layer Doesn¶t undergo mitosis

o Osteocytes Exchange nutrients and waste with blood Doesn¶t undergo mitosis

o Osteoclasts Resorb bone matrix and release nutrients into the blood.

y

Spongy Bone o Red bone marrow o Red blood cells develop here

y

Compact bone o Made of Haversian Canals o Yellow bone marrow, which are adipose cells for fat storage.

y y

Cartilage o Flexible connective tissue, composed of collagen Facts o Calcium is stored in the bone matrix as hydroxyapatite o Bone acts as storage site for Calcium ions and HPO4-2

Skin

y

Functions o Thermoregulate o Protection o Environmental sensory input o Excretion o Immunity o Blood reservoir o Vitamin D synthesis

y

Epidermis o Composed of 5 layers made of epithelial tissue o Top most layer of skin o No blood vessels

y

Dermis o Contains blood vessels, nerves, glands, hair follicles o Made of mesodermal cells.

Population

y

Phenotype o Expression of Traits

y y

Genotype o Genetic Make-up Law of Independent Assortment o Genes on different chromosomes are independent of each other o Genes on the same chromosome are more likely to pair if they are located closely.

y y

Dihybrid Cross o Gives a 9:3:3:1 genotype ratio Sex chromosomes o 23rd chromosome o Genes on here ate sex linked

y y y

Make up o Kingdom, phylum, class, order, family, genus, species Domains o Bacteria, Archae, Eukarya Species o Usually organisms within the same species can reproduce and form fertile offspring

y

R-selection o Reproducing in large numbers with little or no parenting o Exponential population growth o Found in rapidly changing environments

y

K-selection o Small, slow maturing offspring with strong parental care o Sigmoidal growth curve o Levels off at carrying capacity

y

Speciation

o Process by which new species are formed y Adaptive radiation o Several species arise from single ancestral species  y y Example is finches

Divergent Evolution o One species split into two species over time. Convergent Evolution o Have similar features, but evolved separately  Example is bats and birds

y y

Polymorphism o Distinct form, like flower colors Hardy-Weinberg Equilibrium o There is no change in the gene pool if there is:      Large population Mutational Equilibrium Immigration and Emigration must not change gene pool y Migration

Random Mating No selection for the fittest organism

y

Genetic drift o One allele permanently lost due to death of all members processing it o Allele fixation, and occurs most commonly in small population with no gene flow.

y

Cells o First layers evolved from coavervates  Lipid or protein bilayer bubbles

y

Chordata o Bilateral symmetry o Deuterstomes   Anus develops from blastopore Humans

o Chordate characteristics    y y Vertebrata o Notochord replaced by segmented cartilage and bone structure Humans o Kingdon, phylum, class, order, family, genus, species. o Eukarya, Animalia, Chordata, Vertebrata, Mammalia, Primata, Homididae, Homo, Sapiens Coelom is the body cavity Possess notochord for axial support Pharyngeal slits, dorsal nerve cord, and tail

Physics

Units and Kinematics

y

There are only two kinds of numbers: Scalars and vectors. Scalars have magnitude only and include distance, speed, mass, pressure, energy, and work. Vectors have magnitude and direction and include displacement, velocity acceleration, force and electric and magnetic fields. Vector addition or subtraction is usually best accomplished by resolving the vectors into their x and y components first.

y

Average velocity is calculated as the total displacement divided by total time. Average speed is calculated as the total distance divided by total time. The magnitude of the average velocity may be equal to or less than average speed, but it can never be greater. Instantaneous speed is always equal to the magnitude of the instantaneous velocity.

y

Deceleration is nothing other than acceleration in the direction opposite of that of the initial velocity. Such negative accelerations will cause objects to slow down and possibly even stop and reverse direction.

y y

Constant acceleration implies a constant force. Objects in free fall experience acceleration equal to that of gravity (9.8m/s), discounting air resistance. Objects that achieve terminal velocity experience a net force equal to 0 and have an acceleration of 0 because the upward air resistance force exactly balances the downward force of gravity.

y

Projectile motion is motion in two directions. To solve projectile motion problems, you must resolve the initial velocity into its x and y components. For projectile motion involving gravity, only the y-component (vertical) velocity vector will change at the rate of g, the x component (horizontal) velocity vector is constant discounting the force of air resistance.

Newtonian Mechanics

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Newtonian mechanics is all about the relationships among objects, forces, accelerations, and energies. Newton¶s three laws express the fundamental relationships among force, mass, and acceleration. The first law is actually a special case of the second law in which the object experiences a net force equal to 0 and therefore doesn¶t accelerate.

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Newton¶s third law does not require objects to be in direct physical contact. Many equal and opposite forces can be exerted between objects that are separated by even great distances. Gravitational and electrostatic forces are two types that can exist over large distances of separation. Normal force is a special kind of reactive force between objects that are in direct physical contact.

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Always draw a free-body diagram when working through problems of Newtonian mechanics. Be especially mindful to practice drawing free-body diagrams of objects on inclined planes. In order to resolve the forces into their x and y components you must know the trigonometric functions of sine and cosine for the classic right triangles.

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The magnitude of gravitational force between two objects is inversely proportional to the square of the distance separating their respective centers of gravity. This equation is in the same form as the electrostatic force equation, but the force due to mass s much smaller than the force due to charge.

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³Little g´ is an approximation of the acceleration due to gravity on an object close to the surface of the earth. Although g is given as a constant, 9.8 m/s, in reality the true acceleration due to gravity depends on r, and can be determined with the gravitational force equation.

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There are three types of motion being tested: translational, rotational, and circular. Translational and circular motion are caused by forces that cause objects to move without rotating; rotational motion is caused by forces applied perpendicularly to a fulcrum, generating torque, causing rotations around the fulcrum.

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In uniform circular motion, the centripetal force vector and the centripetal acceleration vector point directly to the center of the circular pathway. The

instantaneous velocity vector is tangential to the circular pathway at any given point. y All friction forces act in the direction opposite or opposing intended or actual motion. The forces of air resistance, static friction, and kinetic friction are commonly encountered on the test. For an object in contact with a surface, the maximum value of static friction will always be greater than the constant value of kinetic friction. y Translational equilibrium occurs when the vector sum of forces acting on an object is equal to 0. There is no net acceleration and the Object continues in a constant motional behavior. Translational equilibrium does not require that an object be stationary, only that its motional behavior (stationary or moving) be constant. y Rotational equilibrium occurs when the vector sum of torques acting on an object is equal to 0. There is no net rotational acceleration and the object continues in a constant motional behavior. As with translational equilibrium, there is no requirement that the object be stationary, only that its motional behavior (stationary or rotating) be constant.

Work, Energy, and Momentum

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Energy is a property of characteristic of a system to do something or make something happen including the capacity to do work.

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Kinetic energy is energy of motion. Potential energy is energy stored within a system and exists in forms such as gravitational, electric and mechanical. In the absence of friction forces, total mechanical energy of a system will be conserved. That is to say, the sum of a system¶s potential energy and kinetic energy will be constant.

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Work is a process by which energy is transferred from one system to another. It involves the application of force through a displacement (or distance). The rate at which work is done, or energy is transferred, is the power loss (or gain) of the system.

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The work-energy theorem states that when net work is done on or by a system, the system¶s kinetic energy will change by the same amount When net work is done on a system, the system¶s kinetic energy will increase; when net work is done by a system, the system¶s kinetic energy will decrease.

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Momentum is a quality of objects in motion and is the product of mass and velocity. Inertia is the tendency of an object to resist changes in its motion. Impulse is a change in momentum achieved by the application of force through some period of time.

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There are three types of collision for which the systems total momentum is conserved: completely elastic, inelastic, and completely inelastic collisions. Only in a completely elastic collision is the system¶s total kinetic energy also conserved. In the inelastic collisions, kinetic energy is transformed into another form such as heat, light, or sound.

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Simple Machines such as inclined planes, levers, and pulleys provide the benefit of mechanical advantage, which is the factor by which the machine multiplies the input force or torque. Mechanical advantage makes it easier to accomplish a given amount of work since the input force necessary to accomplish the work is

reduced. The distance through which the reduced input force must be applied, however, is increased by the same factor. y For all machines that provide mechanical advantage, input work = out put work, discounting energy lost due to friction. If the work of friction is accounted for, then the ratio of output work to input work is a measure of the machines efficiency. y The center of mass is the point within a two or three-dimensional object at which all the object¶s mass could be represented as a single particle. The center of mass and the center of gravity are the same point within an object.

Thermodynamics

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There are four numbered laws of thermodynamics: zeroth, first, second, and third. These laws are principles that describe the nature and behavior of energy and its relationship to heat, work, and temperature.

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The zeroth law of thermodynamics states that objects are in thermal equilibrium when they are at the same temperature. Objects in thermal equilibrium experience no net exchange of heat energy. Temperature and heat are not the same thing. Temperature is a qualitative measure of how hot or cold an object is; quantitatively, it is related to the average kinetic (motional) energy of the particles that make up a substance. Heat is a quantity of energy that is transferred from a hot object to a cold one.

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All materials have certain physical properties that change as a result of a change in temperature. Some of these temperature dependent properties include length, volume, and conductivity. Thermal expansion is the change in length or volume as a function of the change in temperature.

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The first law of thermodynamics is a statement of energy conservation: the total energy in the universe can never decrease or increase. For a closed system the total internal energy is equal to the heat into or out of the system minus the work done by or on the system.

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Specific heat is the amount of energy necessary to raise one kilogram of a substance by one degree Celsius or one unit Kelvin. The specific heat of water is 1,000 cal/kg

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When heat energy is transferred into or out of a system, the system¶s temperature will change in proportion to that amount of energy, as long as no phase change is occurring. During a phase change, the heat energy is associated with changes in the particle¶s potential energy, not kinetic energy, and so there is no change in temperature.

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There are three special cases of the first law of thermodynamics in which one of the conditions of the gas system is held constant. For isovolumetric processes, the volume is constant and no work is done. For adiabatic processes, no heat is

exchanged. For closed cycle processes, the internal energy (and hence, temperature) is constant. y The second law of thermodynamics states that in a closed system (up to and including the entire universe), energy will spontaneously and irreversibly go from being localized to being spread out. y y Every real process is ultimately irreversible; under highly controlled conditions, certain equilibrium processes, such as phase changes, can be treated as reversible. Entropy is measure of how much energy has spread out or how spread out energy has become.

Fluids and Solids

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Fluids are substances that have the ability t flow and conform to the shape of their container. They can exert perpendicular forces, but they cannot withstand shear forces. The category of fluids includes both liquids and gases. Liquids are assumed incompressible.

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Solids are substances that do not flow and are sufficiently rigid to maintain their shape independent of any container. They can exert perpendicular forces and can withstand shear forces.

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The density of any fluid or solid is defined as the mass per unit volume. For a constant mass, there is an inverse relationship between volume and density. Thus, the density of an object that experiences thermal expansion decreases as its volume increases.

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Pressure is defined as a measure of the force per unit volume. Pressure is a scalar quantity; it has no direction. The pressure exerted by a gas against the walls of its container will always be perpendicular (normal) to the container walls.

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Gauge pressure is defined as the pressure above atmospheric pressure due to the weight of the fluid sitting above the point of measurement. Pressure can be measured either as an absolute pressure, which is the sum of the pressure at the surface plus the gauge pressure, or simply as the gauge pressure.

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Pascal¶s principle states that an applied pressure to an incompressible fluid will be distributed undiminished throughout the entire volume of the fluid system. This principle is the basis of hydraulic machines.

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Archimedes¶ principle states that the volume of fluid displaced by an object placed in it will generate a buoyant force against the object that is equal to the weight of the fluid displaced.

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Incompressible fluids will flow with conservation of energy as a result of the fluid¶s very low viscosity and laminar flow. The continuity expression is a statement of conservation of mass.

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Bernoulli¶s equation is an expression of conservation of energy for a flowing fluid: the sum of the static pressure and the dynamic pressure will be constant

between any two points in a closed system. For horizontal flow, there is an inverse relationship between pressure and velocity; as pressure decreases, velocity will increase. y The elasticity of solid materials can be measured by any one of the three moduli: Young¶s, shear, and bulk. All three measure stress in the same way, as pressure (F/A). The three moduli differ in the way they measure strain.

Electrostatics

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Charges are either positive or negative. The fundamental unit of charge is equal to the charge of a single proton or a single electron. Protons have positive charge, while electrons have negative charge.

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Coulomb¶s law gives the force between two charges that are separated by some distance. The force vector lies along the straight line that connects the two charges. Like charges exert repulsive forces, while unlike charges exert attractive forces.

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Coulomb¶s law is analogous to the gravitational force equation, except that it has a much larger constant and uses charge rather than mass. Electrostatic and gravitational forces are inversely proportional to the square of the distance between the two charges or masses, respectively.

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Every charge sets up an electric field which surround it and by which it exerts forces on other charges. The electric field is defined as the ratio of force that is exerted (or would be exerted) on a test charge that is (or could be) at some point in space within the electric field. Electric field vectors can be represented as field lines, which radiate outward from positive source charges and radiate inward from negative source charges.

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Positive test charges will move in the direction of the field lines; negative test charges will move in the direction opposite of the field lines. The electric potential energy of a charge is the amount of work it took to put the charge in a given position. It is analogous to gravitational potential energy. When like charges move away from each other, their electrical potential energy decreases. When unlike charges move toward each other, their electrical potential energy decreases.

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Electric potential is the electric potential energy per unit charge. Different points in space of an electric field surrounding a source charge will have different electric potential values. Test charges will move spontaneously in whichever direction results in a decrease in their electrical potential energy. Positive test

charges will move spontaneously from high potential to low potential. Negative test charges will move spontaneously from low potential to high potential. y Equipotential lines are concentric lines (or concentric spheres in 3-D space) of points in an electric field that have the same electric potential. Work will be done when charge is moved from one equipotential line to another, and the work is independent of the pathway taken between them. no work is done when a charge moves from a point on one equipotential line to another point on the same equipotential line. y y Two charges of opposite sign separated by a distance d, generate an electric dipole of magnitude p= qd. In an external electric field an electric dipole will experience a net torque until it is aligned with the electric field vector. However, an electric field will not induce any translational motion, regardless of its orientation with respect to the electric field vector.

Magnetism

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Magnetic fields are created either by magnets or moving charge. The SI unit for magnetic field is the tesla; smaller magnetic fields are measured in gauss.

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Materials are classified as diamagnetic, in which all electrons are paired, and these materials are weakly antimagnetic; paramagnetic in which some electrons are unpaired and these materials become weakly magnetic in an external magnetic field; and ferromagnetic, in which some electrons are unpaired, and atoms are organized into magnetic domains, and these materials are strongly magnetic. Ferromagnetic materials become permanently magnetized at temperatures below their respective Curie temperatures.

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Straight current-carrying wires create magnetic fields that are perpendicular concentric circles surrounding the wire. The strength of the field decreases as the distance from the wire increases. Use the first right hand rule to determine the direction of the magnetic field vector.

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Circular loops of current-carrying wires create magnetic fields that are also perpendicular concentric circles surrounding the wire. We can calculate the magnitude of the magnetic field at the center of the loop of wire, which decreases as the radius of the loop increases. Use the first right hand rule to determine the direction of the magnetic field vector.

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External magnetic fields exert forces on charges only if they are moving with a velocity that has a component perpendicular to the magnetic field vector. Point charges moving into a magnetic field perpendicular to the magnetic field vector will assume uniform circular motion for which the centripetal force is the magnetic force acting on the point charge. Use the second right hand rule to determine the direction of the magnetic force acting on the moving charge.

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A current carrying wire placed in an external magnetic field will experience a magnetic force on it so long as the current has a directional component that is perpendicular to the magnetic field vector. Use the third right hand rule to determine the magnetic force on the current-carrying wire.

DC and AC Circuits

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Current is the movement of charge between two points that exist at different electric potentials. Current, by convention, is defined as the movement of positive charge from the higher potential (positive) end of a voltage source to the lower potential 9negative) end. In actuality, the negative charge (electron) is moving from the lower potential end to the higher potential end. Current is measured in Amperes.

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Kirchhoff¶s laws are expressions of conservation of charge and energy. The first law states that the sum of currents directed into a point within a circuit equals the sum of the currents directed away from that point. The second law states that the sum of the voltage sources is equal to the sum of the voltage drops around a closed circuit loop.

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Resistance is the opposition to the movement of electrons through a material. Materials that have low resistance are called conductors. Conductive materials that have moderate resistance are called resistors. Materials that have very high resistance are called insulators. Resistance is related to resistivity, proportional to length of the resistor and inversely proportional to the cross-sectional area of the resistor.

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Ohm¶s law states that for a given resistance, the voltage drop across a resistor is proportional to the magnitude of the current through the resistor. Resistors in series are additive to give a resultant resistance that is the sum of all the individual resistances. Resistors in parallel cause a decrease in overall resistance.

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For resistors in parallel, the magnitude of current through each circuit division will be inversely proportional to the magnitude of the individual resistances of each circuit division.

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Capacitors in series cause a decrease in overall capacitance. Capacitors in parallel are additive to give a resultant capacitance that is the sum of all the individual capacitances.

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Dielectric materials act as insulators and increase the capacitance by a factor equal to the material¶s dielectric constant K. Direct current (DC) is in one direction only; alternating current (AC) reverses direction periodically. For AC circuits, use the rms values of current and voltage for Ohm¶s law applications.

Periodic Motion, Waves, and Sound

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Periodic Motion is repetitive motion about an equilibrium position. The simple harmonic motion demonstrated by springs and pendulums is an important type of periodic motion.

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Springs are governed by Hooke¶s law, which states that the restoring force is proportional to the displacement and always directed toward the equilibrium position. Springs experience maximum restoring force, maximum acceleration, maximum potential energy, and minimum kinetic energy at maximum displacement. They experience minimum restoring force, minimum acceleration, minimum potential energy, and maximum kinetic energy at minimum displacement. The angular frequency of springs is a function of the spring constant and the mass attached to the spring, but not its displacement.

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Pendulums are governed by a restoring force that is a function of gravity. The equilibrium position of a pendulum is the alignment with the gravitational acceleration vector (that is, the vertical position). Pendulums experience maximum restoring force, maximum acceleration. maximum potential energy and minimum kinetic energy at maximum angular displacement. Pendulums experience minimum restoring force, minimum acceleration, minimum potential energy, and maximum kinetic energy at minimum angular displacement. The angular frequency of pendulums is a function of the acceleration of gravity and the length of the pendulum arm.

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Waves can be transverse (oscillation of wave particles perpendicular to the direction of propagation of the wave) or longitudinal (oscillation of the wave particles along the direction of propagation of the wave). Water waves and EM waves are transverse; sound waves are longitudinal.

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Waves meeting in space in phase result in constructive interference; waves meeting in space out of phase result in destructive interference. Sound waves are longitudinal waves of oscillating mechanical disturbances of a material. The pitch of a sound is related to its frequency; the loudness of a sound is related to its intensity (related to its amplitude)

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The Doppler effect is the shift in the perceived frequency of a sound compared to the actual frequency of the emitted sound when the source of the sound and the detector are moving relative to each other. When they are moving toward each other, the apparent frequency will be higher than the actual frequency; when they are moving away from each other, the apparent frequency will be lower than the actual frequency.

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Standing waves are produced by the constructive and destructive interference of two waves of the same frequency traveling in opposite direction in the same space. The resultant wave appears to be standing still; the only oscillation is that of the amplitude at points called anti-nodes. Points where there is no oscillation of amplitude are called nodes.

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Strings secured at both ends and open pipes (open at both ends) support standing waves and the length of the string or pipe is equal to integer multiple of the halfwavelength.

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Closed pipes (closed at one end) support standing waves and the length of the pipe is equal to odd integer multiples of the quarter-wavelength.

Light and Optics

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Electromagnetic waves are transverse waves consisting of an oscillating electric field and oscillating magnetic field. The two fields are perpendicular to each other and to the propagation of the wave. The EM spectrum includes, from low to high energy, radio waves, microwaves, infrared, visible, ultraviolet, x-ray, and gamma-ray radiation.

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Reflection is the rebounding of incident light waves at the boundary of a medium. The law of reflection states that the angle of incidence will equal the angle of reflection, when each is measured from the normal.

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Mirrors reflect light to form images of objects. Spherical mirrors have centers and radii of curvature as well as focal points. Concave mirrors are converging mirrors and will produce real, inverted, or virtual, upright images. Convex mirrors are diverging mirrors and will only produce virtual, upright images. Plane mirrors may be thought of as spherical mirrors with infinite radii of curvature. Plane mirrors produce only virtual, upright images.

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Refraction is the bending of light as it passes from one medium to another and changes speed. Refraction depends on the wavelength (causing dispersion through a prism). The law of refraction is Snell¶s law, which states an inverse relationship between the index of refraction and the sine of the angle when measured from the normal.

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Total internal reflection occurs when the angle of incidence is greater than the critical angle for light leaving a medium with a higher index of refraction and entering a medium with a lower index of refraction. The internally reflected light does not actually leave the original medium; rather, it is totally reflected back into it.

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Lenses refract light to form images of objects. Thin, bilaterally symmetrical lenses have equal focal points on each side. Convex lenses are converging lenses and will produce real, inverted, or virtual, upright images. Concave lenses are diverging lenses and will only produce virtual, upright images.

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Diffraction is the bending and spreading out of light waves as they pass through a narrow slit. Interference demonstrates the wave/particle duality of light. Young¶s double-slit experiment shows the constructive and destructive interference of waves as light passes through a double slit to produce, respectively, maxima and minima of intensity.

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Plane-polarized light has been passed through a polarizer and the electric fields of all the waves are oriented in the same direction.

Atomic Phenomena

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Blackbody radiators are also ideal absorbers: they will radiate an amount of energy equal to the amount they absorb, but at different peak wavelengths depending on the temperature.

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The peak wavelength for a blackbody radiator is the wavelength at which the object radiates the greatest amount of energy. The peak wavelength is inversely proportional to the absolute temperature.

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The intensity of energy being radiated by a blackbody is proportional to the fourth power of the absolute temperature. The photoelectric effect is the ejection of an electron from the surface of a metal in a vacuum due to an incident photon whose frequency (energy) is at least as great as the threshold frequency (energy known as the work function) necessary to eject the electron from that particular metal. The greater the energy of the incident photon above the threshold energy, the more kinetic energy the ejected electron will possess.

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Once the threshold frequency has been exceeded, the magnitude of the current of the ejected electrons will be proportional to the intensity of the beam of photons. The Bohr model of the hydrogen atom proposes a dense nucleus consisting of a single proton surrounded by a single electron traveling in orbits of discrete energy values. in order for the electron to jump from a lower=energy orbital to one of higher energy, the electron must absorb an amount of energy exactly equal to the difference between the two energy levels.

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Fluorescence is the phenomenon that is observed when a substance flows with visible light upon being excited by higher-energy light, typically in the UV range. The electrons jump to an excited state by absorbing the high-frequency photons and then return to their ground state in multiple steps, releasing lower-frequency photons with each step. These lower-frequency photons are in the visible range.

Nuclear Phenomena

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Atomic number is the number of protons in the nucleus; all the atoms of a given element have the same number of protons and no two elements have the same atomic number.

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Atomic mass is the number of protons and neutrons in the nucleus. Atoms of the same element may have different numbers of neutrons and therefore will have the same atomic number but different mass numbers. Atoms of a given element that have different mass numbers are called isotopes.

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The atomic mass is the mass of a single atom of a given element in atomic mass units (amu). The average mass of a single proton or neutron is one amu, so the atomic mass of an atom is equal to the mass number of that atom. Atomic weight is the mass of one mole of atoms of a given element in grams. One mole of an atom or a compound is the number of atoms or molecules equal to 6.022 x 1023 (Avogadro¶s number)

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Nuclear binding energy is the amount of energy that is released when the nucleons (protons and neutrons) bind together through the strong nuclear force. The more binding energy per nucleon released, the more stable the nucleus. The mass defect is the difference between the mass of the unbound constituents and the mass of the bound constituents in the nucleus. The unbound constituents have more energy and therefore more mass than the bound constituents. The mass defect is the amount of mass converted to energy through the nuclear reactions of fusion or fission.

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Fusion occur when small nuclei combine into larger nuclei. Fission occurs when a large nucleus splits into smaller nuclei. Energy is released in both processes since the nuclei formed in both processes are more stable.

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Radioactive decay includes alpha decay

General Chemistry

Molecules, Atoms, and Quantum Mechanics
A ZX

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o X is the symbol o A is the mass, which is protons + neutrons o Z is the atomic number, which is proton number. y Zeff o Increases from left to right o Increases from Top to bottom y Ionization energy o Increases left to right o Increases from bottom to top y Electronegativity o Increases left to right o Increases from bottom to top y Electron Affinity o Increases left to right o Increases from bottom to top y y y Combination o A+B C

Decomposition o C A+B

Single Displacement o A+ BC B+ AC

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Double Displacement o AB+CD AD+BC

Quantum numbers o 1st number is the shell   Symbol is n o 2nd number is l Goes from 0-4

  

s,p,d,f l = n-1

o 3rd number is magnetic number ml = -l to +l y  Example: n=1, l=0, m=0 or n=3, l=2, m=-2,-1,0,1,2

o 4th number is electron spin ms= ½ or -1/2

Gases, Kinetics, and Chemical Equilibrium

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(PV)/(RT) = 1 for an ideal gas Since Vreal > Videal o (PV)/(RT) > 1  Then deviation due to molecular volume is greater than intermolecular forces o (PV)/(RT) <1  Then deviation due to intermolecular forces is greater than molecular volume

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Slowest step in a reaction o Rate determining step (RDS) o Also any step before the rate determining step contributes as well

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Q o The reaction quotient o (products coefficient)/ (reactants coefficient)

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K o Equilibrium constant o (productsCoefficient)/(reactantsCoefficient) o Q=K at equilibrium o Q>K   Then left shift because of high concentrations of products

o Q<K right shift Then right shift because of high concentration of reactants

o Liquids and solids are not included in equilibrium y y At high pressure o Gasses intermolecular forces cause a lower volume than expected At lower temperatures o Gasses intermolecular forces cause a lower volume

Thermodynamics

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Extensive properties change with amount, whereas intensive properties don¶t (U = q +W o If there is no change in Volume then work = 0 because Work is equal to constant pressure multiplied by change in volume. o (U= q

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(S o Entropy o A reaction must increase the entropy of the universe to proceed spontaneously o Decrease in amount of moles of gas is a decrease in entropy

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At constant pressure, the change in enthalpy ((H) is equal to heat (q) -(G o Spontaneous reaction and increase in entropy ((S) in the universe o Equilibrium is when (G is equal to 0.

Solutions

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Solution o Mixture of two or more compounds in a single phase

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Solvent o Compound that there is more of Solute o Compound that there is less of Negative heat of solution (-(H) is equal to heat given off, stronger bonds, lower vapor pressure, and a higher boiling point.

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When solutions form, entropy increases Vapor pressure increases with temperature If product is added to a solution, the reaction will shift towards the reactants.

Heat Capacity, Phase Change, and Colligative Properties

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Critical point o Combination of unit temperatures o Substance can¶t be liquefied regardless of pressure

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Critical temperature o When an increase in pressure has no effect and the substance wont liquefy o Temperature where critical point occurs

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Critical pressure o The pressure where the critical point occurs q= mc(T Colligative o Depend on number of particles o Not type

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Boils o When vapor pressure is equal to atmospheric pressure o Non-volatile solute   Doesn¶t contribute to pressure Lowers vapor pressure and increases boiling point.

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Exothermic is equal to an increase in solution temperature, which is equal to stronger bonds being formed, which is equal to a lower vapor pressure, which is equal to a higher boiling point.

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If you compare critical point graphs, compare the slopes to discover which one is more dense.

Acids and Bases

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Bronsted/ Lowry o Acids donate protons o Bases accept proton

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Lewis o Acid accepts pair of electrons o Base donate electrons

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pH is equal to the negative log of hydrogen ion concentration (-log(H+)) o Example is when H+ =10-3, pH =3 Stronger acids have weaker conjugate bases Stronger bases have weaker conjugate acids Kb is equal to conjugate base + water
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products = (products)/(reactants)

o Use this when OH is on the right Kw = Kb x Ka Equivalence point o Same number of moles of acid and base Half equivalence point o ½ of the acid neutralized by base o Most well buffered o Midpoint of graph closest to a straight line y To buffer o Start with an acid whose pKa is close to the pH we want o Buffer solution is when a weak acid and its conjugate base are in equal amounts.

Electrochemistry

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Atom that loses an electron is oxidized Atom that gains electrons is reduced Reduction always occurs at the cathode. Galvanic or voltaic cells are spontaneous Electrolytic cells are not spontaneous o Need energy for the reaction to take place +E is spontaneous -E is nonspontaneous.

Atomic Structure

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The subatomic particles include the proton, which has a positive charge; the neutron, which has no charge; and the electron, which has a negative charge. The nucleus contains the protons and neutron, while the electrons reside in regions of space. The element¶s atomic number is its number of protons, while the sum of an electron¶s protons and neutrons is its mass number.

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Isotopes are atoms of a given element that have different mass numbers because they have different numbers of neutrons in their nuclei. Because they have the same atomic number, they are all of the same elemental type. Most isotopes of elements are identified by the element followed by the mass number (e.g. carbon12, carbon-13, carbon-14). The three isotopes of hydrogen go by different names: protium, deuterium, and tritium.

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Bohr proposed a model of the atom with a dense, positively charged nucleus surrounded by electrons revolving around the nucleus in defined pathways of distinct energy levels called orbits.

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The energy of an electron is quantized, which is to say that there is not an infinite range of energy levels available to an electron. Electrons can exist only at certain energy levels and the energy of an electron increases the farther it is from the nucleus. The energy difference between energy levels is called a quantum.

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In order for electrons to jump from a lower energy level to a higher one, it must absorb an amount of energy precisely equal to the energy difference between the two levels. Every element has a characteristic atomic absorption spectrum. When electrons return from the excited state to the ground state they emit an amount of energy that is exactly equal to the energy difference between the two levels. Every element has a characteristic atomic emission spectrum. Sometimes the electromagnetic energy emitted corresponds to a frequency in the visible light range.

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The quantum mechanical model posits the electrons do not travel in defined orbits but rather in complex patterns called orbitals. An orbital is a region of space around the nucleus defined by the probabilities of finding an electron in that

region of space. The Heisenberg uncertainty principle states that it is impossible to know at the same time both an electron¶s position and its momentum. y There are four quantum numbers. These numbers completely describe any electron in an atom. The principal quantum number, n, describes the average energy of an orbital. The azimuthal quantum number, l, describes the subshells within a given principal energy level. The magnetic quantum number, ml, specifies the particular orbital within a subshell where an electron is likely to be found at a given moment in time. The spin quantum number, ms, indicates the spin orientation of an electron in an orbital. y The system of designating the placement of electrons into the principal energy levels, subshells, and orbitals is electron configuration. A neutral magnesium has 12 electrons: two in the s-orbital of the first energy level, two in the s-orbital of the second energy level, 6 in the p-orbitals of the first energy level, and 2 in the sorbital of the third energy level. The two electrons in the s-orbital of the third energy level are the valence electrons for the magnesium atom. y Electrons fill the principle energy levels and subshells according to increasing energy, which can be determined by the (n+1) rule. Electrons fill orbitals according to Hund¶s rule, which states that electrons prefer to be unpaired with parallel spins. y Valence electrons are those electrons in the outermost shell and/or those available for interaction (bonding) with other atoms. For the representative elements, the valence electrons are found in s- and/or p- orbitals. For the transition elements, the valence electrons are found in s-,d-, and f- orbitals. Many atoms interact with other atoms to form bonds so as to complete the octet in the valence shell.

The Periodic Table

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The periodic table of elements organizes the elements according to their atomic number and reveals a repeating pattern of similar chemical and physical properties. Elements in the same row are in a period, while elements in a column are in a group. Elements in the same period have the same principal energy level, n. Elements in the same group have the same valence shell electron configuration.

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The valence electrons are those located in the outer shell and/or are available for interaction (bonding) with other atoms. The representative elements have their valence electrons in either s- or s-and p- orbitals. The non-representative elements (the transition elements) have their valence electrons either in s- and dor in s-,d-, and f- orbitals.

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Effective Nuclear charge, (Zeff), is the net positive charge experienced by electrons in the valence shell. Zeff increases from left to right across a period, with little change in value from top to bottom in a group. Valence electrons become increasingly separated from the nucleus as the principal energy level increases, n, from top to bottom in a group. These two trends are the basis for all the other trends exhibited by the elements in the periodic table.

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Atomic radius increase from right to left across a period and also increases from top to bottom in a group. Ionization energy (IE) is the amount of energy necessary to remove an electron from the valence shell. It increases from left to right across a period and decreases from top to bottom.

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Electron affinity is the amount of emery released when n atom gains an electron in its valence shell. it increases from left to right across a period and decreases from top to bottom in a group.

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Electronegativity is a measure of the attractive force that an atom in a chemical bond will exert on the electron pair of the bond. It increases from left to right across the period and decreases from top to bottom in a group.

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There are three general classes of elements:

o The metals, located on the left and middle of the periodic table, including the active metals and the transition metals. o The nonmetals, located in the upper right side of the periodic table, including hydrogen, carbon, oxygen, nitrogen, and phosphorus, among others. o The metalloids or semimetals, located in a staircase formation between the metals and nonmetals, with qualities and behaviors that are combinations of the metals and nonmetals. y The alkali and alkaline earth metals are the most reactive of all metals; they exist only in their ionic forms, having given up one or two electrons, respectively, in order to achieve the electronic configuration of the prior noble gas. The transition metals are less reactive, and many can have two or more oxidation states. y The halogens are very reactive nonmetals and are highly electronegative. They need only one electron to complete their octets and are naturally found only in the anionic state. The noble gases are the least reactive of all the elements because they have the stable octet in their valence shell. The have very high ionization energies and virtually nonexistent electronegativities.

Bonding and Chemical Interactions

y

Atoms come together to form compounds through bonds. Many atoms interact with other atoms in order to achieve the octet electron configuration in their valence shell. There are two types of bonds: ionic and Covalent.

y

Ionic bonds form when a very electronegative atom gains one or more electrons from a much less electronegative atom, and the strong electrostatic force of attraction between opposite charges holds the resulting anion and cation together. Covalent bonds form when two atoms share one or more pairs of electrons. The force of the bond is due to the electrostatic attraction between the electrons in the bond and each of the positively charged nuclei of the bonding atoms.

y

Covalent bonds are characterized by their length, energy, and polarity. A single covalent bond exists when two atoms share one pair of electrons; a double bond exits when two atoms share two pairs of electrons; and a triple bond exists when two atoms share three pairs of electrons. Triple bonds are the shortest and have the highest bond energy. Single bonds are the longest and have the lowest bond energy.

y

Although all covalent bonds involve a sharing of one or more electron pairs, the electron density of the bonding electrons may not be distributed equally between the bonding atoms. This gives rise to a polar bond, with the more electronegative atom receiving the larger share of the bonding electron density.

y

Lewis structures are bookkeeping devices used to keep track of the valence electrons of atoms and their various possible different arrangements in a compound. Evaluation of formal charge on each atom in the arrangement can help determine which arrangement is most likely to be representative of the actual bond connectivity. Lewis structures that demonstrate the same atomic arrangement but differ in the distribution of electron pairs are called resonance structures. The actual molecular positioning of electrons is a ³weighted´ hybrid of all the possible resonance structures called a resonance hybrid.

y

VSEPR theory helps us predict the actual three-dimensional arrangement of bonded and nonbonded electron pairs around the central atom in a compound.

The theory states that nonbonded electrons (lone pairs) exert strong electrostatic repulsive forces against the bonded pairs of electrons and, as a result, the electron pairs arrange themselves as far apart as possible in order to minimize the repulsive forces. y A molecular dipole is the resultant of all the bond dipole vectors in the molecule. A compound consisting of only nonpolar bonds will by definition be nonpolar. A compound consisting of one polar bond will by definition be polar (although perhaps insignificantly). A compound consisting of two or more polar bonds have be polar or nonpolar depending on the molecular geometry and the vector addition of the bond dipoles. y Atomic orbitals overlap their + and ± lobes to result in bonding or antibonding molecular orbitals. When the signs of the overlapping atomic orbitals are the same, the result is a bonding molecular orbital. When the signs are opposite, the result is an antibonding orbital. y Sigma bonds involve head-to-head (or end-to-end) overlap of electron cloud density and thus allow for relatively low-energy rotation. Pi bonds involve parallel overlap of electron cloud density and thus do not allow for low-energy rotation. y The intermolecular interactions are electrostatic interactions that weakly hold molecules together. They generally are significant only over short distances and in the solid or liquid state. The weakest intermolecular interaction is the dispersion force (London force), which results from the moment-by-moment changing unequal distribution of the electron cloud density across molecules. A more moderate-strength intermolecular interaction is the dipole-dipole interaction, which exists between the opposite ends of permanent molecular dipoles. The strongest of these intermolecular interactions is the hydrogen bond, which is a special case of the dipole-dipole interaction between the hydrogen atom attached to either oxygen, nitrogen, or fluorine, and another oxygen, nitrogen, or fluorine on another- and sometimes, if the molecule is large enough, even the same molecule. One of the most important occurrences of hydrogen bonding is that between water molecules.

Compounds and Stoichiometry

y

A compound is a pure substance composed of two or more elements in a fixed proportion. Compounds can react with other elements or compounds to form new compounds and be broken down by chemical means to produce their constituent elements or other compounds, which can themselves go on to become involved in other reactions.

y

Molecular weight is the mass in amu of the constituent atoms in a compound, given by the molecular formula, which gives the exact number of atoms of each element in a compound. Empirical formula weight is the mass of the constituent atoms in a compound¶s empirical formula, which is the smallest whole number ratio of the elements in a compound. Molar mass is the mass in grams of one mole (6.022 x 1023 molecules) of a compound.

y

An equivalent is a measure of capacity to react in a certain way. One equivalent is an amount of a chemical compound equal to one mole of hydrogen ions or hydroxide ions in acid-base reactions or one mole of electrons in redox chemistry. Gram equivalent weight is the mass in grams of a compound that will yield one equivalent of hydrogen ions, hydroxide ions, or electrons. Normality is the ratio of equivalents per liter.

y y

Combination reactions occur when two or more reactants combine to form one product. Decomposition reactions occur when one reactant is chemically broken down into two or more products, usually by heat or electrolysis.

y y

Single displacement reactions occur when an atom or ion of one compound is replaced by an atom or ion of another element. Double displacement reactions occur when elements from two different compounds trade places with each other to form two new compounds. Neutralization reactions are a specific type of double displacement in which an acid reacts with a base to produce a solution of salt and water.

y

Net ionic equations ignore spectator ions to focus only on the species that actually participate in the reaction.

y

The steps for balancing chemical equations are: o Balance the nonhydrogen and nonoxygen atoms o Balance the oxygens o Balance the hydrogens o Balance charge is necessary

y

Balanced reactions are essential for calculating limiting reactant (the reactant that will be consumed first in a chemical reaction) and yields. Theoretical yield is the maximum amount of product that can be formed, assuming all limiting reactant is consumed. Actual yield is the amount of product collected from a chemical reaction. Percent yield is the ratio of actual yield divided by theoretical yield, multiplied by 100 percent.

Chemical Kinetics and Equilibrium

y

Reaction mechanisms propose a series of steps, the sum of which gives the overall reaction that explains the chemical processes in the transformation of reactants into products. The slowest step in a reaction mechanism is the rate-determining step, and it limits the maximum rate at which the reaction can proceed.

y

Reaction rates can be measured in terms of the rate of disappearance of reactant or the appearance of product, as measured by changes in their respective concentrations. The generic rate law is rate= k(A)x(B)y, and a particular reaction¶s actual rate law usually must be determined by analyzing experimental rate data that relate concentrations of reactants to rates of product formation.

y

y

In order for a reaction to occur, molecules of reactants must collide with each other at the proper angle and with an amount of kinetic energy at least as great as the energy maximum of the transition state, known as the energy of activation, Ea.

y

Reaction rates can be increased by increasing reactant concentrations (except for zero-order reactions), increasing the temperature, changing the medium, or adding a catalyst.

y

Reversible chemical reactions will eventually ³settle´ into an energy minimum state (for which there is maximum entropy) called equilibrium. This is a dynamic equilibrium in which the concentrations of reactants and products are constant because the rates of the forward and reverse reactions are equal.

y

The law of mass action gives the equilibrium constant (Keq) expression. It states that at equilibrium, the ratio of products to reactants will be constant. At equilibrium, the ratio of the forward rate to the reverse rate will be equal to one; however, the ratio of the equilibrium concentrations of products to reactants will usually not be equal to one.

y

The reaction quotient, Qc, is a calculated value involving reactant and product concentrations at any time within a reaction. Comparison of the calculated Qc value to the known Keq value will tell you ³where´ the reaction is with respect to its equilibrium state.

y y

Pure solids and pure liquids are not included in the law of mass action, and Keq is temperature-dependent. Le Chatelier¶s principle states that a chemical system that experiences a stress (changes to concentration, pressure, or temperature) will react in whichever direction results in the reestablishment of the equilibrium state.

Thermochemistry

y

Systems can be characterized as isolated (no heat or matter exchange), closed (no matter exchange), or open (both heat and matter exchange possible)

y

Some processes are identified by some constant property of the system: isothermal (constant internal energy/temperature), adiabatic(no heat exchange), and isobaric (constant pressure)

y

State functions are physical properties of a system that describe the equilibrium state; as such, changes in state functions are pathway-independent. Some examples of state functions are temperature, volume, pressure, internal energy, enthalpy, entropy, and Gibbs free energy.

y

Standard state of a substance is the most stable form (phase) of the substance under standard state conditions (298K and 1 atm). Standard enthalpy, standard entropy, and standard free energy changes are measured under standard state conditions.

y

Heat and temperature are not the same thing. Temperature is a scale related to the average kinetic energy of the molecules in a substance. Heat is the transfer of energy that results from two objects at different temperatures being put in thermal contact with each other. Heat energy transferred from one substance to another is measured by the methods of calorimetry.

y

Enthalpy is a measure of the potential energy of a system fond in the intermolecular interactions and bonds of molecules. Hess¶s law states that the total change in the potential energy of a system is equal to the changes in potential energies of the individual steps (reactions) of the process.

y

Entropy is a measure of the degree to which energy has been spread out through a system or between a system and its surroundings. It is a ratio of heat transferred per unit Kelvin. Systems reach maximum possible entropy (maximum possible energy dispersal) only at equilibrium.

y

Gibbs free energy is a calculation involving both enthalpy and entropy values for a system. The change in Gibbs function determines whether a process is spontaneous or nonspontaneous. When the change in Gibbs function is negative,

the process is spontaneous, but when the change in Gibbs function is positive, the process is nonspontaneous. y Temperature-dependent processes are those that change between spontaneous and nonspontaneous at a certain temperature. For example: water freezes spontaneously only at temperatures below 273 K, and boils spontaneously only at temperatures above 373K. y The larger and more positive the value of the equilibrium constant is, the more spontaneous a reaction will be (that is, the more negative the change in Gibbs function for the system as it moves from its initial position to its equilibrium).

The Gas Phase

y

Gases are the least dense phase of matter. They are classified, along with liquids, as fluids because they flow in response to shearing forces and conform to the shape of their container. Unlike liquids, however, gases are compressible.

y

The state of a gas system can be characterized by four properties: pressure, volume, temperature, and number of moles. Standard temperature and pressure (STP) is a set of conditions common in the study of gases; standard temperature is 273 K (00 C) and standard pressure is 1 atm.

y

Ideal gases are described by the kinetic molecular theory of gases, which characterizes gases as composed of particles with negligible volume, no intermolecular forces, in continuous and random motion, undergoing elastic collisions with each other and the walls of their container, and having an average kinetic energy that is proportional to the temperature.

y

Graham¶s law of diffusion and effusion states that for two or more gases at the same temperature, a gas with lower molar mass will diffuse or effuse more rapidly than a gas with higher molar mass.

y

Regardless of chemical identity, equal amounts of gases occupy the same volume if they are at the same temperature and pressure. For example, one mole of any gas occupies 22.4 liters at STP.

y y y y

The ideal gas law, PV = nRT, describes the mathematical relationship between the four variables of the gas state for an ideal gas. Boyle¶s law is a special case of the ideal gas law for which temperature is held constant; it shows an inverse relationship between pressure and volume. Charles¶s law s a special case of the ideal gas law for which pressure is held constant; it shows a direct relationship between temperature and volume. Dalton¶s law of partial pressure states that the individual gas components of a mixture of gases will exert individual pressures, called partial pressures, in proportion to their mole fractions. The total pressure of a mixture of gases is equal to the sum of the individual partial pressures of the individual gas components.

y

The behavior of real gases deviates from that predicted by the ideal gas law, especially under conditions of very high pressure or very low temperature. The van der Waals equation of state is used to correct for deviations due to intermolecular attractions and molecular volumes.

Phases and Phase Changes

y

In the solid and liquid phases, the atoms, ions, or molecules are sufficiently condensed to allow the intermolecular forces, such as van der Waals, dipoledipole, and hydrogen bonds, to hold the particles together and restrict their degrees of freedom of movement.

y y

Solids are defined by their rigidity (ability to maintain a shape independent of a container) and resistance to flow. The molecular arrangement in solids can be either crystalline or amorphous. Crystalline structure is a three-dimensional lattice arrangement of repeating units called the unit cell. Amorphous solids lack this lattice structure.

y

Liquids are defined as fluids because they flow in response to shearing forces and assume the shape of their container.

y

Liquids like water and alcohol will mix together and are called miscible; liquids like water and oil will not mix together and are called immiscible. Agitation of immiscible liquids will result in an emulsion.

y

Phase equilibria will exist at certain temperatures and pressure for each of the different phase changes: fusion (crystallization), vaporization (condensation), and sublimation (deposition).

y y y

The change in Gibbs free energy for phase equilibria is zero. The phase diagram is a given system that graphs the phases and phase equilibria as a function of temperature and pressure. The phase diagram for a solution consisting of multiple components will indicate the composition of the liquid and the vapor at different temperatures and pressures.

y

The colligative properties-vapor pressure depression, boiling point elevation, freezing point depression, and osmotic pressure- are physical properties of solutions that depend upon the concentration of dissolved particles but not upon their chemical identity.

Solutions

y

Solutions are homogenous mixtures of two or more substances that combine to form a single phase, generally the liquid phase. The most important kind of solution for the MCAT is the aqueous solution. Solvents dissolve solutes by a process of surrounding the solute particles and interacting with them by way of electrostatic forces; this is called solvation.

y y

Most dissolutions are endothermic. However, the dissolution of gas into liquid is exothermic. Solubility is the maximum amount of substance that can be dissolved in a particular solvent at a particular temperature. Molar solubility is the molar concentration of solute in a saturated solution.

y

Units of solution concentration include: percent composition by mass (mass of solute divided by mass of solution times 100%) mole fraction (moles of solute divided by total number of moles of substances in solution), molarity (moles of solute divided by liters of solution), molality (moles of solute divided by kilograms of solvent), and normality (number of equivalents divided by liters of solution.)

y

A standard solution is in equilibrium for that particular temperature. Ksp is the solubility product constant for a given solute in a given solvent at a given temperature.

y

Calculation of the ion product (IP), followed by comparison to the known Ksp, helps t determine if a solution is unsaturated (IP < Ksp), saturated (IP=Ksp), or super saturated (IP> Ksp)

y

When an ionic compound is dissolved into a solution that already contains one of the constituent ions, the molar solubility for that ionic compound will be significantly decreased from the value normally demonstrated by the same ionic compound in the pure solvent at the same temperature. This is the common ion effect. It is an application of Le Chatelier¶s principle to solutions.

Acids and Bases

y

There are three definitions of acids and bases: Arrhenius: acids produce hydrogen ions and bases produce hydroxide ions in aqueous solutions; Bronsted-Lowry: acids donate hydrogen ions and bases accept hydrogen ions; and Lewis: acids accept electron pairs and bases donate electron pairs.

y

Water is an amphoteric species (both acid and base) and auto-ionizes to produce equilibrium concentrations of hydrogen ions and hydroxide ions equal to 10-7 M at 298K. The Kw for water at 298K is 10-14. All aqueous acid or base solutions are defined by the equilibrium constant for water.

y

pH and pOH scales are logarithmic and express the negative log of the molar concentration of the hydrogen ions or hydroxide ions, respectively. For aqueous solutions at 298K, a pH less than 7 is acidic and a pH greater than 7 is basic: a pH of 7 is neutral.

y

Strong acids and bases dissociate completely in aqueous solutions. Examples of strong acids include HCl, H2SO4, and HNO3. Examples of strong bases are: NaOH and KOH.

y

Weak acids and bases dissociate incompletely in aqueous solutions. They have Ka¶s or Kb¶s less than 1. Examples of weak acids include CH3COOH, H2CO3, and H2O. Examples of weak bases include NH3 and H2O.

y

Bronsted-Lowry acid-base reactions always involve chemical pairs called conjugates: strong acid produces weak conjugate base; strong base produces weak conjugate acid; a weaker acid produces a stronger conjugate base; a weaker base produces a stronger conjugate acid.

y

An equivalent is equal to one mole of charge (hydrogen ions or hydroxide ions). Equivalent weight is the mass in grams of an acid or base compound that yields one acid or base equivalent (i.e., one mole of charge). Normality is the number of acid or base equivalents per liter of solution.

y

Acid-base titration is used to determine the molar concentration of a known acid or base solution. The equivalence point is the point in the titration at which the equivalents of acid equal the equivalents of base.

y

Strong acid/ strong base titration has an equivalence point at pH 7. Strong acid/ weak base titration has an equivalence point at pH less than 7. Strong base/weak acid titration has an equivalence point at pH greater than 7. Indicators approximate the equivalence point b a steady color change at the end point.

y

Buffers are weak acid/ conjugate base or weak base/ conjugate acid systems that act to absorb strong acids or bases from solutions thereby minimizing pH changes within the buffered region. Buffers are most effective within +/- 1 of pKa or pKb.

Redox Reactions and Electrochemistry.

y

Oxidation is loss of electrons; reductions is gain of electrons. Oxidation and reduction always occur as pairs reactions, in accordance with the law of conservation of charge.

y

The oxidizing agent is the chemical species that causes another species to be oxidized and is itself reduced. The reducing agent is the chemical species that causes another species to be reduced and is itself oxidized. Assign oxidation numbers to identify the oxidizing and reducing agents.

y

Redox reactions can be balanced by the half-reaction method: o Separate the half-reactions o Balance the atoms in each half-reaction. o Balance the charges in each half-reaction. o Add the half-reactions o Confirm balance of mass and charge in redox reaction.

y y

There are two basic types of electrochemical cells: galvanic (voltaic) cells and electrolytic cells. Concentration cells are a special type of galvanic cell. Galvanic cells have spontaneous redox reactions, generate current, and supply energy. The (G is negative and the Ecell is positive.

y

Concentration cells have spontaneous redox reactions, generate current, and supply energy. Current is dependent upon ion concentration gradient, not the difference in reduction potential between two different electrodes. The (G0 and the E0cell are both 0, because the current ceases when the concentrations of the ion are equal in both compartments.

y

Electrolytic cells have nonspontaneous redox reactions, require external voltage to generate current, and consume energy. The (G is positive and the Ecell is negative.

y

Reduction potential, measured in volts (V), is a measure of a chemical species¶ tendency to be reduced (gain electrons) relative to the standard hydrogen electrode (SHE). The higher the reduction potential, the greater the tendency to gain electrons and be reduced.

y y

The standard EMF of a cell is the difference between the standard reduction potential of the cathode minus the standard reduction potential of the anode. The Nernst equation is useful for calculating Ecell for all ion concentration.

Organic Chemistry

Nomenclature Concepts y y y y y y y Identify the backbones (longest chain of carbons) Number the chain, keeping number for the substituents as low as possible. Name substituents Assign numbers Put the whole name together, remembering to alphabetize substituents Multiple bonds should be on the main carbon backbone whenever possible -OH is a high-priority functional group, placed above multiple bonds in numbering. More oxidized groups have even higher priority. y y y Haloalkanes, ethers, and ketones, are often given common names Aldehydes and carboxylic acids are terminal functional groups. If present, they define C-1 on the carbon chain Remember to specify the isomer, if relevant such as cis or trans, R or S.

Isomers

Concepts y y y y y Structural isomers share only a molecular formula, they have different physical and chemical properties. Stereoisomers share the same molecular formula and the same atomic connectivity, but differ in their three-dimensional shape. Geometric isomers differ in positioning around a double bond, and they differ in many chemical and physical properties A chiral, sterogenic, center has four different groups attached to the central carbon and is give the absolute configuration of either R or S. Enatiomers have the same chemical and physical properties in an achiral environment, they differ only in the way they rotate plane-polarized light and how they react in chiral environments y Diasteromer (non-mirror image stereoisomers), which differ at some but not all chiral centers, have different chemical and physical properties. Cis-trans isomers are also diasteriomers y y Meso compounds have an internal plane of symmetry and are not optically active Conformational isomers are the same compound at different points in rotation around a single bond. y y The chair conformation is the most favored position for cyclohexane. In ring structures, big bulky groups prefer to be in the equatorial position.

Bonding

Concepts y y y y y y y The principal quantum number, n, determines distance from nucleus and energy level. Possible values are 1,2,3 etc. The azimuthal quantum number, l, determines the shape of the orbital. Possible numbers are n-1. Corresponding to s,p,d,f orbitals. Bonding orbitals share the same sign and are energetically favorable Antiboding orbitals have opposite signs and are energetically unfavorable Single bond is equal to one sigma bond, sp3 hybridized, 109.50 bond angles Double bond is equal to one sigma bon + one pi bond, sp2 hybridized, 1200 bond angles Triple bonds are equal to one sigma bond + two pi bonds, sp hybridized, 1800 bond angles.

Alkanes, Alkyl Halides, Substitution Reactions

y

Physical properties of alkanes: Higher chain length means: o Higher boiling points, o Higher melting points, o Higher density.

y

Physical properties of alkanes: Increased Branching means: o Lower boiling point o Decreased density.

y

Free Radical Halogenation steps: o Initiation o Propagation o Termination

y y y y y y y y y y y y y y

Nucleophiles are electron rich Electrophiles are electron deficient. Solvents affect nucleophilicity Weak bases make good leaving agents Sn1 has two steps Sn2 has one step Sn1 is favored in protic solvents Sn2 is favored in aprotic solvents Sn1: 30>20>10 Sn2: 10>20>30 Sn1 rate: k(RX) Sn2 rate: k(Nu)(RX) Sn1 has racemic products Sn2 has inverted products

Alkenes, Alkynes, and Elimination

y y y y y y y

Alkene is a carbon-carbon double bond Alkyne is a carbon-carbon triple bond Sn2 versus E2 is easier to control than Sn1 and E1 Eliminations and substitutions compete in reaction vessels Strong bulky bases are used in E2 Lots of oxygen is an attribute of an oxidizing agent like KMnO4 or Ozone Hot acidic KMnO4 cleaves double and triple bonds, fully oxidizes carbons of bond

y y y

Cold dilute KMnO4 turns double bonds into vicinal alcohols Electrophilic addition follows Markovnikov¶s rule except with hydroborationoxidation Radical addition is anti-Markonikov

Aromatic Compounds

y

Aromatic compounds are planar, cyclic, conjugated compounds with 4n +2 pi electrons

y y y y y y y y

Cyclic, conjugated polyenes with 4n pi electrons are anti-aromatic and not usually found When named as a substituent benzene is called a phenyl group A 1,2 di-substituted compound is called Ortho A 1,3 di-substituted compound is called meta A 1,4 di-substituted compound is called Para Activating is Ortho/Para directing and electron donating Deactivating is meta directing and electron withdrawing The most common Electrophilic Aromatic Substitutions are halogenation, sulfonation, nitration, and acylation.

Alcohols and Ethers

y y y y y y y y y y y y y y y

Alcohol is equal to an OH attached to an R group Alcohols and any other compound that has a hydrogen bonded to an O,N, or F will undergo hydrogen bonding, leading to a relatively high boiling point. Whereas alkyl groups stabilize positive charges, they destabilize negative charges Alcohols can be made by: nucleophilic substitution, electrophilic addition to a double bond, or nucleophilic addition to a carbonyl If a reactant has a lot of oxygen, its an oxidizing agent If a reactant has a lot of hydrogen it is a reducing agent. Terminal alcohols are oxidized to carboxylic acids, Secondary alcohols are oxidized to ketones Tertiary alcohols cannot be oxidized. PCC only oxidizes terminal (primary) alcohols to aldehydes The oxygen of alcohols or ethers can be protonated to make them into better leaving groups. Cleavage of straight-chain ethers is acid-catalyzed Cleave of cyclic ethers (epoxides) can be carried out in acid or base. Nucleophilic epoxide cleavage has Sn2 character Acid-catalyzed cleavage has Sn1 and Sn2 character.

Aldehydes and Ketones

y y y y y y y

In a carbonyl, the carbon is partially positive, and the oxygen is partially negative Aldehydes are terminal functional groups Ketones are midchain functional groups Aldehydes can be synthesized from primary alcohols with PCC Aldehydes can be oxidized to carboxylic acids, or reduced to primary alcohols Ketones cannot be further oxidized, but can be reduced to secondary alcohols The enol form is significant because it can act as a nucleophile, but it is not prevalent in solution.

y y y

Many molecules will add to the electropositive carbonyl carbon Ammonia derivatives often add in condensation reactions, removing water and forming a C double bond N. The Wittig reaction swaps out a C double bond O for a Carbon-Carbon double bond.

y

The Wolf-Kishner reduction and the Clemmensen reduction reduce ketones or aldehydes to alkanes.

Carboxylic Acids

y y y y

Carboxylic acids have the highest priority in nomenclature Carboxylic acids hydrogen bond better than alcohols, and as such have higher boiling points. The acidity of a carboxylic acid is enhanced by resonance between its oxygen atoms Acidity can be further enhanced by substituents that delocalize the negative charge through resonance, or with electron-withdrawing groups, such as halides.

y y y

Primary alcohols or aldehydes can be oxidized to carboxylic acids Carboxylic acids can also be synthesized from the carbonation of organometalic reagents, or by hydrolyzing nitriles Carboxylic acids can be reduced to primary alcohols or stopped at the aldehyde level with a bulky hydride reagent.

y y y

Carboxylic acids with long chains form soaps when neutralized with NaOH or KOH. Carboxylic acids readily undergo nucleophilic acyl substitution. 1,3-Dicarboxylic acids and other Beta-keto acids may spontaneously decarboxylate when heated, producing a ketone, or a mono carboxylic acid in the case of the dicarboxylic acid, and carbon dioxide.

Carboxylic Acid Derivatives

Acyl Halides

y y y y

Can be formed by adding RCOOH + SOCl2 or PCl3 or PCl5 or PBr3 Undergo many different nucleophilic substitutions, H2O yields carboxylic acid, whereas ROH yields an ester, and NH3 yields an amide. Can participate in Friedel-Crafts acylation to form an alkyl aryl ketone. Can be reduced to alcohols or, selectively, to aldehydes.

Anhydrides

y y y Esters

Can be formed by RCOOH + RCOOH, which is condensation, or RCOO- + RCOCl, which is substitution. Undergo many nucleophilic substitution reactions, forming products that include carboxylic acids, amides, and esters. Can participate in Friedel-Crafts acylation

y y y y y y

Formed by RCOOH + ROH, or even more easily by acid chlorides or anhydrides + ROH. Hydrolyze to yield acids + alcohols Adding Ammonia yields an amide Reaction with Grignard Reagent (2 moles) produces a tertiary alcohol In the Claisen condensation, analogous to the aldo condensation, the ester acts both as nucleophile and electrophile, but note the product difference Very important in biological processes, particularly phosphate esters, which can be found in membranes, nucleic acids, and metabolic reactions.

Amides

y y y

Can be formed by acid chlorides +amines, or acid anhydrides + ammonia Hydrolysis yields carboxylic acids or carboxylate anions Can be transformed to primary amines via Hofman rearrangement or reduction

Amines and Nitrogen-Containing Compounds

y y y

The suffix-amine is used when the amine has the highest priority The prefix-amino is used when the amine does not have the highest priority Remember the nitrogen-containing functional groups: amides, carbamates= urethanes, isocyannates, enamines, imines, nitriles= cyanides, nitro, diazo, azide, carbene, nitrene.

y y y y y y y

The boiling point of amines is between alcohols and alkanes Certain amines can be optically active if inversion is inhibited by sterics Amines have lone pairs, so they are bases and nucleophiles A nitrogen double bonded to carbon (imine) acts like an oxygen double bonded to carbon (carbonyl). Addition of ammonia to an alkyl halide and the Gabriel synthesis are both Sn2 reactions Many nitrogen-containing functional groups are easily reduced to amines Exhaustive methylation = Hofmann elimination. In this reaction, the nitrogen of an amine is released as trimethlamine and the substituent is converted into the least substituted alkene.

Purification and Separation

y

Extraction: o Separates dissolved substances based on differential solubility in aqueous versus organic solvents

y y

Filtration: o Separates solids from liquids. Recrystilization: o Separates solids based on differential solubility, temperature is really important here.

y

Centrifugation o Separates large things, such as cells, organelles, and macromolecules, based on mass and density

y y

Sublimation o Separates solids based on their ability to sublime. Distillation o Separates liquids based on boiling point, which in turn depends on intermolecular forces.

y

Chromatography o Uses a stationary phase and a mobile phase to separate compounds based on how tightly they adhere. Generally due to polarity, size, or charge.

y

Electrophoresis o Separates biological macromolecules, such as proteins or nucleic acids, based on size and sometimes charge.

Spectroscopy

y y y y

Infrared spectroscopy is used to find functional groups Carbonyls: o Sharp peak at 1,700 Hydroxides: o Sharp peak at 3,300 Amines: o Sharper peaks at 3,300 and 3,400 for primary amines o Secondary Amines have one peak.

y y

H-NMR is useful to find the structure of a compound, and can also reveal the functional groups. H-NMR measures how deshielded (how much electron density has been pulled away) protons are on a molecule. Sigma bonds= 0-12, the more deshielded the proton is, the further down-field it will be.

y

In H-NMR, protons that are three bonds apart experience coupling. If there is one proton three bonds away, it is a doublet; if there are two, it is a triplet; if there are three, it is a quartet.

y y y

C-NMR is similar to H-NMR, but Sigma bonds = 0-210. UV spectroscopy is useful for conjugated compounds Mass spectroscopy can be used to find the mass of the compound, and the masses of fragments of the compound.

Carbohydrates

y y y y y y y y

Carbohydrates have the general formula Cn(H20)n Aldoses are sugars with aldehydes at the C-1 position Ketoses are sugars with ketones at the C-2 position. L-sugars have the highest numbered chiral hydroxyl group on the left side of the sugar D sugars have the highest number chiral hydroxyl group on the right side of the sugar. D-glucose and L-glucose are enantiomers o Non-superimposable mirror images Any sugars that differ at only one chiral center are known as epimers Sugars can undergo intramolecular reactions that form rings. o Pyranose rings are six-membered sugar rings, o Furanose rings are five-membered rings

y

C-1 becomes chiral when a ring is formed, this newly chiral atom is known as the anomeric carbon. o For glucose, the anomeric carbon can either be alpha, which is up; or beta, which is down.

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Changing back and forth between the alpha and beta position is known as mutarotation. The key reactions of monosaccharides are: o Ester formation o Oxidation and o Glycosidic reactions

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Polysaccharides: o Cellulose is a chain of glucose with 1,4-Beta-glycosidic bonds o Starch and glycogen are mostly 1,4-Alpha-glycosidic bonds (with some 1,6-Beta-glycosidic bonds that form branches off the chain).

Amino Acids, Peptides, and Proteins

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Amino acids contain a carboxyl group, an amino group, a hydrogen, and an Rgroup attached to its central alpha-carbon.

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There are 20 naturally occurring amino acids, all of which are L-enantiomers. Amino acids are amphoteric species, they can function as acids or bases. In a neutral solution, non-polar and polar amino acids exist as zwitterions, acidic amino acids exist as negatively charged ions, and basic amino acids as positive ions.

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All amino acids have at least two pKa¶s and the isoelectric point (pI) is between the two pKa¶s During Titration, when pH=pKa, concentration of the protonated species is equal to that of the deprotonated species. This region is known as the buffer zone, and pH changes very little during this region (appears as a horizontal line)

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During titration, when pH=pI, all of the species have been deprotonated, and pH changes drastically (appears as a somewhat vertical line). Non-polar amino acids are hydrophobic, so they are often found buried within protein molecules. Polar, acidic, and basic amino acids are hydrophilic and are often found on the surface of proteins. Primary structure is determined by the amino acid sequence (N C) Secondary structure is determined by local hydrogen bonding Tertiary structure (the three-dimensional shape) is determined largely by hydrophobic interactions, but also disulfide bonds Quaternary structure is from the aggregation of more than one polypeptide subunits. Conjugated proteins derive part of their function from prosthetic groups o Which can be either organic molecules or metal ions.