CH 4: AAs and Proteins Flashcards
What are proteins?
Macromolecules
Purpose: enzymes, hormones, receptros, channels, transporters, antibodies, and support
Why are side chains unique?
Variable R-group
Influence AA physical and chemical properties
What are the 2 Acidic/Hydrophilic AAs?
Aspartic acid (Asp) D
Glutamic Acid (Glu) E
E comes after D
What are the 3 Basic/Hydrophilic AAs?
HIstory of ARGentina was a LY
Lysine (Lys) K
Arginine (Arg) R
Histidine (His) H: “His goes both ways” proton donor or acceptor
What are the 9 HydroPHOBIC/NONpolar AAs?
- Glycine (Gly) G
- Alanine (Ala) A
- Valine (Val) V
- Leucine (Leu) L
- Isoleucine (Ile) I
- Phenylalanine (Phe) F
- Tryptophan (Trp) W
- Methionine (Met) M
- Proline (Pro) P
Phenylalanine and Tryptophan are aromatic
1st five: aliphatic (alkyl)
What are the 6 Polar/Hydrophilic AAs?
Neutral
STY CNQ
1. Serine (Ser) S
2. Threonine (Thr) T
3. Tyrosine (Tyr) Y
4. Asparagine (Asn) N
5. Glutamine (Gln) Q
6. Cysteine (Cys) C
What are the 2 sulfur-containing AAs?
- Cysteine (Cys) C: POLAR
- Methionine (Met) M: NONPOLAR
Why is Proline (Pro) P unique
Its amino group is covalently bound ot NP side chain
This forms a secondary alpha-amino structure and ring
What are the 9 essential AAs
PVT TIM HaLL
1. Lysine (Lys) K
2. Histidine (His) H
3. Threonine (Thr) T
4. Valine (Val) V
5. Leucine (Leu) L
6. Isoleucine (Ile) I
7. Phenylananine (Phe) F
8. Tryptophan (Trp) W
9. Methionine (Met) M
Which of the following AAs are most likely to be found on the exterior of a protein at pH 7.0
1. Leucine (Leu) L
2. Alanine (Ala) A
3. Serine (Ser) S
4. Isoleucine (Ile) I
- Serine POLAR
Amphoteric
Includes all AAs
Can act as acids of bases
Henderson-Hasselbalch Equation
Relationship bw pH, pKa, and equilibrium in acid-base rxn
pH= pKa + log ([A-]/[HA]) = pKa = log([base form]/[acid form])
When the pH of the solution is LESS than the pKa of an acidic group, the acidic group will mostly be in its…
protonated form
When the pH of the solution is GREATER than the pKa of an acidic group, the acidic group will mostly be in its…
DEprotonated form
Which functional group of AAs has a stronger tendency to donate protons: carboxyl groups (pKa = 2.0) or ammonium groups (pKa = 9)?
Which group will donate protons at the lowest pH (highest [H+])?
HIGH pKa = weak acid
LOW pKa = strong acid and DEprotonate easier
Carboxyl group
Ammonium group
Protonated (AKA acidic) form of an amine
pKa bw 9-10
Zwitterion
Molecule w positive and negative charges that balance
AKA dipole ion
Isoelectric point (pI)
pH at which a molecule is uncharged (zwitterionic)
Peptide bonds
Covalent bonds that link AA together into polypeptide chains
Disulfide Bridges
Covalent bonds bw cysteine R-groups
Backbone
NCCNCC pattern formed from AAs in polypeptides
Residue
Refers to individual AAs when part of polypeptide chain
Proteolysis or Proteolytic cleavage
Hydrolysis of protein by another protein
Proteolytic Enzyme or Protease
Protein that does cutting
Denatured
Improperly folded, non-functional proteins
Disrupt protein shape WO breaking peptide bonds
Can occur dt:
1. Urea (H-bonds)
2. pH extremes
3. Temperature extremes
4. Salt concentration (tonicity)
Primary Structure
AA order in polypeptide chain
Bond: peptide
Secondary Structure
Initial folding of polypeptide chain
a-helix and B-pleated sheet
Bonds: H-bonds,
What are the 2 types of B-pleated sheets
parallel and antiparallel
Tertiary Structure
Interactions bw AA residues located more distantly in the polypeptide chain
Bonds/interactions: hydrophobic/hydrophilic interactions
1. (N-C) van der Waals forces bw NP side chains
2. (N-C)H-bonds bw polar side chains
3. (Cov) Disulfide bonds bw cysteine residues
4. (N-C) Electrostatic interactions bw acidic and basic side chains
Hydrophobic Effect
HydroPHOBIC R-groups fold into interior of protein while hydroPHILIC R-groups are exposed to water on surface of protein
Quaternary Structure
Interaction bw polypeptide subunits
Bonds/interactions: same as tertiary
NO peptide bond involvement
Reaction coupling
A favorable rxn used to drive an unfavorable one
Possible dt additive free energy changes
Hydrolase
HYDROlyses (AKA breaks) chemical bonds
includes ATPases, proteases, etc
Isomerase
rearranges bonds win a molecule to form an ISOMER
Ligase
forms a chemical bond
EX: DNA ligase
Lyase
BREAKS chemical bonds
NOT BY oxidation or hydrolysis
EX: pyruvate decarboxylase
Kinase
transfers P group to a molecule from a HIGH energy carrier like ATP
EX: phosphofructokinase (PFK)
Oxidoreductase
runs redox rxns
EX: oxidases, reductases, dehydrogenases, etc
Polymerase
polymerization: addition of nucleotides to the leading strand of DNA by DNA polymerase III
Phosphatase
removes P group from a molecule
Phosphorylase
transfers P group to a molecule from inorganic phosphate
EX: glycogen phosphorylase
Protease
hydrolyzes peptide bonds
EX: trypsin, chymotrypsin, pepsin
Active site
region in an enzyme that’s directly involved in catalysis
Active site
region in an enzyme that’s directly involved in catalysis
Substrates
reactants in an enzyme catalyzed rxn
Active site model
AKA “lock and key hypothesis”
States: substrate and active site are perfectly complementary
Induced fit model
Substrate and active site differ SLIGHTLY in structure
Binding of the substrate induce conformational change in enzyme
Protease Active site
Protein cleaving
Active site has serine residue
OH group is NUC and attacks carbonyl C of an AA residue in polypeptide chain
Recognition Pocket
Usually found in proteases
Pocket in structure that attracts certain residues on substrate polypeptides
Cofactors
Metal ions or small molecules (not proteins)
Required for activity in many enzymes
Coenzyme
Organic molecule cofactor
Bind to substrate during the catalyzed reaction
Covalent Modification
Proteins can have diff groups covalently attached to them
Regulates activity, lifespan, and location
EX: P from ATP by protein kinase to hydroxyl of serine, threonine, or tyrosine
Phosphorylation either in/activates enzyme
Protein phosphorylases use INorganic phosphate INSTEAD of ATP
Protein phosphatases reverse phosphorylation
Proteolytic Cleavage
many enzymes/proteins synthesized in inactive forms (AKA zymogens)
Activated by cleavage by a protease
Consitutive Activity
When proteins show continuous rapid catalysis if their regulatory subunit is removed
Allosteric Regulation
Modification of active-site activity thru interactions of molecules w other specific sites on the enzyme
Noncovalent and reversible
Can increase or decrease catalysis
Feedback Inhibition (AKA negative feedback)
End product shuts off enzyme eaerlier in pathway
Feedforward Stimulation
Stimulation of enzyme by substrate or molecule used in synthesis of the substrate
Enzyme kinetics
Rate of formaiton of products from substrates in presence of enzyme
Reaction rate (V)
amt of product formed per unit time
mol/s
depends on substrate concentration [S] and enzyme
Saturated (Vmax)
when theres so much substrate that every active site is continuously occupied and adding more substrate doesn’t increase the reaction rate
Michaelis constant (Km)
substrate concentration where reaction velocity is half its max
Formula: Vmax/2
Positive Cooperativity
binding of substrate to one subunit increases the affinity of the other subunits for substrate
Negative Cooperativity
binding of substrate to one subunit reduces the affinity of other subunits for substrate
Competitive Inhibition
molecules compete w substrate for binding st active site
inhibition can be overcome by adding more substrate
then can outcompete the inhibitor (Vmx NOT affected)
can get to the same Vmax but takes more substrate (INCR Km)
Vmax NO change; Km INCR
Noncompetitive Inhibitors
Bind at allosteric site NOT active site
Amt of substrate added DOES NOT displace inhibitor from site (DECR Vmax)
Also affects Vmax/2
DOES NOT affect Km since substrate can still bind to active site BUT inhibitor prevents catalytic activity of the enzyme
Vmax DECR; Km NO change
Uncompetitive Inhibitor
Inhibitor only able to bind to the enzyme-subtrate complex
Bind to allosteric sites (like noncompetitive inh)
DECR Vmax (limit amt of E-S complex converted to product) and DECR Km
Vmax DECR; Km DECR
Mixed type inhibition
Inhibitor can bind to EITHER unoccupied enzyme of E-S complex
Km INCR
if enzyme has GREATER affinity for the inhibitor in free form
Km DECR
if E-S complex has greater affinity for inhibitor
if there’s EQUAL affinity in both forms–> actually noncompetitive
Vmax DECR; Km varies
Lineweaver-burk slope
Km/Vmax
lineweaver-burk y-int
1/Vmax
lineweaver-burk x-int
-1/Km
