CHEM 431 Exam 1

What are the four levels of cellular organization?

1. Monomeric units

2. Macromolecules

3. Supramolecular complexes

4. The cell and its organelles

What functional group does Arginine belong to?

Guanidinium

What functional group does Histidine belong to?

Imidazole

What is an amphipathic molecule? Give an example

A compound with regions of hydrophobicity and hydrophilicity

EX: Phenylaniline

Why are hydrogen bonds easy to break?

Because they are noncovalent

Which AA(s) has an R-group that is not good at hydrogen bonding?

Cysteine

Which AA(s) has an R-group that is very good at hydrogen bonding?

Asparagine and Glutamine

What is the equation for Gibbs free energy?

ΔG = ΔH - TΔS

• ΔG = change in Gibbs free energy

• ΔH = change in enthalpy

• T = abs. temp. in K

• ΔS = change in entropy

What is an exergonic reaction?

Reactions where ΔG is negative (favorable, exothermic)

What is an endergonic reaction?

Reactions where ΔG is positive (unfavorable, endothermic)

A lower pH indicates what kind of environment?

Acidic environment (lots of H⁺ in the system)

At 25°C, [H₂O] =

55.5 M

A proton donor is a…

Acid

A proton acceptor is a…

Base

What happens to a strong acid/base in H₂O?

It will dissociate 100%

EX: 0.5 mol HCl in H₂O → there will be 0.5 mol protons at the end

What can both give and receive protons?

Weak acids/bases

What is the average molecular weight of amino acids?

110 Da (g/mol)

What is the pK₁ of amino acids?

pK₁ = 2.0

What is the pK₂ of amino acids?

pK₂ = 9.5

What is a peptide bond?

A bond between two amino acids

Always between α-carboxyl group of 1st amino acid and α-amine group of 2nd amino acid

What kind of reaction does the formation of an H₂O molecule indicate?

A condensation reaction

When naming polypeptides, what do you always start and end with?

Start: amino-terminal

End: carboxyl-terminal

How many residues can a oligopeptide have?

2-20 residues

How many residues can a polypeptide have?

More than 20 residues

Which amino acids can be biologically active by themselves?

Glutamate, Glycine, and neurotransmitters

What is a primary AA structure/sequence comprised of?

A single polypeptide chain - amino acid residues

What is a secondary AA structure/sequence comprised of and what are the most common arrangements?

Comprised of short pieces of the primary structure

Arrangements: α-helices or β-confirmations

What is a tertiary AA structure/sequence comprised of?

Secondary structures folded onto each other

What is a quaternary AA structure/sequence comprised of?

Assembled subunits of more than 1 sequence of amino acids

What is a conjugated protein?

A protein that requires additional chemical components (prosthetic groups) to function

Lipoprotein prosthetic group

Lipids

Glycoprotein prosthetic group

Carbohydrates

Phosphoprotein prosthetic group

Phosphate groups

Hemoprotein prosthetic group

Heme

Flavoprotein prosthetic group

Flavin nucleotides

Metalloprotein prosthetic group

Iron, zinc, Ca²⁺, molybdenum, copper (wide variety of protein types)

Describe the binding and removal of prosthetic groups on a protein

Prosthetic groups are covalently bound to or are otherwise not easily removed from the protein

Steps for determining the primary sequence of a protein

1. Treat polypeptide w/ FDNB → Blast with HCl (or strong acid) → Identify the amino acid

2. Treat w/ 2-mercaptoethanol OR dithiothreitol: puts protein under reducing conditions and cleaves disulfide bonds

3. Hydrolyze polypeptide → Separate AAs → Derivatization of AAs → Measure the amounts of each type of amino acid

4. Sequence the polypeptide chains

5. Edman Degradation Procedure: use phenyl isothiocyanate (reacts with α-amine to liberate amino acid from end of chain) → treat w/ CF₃COOH (weak acid) to break it off

6. Organize and complete the structure

Trypsin cleavage points

Lys, Arg (C)

“You’re trippin’ if you listen and argue”

Chymotrypsin cleavage points

Phe, Trp, Tyr (C)

“The chimes are forever too tiny”

Pepsin cleavage points

Leu, Phe, Trp, Tyr (N)

“Pepsi never leaves freaks tripping tires”

Cyanogen bromide cleavage points

Met (C)

V8 protease cleavage points

Asp, Glu (C)

“I ate asparagus and glue cake”

Define conformation

The spatial arrangement of atoms in a protein

Define native conformation

The conformation of a protein when it is in its functional state (folded)

Define stability

Tendency to maintain a native conformation

Number of amino acid residues to do 1 full turn on the α-helix

3.6 residues

Height between 1 full turn on an α-helix

0.54 nm

What amino acids are best for stabilizing an α-helix?

Methionine, Alanine, Leucine, Glutamate, and Lysine (MALEK)

What amino acids are the worst for stabilizing an α-helix?

Proline and Glycine

Dense regions of AAs with (+) or (-) R-groups will…stabilize/destabilize

Destabilize

AAs 3-4 residues apart with (+) or (-) R-groups will…stabilize/destabilize

Stabilize

AAs 3-4 residues apart with aromatic R-groups will…stabilize/destabilize

Stabilize

AAs that are (+) at the C-terminus and (-) at the N-terminus will…stabilize/destabilize

stabilize

2 or more β-strands can be used to make…

• Parallel β-sheets

• Antiparallel β-sheets

What kind of R-groups promote β-strands?

Smaller R-groups

EX: Glycine and Alanine

What makes antiparallel β-sheets stronger than parallel β-sheets?

H-bonds in antiparallel are perfectly aligned and the R-groups are slightly more offset

What are the two types of β-turns?

• Type 1: Always has a Proline in the second position

• Type 2: Always has a Glycine in the third position

Where does a protein live if it has a lot of disulfide bonds?

Outside of a cell (most proteins don’t have disulfide bonds inside a cell)

What are the factors that can denature a protein?

Heat, pH, organic solvents, chemical treatment

What primarily maintains the α-helix conformation, once formed?

Hydrogen bonds

Which amino acids are forbidden for an α-helix conformation?

Proline (conformational restriction) and Glycine (flexibility)

How many H-bonds in a β-turn?

One

If you have an acidic amino acid, what is it making a salt-bridge with at the middle of the protein, if found there?

A complimentary basic amino acid

Proteins almost always go from a long, linear structure to their properly folded state all by themselves in a _____ manner

spontaneous

What is the role of water in protein folding?

1. Start with a string of amino acids

2. First things to fold are secondary structure (especially α-helix)

3. Molten globule state - trying to orient itself

4. Hydrophobic amino acids properly align in the core, excluding water

5. Other pieces fall into their final positions

What do you add to a protein to denature it?

Reducing agents:

• Dithiothreitol

• β-mercaptoethanol

To make sure any breakable disulfide bonds will break and so random proteins won’t form in its unfolded state

Where does the information about the structure a protein should be in come from?

The actual list of amino acids in the protein - no external forces for proper folding

What are the characteristics of a globular protein?

• Polypeptide chains arranged in a generally spherical shape (compact)

• Soluble in H₂O

• Include most enzymes and regulatory proteins

What are the characteristics of a fibrous protein?

• Polypeptide chains arranged in long strands or sheets

• Insoluble in H₂O

• Very strong and/or flexible

What are the characteristics of α-keratin?

• Fibrous protein only found in mammals

• Made up of right-handed α-helices

• Supertwist between helices is left-handed

• Rich in hydrophobic residues: Ala, Val, Leu, Ile, Met, & Phe (VIMFAL)

Name the structures of α-keratin as the # of coils increases

1 coil = keratin α-helix

2 coils = two-chain coiled coil (wrapped left-handed)

4 coils = protofilament

Multiple protofilaments = protofibril (takes a minimum of double the # of protofilaments - 8, held together by disulfide bonds)

What are the characteristics of a collagen triple helix?

Give examples

• A secondary structure

• High tensile strength w/o stretch

• Unique left-handed triple helix containing 3 residues/turn

• Contains tripeptide units:

  • Gly - X - Pro

  • Gly - X - Hydroxyproline

EX: tendons, bone, cartilage, cornea

Define motif

A recognizable folding pattern involving 2 or more secondary structures

Define domain

A part of a polypeptide that is independently stable - can be separated from the rest of the protein and retain its function

Name the common motifs

• β-α-β Loops: α-helix linking 2 parallel β-sheets

• β Barrel: multiple antiparallel β-sheets

What does FNDB react with and what does it do?

Reacts with the N-terminal amino acid

Will determine the number of subunits if there are more than one

ΔG < 0

spontaneous

ΔG > 0

non-spontaneous

ΔG = 0

equilibrium

[H⁺] → pH

pH = -log[H⁺]

pH → M

10^-pH

Ka → pKa

pKa = -log(Ka)

pKa → Ka

10^-pKa

[A^-] =

[HA] =

[A^-] = deprotonated, conc. of conjugate base

[HA] = protonated, conc. of conjugate acid

molarity =

moles/L

[A^-] + [HA]

pKa > pH

protonated

pKa < pH

deprotonated

pKa = pH

take average charge