bc review

All of the amino acids, except cysteine has a _____ configuration. Cysteine has a ____ configuration.

L; R

Non-polar amino acids are found in the interior or exterior of proteins?

Interior

Polar molecules amino acids are found in the interior or exterior of proteins?

Exterior

Acidic residues have an additional _______ charge beyond the C terminus

negative

Basic residues have an additional _______ charge beyond the N terminus

positive

At low pH, amino acids are more ___________ with a net ______ charge

protonated; positive

At high pH, amino acids are more __________ with a net ______ charge

deprotonated; negative

At 7.4 pH, amino acids exist in dipolar, _________, form. Why?

zwitterionic, b/c the N terminus is protonated (NH3+) and the C terminus is deprotonated (COO-)

List the non-polar amino acids:

Glycine, Leucine, Alanine, Methionine, Valine, Isoleucine, Proline, Tryptophan, Phenylalanine (GLAM VIP WF)

List the uncharged, polar amino acids:

Glutamine "Queen Glutamine", Threonine, Serine, Tyrosine ("Y, Try, Tyrosine"), Asparagine ("Asparagus iN my diet"), Cysteine (QT SYNC)

Which of the polar amino acids have an -OH in the side chain?

Tyrosine, Threonine, and Serine (YTS)

List the acidic and basic amino acids:

Glutamate, Aspartate (ED) (Every Dog)

Histidine, Arginine, Lysine (HRK) (Hates Red Kool-Aid)

What does it mean when pH=pka

Half are protonated and half are deprotonated

If the pka of the carbonyl group is 3.1 , what happens when the pH is above and below the pka?

Above pka = conjugate base will predominate (COO-)

Below pka = acid will predominate (COOH)

If the pka of the amino group is 8, what happens when the pH is above and below the pka?

Above the pka = conjugate base will predominate (NH2)

Below the pka = acid will predominate (NH3+)

How are amino acids linked together?

Peptide bonds

The forward reaction of peptide bond formation is a _______________ reaction

dehydration

Peptide bonds are thermodynamically ______________

favorable

How does the forward reaction occur in peptide bond formation?

Use of ATP

Peptide bonds are kinetically _____________

unfavorable

What is acid hydrolysis?

Splitting a peptide bond with heat; nonspecific

Proteolysis

specific cleavage certain bonds-- can choose which peptide bond to cleave

Why is the trans configuration favored in peptide bonds?

\- More stable (less steric hindrance than cis configuration, no electrostatic repulsion)

\- Lower in energy

Secondary structure

Primary structure folds and forms either alpha helix or beta sheets

Where is the backbone located on the alpha helix?

Inner portion

Where is the side chain (R group) located on the alpha helix?

Outer portion

What type of bond/interactions occur between amino acid backbones in secondary structures?

Hydrogen bonding (N-H and C=O)/Non-covalent interactions

How frequently does hydrogen bonding in the alpha helix occur?

Every 4 units

Which two amino acids disrupt the alpha helix?

Proline and glycine

Why is the right-hand alpha helix preferred?

Less steric hindrance between side chains

Which type of beta sheets are most common?

Antiparallel beta sheet

Antiparallel beta sheets consist of:

2 linear polymers in opposite direction

Parallel beta sheets consist of:

2 linear polymers in same direction

What are beta turns?

180 degree turns by 4 amino acids and stabilized by a hydrogen bond of the C=O and N-H

What two amino acids are common in beta turns?

Proline and glycine

What types of bonds are in the tertiary structure?

\- Ionic bonding

\- Hydrogen bond

\- Disulfide bonds

\- Dispersion forces

Which type of bond is the only covalent bond in the tertiary structure?

Disulfide bond

What type (covalent/noncovalent) of bonds are in the quaternary structure?

non-covalent

Isoelectric point (pI) equation for neutral amino acid:

pI = (pka NH + pka COOH)/2

pI equation for acidic amino acid:

pI = (pka R group + pka COOH)/2

pI equation for basic amino acid:

pI = (pka R group + pka NH)/2

Cofactors are…

Nonprotein enzyme helpers

Do cofactors bind to the enzyme?

No

Apoenzyme is the…

Inactive portion of the protein

Apoenzyme + cofactor =

holoenzyme

Coenzymes:

Small organic compounds that loosely/strongly bind to the active site of the enzyme

What is the difference between cofactors and coenzymes?

* Cofactors are inorganic compounds, and coenzymes are organic
* Cofactors do not bind to the enzyme, and coenzymes do bind loosely to the enzyme

What are tightly bound coenzymes called?

Prosthetic groups

How do active sites establish microenvironments?

Create non-polar environments where bonds can break/form more easily

How do substrates bind reversibly through active sites?

Non-covalent interactions: hydrogen bonding, electrostatic interactions, and hydrophobic interactions

What are allosteric sites?

non-catalytic regions of the enzyme that bind regulators

Lock and Key model

Substrates fit precisely into active sites

\*No alteration to tertiary or quaternary structure needed

Induced fit model

Substrate induces change on enzyme shape--requires energy; therefore, endergonic

Products form __________ when there is a high enzyme concentration.

Quickly

The addition of more substrate _______ the rate of reaction

Increases

If substrates outnumber enzymes, then the reaction reaches ____________

Saturation

If the reaction reaches saturation, then the enzyme is working at ________________

maximum velocity; vmax

How do you increase the vmax?

Increase the enzyme concentration

When the reaction rate is equal to half of vmax:

Km = \[S\]

What does Km represent?

* Michaelis constant
* Measures the affinity an enzyme has for a substrate

Increase Km means . . .

Enzyme has low affinity for substrate

Decrease Km means . . .

Enzyme has high affinity for substrate

Where does the inhibitor bind to in the enzyme in competitive inhibition?

Active site

How does competitive inhibition affect Km?

Increases Km

Does competitive inhibition affect Vmax?

No

Where does the inhibitor bind to in the enzyme in noncompetitive inhibition?

Allosteric site

How does noncompetitive inhibition affect Km?

No change

Does noncompetitive inhibition affect Vmax?

Decreases

Where does the inhibitor bind to in the enzyme in uncompetitive inhibition?

Allosteric site

How does uncompetitive inhibition affect Km?

Decreases

Does noncompetitive inhibition affect Vmax?

Decreases

Competitive inhibitors bind only to ____________

free enzymes \[E\]

Uncompetitive inhibitors bind only to _____________

enzyme-substrate complex \[ES\]

Noncompetitive inhibitors have equal binding affinity for

free enzymes \[E\] and enzyme-substrate complex \[ES\]

Mixed inhibitors bind to ______________

both, free enzymes \[E\] and enzyme-substrate complex \[ES\]

\*can have a higher affinity for one over the other

A mixed inhibitor is more competitive when…

Ki \[E\] < Ki \[ES\]

A mixed inhibitor is more uncompetitive when…

Ki \[E\] > Ki \[ES\]

What does Ki mean?

Similar to Kd, Ki is binding affinity for inhibitors.

Low Ki means…

Strong affinity

High Ki means…

Weak affinity

How is Km affected when a mixed inhibitor is more competitive?

Increased

How is Km affected when a mixed inhibitor is more uncompetitive?

Decreased

How is Vmax affected when a mixed inhibitor is competitive?

Decreased

How is Vmax affected when a mixed inhibitor is uncompetitive?

Decreased

Cell adhesion molecules (CAM)

Allow cells to bind to other cells or surfaces

Cadherins

Integrins

Selectins

Cadherins

calcium-dependent glycoproteins that hold similar cells together

Integrins

Two membrane-spanning chains and permit cells to adhere to proteins in the extracellular matrix.

Selectins

Allow cells to adhere to carbohydrates on the surfaces of other cells

Commonly used in the immune system

Voltage-gated channels

open and close in response to changes in membrane potential

Ligand-gated channels

Respond to neurotransmitters or hormones

Ligand-binding domain

Stimulated by ligand and induces a conformational change that activates the catalytic domain

Activation of the catalytic domain can trigger a second messenger, which relays what?

a signal from the cell surface to the intracellular target

What are G protein-coupled receptors?

Cell surface receptors that transmit extracellular signals into intracellular responses

What do G-protein-coupled receptors do?

Modulates intracellular signaling pathways and influence physiological processes

Where do negative charged molecules migrate to in electrophoresis?

Anode

Where do positive charged molecules migrate to in electrophoresis?

Cathode

If a molecule is small in size, how fast will it migrate in electrophoresis?

Fast

If a molecule is large in size, how fast will it migrate in electrophoresis?

Slow

What does native PAGE analyze?

* Proteins are in native state


* Compare molecular size or charge of proteins

What are the limitations of native PAGE?

Many proteins experience same migration