Biology Revision Notes Custom Part 1

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Biology Revision Notes Custom (Part 1 of part one)

Cell Types


Cells are structural and functional units



Small cells: bigger surface area per volume → allows exchange of more nutrients/waste



Large cells: smaller surface area per volume → problems to transport waste out of cell



More nutrients → more waste

Table 1-10-1: Differences between prokaryotic and eukaryotic cells

Feature

Prokaryotic (bacteria)

Eukaryotic (plant/animal/fungi)

Size

Small cells - 5µm

Large cells - 50µm

Capsule (protection)

Present

Absent
In fungi (chitin)

Cell wall

Present (peptidoglycan)

In plants (cellulose)
NOT in animals

Plasma membrane

Present

Present

Absent

Only in plant cells

Absent

Present

Absent

Present

Absent

Present

Absent

Present

Small ribosomes, always

Larger ribosomes free in cytoplasm

free in the cytoplasm

and attached to rough ER

Nucleus

Absent

Present

- Nuclear envelope

\ Absent

\ Present

- Nucleoli

\ Absent

\ Present

- Chromosomes (DNA)

Single and circular

Many and linear

Centriole (for mitosis)

Absent

Only in animal cells

Cytoplasm
- Chloroplast
- Lysosomes
- Golgi Apparatus
- Endoplasmic Reticulum
- Mitochondria
- Ribosomes

1

Cell Ultra-Structure

Cell wall (plant cells only)


Made up of cellulose fibres which provide strength



Cell does not burst if surrounding solutions become dilute

Nucleus (5µm)


Contains chromosomes (genes made of DNA which control cell activities)



Separated from the cytoplasm by a nuclear envelope



The envelope is made of a double membrane containing small holes



These small holes are called nuclear pores (100nm)



Nuclear pores allow the transport of proteins into the nucleus

Rough Endoplasmic Reticulum (rough ER)


Have ribosomes attached to the cytosolic side of their membrane



Found in cells that are making proteins for export (enzymes, hormones, structural proteins,
antibodies)



Thus, involved in protein synthesis



Modifies proteins by the addition of carbohydrates, removal of signal sequences



Phospholipid synthesis and assembly of polypeptides

Smooth Endoplasmic Reticulum (smooth ER)


Have no ribosomes attached and often appear more tubular than the rough ER



Necessary for steroid synthesis, metabolism and detoxification, lipid synthesis



Numerous in the liver

2

Ribosomes (20-30nm)


Small organelles often attached to the ER but also found in the cytoplasm



Large (protein) and small (rRNA) subunits form the functional ribosome
o

Subunits bind with mRNA in the cytoplasm

o

This starts translation of mRNA for protein synthesis (assembly of amino acids into
proteins)





Free ribosomes make proteins used in the cytoplasm. Responsible for proteins that
o

go into solution in cytoplasm or

o

form important cytoplasmic, structural elements

Ribosomal ribonucleic acid (rRNA) are made in nucleus of cell

Golgi apparatus


Stack of flattened sacs surrounded by membrane



Receives protein-filled vesicles from the rough ER (fuse with Golgi membrane)



Uses enzymes to modify these proteins (e.g. add a sugar chain, making glycoprotein)



Adds directions for destination of protein package - vesicles that leave Golgi apparatus move to
different locations in cell or proceed to plasma membrane for secretion



Involved in processing, packaging, and secretion



Other vesicles that leave Golgi apparatus are lysosomes

Vacuole and vesicles


Membranous sacs of liquid which store substances - vacuoles are storage areas

3

Lysosomes (0.05 to 0.5 micron)


Performs intracellular digestion - more numerous in cells performing phagocytosis



Limiting membrane keeps digestive enzymes separate from the cytoplasm



Lysosomal enzymes digest particles



o

They function optimally at pH 5 and are mostly inactive at cytosolic pH

o

Lysosomal enzymes are synthesized on rough ER

o

Transferred to the Golgi apparatus for modification and packaging

Primary lysosomes are small concentrated sacs of enzymes (no digestion process)
o

Primary lysosomes fuse with a phagocytic vacuole

o

Become secondary lysosomes

o

Digestion begins

o

Nutrients diffuse through lysosomal membrane into the cytosol

Mitochondria (1µm in diameter and 7µm in length)


Mostly protein, but also contains some lipid, DNA and RNA



Power house of the cell
o

Energy is stored in high energy phosphate bonds of ATP

o

Mitochondria convert energy from the breakdown of glucose into adenosine
triphosphate (ATP)

o

Responsible for aerobic respiration



Metabolic activity of a cell is related to the number of cristae (larger surface area) and mitochondria



Cells with a high metabolic activity (e.g. heart muscle) have many well developed mitochondria

4

Chloroplast (4-6µm in diameter and 1-5µm in length)


Only in photosynthesising cells (plants)



Light energy, CO2, and H2O are converted to produce carbohydrates and O2



Inner membrane has folds, called lamellae (where chlorophyll is found), which surround a fluid,
called stroma

5

Cell division


Occurs in the nucleus of eukaryotic cells by mitosis and meiosis
o

Replacement of the entire lining of your small intestine

o

Liver cells only divide for repairing

o

Nerve cells do not divide

Chromosomes


Long and thin for replication and decoding



Become short and fat prior mitosis → easier to separate due to compact form

Meiosis (reduction division)


During the production of sex cells (gametes) in animals



In spore formation which precedes gamete production in plants



Haploid gametes (sperm ovum) - sexual reproduction



DNA in a cell replicates only once, but cell divides twice

The Cell Cycle


Interphase
o

G1: Protein synthesis and growth (10 hours)


Preparation for DNA replication (e.g. growths of mitochondria)



Differentiation, only selected genes are used to perform different functions in
each cell

o

S: DNA Replication (9 hours)

o

G2: short gap before mitosis, organelles and proteins for mitosis are made (4 hours)



G0: Resting phase (nerve cells)



M-phase
o

Mitotic division of the nucleus (Prophase, Metaphase, Anaphase, Telophase)

6

o

Cytokinesis (division of the cytoplasm)

Interphase


Phase with highest metabolism (mitochondria have a high activity)



Muscles never complete the whole cycle

Mitosis


Process of producing 2 diploid daughter cells with the same DNA by copying their chromosomes
(clones)



Chromosomes can be grouped into homologous pairs



Mitosis occurs in
o

Growth

o

Repair

o

Replacement of cells with limiting life span (red blood, skin cells)

o

Asexual replacement



Controlled process, cancers result from uncontrolled mitosis of abnormal cells



Division of the nucleus (karyokinesis) and the cytoplasm (cytokinesis) are two processes of mitosis



Division of cytoplasm after nucleus. Delayed if cells have more than one nucleus (muscle)



Active process that requires ATP

Prophase


Chromosomes become shorter and thicker by coiling themselves (condensation)



This prevents tangling with other chromosomes



Nuclear envelope disappears/breaks down



Protein fibres (spindle microtubules) form



Centrioles are moving toward opposite poles forming the spindle apparatus of microtubule

7

Metaphase


Centrioles at opposite poles



Chromosomes line up on the equator of the spindle



Centromeres (kinetochores) attach to spindle fibres



Kinetochores consist of microtubules and "motor" proteins which utilise ATP to pull on the spindle

Anaphase


Spindle fibres pull copies of chromatids to spindle poles to separate them



Mitochondria around spindle provide energy for movement

Telophase


Chromatid at the pole



Sets of chromosomes form new nuclei



Chromosomes become long and thin, uncoil!



Nuclear envelopes form around the nucleus

8

Enzymes


All enzymes are globular proteins and round in shape



They have the suffix "-ase"



Intracellular enzymes are found inside the cell



Extracellular enzymes act outside the cell (e.g. digestive enzymes)



Enzymes are catalysts → speed up chemical reactions
o

Reduce activation energy required to start a reaction between molecules

o

Substrates (reactants) are converted into products

o

Reaction may not take place in absence of enzymes (each enzyme has a specific catalytic
action)

o




Enzymes catalyse a reaction at max. rate at an optimum state

Induced fit theory
o

Enzyme's shape changes when substrate binds to active site

o

Amino acids are moulded into a precise form to perform catalytic reaction effectively

o

Enzyme wraps around substrate to distort it

o

Forms an enzyme-substrate complex → fast reaction

o

E + S → ES → P + E

Enzyme is not used up in the reaction (unlike substrates)

Changes in pH


Affect attraction between substrate and enzyme and therefore efficiency of conversion process



Ionic bonds can break and change shape / enzyme is denatured



Charges on amino acids can change, ES complex cannot form



Optimum pH



o

pH 7 for intracellular enzymes

o

Acidic range (pH 1-6) in the stomach for digestive enzymes (pepsin)

o

Alkaline range (pH 8-14) in oral cavities (amylase)

pH measures the conc. of H+ ions - higher conc. will give a lower pH

Enzyme Conc. is proportional to rate of reaction, provided other conditions are constant. Straight line
Substrate Conc. is proportional to rate of reaction until there are more substrates than enzymes present.
Curve becomes constant.

9

Increased Temperature


Increases speed of molecular movement → chances of molecular collisions → more ES complexes



At 0-42 °C rate of reaction is proportional to temp



Enzymes have optimum temp. for their action (varies between different enzymes)



Above ≈42°C, enzyme is denatured due to heavy vibration that break -H bonds
o

Shape is changed / active site can't be used anymore

Decreased Temperature


Enzymes become less and less active, due to reductions in speed of molecular movement



Below freezing point
o

Inactivated, not denatured

o

Regain their function when returning to normal temperature



Thermophilic: heat-loving



Hyperthermophilic: organisms are not able to grow below +70°C



Psychrophiles: cold-loving

Inhibitors


Slow down rate of reaction of enzyme when necessary (e.g. when temp is too high)



Molecule present in highest conc. is most likely to form an ES-complex



Competitive Inhibitors



o

Compete with substrate for active site

o

Shape similar to substrates / prevents access when bonded

o

Can slow down a metabolic pathway

[EXAMPLE] Methanol Poisoning
o

Methanol CH3OH is a competitive inhibitor

o

CH3OH can bind to dehydrogenase whose true substrate is C2H5OH

o

A person who has accidentally swallowed methanol is treated by being given large doses
of C2H5OH

o

C2H5OH competes with CH3OH for the active site

10





Non-competitive Inhibitors
o

Chemical does not have to resemble the substrate

o

Binds to enzyme other than at active site

o

This changes the enzyme's active site and prevents access to it

Irreversible Inhibition
o

Chemical permanently binds to the enzyme or massively denatures the enzyme

o

Nerve gas permanently blocks pathways involved in nerve message transmission, resulting
in death

o

Penicillin, the first of "wonder drug" antibiotics, permanently blocks pathways certain
bacteria use to assemble their cell wall component (peptidoglycan)

End-product inhibition


Metabolic reactions are multi-stepped, each controlled by a single enzyme



End-products accumulate within the cell and stop the reaction when sufficient product is made



This is achieved by non-competitive inhibition by the end-product



The enzyme early in the reaction pathway is inhibited by the end-product

The metabolic pathway contains a series of individual chemical reactions that combine to perform one or
more important functions. The product of one reaction in a pathway serves as the substrate for the
following reaction.

11

Genes, DNA, RNA


Nucleic acids carry the genetic code that determines the order of amino acids in proteins



Genetic material stores information, can be replicated, and undergoes mutations



Differs from proteins as it has phosphorus and NO sulphur

DNA Deoxyribonucleic Acid


Nucleotides are smaller units of long chains of nucleic acids. Each nucleotide has
o

A pentose sugar (deoxyribose in DNA, ribose in RNA)

o

A phosphate group

o

An organic base which fall into 2 groups,


Purines (double rings of C and N - bigger)




Pyrimidines (single ring of C and N - smaller)




Adenine or Guanine
Thymine or Cytosine

Base pairing by weak hydrogen bonds


Adenine-Thymine 2 H- bonds



Cytosine-Guanine 3 H- bonds



Chains are directional according to the attachment between sugars and phosphate group



They are antiparallel which is essential for gene coding and replication



DNA molecule has 2 separate chains of nucleotides hold together by base pairing / DNA normally
twist into a helix (coil) / forms a double helix

Ribonucleic Acid (RNA)


Ribose instead of deoxyribose



Single chain (shorter than DNA - lower molecular mass)



Base difference: Uracil instead of Thymine. Adenine, Guanine and Cytosine are the same
o

Ribosomal RNA (rRNA)


Located in the cytoplasm - ER



Reads mRNA code and assembles amino acids in their correct sequence to make a
functional protein (translation)

o

Messenger RNA (mRNA)

12

o



Commutes between nucleus and cytoplasm



Copies the code for a single protein from DNA (transcription)



Carries the code to ribosomes in the cytoplasm

Transfer RNA (tRNA)


In the cytoplasm



Transfer amino acids from the cytoplasm to the ribosomes

The Genetic Code


DNA codes for assembly of amino acids / forms a polypeptide chain (proteins - enzymes)



The code is read in a sequence of three bases called



o

Triplets on DNA

e.g. CAC TCA

o

Codons on mRNA

e.g. GUG AGU

o

Anticodons on tRNA

e.g. CAC UCA

o

(must be complementary to the codon of mRNA)

Each triplet codes for one amino acid / single amino acid may have up to 6 different triplets for it
due to the redundancy of the code / code is degenerate. Some amino acids are coded by more
than one codon



Same triplet code will give the same amino acid in virtually all organisms, universal code



We have 64 possible combinations of the 4 bases in triplets, 43



No base of one triplet contributes to part of the code next to it, non-overlapping



Few triplets code for START and STOP sequences for polypeptide chain formation



eg START AUG and STOP UAA UAG UGA

DNA Replication (Semi-Conservative Replication)


Happens during Interphase 'S'



Separate the strands, a little at a time to form a replication fork



Events:
o

Unwinding / Enzyme DNA helicase separates 2 strands of DNA by breaking hydrogen
bonds

o

Semi-conservative replication / each strand acts as a template for the formation of a new
strand

o

Free DNA molecules join up to exposed bases by complementary base pairing

13

o



Adenine with Thymine (A=T 2 -H bonding)



Cytosine with Guanine (CΞG 3 -H bonding)

For the new 5' to 3' strand the enzyme DNA polymerase catalyses the joining of the
separate nucleotides

o

"All in one go" → completed new strand

o

For the 3' to 5' strand DNA polymerase produces short sections of strand but these
sections have to be joined by DNA ligase to make the completed new strand. Specific base
pairing ensures that two identical copies of the original DNA have been formed

Transcription: DNA to mRNA


DNA in nucleus unzips - bonds break



Single template strand of DNA used for mRNA (triplet on DNA = codon for amino acid on mRNA)



Enzyme RNA polymerase joins nucleotides together



Free RNA nucleotides are assembled according to the DNA triplets (A-U / C-G / T-A)



mRNA bases are equivalent to the non-template DNA strand



Start and stop codons are included



Introns (Non-coding) and exons (coding) DNA sequences are present in the primary mRNA
transcript. Introns are removed before the mRNA is translated so that exons are only present in the
mature mRNA transcript

[EXAM] Total number of bases in the DNA sense strand and total number of bases in the mRNA are
different


mRNA moves into cytoplasm and becomes associated with ribosomes

Translation: mRNA to Protein via tRNA


Translation is the synthesis of a polypeptide chain from amino acids by using codon sequences on
mRNA



tRNA with anticodon carries amino acid to mRNA associated with ribosome



"Anticodon - codon" complementary base pairing occurs



Peptide chain is transferred from resident tRNA to incoming tRNA



tRNA departs and will soon pick up another amino acid

14

Requirement for Translation


Pool of amino acids / building blocks from which the polypeptides are constructed



ATP and enzymes are needed



Complementary bases are hydrogen-bonded to one another



Structure involved in translation



Messenger RNA (mRNA)

Carries the code from the DNA that will be translated into an amino acid sequence


Transfer RNA (tRNA)

Transfer amino acids to their correct position on mRNA strand


Ribosomes

Provide the environment for tRNA attachment and amino acid linkage

DNA and Inheritance


Reactions in cells is referred to as cell metabolism



A sequence of chemical reactions is called a metabolic pathway



Different forms of the same gene are alleles



A gene is the length of DNA that carries the code for a protein (enzyme)
o

Enzyme effect the cell's metabolism

o

Visible changes are described with the phenotype



The phenotype is influenced by the metabolic pathway



Therefore
o

DNA controls enzyme production

o

Enzymes control metabolic pathways

o

Metabolic pathways influence the phenotype of an organism

Gene Mutations


Deletion, reading frame shifts



Substitution, one base replaced by another



Duplication, repetition of part of the sequence

15



Addition, Addition extra base



Change in one or more nucleotide bases in the DNA



Change in the genotype (may be inherited)

Cystic Fibrosis - Defective Gene


Mutation causes the deletion of 3 bases in DNA. One amino acid (phenylalanine) is not coded for in
the Cystic Fibrosis Transmembrane Regulator CFTR protein



Faulty CFTR protein cannot control the opening of chloride channels in the cell membrane



Results in production of thick sticky mucus, especially in lungs, pancreas and liver



Organs cannot function normally and infection rate increases

Phenylketonuria (PKU) - Defective Gene


Gene mutation in DNA coding for the enzyme phenylalanine hydroxylase



Phenylalanine hydroxylase not produced



Amino acid phenylalanine cannot be converted to the amino acid tyrosine



Tyrosine is necessary to produce the pigment melanin



Phenylalanine collects in the blood and causes retardation in young children



Managed by controlling diet to eliminate proteins containing phenylalanine



Disease is tested by drops of blood taken from the baby

16

Biology Revision Notes Custom (Part 1 of part two)

Large Molecules




Monomer (-OH) + Monomer (-H) → Polymer + H2O(l)
o

Condensation: monomers (e.g. amino acids) join to form polymers (e.g. proteins)

o

Glycosidic bond forms when two carbohydrate monomers join together

o

Hydrolysis: break down of a polymer; reverse reaction

Polymers are also called macromolecules (e.g. starch, proteins, triglyceride)

Carbohydrates


Organic molecules in which C, H and O bind together in the ratio Cx(H2O)y



Serve as an energy source important for the brain and cellular respiration



Plants produce carbohydrates by using energy from sunlight
o

6CO2 + 6H2O + energy (from sunlight) → C6H12O6(carbohydrate) + 6O2



Animals eat plant materials to obtain the produced carbohydrates



They can then be used in animal metabolism to release energy
o

C6H12O6 + 6O2 → 6CO2 + 6H2O + energy

Monosaccharides
Triose (3 carbons)

Product of respiration and photosynthesis

Pentose (5 carbons)

Found in RNA and DNA

- Ribose

nucleic acids

- Deoxyribose
Hexose (6 carbons)

Source of energy in respiration

- Glucose

Main energy source in brain

- Fructose

Found in sweet-tasting fruits

- Galactose

17

Disaccharides (two sugar residues)
Sucrose (glucose + fructose)

Transport carbohydrates in plants

Maltose (glucose + glucose)

Formed from digestion of starch

Lactose (glucose + galactose)

Carbohydrates found in milk

Polysaccharides (many sugar residues)
Starch (alpha-glucose)

Main storage of carbohydrates
- in plants

Glycogen (alpha-glucose)

- in humans and animals

Cellulose (beta-glucose)

Important component of the plant cell wall

Starch


Consists of amylopectin and amylose (both are made of α-glucose)
o

Amylopectin is branched via 1,6-glycosidic bonds

o

Amylose forms a stiff helical structure via 1,4-glycosidic bonds

o

Both are compact molecules → starch can be stored in small space



The ends are easily broken down to glucose for respiration



Does not affect water potential as it is insoluble



Readily hydrolysed by the enzyme amylase found in the gut and saliva



Major carbohydrate used in plants



o

Found as granules (chloroplast)

o

Each granule contains amylopectin combined by a larger amount of amylose

Commonly used sources are corn (maize), wheat, potato, rice

Glycogen


Branched, storage, polymer of glucose linked via glycosidic bonds



Found in skeletal muscle and in the liver



Chains are linked by alpha-1,4-linkage, branches are linked by alpha-1,6-linkages



Glycogen is broken down to glucose by glycogenolysis (glycogen phosphorylase)



Major site of daily glucose consumption (75%) is the brain via aerobic pathways



Most of the remainder is utilized by erythrocytes, skeletal muscle, and heart muscle

18



Glucose is obtained from diets or from amino acids and lactate via gluconeogenesis



Storage of glycogen in liver are considered to be main buffer of blood glucose levels

Cellulose


Polysaccharide consisting of long beta-glucose chains



Linked together by hydrogen bonds to form microfibrils



Structural function is a important component of plant cell walls



Its tensile strength helps plant cells in osmosis //cell does not burst in dilute solutions

Proteins
Structure


Proteins are polymers of amino acids



Proteins are made up by different combinations of 20 amino acids
o

They have a general structure:

o

The difference between different amino acids is found in the R-group

o

When two amino acids join together, they release -H and -OH groups highlighted in red
below







o

Peptide bond is formed between alpha-carbon and nitrogen

o

Condensation reaction

Primary structure of a protein
o

Sequence of amino acids

o

Joined together by covalent peptide bonds

Secondary structure
o

Hydrogen bonds between amino acids

o

Made of a combination of alpha-helices and beta-pleated sheets

o

Proportion of α-helix and β-sheet depends on sequence (primary structure)

Tertiary structure
o

Complex globular shape

o

Folding and twisting of polypeptides (H-bond)

19

o




Polypeptides contain many peptide bonds

Quaternary structure
o

Several polypeptide chains //several tertiary structures combined

o

Haemoglobin has 4 polypeptide chains

o

Collagen has 3 polypeptide chains, twisted around each other

o

Globular proteins are soluble and has folded chains

o

Fibrous proteins are insoluble and long, thin, twisted chains

Same amino acid sequence → same shape always

Bonds Found in Proteins






Hydrogen bonds
o

Between R-groups are easily broken, but are numerous

o

The more bonds, the stronger the structure

Disulphide bonds
o

Between sulphur-containing amino acid cystine

o

Strong bonds found in skin and hair

Denaturation
o

Destruction of tertiary structure, can be done by heat

o

Protein structure is lost and cannot reform → dysfunctional

Absorption and Function




Absorption of proteins in the digestive tract
o

Proteins are taken in as food

o

They are broken down in the digestive tract into their individual amino acids

o

Amino acids are recombined in the body to form different proteins

o

Good food sources include beans, milk, cheese, fish, meat

Several substances are composed of proteins with distinct functions
o

Keratin, collagen are main components in hair, muscles, tendons, skin

o

Enzyme amylase digests starch

o

Haemoglobin transports O2 in the blood stream

o

Insulin regulates glucose storage

20

Lipids


Easily dissolved in organic solvents but not in water



Triglycerides (fats and oils)







o

Serves as an energy reserve in plant and animal cells

o

Consists of 3 fatty acids linked by ester bonds to glycerol

o

Excess energy available from food/photosynthesis is stored as triglycerides

o

Can be broken down later to yield energy when needed

o

Fats and oils contain twice as many energy stored per unit of weight as carbohydrates

o

Triglycerides (TG) are also called triacylglycerides (TAG)

Saturated fatty acids
o

-COOH group without double bonds in the carbohydrate chain

o

May cause blockage of arteries which can lead to strokes and heart attacks

o

High melting point / solid at room temperature (fats) / typical animal fats

Unsaturated fatty acids
o

-COOH group with double bonds in the carbohydrate chain

o

Low melting point / liquid at room temperature (oils)

o

Found in plants

Phospholipids
o

Formed by replacing one fatty acids in a triglyceride with a phosphate group

o

Phosphate is polar / hydrophilic / does mix with H2O

o

Fatty acid tails remain non-polar / hydrophobic / insoluble, does not mix with H2O

o

Form a ball called a micelle when placed in a polar solution (e.g. water)

21

Fluid-mosaic model


Plasma membrane consists of a phospholipid bilayer studded with proteins, polysaccharides, lipids



The lipid bilayer is semipermeable



o

Regulates passage of substances into and out of the cell

o

H2O and some small, uncharged, molecules (O2, CO2) can pass through

Phospholipids have two parts
o

"Head": hydrophilic → attracts and mixes with H2O

o

Two "fatty acid tails": hydrophobic

Function of proteins


Carrier (change shape for different molecules) for water-soluble molecules such as glucose



Channels for ions (sodium and chloride ions)



Pumps use energy to move water-soluble molecules and ions



Adhesion molecules for holding cells to extracellular matrix



Receptors enable hormones and nerve transmitters to bind to specific cells



Recognition sites, which identify a cell as being of a particular type



Enzymes, which speed up chemical reactions at the edge of the membrane

22



Adhesion sites, which help some cells to stick together



E.g. glycoprotein acts as a receptor and recognition site

Passive transport


Uses energy from moving particles (Kinetic Energy)

Diffusion


Substances move down their conc. gradient until the conc. are in equilibrium



Microvilli are extensions of the plasma membrane



o

They increase the surface area of the membrane, therefore

o

They accelerate the rate of diffusion

Fick's law → rate of diffusion across an exchange surfaces (e.g. membrane, epithelium) depends
on



o

surface area across within diffusion occurs (larger)

o

thickness of surface (thinner)

o

difference in concentration gradient (larger)

o

Fick’s law = (surface area x difference in conc gradient) / thickness of surface

Temperature increases rate of diffusion due to increasing K.E. (kinetic energy)

Facilitate diffusion


Transmembrane proteins form a water-filled ion channel
o

Allows the passage of ions (Ca2+, Na+, Cl-) down their conc. gradient //passive - no ATP
required



o

Some channels use a gate to regulate the flow of ions

o

Selective permeability - Not all molecules can pass through selective channels

How do molecules move across the membrane?
o

Substrate (molecule to move across the membrane) binds to carrier protein

o

Molecule changes shape

23

o


Release of the molecule (product) at the other side of the membrane

Example
o

If you want to move a muscle a nerve impulse is sent to this muscle

o

The nerve impulse triggers the release of a neurotransmitter

o

Binding of the neurotransmitter to specific transmembrane proteins

o

Opens channels that allow the passage of Na+ across the membrane

o

In this specific case, the result is muscle contraction

o

These Na+ channels can also be opened by a change in voltage

Osmosis


Special term used for the diffusion of water through a differentially permeable cell membrane



Water is polar and able to pass through the lipid bilayer



Transmembrane proteins that form hydrophilic channels accelerate osmosis, but water is still able
to get through membrane without them



Osmosis generates pressure called osmotic pressure
o

Water moves down its concentration gradient

o

When pressure is equal on both sites net flow ceases (equilibrium)

o

The pressure is said to be hydrostatic (water-stopping)

Water potential


Measurement of the ability or tendency of water molecules to move



Water potential of distilled water is 0, other solutions have a negative water potential



Measured in kPa - pressure



Hypotonic
o

Solution is more dilute / has a lower conc. of solute / gains water by osmosis

o

Cells placed in a hypotonic solution will increase in size as water moves in

o

For example, red blood cells would swell and burst

o

Plant cells are unable to burst as they have a strong cellulose cell wall

24





Hypertonic
o

Solution with a higher conc. of solutes / loses water by osmosis

o

Cells will shrink in hypertonic solutions

Isotonic
o

Solutions being compared have equal conc. of solutes

o

Cells which are in an isotonic solution will not change their shape

o

The extracellular fluid of the body is isotonic



Molecules collide with membrane / creates pressure, water potential



More free water molecules, greater water potential, less negative



Solute molecules attract water molecules which form a "shell" around them
o

water molecules can no longer move freely

o

less "free water" which lowers water potential, more negative

Active Transport


Movement of solute against the conc. gradient, from low to high conc.



Involves materials which will not move directly through the bilayer



Molecules bind to specific carrier proteins / intrinsic proteins



Involves ATP by cells (mitochondria) / respiration
o

Direct Active Transport - transporters use hydrolysis to drive active transport

o

Indirect Active Transport - transporters use energy already stored in gradient of a directlypumped ion



Bilayer protein transports a solute molecule by undergoing a change in shape (induced fit)



Occurs in ion uptake by a plant root; glucose uptake by gut cells

Endocytosis and Exocytosis


Substances are transported across plasma membrane in bulk via small vesicles



Endocytosis
o

Part of the plasma membrane sinks into the cell

o

Forms a vesicle with substances from outside

o

Seals back onto the plasma membrane again

o

Phagocytosis: endocytosis brings solid material into the cell

25

o


Pinocytosis: endocytosis brings fluid materials into the cell

Exocytosis
o

Vesicle is formed in the cytoplasm //May form from an edge of the Golgi apparatus

o

Moves towards plasma membrane and fuses with plasma membrane

o

Contents are pushed outside cell

o

Insulin is secreted from cells in this way

26

Biochemistry of Respiration


Oxidative breakdown of organic molecules to store energy as ATP



Animals and plants respire; FAD and NAD are coenzymes

Aerobic respiration


C6H12O6 + 6O2 → 6CO2 + 6H2O + energy



Complete oxidation of an organic substrate to CO2 and H2O using free O2



Production of CO2, NADH + H+ and FADH + H+, 38ATP

1) Glycolysis → cytoplasm


Glucose enters cell by facilitated diffusion



ATP activates glucose to produce 2 unstable compounds



Substrate-level phosphorylation produces 4ATP



Net yield of 2ATP and 2reducedNAD per glucose molecule

2) Link reaction → matrix of mitochondria


Pyruvate enters matrix of mitochondrion for further reaction



Net yield of 2reducedNADH per glucose

3) Krebs cycle → matrix of mitochondria


Citrate is gradually broken down to re-form oxaloacetate



Substrate-level phosphorylation forms 2ATP



Removal of hydrogen from respiratory substrate



Net yield of 2ATP, 2reducedFADH, 6reducedNADH per glucose

4) Electron Transport Chain ETC → inner membrane/cristae of mitochondria


Reduced coenzymes arrive at ETC



Split into coenzyme + 2H+ + 2e- by hydrogen carriers



2e- are transferred to electron carriers (cytochrome)

27



Pass down ETC by redox reaction and release energy as they go



Energy produces ATP by oxidative phosphorylation



Final electron acceptor 1/2O2 is reduced by 2H+ and 2e- to produce H2O



Net yield of 34ATP (30NADH, 4FADH) per glucose



//Cytochromes are iron-containing proteins → cytochrome a3 also contains copper and is
irreversibly damaged by cyanide

IMG 5-14-8

Anaerobic respiration (fermentation)


Substrate-level phosphorylation: 2ADP + 2Pi → 2ATP directly by enzymes in glycolysis



No O2 to accept electrons from NADH + H+ → no Krebs cycle or ETC



NADH + H+ reduces (gives off H+ ions to) pyruvate to produce
o

Lactate C3 in animal cells → can be re-oxidised

o

Ethanol C2 in yeast cells → irreversible, CO2(g) lost



Regenerates NAD



NAD can be re-used to oxidise more RS/allows glycolysis to continue



Can still form ATP/release energy when O2 is in short supply

Role of ATP


Adenosine (ribose + adenine) triphosphate (3 phosphate groups)



Produced by adding Pi to ADP → phosphorylation



Breaks down to ADP (adenosine diphosphate) and Pi (inorganic phosphate ion) by hydrolysis



ATP is useful as an immediate energy source/carrier because
o

Energy release only involves a single reaction

o

Energy released in small quantities

o

Easily moved around inside cells, but cannot pass through cell membranes

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Light-dependent reaction cannot be the only source of ATP
o

"Photosynthesis cannot produce ATP in the dark

o

Need more ATP than can be produced in photosynthesis

o

Cannot be produced in plant cells lacking chlorophyll

o

ATP cannot be transported"1

Central molecule in metabolism (ATP hydrolysis)
o

Muscle contraction → changes of position of myosin head relative to actin

o

Protein synthesis → ATP "loads" amino acids onto tRNA

o

Active transport → driven by phosphorylation of membrane-bound proteins

o

Calvin Cycle → cyclic reduction of CO2 to TP

o

Nitrogen fixation → involves ATP-driven reduction of molecular nitrogen

ATP in liver is used for active transport / phagocytosis / synthesise of glucose, protein, DNA, RNA,
lipid, cholesterol / urea in glycolysis / bile production / cell division

Brown fat


White fat insulates the body and reduces heat loss



Brown fat cells in mitochondrial membrane produce heat



Mitochondria in other tissue / chemiosmosis



o

H+ ions pass back from space between two mitochondrial membranes into matrix

o

Through pores which are associated with the enzyme ATP synthetase

o

Energy from the ETC will be used to produce ATP

Mitochondria in brown fat
o

H+ ions flow back through channels not associated with ATP synthetase

o

Energy produces heat instead of ATP

o

Found in chest, larger arteries for heat distribution round the body or in hibernating
mammals

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