Biochemistry Exam 2

Biochemistry Exam 2

1. Theme E: binding sites

   • Binding sites of proteins
     • P- proteins L- ligands Ps binds to Ls (which are smaller molecules) This is the first step to performing various functions
     • functions
       • Enzymes (P) bind to substrates, products & activators
       • Hormone receptors bind to hormones
       • Immunoglobins bind to antigens
       • Hemoglobin & myoglobin bind to O2 and CO2
     • interaction between P and L takes place @ binding site
     • Oligometric protein= more than 1 binding site
     • catalytic proteins binding site= active ite
   • Properties of binding sites
     • site is small
     • occurs in cavity on the protein's surface
     • binding site is complex (3D)
       • consists of groups of amino acid residues
         • from different parts of the linear amino acid chain
       • these groups are brought together by polypeptide folding
     • water is excluded from cavity
       • helps to prevent ligand from having to compete with water 
     • cavity contains polar residues
       • necessary for specificity & catalysis (in enzymes)
     • non-polar residues
       • makes it more energetically favorable for a non-polar ligand to bind (hydrophobic effect)
     • ligands bind to proteins through weak non-covalent forces
       • bonds that play a role in ligand binding
         • electrostatic
         • hydrogen
         • v/d Waals
         • hydrophobic interactions
   • Specificity of ligand binding
     • depends on arrangement of atoms in binding site
     • ligands only bind when the site is complementary
     • Fisher's lock & key hypothesis
       • if they dont fit 100% the reaction wont happen
       • enzyme = lock
       • substrate = key
     • Koshland's induced fit model
       • ligand binds specifically to protein but only after a conformational change is brought about  -by binding -makes site complementary

2. Theme F:

   • type of enzymatic reactions
     • redox
       • enzyme: oxidoreductases A*- + B ->  A + B*-
     • single replacement
       • enzyme: transferases AB + C -> A + BC
     • double replacement / acid/base
       • enzyme: hydrolases AB + CD -> AC + BD
     • decomposition
       • Enzyme: lysases AB -> A + B
     • isomerisation
       • enzyme: isomerases AB -> BA
       • L formation to D formation
     • synthesis
       • enzyme: ligases A + B -> AB
   • chemical kinetics
     • reaction rate
       • (V) amount of product formed per unit time
   • transition states & reaction rates
     • free energy of substrates & products does NOT affect RXN rate
     • rxn proceeds via high energy state
     • transition state
       • intermediate between substrate & product high free energy
   • Enzymes as catalysts
     • -enzymes speed up rxns by 10^8 to 10^13 -decreases activation energy -eqm remains unchanged
     • weak binding of substrate
       • -binding of substrate may not be too strong -Km must be optimised for effective catalysis    -low enough for proximity of         substances    -high enough that ES -complex     is not too stable
     • proximity effect
       • -correct positioning of substrates    -lowers degree of freedom
     • induced fit
       • -during substrate binding there's a distortion of structure towards the transition state
     • stabilisation of transition state
       • -enzymes bind to transition state stronger than to substrate most important factor in the speed up of rxns
     • mechanisms of enzyme action
       • nucleophilic substitution
         • nucleophilic substitution: -nucleophile:   - e- rich   - (-) charged   - unshared electron pair-electrophile    - e- poor    - (+) charged    -empty orbital redox reactions: -oxidation    -loss of electron    -caused by oxidising agent         which gets reduced -reduction    -gain of electrons    -caused by reducing agent         which gets oxidised -biological oxidation    -addition of oxygen    -removal of e-
     • chemical catalysis
       • acid/base catalysis
         • -increases the rate of rxn through catalytic proton ttransfer -catalysed by H+ or OH- diffusing out of solution (specific a/b) -H+ or OH- formed in transition state by another molecule or group (general a/b)    -general acid vs general base    -ionisable group will have pKa        close to pH
       • covalent catalysis
   • Effect of pH on enzyme activity
     • different optimum pH for different enzymes
     • change in pH causes change in shape & charge of substrate
     • substrate cannot bind to active sire or undergo catalysis
   • Serine proteases
     • class of enzymes- hydrolyse peptide bonds in (digestive)protein
     • Ser: a catalytic amino acid residue
     • enzyme family
       • Trypsin
         • positive charged residue -Lys, Arg
       • Chemotrypsin
         • large hydrophobic residue -Tyr, Phe, Trp, Leu
       • Elastase
         • small side chain -Gly, Ala
   • Reversible enzyme inhibition
     • inhibitor: -a small molecule binds reversibly to an enzyme and influences the activity of that enzyme
     • Competitive
       • E + I = EI
       • Km = increases
       • decrease in substrate affinity
       • doesn't influence Vmax
       • SKEW X ON Y-AXIS
     • Uncompetitive
       • ES + I = ESI
       • Km = decreases
       • TWO PARALELL LINES
     • Mixed
       • SKEW X NOT ON Y-AXIS
       • Kic not = Kiu
     • Non-competitive
       • Kic = Kiu
   • Regulation of enzyme activity
     • what controls enzyme activity?
       • substrate level control
         • -substrate increases rate -product reduces rate
       • feedback control
         • -prevents accumulation of intermediates
     • allosteric regulation
       • regulatory molecule binds to different area to active site
         • area where molecule binds is known as allosteric site
     • properties of alllosteric enzymes
       • -generally have multiple active sites -activity changes due to metabolic activators and inhibitors -allosteric modulators bind non-covalently to enzyme
     • covalent modification
       • -activity of enzyme can be modulated by covalent attachment or removal of groups -slower than allosteric regulation -reversible but requires enzymes that catalyse the conversion -modified enzymes can be regulated allosterically or covalently

3. Theme G

   • Cofactors
     • -ions or molecules that are bound to proteins to aid in catalysis -can increase catalytic scope of enzymes
     • essential ions
       • activator iond
         • -loose -participate in binding of substrate
       • metal ions
         • -tight -participate directly in catalysis
     • coenzymes
       • cosubstrates
         • -loose -group transfer reagents
       • prosthetic group
         • -tight -group-transfer reagents
   • Essential ions
     • -most enzymes need essential ions for full catalytic activity -held by covalent bonds from amino acid side chains -can also be bound in prosthetic group
     • metal-activated enzymes
       • K+ Mg 2+ Ca 2+ Mg-ATP (Mg stabilizes phosphate bonds)
     • metalioenzymes
       • Zn Fe Cu Co
     • metals & trace elements
   • Coenzymes
     • -classified based on interaction with apo-enzyme
     • cosubstrates
       • -act as substrate in enzyme-catalysed rxns -chemically unchanged -dissociate to be converted by another enzyme ti the original form
     • prosthetic groups
       • -remain attached to enzyme-catalyzed rxns -sometimes covalently bound to enzyme (otherwise strong non-covalent bonds) converted back to original form during rxn
   • Cosubstrate -> NAD+ & NADP+
     • -nicotinamide adenine dinucleotide (phosphate) -coenzyme in redox rxns
     • oxidised form (oxidising agent)
       • Hydride donor
     • reduced form (reducing agent)
       • Hydride acceptor
     • hydride ion transfer
     • enzyme: dehydrogenase
       • -enzyme that converts alcohol to aldehyde or ketone
   • Cosubstrate => coenzyme A (CoA)
     • -many metabolic processes depend on CoA -responsible for transfer (activation) of acyl groups
     • acyl group transfer/activation
       • what is an acyl group? -usually derived from carbox acids -formula for acyl is: R - C=O -
     • Acetyl-CoA
       • -key metabolite  -metabolises: fats, proteins and carbs
   • Prosthetic group => FAD & FMN
     • FAD = Flavin adenine dinucleotide
     • FMN = Flavin mononucleotide
     • derived from riboflavin
       • coenzymes in redox reactions
         • strong non-covalent bonds
   • Lipid vitamins
     • Vit A
       • trans-retinol
       • gene expression & vision
     • Vit D
       • D3 = cholecalciferol
       • Ca 2+ utilisation control
     • Vit E
       • alpha - tocopherol
       • anti-oxedant
     • Vit K
       • phylloquinone
       • protein modification rxn -> blood clotting

4. Theme H

   • Carbohydrates
   • Glyceryde
   • Fisher projections
   • Sterioisomers
   • Dihydroxyacetone
   • Cyclisation of Aldoses & ketoses
   • Alpha vs Beta Anomers
   • Hexose Rings
   • Conformations of Monosaccharides
     • Derivatives of Monosaccharides
   • Sugar Phosphates
     • Sugar Alcohols
       • Sugar Acids
         • Amino Sugars
           • Deoxy Sugars
   • Common Monosaccharide Abbreviations
   • Disaccharides
   • Polysaccharides
   • Reducig Sugars
   • Starch
   • Storage Polysaccharides
   • Structural Polysaccharide
   • Cellulose
   • Chitin
   • Glycocongugates