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72 Cards in this Set

  • Front
  • Back
Amino Acids-
standard amino acids- 20 amino acids used in most protein synthesis
Amino Acids
standard amino acids- 20 amino acids used in most protein synthesis
Carboxyl group
alpha carbon
amino group
R- group – gives amino acid its specific properties in proteins
- can act as both an acid (COOH)and a base (NH2)
have both + and – charge at neutral pH
Amino acid Classes
Neutral nonpolar
Neutral Polar
Acidic, Basic, Other
AA Neutral nonpolar
A. Aromatic- have unsaturated cyclic hydrocarbons
Phe Trp
B. Aliphatic- non aromatic
gly ala val Leu Ile Met Cys Pro, gly-
high degree of freedom
Pro- 2ndary amine rigid structure
cys- sulfhydryl group reactive
disulfide bonds- cys-cys linkages part of tertiary protein structure
AA Neutral Polar
form Hydrogen bonds interact with water found in active sites of enzymes
ser thr tyr asn gln
AA Acidic
acid r groups, - charge at neutral pH
asp glu
AA Basic-
+ charge at neutral pH
Arg lys His
His- partially ionized at neutral pH acts as buffe
Other Amino Acids
1. Chemical messengers neurotransmitters
2. Precursors for other biological molecules
nucleotides, heme, chlorophyll
3. metabolic intermediates
urea cycle
Isoelectric point
pH at which the molecule has no net charge-
pI =(pK1 + pK2) / 2
Structure of dipeptide
No rotation about peptide bond
resonance stabilization
main chain- repetitive series linked by peptide bonds
side chains- R groups
Calpha – N bond angle = phi
Calpha – C bond angle = psi
polypeptide chains less than 50 residues long
relatively simple structure
many biological functions
Glutathione- acts as antioxidant reduces HOOH
HOOH binds hemoglobin→ forms methemoglobin→ can’t bind O2
longer than 50 residues
classified by function, shape and composition
Proteins Shape
fibrous or globular
Protein Composition-
simple proteins- contain only amino acids
conjugated proteins- have prosthetic group
Apoprotein- conjugated protein without prosthetic group
holoprotein-with prosthetic group, multiple types
Protein structure
Primary, secondary, (alpha, beta, turns), super secondary, Tertiary
Primary Structure
dictates all further organization
homologous proteins – have similar primary structure→ usually similar in function
used as a measure of evolutionary relationship
Secondary Structure
localized repeating patterns
stabilized by H-bonds
Phi and psi are equal in all residues in the pattern
R groups dictate the bond angles
Alpha helix
Type of secondary structure
- rigid rod like structure
a. right hand coil
b. tightly packed
c. H-bonds between the NH2 group of one residue and the COO group of the a.a. four residues away
d. 3.6 residues /turn
e. R groups on outer surface of helix
f. 54 nm pitch
Beta Sheet
extended structure composed of beta strands
beta strands are H bonded to adjacent beta strands
2 structures-
1. parallel – adjacent strands run in the same direction
2. antiparallel – adjacent strands run in opposite directions more stable than parallel sheets due to more efficient H bonds
Beta turn
omega loop
t looser turn usually has binding functionight turn about 4 amino acid,
Super secondary structure
. - localized arrangement of secondary structures:
1. Beta-alpha-beta-two beta sheets are linked by an alpha helix
2. Beta meander- series of antiparallel beta sheets
3. Alpha Alpha unit – 2 alpha helices linked by turn
4. Beta barrel – beta sheet folds up on itself to form tube
Tertiary Structure
three-dimensional conformation of a protein
Forces involved in tertiary structure
Hydrophobic interactions, Ionic bonds, Hydrogen bonds, London forces, Covalent bonds
Quaternary Structure
- similar type of interactions that occur in tertiary structure but between two different polypeptide chains
Polymeric proteins- proteins that contain multiple subunits
Homopolymers- one type of subunit
Heteropolymers- different types of subunits
Small molecule that binds a specific site on a protein
binding of a ligand effects the binding of subsequent ligands, causes conformational change in protein structure.
Two types of allosteric effectors:
homotropic- substrate molecules
heterotropic- other molecules
- binding of one substrate molecule leads to an increased affinity for subsequent substrate molecules
Protein –Ligand interactions:
Ka = [PL]/ [P] [L]
[L] >>> [P]
[L] = [L]T
essentially, the free ligand is equal to the total ligand
The association constant
Ka[L] = [PL] / [P]
occupied binding sites/ total binding sites
dissociation constant
Kd () = 1/Ka
= [L] / ([L] +Kd)
hemoglobin A – present in adult humans
tetramer :
2 alpha-subunits
each subunit contains a heme prosthetic group
heme- protoporphorin ring with bound Fe2+
Fe2+ - coordinated on 4 sites by heme, 5th site by his, 6th site binds O2
Tense to Relaxed transition:
corresponds to low affinity to high affinity binding modes
mechanism of transition from T to R
0.4 angstrom movement of Fe movement of coordinated His
His pulls associated alpha-helix C-terminus of alpha-helix is at dimer interface rotation of dimers with respect to each other  communication between subunits
2,3 Bisphosphoglycerate (2,3-BPG
)- binds a pocket present only in T form
stabilizes the T form ↓ O2 affinity:
At lungs O2 binds T form  displaces 2,3-BPG
At tissues low O2 leads to dissociation of O2 RT transition BPG binds  further dissociation of O2 and no O2 binding (prevents back reaction)
The Bohr Effect
- H+ and CO2 promote the release of O2

Metabolically active tissues (muscle) produce high concentrations of H+ and CO2
Low pH
decrease in O2 affinity for Hgb
His 146- when protonated it forms salt bridge with asp 94  stabilization of T form
binds amino terminus
 forms carbamate anion
 forms salt bridges at interface
 stabilizes T form
Delta G‡ = - RT ln[S‡]/[S]
S‡=Transition state
How do enzymes reduce the activation energy
Formation of enzyme-substrate complex (ES complex)- enzymes bring substrates together in favorable conformations.
Evidence for ES complex
1. Enzymes are saturable- enzyme catalyzed reactions reach a maximal velocity at high sustrate concentration.
2. X-ray crystallography – high resolution images of enzymes bound to substrate or substrate analogs.
3. Spectroscopic studies- many enzymes spectroscopic properties are altered upon substrate binding
Active sites:
1. Active sites form 3D cleft – a.a.s from distant regions in the 1o sequence make up a cleft or crevice. usually hydrophobic, with certain polar or charged residues critical to substrate binding.
2. Active sites represent a small portion of total volume of enzyme.
3. Substrates bind through multiple weak interactions → the active site and substrate must have complementary shapes.
4. Specificity depends on the precise arrangement of atoms in the active site.
lock and key model
enzyme has exact complementarity to substrate
Induced fit
Enzyme changes shape upon substrate binding.
Michaelis-Menton Model
reaction velocity varies with substrate concentration and approaches a maximum velocity asymptotically
What is this
See image
What is this
The Michaelis-Menton equation
KM = (k-1 k2)/k1
Lineweaver- Burke:

1/Vo = 1/Vmax + KM/Vmax * 1/[S]
Significance of KM and Vmax

1. Km = substrate concentration where ½ active sites are filled
provides a measure of substrate required for catalysis:

set [S] = KM
then V0 = Vmax (1/2)
if KM is known fES can be calculated at any [S]:
fES = V0/Vmax = [S]/[S]+ KM
2. KM is related to rate constants-
KM = (k-1 +k2)/ k1
So if k2 <<< k-1
then KM = k-1/k1 = Kd = dissociation constant
3. Vmax = k2 [E]t
k2 = Vmax/[E]t = turnover number
V0 = k2 [ES]

[ES] = [E][S]/ KM
V0 = k2/ KM [E][S]
k2/KM = k2/(k2+k-1) x k1 < k1
catalytic perfection
this implies all enzyme substrate interactions are productive
Circe effect
electrostatic forces entice the substrate into the active site
Enzyme Inhibitors
1.bind enzyme with high affinity. Covalent or noncovalent.
Penicillin- covalently binds transpeptidase blocks cell wall synthesis killls bacteria
Aspirin- binds cyclooxygenase  blocks inflammatory response.
Rapid dissociation of E-I complex.
1.Competitive- inhibitor mimics substrate  binds to active site and prevents substrate binding.
2.Noncompetitive inhibition- Inhibitor binds outside active site.
Blocks catalysis  decreases turnover number
3.Uncompetitive Inhibition- inhibitor only binds to ES complex; affects KM and Vmax Not very common
Which chart is which inhibitor?
Allosteric Enzymes
Don’t obey M and M kinetics.
Contain multiple subunits
multiple active sites- binding of substrate to 1 active site affects the others
binding of substrate to one active site  increased affinity of other active sites for substrate
Enzyme Mechanism
Four basic strategies:
1. Covalent catalysis- active sit contains a reactive group, often a nucleophile. forms temporary covalent bond with some aspect of substrate.
2. General Acid –Base catalysis- Involves proton transfer. Histidine is a good proton donor and acceptor.
3. Metal ion catalysis:
a. act as electrophilic catalyst- stabilize a negative charge
b. generate a nucleophile – increase acidity of a moiety.
c. may bind substrate
4. Catalysis by approximation- bring two substrates into proper orientation.
- protease, cleaves on the carboxyl side of aromatic or large hydrophobic residues
burst phase
initial rate of product formation was much greater than rate at steady state.
Active Site
contains catalytic triad:
ser195- H-bonded to
his57- H-bonded to
Mechanism of chymotrypsin catalysed peptide hydrolysis
1. Substrate Binding
2. alkoxide anion (OH group of ser195)- attacks carbonyl center of peptide bond  forms unstable tetrahedral intermediate.
(-) charge on O derived from carbonyl center.

oxyanion hole – contains NH3 groups from gly193 and ser195
stabilize the transition state and oxyanion
3. e- from peptide bond transferred to proton from (+) his57 cleavage of peptide bond and formation of primary amine H-bonded to his57.
4. Departure of amino product
5. H-bonding of H2O to His57
6. HOH attacks the carbonyl center of acyl-enzyme intermediate (ser195 OH)  forms tetrahedral intermediate
7. Collapses to form the carboxylic product
8. Release of product frees the enzyme
Enzyme Regulation
1. Allosterism
2. Isoenzymes
3. Reversible Covalent modification (Phosphorylation)
4. Proteolytic activation
Proteolytic cleavage
zymogens are activated by cleavage of one or more peptide bonds to produce active enzyme.
How does enzyme set up?
Like this
Enzyme set at work
cAMP binding sites – 2 on each R subu