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Biochem final Exam Study Guide, Study Guides, Projects, Research of Biochemistry

Virginia State University (VSU)Biochemistry

Biochem final Exam Study Guide

Typology: Study Guides, Projects, Research

2023/2024

Available from 07/23/2024

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Biochem final Exam Study Guide
1.first law of thermo: - energy conserved in a closed system
- ”E = Ef - Ei = q + w (heat + work)
- chemical bonds store energy
2.enthalpy: - energy available to do work
- ”H = E” + ”(PV)
- ”PV)=0 under 1 atm
- ”H = Hf - Hi
3.entropy: - universe tends towards disorder
- S” sys + ”Ssurr = ”Suni > 0
- Increases from s’l’g
- ”S° = S°f - S°i
4.Gibbs free energy: - ”G= 0 at equilibrium
- Q=Keq when at equilibrium
- Keq= 1 at equilibrium if dG°=0
- Keq > 1 prod favored
- Keq < 1 react favored
- ”G = Gprod - Greact
- ”Gtot = ”Grxn1 + Grxn2
- ”G = ”H - TS”
- G” - energy change
- ”G°- under std conditions
- ”G°'- under std biological conditions (1 atm, 298 K, pH 7)
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Biochem final Exam Study Guide

  1. first law of thermo: - energy conserved in a closed system
  • ”E = Ef - Ei = q + w (heat + work)
  • chemical bonds store energy
  1. enthalpy: - energy available to do work
  • ”H = E” + ”(PV)
  • ”PV)=0 under 1 atm
  • ”H = Hf - Hi
  1. entropy: - universe tends towards disorder
  • S” sys + ”Ssurr = ”Suni > 0
  • Increases from s’l’g
  • ”S° = S°f - S°i
  1. Gibbs free energy: - ”G= 0 at equilibrium
  • Q=Keq when at equilibrium
  • Keq= 1 at equilibrium if dG°=
  • Keq > 1 prod favored
  • Keq < 1 react favored
  • ”G = Gprod - Greact
  • ”Gtot = ”Grxn1 + Grxn
  • ”G = ”H - TS”
  • G” - energy change
  • ”G°- under std conditions
  • ”G°'- under std biological conditions (1 atm, 298 K, pH 7)
  1. le chatlier's principle: - initial rates are quicker and slow until equilibrium
  • ”G = G” ° + RTln(Q)
  • manipulating concentrations can change rxn direction
  1. acids/bases: - acid strength specified by Ka
  • pH=-log[H+]
  • acidic solutions have pH<
  1. henderson hasselbach: - to calculate pH for weak acid/base
  • pKa= pH + log (HA/A)
  • pH = pKa when acid and CB are equal
  • pH > pKa deprotonated form higher conc
  • 1 pH unit away= 90% protonated deprotonated
  • 2 pH unit away= 99% protonated deprotonated
  1. titration curve midpoint: - pH vs [H+]
  • pH at midpoint= pKa, where [HA] = [A-], flat slope, pH insensitive, added H+ and OH- react with A- or HA
  • buffering capacity max when pH=pKa
  1. polyprotic acids: - can lose more than 1 proton
  2. [H+] and [OH] in H2O: 1 x 10^-7 M for both Kw= [H+][OH-]= 1 x 10^- Keq= e^(-dG/RT)
  3. water: - strong dipole
  • surface tension
  • solid less dense
  • high heat of vaporization

tryptophan

  1. polar aa: serine threonine asparagine glutamine tyrosine +12. cysteine +8.
  2. isoelectric point: - pH at which net charge on molecule is 0
  • around 6 for average aa
  • pI= (pKa1 + pKa2)/ 2
  1. torsion angles: - phi= Calpha and N bond,
  • psi= Calpha and C bond
  • proline values limited to 60°
  • glycine is the only residue without a C beta atom (less hindered)
  1. Ramachandran plot: - allowed conformations of polypeptides
  2. a helix: - H-bonding, right handed
  • phi= 60, psi= 60
  • vanderwalls interactions in core
  • N terminus slightly +, C slightly -
  1. helical wheel diagram: n and n+4 are alpha bonded in the helix
  2. favored aa for a helix: skinny, long MALKR PG disfavored
  1. B-sheet: - H-bonding between strands
  • 2-22 polypeptide strands (usually about 6)
  • up to 15 reidue per strand (average 6)
  • side chaines alternate sides
  • antiparallel more stable
  1. B-sheet favored aa: TVIYWFL PG disfavored
  2. B-turns: PG
  3. tertiary structure: - may be separable through protease treatment
  • bi or multi lobule
  • globular
  • membrane- hydrophobic outside (a helix, helical bindle, B-barrel)
  • fibrous- repetative, insoluble, long narrow
  • intrinsically disordered- low hydrophobicity, alternating charge
  1. Hydropathicity Plot: - how hydrophobic aa sequence is
  • sustained peaks over 0 indicative of transmembrane helix
  • can tell if it's helix or not but thats it
  1. quaternary structure: - protein units coming together
  • homopolymer heteropolymer
  1. disulfide bonds: - covalent cysteines
  • stabilize tertiary and quaternary
  • strongest but don't make big contribution
  1. electrostatic interactions: ionic bonds
  1. protein folding models: - hydrophobic collapse model- aa greaseballs se- quester then secondary structures fold
  • framework model- secondary structures first
  • nucleation model- local tertiary fold first
  1. when folding fails: - amyloid fibers- stacked B-sheets held by side chain inter- actions
  • cross strand B-sheet interactions- side chains form H bonds, very stable but wrong
  1. preventing misfolding: chaperons- aide folding, recover heat- denatured pro- teins, requires ATP to defold
  • Hsp70 and GroEL/GroES protein disulfide isomerase- allows disulfides to reshuffle prolyl isomerase- allows transition between cis and trans proline
  1. protein purification techniques: density
  • centrifuge size
  • gel filtration chromotography
  • SDS-PAGE (denaturing gel electrophoresis) charge- ion exchange chromotography
  • isoelectric focusing
  • 2D electrophoresis specificity
  • affinity chromatography
  1. SDS-PAGE (denaturing gel electrophoresis): - polyacrylamide gel, apply elec- tric current (neg bottom pos top)
  • SDS denaturing agent gives protein neg charge
  • larger proteins move slower, small faster
  1. ion exchange chromotography: cation exchange- beads neg charged, pos proteins interact, neg pass through
  1. fraction bound: as [L] increases, fraction bound levels off
  2. classic binding: myoglobin, events independent, hyperbolic
  3. cooperativity: - hemoglobin, not a log scale, uptake and release over smaller concentration gradient
  • N (hill coefficient)- extend to which binding of one ligand influenced
  • slope increases as n increases -once n is not 1, Kd is no longer conc at 1/2 max binding
  • sigmoid
  1. miscroscopic Kd: equilibrium constant
  2. macroscopic Kd: one were calculating from curve
  3. hill plots: slope = n n always less than number subunits
  4. O2 binding models: T state- deox R state- ox concerted model
  • all subunits in T or R sequential model
  • mixture of T and R states, ripple
  1. homotrophic allostery: - same type of molecule as ligand influences affinity (O2 in hb)
  2. heterotrophic allostery: another molecule influences binding affinity
  • Bohr effect- acidify= lower pH= protonates hB= higher Kd, worse affinity
  • higher pH= higher affinity
  • 2,3-BPG- stabilizes T of Hb (deox state), increases Kd, bigger differential between tissues and lungs
  • allow milder conditions
  • specificity (few side products)
  • regulation capacity
  1. prochirality: enzyme can alter one end, orienting non-chiral molecules
  2. substrate binding: lock and key induced fit- binding induces structural change in protein
  3. catalytic strategies: - acid-base catalysis
  • covalent catalysis
  • metal-ion catalysis
  • approximation
  1. cosubstrate: used up in rxn
  2. cofactor: regenerated?
  3. acid-base catalyis: acid- protonate O to allow easier extraction of H from CH, decreases energy of TS base- to abstract proton
  • 2 neg charges, one more likely to retain neutral charge
  • pos on his makes cys deprotonate at lower pKa
  • neutral molecule more stable than charged in hydrophobic core
  1. covalent catalysis: - covalent intermediate formed during rxn
  • 1 TS into multiple
  1. metal ion catalysis: - metal arranges substrate in active site
  • mediates redox
  • activation of water
  1. approximation: - proximity of substrate reduces cost of TS formation
  • enzyme holds subtrates in correct orientation and proximity
  1. serine protease: covalent catalysis coupled with acidbase catalysis
  2. velocity: v= dprod/dt v= - dsubstrate/dt v= k[A][B] mol/s initial v highly dependent on starting concentrations
  3. michaelis menton model: E + S <==> ES <==> EP <==> E + P
  1. K3 not limiting- E + P rapidly disociate
  2. [P] so low that theres no back rxn (K-2=0)
  3. steady state equilibrium between E+S and ES= [ES] doesnt change
  • increasing [E] increases vmax
  • Km= [S] at 1/2 max
  1. lineweaver-burke plots: - Km= m/b
  • Vmax= 1/b
  1. Kcat: turnover weight Kcat=K Kcat= Vmax/[E]
  2. inhibitors: - reversible- competitive, uncompetitive, mixed
  • irreversible
  • activators
  1. competitive inhibiton: - Km increases, Vmax unchanged
  • can be outcompeted at high [S]
  • Vmax decreases, Km depends on a vs a'
  • noncomp- Ki=Ki', Km doesnt change because Km goes up and down by same factor
  1. irreversible inhibition: - inactivate enzyme
  • Koff=
  • permenantly reduces [E]t
  • Vmax reduced, Km doesnt change
  • will look like noncompetitive
  1. allostery and enzynes: - enzymes can have allosteric enhancers/inhibitors
  • ex. ATCase- ATP stimulates, CTP inhibits
  1. nucleotide: - nitrogenous base, sugar, phosphate group
  • ribose and deoxyribose phosphorylated to keep hem in cell
  • deoxy has H instead of 2' OH
  • purine= double ring AG
  • pyrimidine= single ring CG
  1. Hoogsteen base-pair: - N7 acts as acceptor
  • not in DNA
  1. GU wobble pair: - slight angle shift makes it less stable
  2. DNA forms: B- double right handed (normal) A- squished Z- left handed, uncoiling, relief for transcription
  3. DNA stabilization: - pi-stacking between rings
  • supercoiling around histones
  1. DNA melting temp: higher mp:
  • more GC
  • more salt in solvent stabilizes backbone
  • longer Tm= (#A/T)2 + (#G/C)
  1. metabolic flux: direction dependent on concentrations Q>Keq unfavorable Q<Keq favorable
  2. carbohydrate diagram: C1: down= a, up=B C2-4: right side= down C5: OH right/up in D sugar
  3. startch: - plants
  • amylose= a1-
  • amylopectin= a1-4 a1-4, more nonreducing ends, less soluble
  1. cellulose: - plants
  • B1-
  1. glycogen: - animals
  • a1-4 a1-
  • more branches than amylopectin
  • glycogenin (2 UDP-glucose= no reducing end)
  1. regulating glycogen degradation by glycogen phsophrylase: muscle cells
  • phosphorylation state- indirect, insulin causes phosphorylation= active= break down glycogen
  • allosteric AMP- AMP binds at low energy= R state= break down glycogen
  1. malate-aspartate shuttle: - liver, not common in mamal
  • NADH to make malate from oxaloactetate, transferred, converted back (no net loss ATP)
  • x2.
  1. glycerophosphate shuttle: - muscle, common in mamal
  • NADH converted to NAD+, e- transferred to FAD
  • x1.
  1. ATP synthetase: - stator
  • rotor
  • headpiece L- binds ADP + Pi T- ATP bound tightly O- ATP diffuses
  1. decoupling of ETC membrane: energy released through heat, thermogene- sis
  2. transketolase: 2C transfer (ketone donor) requires TPP
  3. transaldolase: 3C transfer, uses schiff's base to hold carbons
  4. lipid functions: - energy storage (triacylglycerides)
  • cell membranes (sphingolipids, glycerophospholipids)
  • endocrine signaling (cholesterol)
  1. hydrocarbon chains: saturated- solid fats, high mp, #C2- 1 (neg ion) monounsaturated- liquid oils, #C2- polyunsaturated- #C*2-
  2. Triacylglycerides: - energy
  • glycerol + 3 fatty acids
  1. essential fatty acids: - omega3 and 6 (counting from end)
  • alpha= count from branch