MCAT Biology

BIOCHEM

• 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

    • Citrate is Krebs Starting Cycle for Making Oxaloacetate 

  • 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

BIOLOGY

Class 4 - 20/06/24:

• Viruses: intracellular parasite

• Virus structure: made up of a capsid(coat) with a nucleic acid genome inside(Can’t have both DNA and RNA)

• Basic Steps: attachment(adsorption) - specific attachment but not infected yet; and injection - penetration - from bacterium to host

• Lytic Cycle: transcribe and translate viral genome; replicate; lysis of host

  • Early genes - hydrolase and capsid

  • Hydrolase: destroy host cell genome

    • Replicate genome

    • Lysis of host and release of viral particles

• Lysogenic Cycle: integrate viral genome into host then induce with normal host activity and excision and lytic cycle happens

  • Transduction - insertion of new DNA that was not present before

• Productive Cycle: does not destroy the host cell

• RNA Viral Genomes: can be both positive and negative types of RNA viruses

  • (+) RNA requires translation of RNA to protein - RNA dependant and RNA polymerases make the proteins

  • (-) RNA need a copy of RNA pol., and translate the now + RNA to proteins that negative

• Prions - do not follow central dogma because they are self-replicating proteins

  • No DNA/RNA

  • no membranes

  • no organelles

  • very small

  • extremely stable

• Prion categories = normal and mutagenic - mutant can lead to cell death

  • Mutant = Bad prions - come from a mutation in a prion, can be inherited, or by ingesting a bad prion → bad ones can make good ones bad too

• Viroids: circular RNA, no capsid, must be co-infected, no protein code - block translation

  • two different mechanisms make viroids -

    • one by taking negative RNA, translating it to positive RNA to form many +RNA to form viroid copies

    • One by taking -RNA and wrap +RNA to form a viroid copy

• Bacteria:

  • Can have three different shapes:

    • Round = coccus

    • Rod = bacilli

    • Spiral = spirillum

    • can have a flagella to move it or cilia

    • Bacteria have a cell wall and a cell membrane

  • gram + = stain dark and have a cell membrane covered by a cell membrane - easier to get in

  • gram - = stain light and have an inner membrane covered by a cell wall covered by an outer cell membrane - harder to get in

  • Temperature-dependent bacteria:

    • mesophiles → 30*C

    • Thermophiles → 100*C

    • psychrophiles → 0*C

  • Oxygen use Bacteria:

    • Obligate aerobe = use it and need it

    • Facultative anaerobe = can use it and survives

    • Tolerant anaerobe = doesn’t need it but can tolerate

    • Obligate anaerobe = can’t use it and can die due to O2

  • Energy/Nutrients of Bacteria

    • Photoauto = uses light and makes it on its own

    • Chemoauto = use chemicals by self

    • Photohetero = carnivorous plants

    • Chemohetero = need other energy sources

• Reproduction - use of binary fission to duplicate identical copies

• Binary Fission - growth follows an exponential growth pattern

• Conjugation(genetic Diversity) - helps to provide genetic diversity, rather than increase population size

  • horizontal gene transfer - donor-to-recipient transfer with direct contact

  • F- is the donor(male) and F+ is the female recipient - gives an F plasmid, not a genome

Class 5 - 27/06/24:

• Cell Biology and organelles

Cell Biology, colligative properties, membranes, mitosis, cancer

• Cell Biology and organelles → Eukaryotes

  • Nucleus and Nucleolus

  • Ribosomes

  • Rough ER

  • Smooth ER

  • Golgi apparatus

  • Lysosomes

  • Peroxisomes

• ALL transcription in the nucleus, and ALL translation in the cytosol

  • Secreted, transmembrane, lysosomal proteins are made in the Rough ER → resident proteins

• Start in the nucleus(transcription, mRNA processes) → goes to the cytosol(begin all translation) → some proteins finish translation in the Rough ER → signal sequence tells the 3 proteins made by the Rough ER

• Components of the cell membrane

  • Phospholipids - the membrane bilayer

  • Cholesterol - stabilizes membrane and keeps it fluid

  • Proteins

  • Carbohydrates

• Colligative properties depend on the number to solute but not their identity

  • Freezing point, boiling point, vapour pressure, osmotic pressure

• Electrolytes: free ions in a solution that come by dissolving ionic substances

  • ex. NaCl → Na + cl-

• Van’t Hoff factor: the number of ions produced per molecule of an electrolyte when dissolved in water

  • ex. NaCl = 2 → 2 ions are produced per NaCl molecule

• Freezing Point depression:

  • The freezing point of 1 KG H2O is OºC

  • FP depression Tf = -kf x i x m

    • kf water = 1.9℃

    • i = Van’t Hoff factor

    • m = # of moles

• Vapour pressure depression:

  • need to raise the temperature to boil and evaporate molecules in a liquid

• Boiling Point elevation:

  • BP Elevation Tb = kb x i x m

    • kb water = 0.5℃

• Osmotic pressure elevation: we care about the number of particles(that change osmolarity)

  • Osmotic pressure = particle [C]

  • TT = i x M x R x T

    • M = molarity

    • R = gas constant

    • T = temperature

• Diffusion: particles moving down a gradient → high [C] to low [C]

• Osmosis: movement of water → water moves from high [C] to low [C]

  • Hypertonic = more particles than…

  • Hypotonic = fewer particles than…

  • Isotonic = the same amount of particles than…

• Pressure is required to resist the movement of water by osmosis

  • osmotic pressure = particle [C]

    • ex. put a RBC(which is 0.9% NaCl into a beaker with 20% NaCl → water wants to leave the cell to equalize it, but the cell will shrivel → hypertonic

    • ex. put the same RBC into a beaker with 1% NaCl, very close to the RBC, some water leaves but not a lot → isotonic

• Passive transport: no energy is needed and relies on the concentration gradient for movement

  • Simple diffusion and facilitated diffusion

    • Simple → works well for small hydrophobic molecules, ex. steroids, CO2, O2, lipids

    • Facilitated → still moves down a gradient and uses small hydrophilic molecules ex. glucose, amino acids, ions, H2O → need helper protein

• Helper Proteins: pores, channels, porters

  • Pores: limits things in/out by size only

  • Channels: highly-specific → Na/K channels

  • Porter: can undergo a conformational change to move molecules → The shapeshifters

• Active transport: requires E and can move molecules without the need of concentration gradients

  • Primary: use ATP

    • Na/K pumps(every 2K for 3 Na)

    • K leak channels → can go by the concentration gradient

    • These maintain osmotic balance, establish e- gradient, set up gradient for secondary transport

• Secondary: uses ATP indirectly and relies on the setup of the primary

• G-Protein: adenylyl cyclase → makes cAMP → activate cAMP-dep kinases → phosphorylates enzymes and changes enzyme activity in cells

  • cAMP is a secondary messenger, signal amplification, fast and temporary

• Phospholipase C → breaks phosphoinostiol biphsophate → breaks into IP3 and DAG → DAG activates kinase and changes enzyme activity

• Cytoskeleton:

  • Microtubules: made of a and b tubulin and are large in diameter and are used for mitotic spindle, intracellular transport, and cilia/flagella

    • Cilia/flagella → 9 microtubules surrounding 2 lone tubules

  • Microfilament: made of actin protein, smaller in diameter, and used for muscle contraction, pseudopod formation, cytokinesis

  • Intermediate filament: several different protein types, medium in diameter, and used in many structural roles

• Cell Junctions:

  • desmosomes = general adhesive junctions

  • tight junctions: seal lumens and separate environments

  • Lumen also has gap junction → cell-to-cell communication

• Cell Cycle: Interphase to mitosis(PMAT)

  • Sister chromatids: absolutely identical → same order, genes, alleles

  • Homologous chromosomes: same genes, same order, but can have different alleles

  • Interpahse: cell growth and synthesis of DNA

    • G1 = cell growth, normal cell activities,

    • S = synthesis of DNA and DNA replication

    • G2 = growth and prepare for mitosis

  • Mitosis = PMAT → ends with two identical daughter cells similar to the parent

    • Prophase: condense DNA, form mitotic spindle, nuclear membrane breaks down

    • Metaphase: chromosomes align on the center

    • Anaphase: the sister chromatids separate and travel to the ends of the two poles and begin cytokinesis

    • Telophase: reverse prophase(DNA un-condenses and nuclear membrane forms again) - cytokinesis finishes

• Cancer: mutation to DNA, starts from a single cell with mutations, goes through the cell cycle rapidly and out of control, spreads to other tissue → Metatsis

  • Two types of Cancer genes: oncogenes and tumour suppressors

• Proto-oncogenes: genes are normally present in the cell and code for proteins that regulate the cell cycle →

  • Active types: fetal development, growth, and healing

  • Inactive types: when healing or growth is not required

• Oncogenes: the mutated version of proto-oncogenes that are permanently on(always active and dividing)

• Tumour suppressor genes: code for proteins that stop the cell cycle, and monitor the genome of cells in the cell cycle, if DNA damaged they initiate repair mechanisms, if DNA cannot be repaired then they initiate cell death(apoptosis)

  • If they lose their function to save or get rid of mutations, cancers can come from those mutations that were not ‘killed’ off by apoptosis

Class 6 - 01/07/24:

• Meiosis - making of 4 cells that differ from the parent cell and each other

  • Non-disjunction - failure to separate DNA during meiosis

• Genetics - study of genes

  • Allele - the genes found on a chromosome

  • Trait - the characteristic that appears from the alleles

    • Polymorphic - several types of one trait

    • polygenic - several genes that determine a trait

• Classical Dominance: homozygous dominant/recessive, heterozygous

  • Genotype: combination of alleles

  • Phenotype: physical characteristics

• Incomplete: display a blend of the parental phenotypes

  • ex. red flower RR x white flower WW = pink flower RW

• Co-dominance: both alleles are expressed independently and at the same time

  • Ex. Blood types → I^A I^B i

• Epistasis: dominance between two different genes - one gene can mask or modify the expression of another gene ex. Albinism

• Test-cross: where one of an unknown genotype is crossed with another of a homozygous recessive genotype

• Backcross - F1 x P

• Mendel’s Laws

  • Law of segregation - alleles separate during gamete formation

  • Law of independent assortment - one allele is independent of another allele

• Single-gene crosses - 4 types

  • Homozygote 1 x Homozygote 1

  • Homozygous dominant x homozygous recessive

  • heterozygote x homozygote dom/rec

  • heterozygoye x heterozygote

• Rules of Probability

  • A AND B - multiply the probabilities

  • A OR B - add individual probabilities

• Linked Genes: genes found close together on the chromosome

  • Dihybrid crosses = crosses between two traits

    • F1xF1 = 9:3:3:1 → unlinked

    • F1xHomozygous recessive Parent = 1:1:1:1 → unlinked

      • When the actual ratio differs from this, they will be linked genes as they don’t follow the expected ratios

• Recombination: genes that do not assort independently

  • recombination frequency = # recombinants/total offspring x 100

    • Tells us the map units(mu) distance between genes on the chromosome

      • 1 mu = 1 cM(Centimorgan)

• Hardy Weinberg: tells us that allele frequencies within a population do not change from generation to generation

  • p + q = 1 → allele frequency where p = dominant allele and q = recessive allele

  • pp + 2pg + qq = 1 → genotype frequency where 2pq is the heterozygous allele

• 5 Conditions where Hardy-Weinberg hold true:

  • No mutation

  • No natural selection

  • No migration

  • Total random mating

  • Large population size

Class 7 - 10/07/2024:

• Neuron Structure

  • Specialized cells of the nervous system

    • Have a soma(central), dendrites, axon. axon terminus

    • Dendrites receive signals

    • Axon sends off signals

      • Axon has myelin covering it

        • Speeds and protects the axon

  • Types of Neurons:

    • Multipolar - connects and receives from many neurons

    • Bipolar - depends on the direction of the synapse - two-sided

    • Unipolar - soma is attached to one node only

• Resting Potentials

  • at -70mV

  • sodium/potassium pump out one net positive ion, creating a Na/K gradient

  • many + ions lost via K leakage channels

  • The result is that the cell is more negative inside than outside

• Action Potentials

  • When the cell reaches positive levels to send a signal across the neuron - All or None event

    • Depolarization - cell becomes more positive

    • Hyper polarization - when the cell becomes more negative

    • Repolarization - return to rest

    • Equilibrium potential - when there is no driving force on the ion, neither +/-

• At -70mV → resting potential

• At -55 → threshold - Na+ channels open

• Depolarization upto +35mV - Na+ channels inactivate and K+ fully open

• Hyperpolarization to -90mV - Na+ and K+ close

• Repolarization to -70mV by Na/K pumps

  • This happens in a matter of 2-3 msec

• Nerve Impulse: by a synapse from neuron-neuron or neuron-organ junction

• Refractory Periods

  • Absolute: not able to fire a second action potential due to Na channels being inactive and the cell is too positive at the moment

  • Relative refractory period: there is a small chance of firing a second AP since Na channels are closed and the cell is too negative

• Electrical Synapse - relatively rare but important in muscle cells

  • Require:

    • Physical connections - gap junctions

    • Always excitatory - AP in post synapse

    • Bi-directional - either pre/post synapse

    • Unregulated

• Chemical Synapse - more common - transport of neurotransmitters

  • One neuron can only make one type of NT but can respond to many

  • NT in the synaptic cleft can be re-uptaken or broken down

  • Response of the post-synapse depends on the receptors, not the NT

  • Need more than one vesicle of NT to make a change to post-synapse

• EPSPs and IPSPs

  • EPSP = excitatory post-synaptic potential → Many accumulate to make an action potential - help reach the threshold

  • IPSP = inhibitory post-synaptic potential → Many accumulate to prevent an AP from reaching a threshold

  • EPSP and IPSP can cancel each other out

• Summation

  • Spatial: The add-up of inputs from multiple sources

  • Temporal: the add-up of frequent impulses from a single source

• General System Functions

  • Sensory Input - PNS

    • Info coming into the CNS

    • carried on the sensory neurons → afferent → towards CNS

  • Integration - CNS

    • decision making

    • interneurons - entirely contained within the CNS

  • Motor Output - PNS

    • commands sent out to the body

    • Carried on the motor neurons → efferent → exit CNS

• Reflexes

  • rapid integration to avoid potential injury

    • Patellar tendon stretch reflex

• CNS Anatomy

  • Telencephalon: cerebrum

    • Cerebral hemispheres - left and right - connected by the corpus callosum

    • Cerebral cortex - divided into 4 lobes

      • Frontal - complex processes and voluntary movement

      • Parietal - general sensations - touch, temperature, taste

      • Temporal lobe - sound and audition and olfactory, STM, language

      • Occipital lobe - Visual sensations

• Diencephalon:

  • Epithalamus: Pineal gland and secretion of melatonin - links to the limbic system

  • Thalamus: sensory - all sensory (except olfactory)

  • Hypothalamus: sends hormones to the pituitary - primary link to endocrine - homeostasis and behaviour/emotions

• Hindbrain:

  • cerebellum - movement and balance

  • Medulla - controls vital autonomic functions and relays info between other areas - respiratory centers located here

  • pons - the role is posture and balance

• Spinal Cord: connects brain and body and is protected by the CSF

• Limbic System: works for emotion and memory

• White Matter vs Grey Matter:

  • White: myelinated axons - cell-to-cell communication

    • CNS to brain = Tract

    • CNS to cord = tract/column

    • PNS = nerve

  • Grey: non-myelinated axons - decision-making

    • CNS to deep brain = nucleus

    • CNS to brain surface = cortex(conscious mind)

    • CNS to cord = horn

    • PNS = ganglion

• PNS

  • all nerves and sensory systems outside of the CNS

• Somatic vs Autonomic

  • Somatic = voluntary control of the skeletal muscles

    • uses Ach only, excitatory only, single neuron effector

  • Autonomic = involuntary control of glands and smooth muscle

    • uses Ach and Norepinephrine, can be excitatory or inhibitory, a chain of two effectors

• Parasympathetic vs. Sympathetic

  • Para = rest and digest

    • decrease HR, breathing, BP

    • Increase Digestion

    • release Ach to organs either inhibit(heart rate down) or excite(increase digest)

  • Symp = fight or flight

    • Fight, flight, fright, sex

    • increase body activity

    • decrease digestion

    • increase blood flow to skeletal muscles

    • release norepinephrine at the organ level

• Sensory receptors - 5 Classes:

  • mechanoreceptors: by physical shape changes, touch

  • Chemoreceptors: by chemicals, pH, O2, taste buds

  • Thermoreceptors: stimulated by temperature, hot or cold

  • Nociceptors: stimulated by pain, free nerve endings, chemicals, heat

  • Photoreceptors: by light, rods and cones

• General Sensory Processing

  • Absolute threshold: the minimum stimulus required to trigger a receptor

  • Difference threshold: how much a stimulus must change to detect it

  • Sensory adaption: receptor stops responding to constant stimulus

    • pain receptors do not adapt

• Bottom-up processing:

  • from the environment to the brain → sensory receptors take in the info, send to the brain, and the brain uses the info

• Top-down processing:

  • from inside to environment → brain applies prior knowledge to identify the environment

• Visual System

• Cone cells: colour vision, stimulated in light only - three kinds: red, green, blue

  • in the Fovea centralis only

• Rod cells: susceptible to light and work in low light conditions

  • Concentrated in the retina

• Auditory System

Class 8 - 20/07/24:

Endocrine system, Cardiovascular system, Immune system

• Endocrine system: hormones → through the bloodstream → no ducts

• Exocrine system: hormones by way of ducts → into the intestinal lumen

• Peptide hormones: made from amino acids, the receptor is on the cell surface, 2nd messengers, fast effects but temporary

• Steroid hormones: made from cholesterol, intracellular binding, binds to DNA and modifies transcription, effects are slower but last longer

• Mechanisms to control hormone release: neural, hormonal, humoral(in the blood)

• Hypothalmus - pituitary: The hypothalamus controls neurally and humoral while the pituitary has divided control

  • Anterior pituitary: made of gland tissue, secretes six major hormones: FLAT PIG

    • Has hormones making cells and many veins

  • Posterior Pituitary: made of nervous tissue, stores and secretes two hormones - Oxytocin and ADH

    • Many neurons and capillaries

• Blood vessels: Veins and arteries

  • Veins: lower pressure, blood moves back to the heart - more rigid and made of collagen

  • Arteries: higher pressure, moves blood away from the heart - more elastic and can control dilation/constriction

  • Capillaries - smallest in size but largest SA → can exchange products like O2

  • The inner layer of blood vessels is endothelial cells

• The heart - 4 chambers:

• Blood carries from aorta to body → vena cava carries blood back to heart from body → into the right atrium → to the right ventricle → to the pulmonary artery to the lungs(deox) → blood coems back from the lungs into the pulmonary veins(oxy) → into left atrum → into left ventricle → to the aorta

• Systole: ventricular contraction - empty

• Diastole: ventricular filling

  • Lub Dub:

    • Lub: close AV valves and begin systole

    • Dub close SL valves and begin diastole

  • systole/diastole = Blood Pressure

  • BP is directly proportional to CO and peripheral resistance

• CO = cardiac output = stoke volume x HR

  • volume pumped per minute x beats per minute

  • Stroke volume = change in blood volume, activity level, posture

• Peripheral resistance = how hard it is to move blood through the vessels

  • Vasoconstriction and Vasodilation

    • Constrict = smaller diameter, lower flow, higher resistance, higher BP

    • Dilate = larger diameter, higher flow, lower resistance, lower BP

• Tetany - tetanic contraction = involuntary muscle contraction from overstimulated neurons and low Ca levels

• Cardiac cell potential: slow opening of CA+ channels, fast depolarization to 20+, then potassium channels open and repolarization back - unstable resting potential due to NA leakages

• Cardiac Conduction: SA node → AV node → HIS Bundle → purkinje Fibers

• Blood composition: 54% plasma, 45% RBC, 1% leukocytes/WBC

• Oxygen Dissociation Curve: oxygen is 3% dissolved in plasma and 97% dissolved in Hb → The higher the O2 levels, the higher Hb saturation, and the more it is exchanged to tissues

• Immunity:

  • Antigen: a foreign protein that can trigger an immune response

  • Antibody: specific marker for anti-gen

  • Pathogen: disease-causing organism

• B cells - humoral immunity - make antibodies

  • Produce and secrete antibodies into the blood - when stimulated, will clone into thousands of B cells to enhance antibody production - rearrange antibody genes(DNA) to generate antibody diversity

• T cells - kill virus-infected cells, and tumour cells, and control the immune response(helper T cells)

• MHC 1 → found on all cells, allows to display of cell contents

• MHC 2 → macrophages and B cells, allows cells to display eaten stuff on the cell surface

• Classes of Antibodies:

Class 9 - 27/07/24:

Renal and Digestive Systems

• Excreroty organs:

  • Colon - elliminates solid waste - material not absorbed into the blood

  • Liver - eliminates hydrophobic wate - material too hydrophoboc to be dissolved into the plasma

  • Kidney: eliminates hydrophilic waste - material eaten and absorbed into teh blood and is dissolved into the plasma

• Kidney -> ureyer -> bladder -> internal sphincter -> external sphincter -> urethra

  • Kidney has the ureter that connects to the renal pelvis, to the medulla and meddulary pyraminds, to the nephrons -> outer side of the kidney is the cortex

• 3 processes to produce urine: 

  • filtration(moving a substance across a membrane using pressure

  • Reabsorption(move a substance from the filterate to the blood(glucose, amino acids, water) -> glomerular filteration 

  • Secretion: move a substance from the blood to the filterate(drugs, toxins, creatine)

• Nephron Sturcture: 

  • Afferent arteriols comes into the glomerulus laeds to the PCT(mostly reabsorption and secretion), then to teh loop of henle - decending is permeabl;e to H2O and the ascending is permeable to salt - DCT is speacialized for absorption and reabsorption then the collecting duct(regulated H2O reabsorption)

• Urine and Blood flow are opposites

• Renin-Angiotensin system: 

  • Angiotensinogen -> angiotensin 1 -> angiotensin 2 -> increases release of aldosterone and leads to sysemic vasocontriction

• Juxtaglomerular apparatus(JGA): contact point between afferent arteriole and distal convoluted tubule

  • Afferent = baroreceptor

  • Distal = chemoreceptor

• ANP - blood pressure regulation:

  • High BP -> arteria of heart stretch -> right atrium releases atrial natriuretic peptide(ANP) -> vasodilation and inhibits renin release

Class 10 - 01/08/24:

Musculoskeletal System and Respiratory System

• Skeletal muscle overview: voluntary function, on the bones, multinucleate and striated appearance

• Hierarchy:

  • protein filament - actin and myosin → they do not shorten

  • Sarcomere - a unit of contraction → Shortening happens here → depolarization

    • 1 sarcomere is one Z line to the next Z line

    • Actin, thin filaments are held by the Z line

    • The myosin, thick filaments, is centred in each sarcomere but doesn’t reach the Z line

    • The I band (isotropic) are the regions with full actin or ½ actin

    • The A band(anisotropic) are the regions where there are both actin and myosin - it is both dark and light - ends at the ends of the myosin

    • H zone is the light zone where there is only myosin and no overlap with actin

    • M line is the middle of the sarcomere

  • Myofibril

    • Covered by sarcoplasmic reticulum(holds Ca)

    • T-tubules - the plasma membrane goes in deep to help action potential travel to the interior of the cell

  • Muscle cell - myofiber

  • Fascicle

  • Whole muscle

• Sliding Filament Theory:

  • Myosin binds to actin (cross bridge formation)→ needs calcium

  • myosin pulls actin towards the center of the sarcomere - power stroke → myosin returns to low-E state

  • Myosin release actin → needs ATP but doesn’t break it down

  • Myosin resets to high-E → ATP hydrolysis

• When you run out of ATP, you can’t relax

• Excitation-contraction coupling:

  • Excitation - depolarize, open voltage-gated Ca channels

  • Troponin binds Ca and changes shape, lifts tropomyosin off myosin binding sites, and myosin binds to actin

  • Contraction occurs

• Motor Neuron - a neuron and all teh muscle cells it controls

  • Contraction of the motor unit is all or none

  • Contraction of the whole muscle is graded

• Large vs. Small:

  • Large is 1000s of m/n

  • Small is 10-20 m/n

• Gross motor control - a few large motor units

• Fine motor control - many many small motor units

• Muscle Energy:

  • Fastest source of E = Creatine (substrate-level phosphorylation)→ reversible process

  • Medium source of E = Glycolysis(fermentation) - 2 ATP per glucose and lactic acid

  • Slowest source of E = aerobic respiration → 30 ATP, H2O, CO2 → store O2(myoglobin)

• Oxygen Debt - extra O2 needed after exercise

  • replenish O2 stores on myoglobin

  • convert lactic acid into something useful → back into pyruvate

• How to repay O2 debt? Bohr effect → pH and temp changes after O2 is used, then Hb is changed - rather than holding lots of O2, gives more of it back to tissues

• Skeletal Muscle Types:

• Slow Twitch- more myoglobin, more blood vessels, slow contraction, higher mitochondria, higher fatigue resistance, the low force generated

• Fast Twitch IIA: medium level of myoglobin and blood vessels, faster contraction, medium mitochondria levels, medium resistance to fatigue, medium force generated

• Fast Twitch 11B: low myoglobin levels, lesser capillary network, fast contraction and higher force, lower mitochondria, lower fatigue resistance

  • Fast twitch makes more glycolytic enzymes - more glycolysis

• Cardiac and Smooth Muscle

  • Cardiac = auto, involuntary, only in heart(vessels have smooth muscle) - uninucleate - striated appearance → the filaments overlap(difference is that some of the calcium for contraction comes from the extracellular environment)

  • Smooth muscle = involuntary, neural, mechanical, hormonally stimulated; located in the walls of hollow organs; uninucleated; non-striated but has bundles of actin and myosin and still needs calcium

• 4 different tissues:

  • Muscle

  • Neural

  • Epithelial

    • First three mostly cells

  • Connective - mostly non-living

• Connective tissue: cells in a matrix

  • matrix is made of fibers and glop(ground substance)

    • Fibers are made of collagen and elastic fibres

    • glop is the glue that holds everything

      • Liquid or solid → blood plasma or bone → in between is cartilage

  • osteoblasts - form new bone - can still divide and make the matrix

  • osteoclasts - break down bone

  • -cyte cells: the mature cells - don’t divide

• Bone helps:

  • Support and movement

  • Store minerals - calcium and phosphate

  • Protection

  • blood cell formation

• Osteoporosis - bone creation is slower than its removal → Weak and brittle bones

• Long Bone anatomy:

  • Shaft = Diaphysis

  • Ends = Epiphysis - holds spongy bone that makes RBC

  • Core = medullary cavity = yellow bone marrow(fat)

  • Surrounding core is compact bone

  • Epiphyseal plate = growth plate

    • ossification greater than cell division

• Compact bone:

  • Osteons → have a central canal → central canal hold blood vessels → central canal made of rings that hold osteocytes

• Bone Turnover:

  • PTH and Calcitonin

    • PTH - increases blood calcium by dissolving bones, increases Ca absorption in intestines and kidneys

    • Calcitonin - builds bone back, and decreases intestinal and kidney absorption

  • Vitamin D(calcitriol) - increases PTH effects and absorption in kidneys

  • osteoclasts - dissolve bone - eat bone, not like bone cells

• Respiratory System:

  • Gas exchange and pH regulation

  • Ventilation = move in the air and out

  • Respiration = gas exchange (External and Internal)

• Conduction zone = ventilation only

  • Air drawn in by the nose → nasal cavity → warmed up and filtered here → tissue is respiratory epithelium(mucus cells and cilia) → air to pharynx(naso, oro and laryngo pharynx) → air to larynx and travels down to trachea → separates to R/L primary bronchi → travels to secondary Bronchi in lobes → travels to tertiary bronchi → travels to terminal bronchioles to reach the respiratory bronchioles

    • The larynx is all cartilage → keeps airways open and separates air and food(epiglottis) and helps produce sound

    • Trachea: a muscle lined with cartilage rings and connective tissue membrane → The muscle can contract and pull the rings together → increases the speed of airflow(ex. coughing)

    • Primary bronchi → cartilage rings → cilia cells

    • Secondary bronchi → oddly shaped cartilage rings, some smooth muscles → short cells, no cilia

    • Tertiary bronchi → all smooth muscle, no cartilage → no cilia, short cells

• Respiratory zone = Gas exchange

  • Air travels from respiratory bronchioles to alveolar ducts → enters alveolar sac and gas exchanges occur in the alveoli by capillary network surrounding the sac → O2 is released into blood and CO2 is picked up → CO2 travels back outside the lungs

    • Alveolar cells:

      • Type 1 = walls of alveoli

      • Type 2 = secrete surfactant → makes breathing easier and reduces tension/friction

• The Lungs: there are two of them → The right lobe has 2 parts and the left lobe has 3

  • lungs stick to chest cavity due to surface tension and slight negative pleural pressure(Inhale) → pressure wants to go positive, hence, becomes like environment(exhale)

  • Inspiration: Active → contraction of the diaphragm

  • Relaxed expiration: Passive → Diaphragm contracts

  • Forced expiration: Active → abdominal muscles contract

• Skin: has 3 layers

  • Epidermis: epithelial tissue

  • Dermis: connective tissue

  • Hypodermis: fat

• Thermoregulaton:

  • Cold = no sweat, shivering, vasocontriction

  • Hot = sweat, no shivers, vasodilation