Class 1 - 01/06/2024:

• Macromolecules - are polymers made from monomers - enzymes that make polymers are polymerases via reactions called polymerization.

• Proteins: made up of amino acids(20 kinds)

  • Have an N-C-C backbone, amine group, carboxylic group, and variable group

  • Bond together by a peptide bond(formed by dehydration synthesis - loss of H2O)

  • 4 types of structures

    • Primary = amino acids joined

    • Secondary = alpha-helix or beta-sheets

    • Tertiary: formation of a polypeptide and side chain interactions - inner core becomes hydrophobic and outer becomes hydrophilic

      • Non-covalent interactions: non-polar/non-polar, polar neutral/polar neutral, acid/base(charged)

      • Covalent: disulphide bridges(harder to break)

    • Quaternary structure: side chain interactions between different polypeptides - subunits come to form larger units

• Carbohydrates: from monosaccharides to disaccharides to polysaccharides;

  • monosaccharides - CnH2On - 3 common are glucose, fructose, galactose - ribose and deoxyribose

  • Disaccharides - 2 monosaccharides - 3 common = maltose, sucrose, lactose - C12H22O11 formula

  • Polysaccharides: many monosaccharides - 3 common are glycogen, starch, and cellulose - function as an energy source

• Lipids: the fats - made of a hydrocarbon structure(many C and H) - saturated fatty acids are solid at room temperature

  

  • Unsaturated are liquid at room temperature due to the double bond

  • Triglyceride: 3 fatty acids combined

  

  • Phospholipids: 2 lipid structures and one phosphate - form the lipid bilayer due to having polar and non-polar sides

    

  • Terpenes: built from isoprene structures and need at least 2 of them - terpenes form waxes and lipid rings like vitamin A

  • Cholesterol and steroid hormones - 3 six-carbon rings and 1 five-carbon ring)

• Thermodynamics: delta G = delta H - TdeltaS

  • G = Gibbs free energy

  • H = enthalpy (potential E)

  • T = temperature

  • S = Entropy (kinetic E)

  • When G<0 = negative G, spontaneous - gives E - exergonic

  • When G>0 = positive, non-spontaneous - needs E - endergonic

  • When G = 0, equilibrium

• Reaction Coupling - using ATP as a source of energy - a very favourable reaction is used to drive an unfavourable one

  • ATP = ADP + Pi → very exergonic

    • Exergonic = giving off E

    • Endergonic = using up E

• Chemical Kinetics: the study of reaction rates - all reaction rates proceed through a transition state which tends to be unstable

  • Activation E = is the required E to produce the TS

  • if Ea is High = slow rate

  • if Ea is low = faster rate

• Reaction Coordinate Graph - shows the energy vs reaction coordinates over time - the smaller the Ea, the better

  • We can make the Ea smaller using catalysts - speeding the reaction up by stabilizing TS and reducing Ea

  

Enzymes: a physiological catalyst - works to speed up a reaction by increasing the rate of reaction, not used up in a reaction, and must be specific

• Structure: an enzyme has an allosteric site and an active site - the active site is where the substrate binds(where the reaction occurs) and the allosteric site is another place for enzyme regulation(inhibition or activation)

  • Two models - active site and induced fit; active is lock and key while the induced fit is when the enzyme needs to change shape to fit a substrate

  • Can perform both positive and negative feedback

• Function: to speed up a reaction

• Regulation: by many inhibitions ways, allosteric site, feedback inhibition

• V vs. [S] Graph: reaction rate in Velocity vs the substrate concentration [S] → vmax is when the enzyme is saturated and depends on enzyme [C], and the [S] becomes constant - Vmax/2 is when the linear part of the graph is equal to [S]

• Km is the substrate [S] required to reach ½ Vmax

• Enzyme Inhibition:

  • Competitive: compete for enzyme binding - same Vmax but the effect on Km is more since you need more substrate - a longer time to reach the same Km - binds at the active site - before substrate binds

  • Non-competitive: it affects the Vmax since we need more enzymes to deal with the substrate, but Km is unchanged since the active site is the same but prevents the activity of the enzyme- binds to the allosteric site before substrate binds

  • Un-competitive: it affects both the Vmax and Km since it binds to the allosteric site after the substrate is bound, which affects both enzyme performance and the amount of product being produced - binds to an allosteric site after the substrate binds

  • Mixed-Type Inhibition: binds at the allosteric site either when the enzyme is bound to the substrate or empty active site. Vmax will become lowered, but Km can vary whether enzyme bound or empty Active site

    • when bound to the substrate, Km decreases(like un-comp)

    • When empty active site, Km increases(like comp)

    

• Lineweaver Burk Plots:

  

Class 2 - 08/06/2024:

• Oxidation-Reduction Reactions - Redox

  • Oxidation is when you gain O, lose H and electrons

  • Reduction is when you lose O, gain H and electron

• Cellular Respiration: When you convert sugar and O2 into carbon dioxide and water

  • a four-step process - glycolysis, PDC, Krebs, and electron transport

• Glycolysis

  • processed in the cytoplasm and doesn’t need O2

  • all cells from all domains perform glycolysis → Sugar split into two pyruvate molecules and 4 ATP and 2 NADH formed at the end

  • Step 1: Got a phosphate from ATP and a glucose → Hexokinase → bam, G-6-P and ADP

  • Step 2: Got a G-6-P and a isomerization → Bam, F-6-P

  • Step 3: Got a F-6-P and an ATP → bam, F1-6-bp and ADP

  • Step 4: Split F1 into two to form 2×3CP

  • Step 5: add 2pi to 2×3CP → Form 2 PEP 2×3CP

  • Step 6: 2 PEP plus 2ADP → Pyruvate kinase → 2 Pyruvate

• PDC - Pyruvate Dehydrogenase Complex: occurs in the matrix of the mitochondria and needs O2

  • Pyruvate is changed from being a 3C molecule to a 2 C molecule and CO2 and NADH are produced; this is from taking pyruvate and coenzyme A to make acetyl-coA

  • Oxidative Decarboxylation does this: release of CO2 and make NADH

• Krebs Cycle: Occurs in the matrix of the Mitochondria and needs O2- Takes 2xacetyl-coA with oxaloacetate to make 2xCO2, NADH and FADH2

  • In order:

    • 2C + Oxaloacetate → citrate(6C) → NADH + CO2 → 5C → NADH and CO2 → 4c → GTP → succinate → fumarate → malate → oxalacetate

• ETC and Oxidative Phosphorylation: occurs in the inner membrane of the mitochondria and needs O2

  • OP is the oxidation of NADH and FADH2 to make ADP into ATP → This makes energy move e- transport chain and pumps protons out of the mitochondria

  • ETC is a chain of 5 e- carriers that perform redox roles(cytochromes)

    • Step 1: NAHD dehydrogenase → reduce NADH, pass e

    • Step 2: coenzyme Q → release FAD from FADH, pass e

    • Step 3: cytochrome C reductase → passes e to next

    • Step 4: cytochrome C oxidase → makes H2O and send to ATP synthase to make ATP

• Total ATP of respiration = 30 ATP made in Euk, and 32 in Prok

• Fermentation

• Gluconeogenesis: the formation of glucose from 2 pyruvates (reverse of glycolysis but some different unique enzymes) - Happens in the body when glycogen stores are depleted in the liver

  • 2 pyruvate with pyruvate carboxylase forms 2 oxaloacetate

  • PEP carboxykinase makes 2 PEP

  • 2 PEP is turned into 2×3CP to then F16CP

  • F16CP is then turned into F6CP to G-6-P

  • G-6-P with glucose-6-phosphatase to make glucose

• Glycogenesis: the formation of glycogen from glucose

  • made by using G-6-P to G-1-P by phosphoglucomutase and then using UDP to make UDP-glucose which is turned into glycogen by glycogen synthase

• Glycogenolysis: breakdown of glycogen to glucose

  • Here glycogen is phosphorylated into G-1-P then isomerized to G-6-P to make glucose again

  • happens in the liver

  • Insulin increases when glucose is high to make glycogen - stores energy for later

• Pentose Phosphate Pathway: takes G-6-P to form NADPH and ribose-5-phosphate. NADPH is important in its role of reducing the power of fatty acid synthesis and helps neutralize reactive O2 species as well as make the building block for nucleotides

• Fatty Acid Oxidation: the fat digestion - the removal of 2C units as acetyl-CoA from a fatty acid and makes 1 FADH2 and 1 NADh - the acetyl is then moved to Krebs or ketone bodies

  • dietary fat chylomicrons move from the lymph system to the liver and organs and then undergo beta-oxidation which then turns the fatty acid into acetyl-coA

• Fatty Acid Synthesis: uses high amounts of ATP and NADPH where 2C units are added to the chain until 16C fat is made

  • using acetyl-coA to make malonyl-CoA

• Ketogenesis: during starvation, acetyl-coA turns into ketone bodies and can supply energy to the brain and lower blood pH

• Protein Catabolism: break down of protein by proteases to amino acids

• Metabolism: when the body is fed, glycolysis, glycogenesis, and fatty acid synthesis is favoured. When the body is starved, glycogenolysis, glucogenesis, and fatty acid oxidation are favoured.

Class 3 - 15/06/24:

• Nucleotide: made up of sugar, base, and phosphates

  • Sugar = deoxyribose or ribose

  • Base = ACTG

  • Phosphates = 3 linked together

• Nucleic Acid Structure: 5’-3’ linkage, antiparallel and complementary, phosphodiester bonds

  • Pyrimindines = U, T, C(smaller)

  • Purines = A, G(bigger)

  • A-T, C-G, A-U(in RNA)

• DNA structure:

  • in prokaryotes, circular DNA genome, formed by methylation, and supercoiling

  • in eukaryotes, several linear chromosomes → (biggest)chromosome, to chromatin, to histones bound to make nucleosomes, to make smaller DNA strands(smallest)

• Centromere: the middle of the chromosome where the spindle fibres attach to - made of heterochromatin and repetitive DNA sequences - short sequences repeat - both single and double-stranded DNA which can loop to form a knot at the end of the chromosome to stabilize it

• Telomere: the ends of a eukaryotic linear chromosome - also has a hand in aging

• DNA protection: the tighter it is, the less likely it will be uncoiled

• The Central Dogma: DNA leads to transcription to RNA that leads to the translation of proteins - the unidirectional flow is a fundamental law - genetic code is by the use of Codons

  • 3 nucleotides = 1 amino acid → 3 bases make a codon

• Codons = words of amino acids

  • Start: AUG

  • Stop = UAA, UAG, UGA

• Humans have 24 chromosomes(including sex), three billion nucleotides, 21000 genes, and large intergenic regions → Everyone is unique

• Mutations: Can be fatal, silent, inside or outside damages

  • Polymerase errors = point mutations, small repeats, insert/deletion, frame-shifts

  • Endogenous damages(physical, reactive O2 species) = oxidized DNA, cross-linked bases, double/single-strand breaks

  • Exogenous damage(radiation, chemicals) = UV, x-rays, chemicals

  • Transposons = large insertions/deletions, inversions, duplications

• Point Mutation: missense, nonsense, silent

• transposons: mobile genetic elements - old and defective

  • They can cut and paste by transposase enzyme, and can paste it somewhere else

  • if inserted in the intergenic region, it has no effect. if inserted in the coding region, can become mutagenic

• Mutation repair:

  • Bad bases: mismatch pathway, nucleotide repair

    • Mismatch: during or after replication - parent strand is methylated, but the daughter is not → can identify parent-daughter

    • Nucleotide Excision repair: can happen at any time in the cell cycle - removes the bad base and replaces it with a good one(ideally before replication)

  • Broken chromosome: homology-directed repair, non-homologous joining

    • Homology-directed: must happen after replication when a sister chromatid is present and must use an identical sister chromatid as a template to fix the broken chromosome

    • Non-homologous end-joining: happens anytime in teh cell cycle and ligate ends are broken together - can be mutagenic since this causes loss of some bases or translocations

  • DNA rearrangement by transposons: can’t repair

• DNA Replication:

  • 4 General rules: semiconservative, 5’-3’, requires RNA primer, and needs a template

  • 5 Main enzymes of replication:

    • Helicase - unwinds DNA

    • Topoisomerase - cuts DNA and relaxes teh supercoiling

    • Primase - synthesizes RNA primer

    • DNA polymerase - replicates the DNA and proofreads

    • Ligase - Links Okazaki fragments

  • Replication starts at the ORI - starts to go from the 5’ end to 3’, both sides in opposite directions

  • In Eukaryotes, many replication bubbles formed(many ORI)

  • Ends of the chromosomes become shortened after replication - shorter telomeres

• Prokaryotic DNA Polymerases:

  • Pol. 2: 5’-3’ AND 3’-5’ exonuclease

    • back-up for DNA Pol.3 and repairs DNA

  • Pol. 1 and 3: are more error-prone 5’-3’ and repair DNA

• Telomerase: elongate the telomeres on the parent strand of the DNA - cells that express telomerase are known as immortal cells ex. spermatogonia, stem cells, cancer cells

  • Has RNA primers and reverse transcriptase enzyme

• DNA vs. RNA:

  • DNA is double-stranded, has thymine, deoxyribose sugar, double helix, one type

  • RNA is single-stranded, has uracil, ribose sugar, many 3D shapes, many types

  • Types of RNA - rRNA, tRNA, mRNA, hnRNA, miRNA, siRNA

• Replication vs. Transcription:

  • Replication has a start site. is in the 5’-3’ direction, has a DNA template

  • Transcription has a stop site, no primer, and no editing - the start for translation

    • Regulated by a promoter - higher affinity for RNA polymerase to get a lot of RNA, has DNA binding proteins, repressors and enhancers

• Transcription in Prox. vs Euk:

  • Prokaryotes: transcription and translation at the same time, no mRNA processing, polycistronic, 1 RNA polymerase

  • Eukaryotes: transcription and translation separate, has mRNA processing(poly-A tail, 5’ G cap, splicing), monocistronic(one RNA, one protein), 3 RNA polymerases

• tRNA and Wobble Pairing:

  • tRNA: transfer RNA - responsible for translocation → has an anticoding region to pair with RNA to code amino acids using codons - needs two ATP to load amino acids

  • The first two bind by Watson-Crick pairing - the third is more flexible, and adenine can be converted into I for more flexibility

  • Wobble base pairing: makes it such that the first two must be the same, but the third, Wobble area, can be flexible - allows for non-traditional pairing

• Ribosomes for Translation: have a large subunit and a small subunit

  • Euk: 60s and 40s → 80s total

  • Prok": 50s and 30s → 70s total

  • In translation, RNA enters the A site and the new-forming amino acid is added to the P site - it stops when a release factor binds and breaks teh bond between the final tRNA and the final amino acid

• Energy Count: translation uses a total of 200 ATP, and is most used in tRNA loading

  • the # of amino acids x 4 = # ATP needed

• Post-translational Modification:

  • Protein folding - by chaperonins

  • Covalent modification - disulphide bridges, phosphorylation, etc

  • Processing - cleavage to form active protein