BIO-2 EXAM 1 Protien

Question 1

Defining Proteins…

Answer 1

Polymer of amino acids

The sequence of amino acids determines protein structure. Protein structure determines the protein function

Question 2

Amino Acids: List the four central carbon atoms

Answer 2

1. Hydrogen
2. Amino Group
3. Acid Group
4. Other
   “R” group determines which amino acid this is

Question 3

“R” groups have which abbreviations… Make sure to know the backbone and groups

Answer 3

One letter
Three letter
EX: Glycerine
GLY
G

Question 4

Protonated or deprotonated…

Answer 4

Controlled by proton concentration or [H+], which is also the pH.

Lower pH means higher [H+]. Makes the amine more likely to protonated

Question 5

How low of a pH is needed to protonate the group? Measured by the pKa…

Answer 5

Most amines have a pKa ~10

If pH < pKa, most molecules will be protonated
If pH > pKa, most molecules will be deprotonated

Question 6

What about carboxylic acids… (pKA)

Answer 6

pKa ~ 4

Question 7

What do protons determine…

Answer 7

protination and deprotination.

Question 8

How to evaluate these situations…

Answer 8

Only Amines (pKa~10) and Carboxylic Acids (pKa~4)

Evaluate each one individually (including side groups)

Think protonated/deprotonated (not charged/uncharged)

Question 9

Connecting Amino Acids…

Answer 9

Amino acids are connected by peptide bonds.

Condensation reaction

Question 10

Defining Protein Structure

Answer 10

Proteins aren’t linear. The primary sequence determines the 3D structure

Secondary structure involves short-range interactions

Through side chains and/or peptide backbone
*Hydrogen bonding
Ionic interactionsHydrophobic interactions/van der Waals
*Disulfide bonds
Covalent through sulfur on Cysteine side chains

Question 11

Characteristics of a Protein Structure…(1) (alpha)

Answer 11

a-helix is a common secondary structure

Hydrogen bonding between peptide backbone

Forms a cylinder

R groups are on the surface

Question 12

Characteristics of a Protein Structure…(2) (beta)

Answer 12

b-sheet is another common secondary structure

Hydrogen bonding between peptide backbone

Forms a flat surface

R groups are on the surface, alternating

Question 13

Characteristics of a Protein Structure… (3) Tertiary structure

Answer 13

Long-range interactions

Same intramolecular forces

Question 14

Characteristics of a Protein Structure… (4) Quaternary structure

Answer 14

Between two proteins

Same intramolecular forces

Question 15

Defining Protein Structure…

Answer 15

Sequence of amino acids determines protein structure

Protein structure determines the protein function

Question 16

Four bonds that are involved in protein structure…

Answer 16

Hydrogen
Ionic interactions
Hydrophobic interactions/van der Waals
Disulfide

Question 17

Protien denaturation…

Answer 17

Loss of 3D structure is denaturation

Too low/high salt concentration

Too low/high pH

Organic solventsHeat

Question 18

Defining Protein Domains…

Answer 18

Proteins can be divided into domains

A (mostly) independently folded portion of the protein

Often shows a discrete function

Question 19

Defining protein add-ons and synthesis…

Answer 19

Many proteins have a prosthetic group
Non-peptide
Stably bound
(Needed for function)

Protein Synthesis:
Peptide bonds synthesized on ribosomes
Secondary and tertiary structure form as translation happens

Question 20

Defining Post-Translational Modifications…

Answer 20

Many proteins are post-translationally modified
EX:
Acetylation
Glycosylation
Acylation
Methylation
etc.