Biochem Review

Amino Acid

Non-polar Amino Acids

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, and Proline

Glycine

Gly, G

Alanine

Ala, A

Valine

Val, V

Leucine

Leu, L

Isoleucine

LIe, I

Methionine

Met, M

Proline

Pro, P

Aromatic Hydrophobic

Tryptophan, Tyrosine, and PhenylAlanine

Tryptophan

Trp, W

Tyrosine

Tyr, Y

Phenylalanine

Phe, F

Polar

Serine, Threonine, Asparagine, Glutamine, and Cysteine

Serine

Ser,S

Threonine

Thr, T

Asparagine*

Asn, N

Glutamine

Gln, Q

Cysteine

Cys, C

Acidic

Aspartic Acid and Glutamic Acid

Aspartic Acid (at a neutral pH, it would be a basic COO-)

Asp, D

Glutamic Acid

Glu, E

Basic

Arginine, Lysine, and Histidine

Arginine

Arg, R

Lysine *

Lys, K

Histidine (at a neutral pH, one amino group is protonated)

His, H

Amphoteric

accept or donate protons

-Under acidic conditions, gain protons

-Under basic conditions, lose protons

NH3 would be protonated to NH4+.

At a pH= 1, what would happen to an AA?

Amino would be protonated and carboxyl would be deprotonated.

At a pH=7, what would happen to an AA?

The carbonyl group would be deprotonated.

At a pH=10, what would happen to AA?

Condensation or dehydration (removal of water)

How to peptide bonds form? (Two processes)

N-terminus

What end does translation start at?

Primary

Linear arrangement to encode for higher levels

-Sequencing can be done here

Secondary

Hydrogen bonding between alpha (Keratin) and beta (fibroin) kinky :)

Tertiary

3D structure of hydrophobic areas facing inward and hydrophilic facing outward (disulfide bond)

Quart-nary

More than one polypeptide with subunits involved

For example, hemoglobin and immunoglobin

More stable by lower surface area, lower amount of DNA needed, Bring catalytic sites closer

Cooperatively or allosteric effects

Several Roles in 4th structure

Prosthetics

organic (vitamins) or metal (Fe)

For example, lipoproteins, glycoproteins, and nucleoproteins along with heme

Denaturation

Interactions between the hydrophobic interactions (higher temperature) or bonds broken between disulfide bridges and HB (urea) lessens a proteins ability to function

SDS

Detergents that solubilize proteins, disrupting covalent bonds, and promoting denaturation

What do enzymes do?

Does not change H, G, or Keq

Lower activation energy

Increases rate of reaction

Appears in reactants and products

pH and temperature

Specific

LIL' HOT

Acronym for type of enzymes

Ligases

addition or synthesis that requires ATP

For example, synthase

Isomerases

rearrangement of bonds

For example, oxireductase, transferase, or ligases

Lyases

cleavage of a single molecule without water

For example, sythnases

Hydrolyases

cleavages of a single molecule with water

For example, phosphates, peptidase, lipase, and nucleases

Oxireductase

NAD+, dehydrogenase, or reductase

Transferase

movement of functional group from one molecule to another

For example, aminotransferase for the TCA or Kinases with pi

Michaelis Menton

Endergonic

Delta G is positive (non-spontaneous)

Exergonic

Delta G is negative (spontaneous) which can reduce energy when released

Yes mam! :)

Can enzymes provide a favorable microenvironment in terms of charge and pH

Hydrogen Bonding, Ionic Interactions, and transient covalent bonds

What interactions lie within an active site?

Lock n' Key

Already in an appropriate conformation for the substrate to bind

-No alternation of tertiary or quartnery structure

Induced Fit Model

The substrate induces a change in the shape of the enzyme (requires energy: endergonic)

Alters between relaxed and tight phase

Apoenzyme

inactive form of enzyme without cofactor

Holoenzyme

active form of enzyme with cofactor

Cofactor

Inorganic, such as metals and dietary minerals

Coenzymes

Small and organic, such as NAD+, Coenzyme A, and vitamins

Water Based Vitamins

B and C

Fat Based Vitamins

A D E K

Km

the lower the Km then the higher affinity for substrate (adding more substrate or enzyme will not affect Km because it strictly deals with ES complex)

K2+K3/K1

V0

(Vmax x [S]) / (Km +[S])

Reaction Mechanism

E+S--> ES--> EP (K1 and K2) ... (K3)

Lineweaver Plot

Cooperatively

Allosteric Sites with a sigmoidal shaped curve

For example, heme or PFK1 in glycolysis

R State

Higher affinity for substrate

T State

Lower affinity for substrate

Temperature ( Higher-> denature)

pH (pH= 7.4)

Salinity ( Interrupts ionic and hydrogen bonding, slight change in conformation, which may lead to denaturing)

What are some local conditions that affect enzyme activity? (Name 3)

Competitive

Noncompetitive

Uncompetitive

Mixed

What are the four reversible inhibitors?

Competitive

Binds directly to active site

Increases the Km

No change in Vmax

Noncompetitive

Binds "equally" to either enzyme or ES complex

Lowers Vmax