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
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
28
•
•
•
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