KA MCAT BIO

Reverse transcription

Conversion of RNA to DNA is called ____

Epigenetics

How different phenotypes can come from same DNA sequence (DNA methylation, Histone modification)

Peptide

Bond between two amino acids

N terminal
C terminal

End of a polypeptide with an amino group

End of a polypeptide with a carboxyl group

Acid hydrolysis
Proteolysis

(Methods of breaking down proteins)

Breaks all peptide bonds with strong acid and heat

Breaks specific peptide bonds with proteases

Histidine

Special amino acid with pKa similar to physiological ph (Can exist in protonated and deprotonated form)

6.5

pKa of histidine

Protonated
Deprotonated

pH < pKa

pH > pKa

Proline

Special amino acid with a secondary alpha amino group
(Introduces kinks to alpha helix)

Glycine

Special amino acid that is very flexible (achiral alpha carbon)

Alpha helix breakers

Proline and glycine are _

Cysteine

Special amino acid that forms disulfide bridge

Oxidizing

What environment allows cysteine to form disulfide bridge? (oxidizing or reducing)

Cystine
Cysteine

Oxidized form of cysteine

Reduced form of cysteine

L (amino acid)
D (amino acid)

Amino acid fischer projection with NH2 on the left

Amino acid fischer projection with NH2 on the right

L

What configuration of amino acids is the only form found in human body

Isoelectric point (pI)

Point on pH scale where molecule exists in neutral form with no charge

Zwitterion

Molecule with both a positive and negative charge present

pI (Isoelectric point)

Average of pKas of all functional groups in molecule =

Nonpolar (hydrophobic)
Polar (Hydrophillic)

Two classes of amino acids

Alkyl
Aromatic

Two types of nonpolar amino acids

Neutral
Acidic
Basic

Three types of polar amino acids

Aspartate

Conjugate base of aspartic acid

Glutamate

Conjugate base of glutamic acid

Amyloid

Clumps of misfolded proteins (builds up and interferes with neurons)

1 (° structure)

(Protein structure)
Linear sequence of amino acids

Peptide bonds

What determines primary protein structure?

2 (° structure)

(Protein structure)
Way linear sequence of amino acids folds over itself

H bonds
(Backbone interactions)

What determines secondary protein structure?

Alpha helix

Name of protein structure

Beta sheet

Name of protein structure

2 (°)

Alpha helix and beta sheet are _ structure

Parallel (sheet)
Antiparallel (sheet)

Beta sheet where C terminals line up and N terminals line up

Beta sheet where C terminals line up with N terminals

3 (° structure)

(Protein structure)
Higher level of polypeptide folding

R group interactions
(Hydrogen bonding)
(Van der waals)
(Hydrophobic packing)
(disulfide bridge)

What determines tertiary structure?

Hydrophobic packing

R group interaction that acts like phospholipid bilayer or soap (3° protein structure)

4 (° Structure)

(Protein structure)
Bonding between multiple polypeptides

Residue
Subunit

Name for an amino acid unit in a polypeptide

Name for an individual polypeptide chain in a protein

Solvation shell

Layer of solvent surrounding a protein

2 3 4
3 4
2 3 4
1

What levels of protein structure does temperature break

What levels of protein structure does pH break

What levels of protein structure do chemicals break

What levels of protein structure do enzymes break

Covalent
Ionic
Hydrogen
Peptide

(Denaturing protein)
What bonds are broken by temperature?

What bonds are broken by pH?

What bonds are broken by chemicals?

What bonds are broken by enzymes?

Native conformation

Functional conformation of a protein found under normal biological conditions

Net negative charge

Electrophoretic separation depends on existence of _

Carbonic Anhydrase

Enzyme in mouth that catalyzes conversion of carbonic acid to CO2 and H2O

Acid
Base
Covalent
Electrostatic
Proximity/Orientation

(Catalytic Strategy)
catalysis is when enzyme acts as an acid
catalysis is when enzyme acts as a base
catalysis is when enzyme forms covalent bonds with other molecules
catalysis is when enzyme stabilizes negatively charged molecule with metal cation
_ effects are when enzyme helps molecules to collide in proper orientation

Transition state

Highest energy point in reaction coordinate diagram

Free energy of activation (activation energy)
Standard free energy change

Difference between energy of reactant and transition state

Difference in energy between reactant and product

EA
Erxn

Abbreviation for free energy of activation
(Not ∆G dagger)

Abbreviation for standard free energy change
(Not ∆G°)

Substrate

Molecule enzyme acts on is called _

Active site

Location on enzyme substrate binds and rxn takes place

Induced fit

After initially binding, enzyme and substrate change shapes to bind tightly

Allosteric site

Place on enzyme that binds regulatory molecules

Activator
Inhibitor

Regulatory molecule that increases enzyme activity

Regulatory molecule that decreases enzyme activity

Ligase

Type of enzyme that combines two molecules

Transferase

Type of enzyme that moves functional groups from one molecule to another

Oxidoreductase

(Oxidase + Reductase)

Type of enzyme that transfers electrons from one molecule to another

Isomerase

Type of enzyme that converts molecule to one of its isomers

Hydrolase

Type of enzyme that uses water to cleave molecule into two other molecules (facilitates hydrolysis reactions)

Lyase

Type of enzyme that catalyzes additions to or formation of double bonds

Coenzyme

Organic molecule that helps enzyme by bringing materials for reaction (NADH)

Cofactor

Molecule that helps enzyme with catalytic mechanism by binding to enzyme or substrate

Vitamin
Mineral

Important organic molecule that must be obtained from diet

Important inorganic molecule that must be obtained from diet

Km (M)

[S] when V0 is 1/2 of Vmax

Kcat (1/s)

Vmax/[E]t
(# of substrate to product in 1 second @ max speed)

Catalytic efficiency

Kcat/Km

Cooperativity

Substrate binding changes subsequent substrate affinity

Positively
Negatively
Non

cooperative binding increases affinity
cooperative binding decreases affinity
_ cooperative binding does not affect affinity

Negatively (cooperative binding)

Cooperative binding type for enzymes with one active site

Feedback loop

Downstream products regulate upstream rxns

Homotropic
Heterotropic

Substrate and regulator are the same molecule

Substrate and regulator are different molecules

Receptor

Class of proteins that receive and bind to signaling molecules (RTK)

Ion channel

Class of proteins that act as a membrane channel for certain ions

Transport (protein)

Class of proteins that transport molecules that include carrier and channel proteins

High
Low

Transport proteins have affinity for ligand at high concentration and affinity for ligand at low concentration

Motor (protein)

Class of proteins that are involved in movement (myosin, kinesin, dynein)

Myosin
Kinesin
Dynein

Three types of motor proteins

Antibody

Class of proteins in the adaptive immune system that flag intruders for destruction

Methylation
Acetylation
Glycosylation

Small post translational modification involving a methyl group

Small post translational modification involving an acetyl group

Small post translational modification involving sugar