Proteins for the MCAT

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Which amino acid category does D belong to?

*Aspartic acid Acidic amino acid (hydrophilic, negatively charged at physiological pH)

Which amino acid category does Glu belong to?

*Glutamic acid Acidic amino acid (hydrophilic, negatively charged at physiological pH)

Name all 5 aliphatic amino acids

*VAIL G 1. Valine (Val, V) 2. Alanine (Ala, A) 3. Isoleucine (Ile, I) 4. Leucine (Leu, L) 5. Glycine (Gly, G)

What level of protein structure is responsible for the formation of multimers?

*multimer: more than 4 polypeptide chains linked to form a functional protein Quaternary structure

If you preformed gel electrophoresis at a pH of 6 to separate alanine, glutamic acid and arginine, which end would each amino acid migrate towards and why?

-Alanine would be neutral so it wouldn't migrate -glutamic acid would be negative so it would migrate towards the cathode (+) end -Arginine would be positive so it would migrate towards the anode (-) end

What are 2 ways to break a peptide bond?

1. Acid/heat hydrolysis (not specific) 2. Proteolysis (specific cleavage by proteases between specific residues)

Name the 7 categories of amino acids used in this class

1. Aliphatic 2. Sulfur-containing 3. Aromatic 4. Imino acid 5. Neutral polar 6. Acidic 7. Basic

Name 2 acidic amino acids

1. Aspartic acid (Asp, D) 2. Glutamic acid (Glu, E)

What 2 ways of denaturing a protein will not affect primary and secondary structures?

1. Changing the pH 2. Adding salts Both of these will affect the interactions between acidic and basic amino acids [ionic salt bridges] --> affects tertiary and quaternary structure

Name 2 sulfur containing amino acids

1. Cysteine (Cys, C)- can form disulfide bonds with other cysteine residues 2. Methionine (Met, M)-cannot form disulfide bonds

What 2 things are important for protein conformational stability?

1. Fidelity to the protein's intended primary, secondary, tertiary and quaternary structure 2. The formation of a solvent shell in aqueous solutions

Name 3 basic amino acids

1. Histidine (His, H) 2. Lysine (Lys, K) 3. Arginine (Arg, R)

Which two amino acids are known for their reactivity and often found within the active/ catalytic sites of enzymes?

1. Histidine (basic amino acid) 2. Cysteine (sulfur-containing amino acid)

What 2 ways of denaturing a protein will affect secondary, tertiary, and quaternary structure but not primary structure?

1. Increasing temperature (amino acids gain energy and bonds vibrate and stretch until all non-covalent bonds are destroyed) 2. Adding chemical detergents (disrupt hydrogen bonding)

Name 3 aromatic amino acids

1. Phenylalanine (Phe, F) 2. Tyrosine (Tyr, Y)- slightly hydrophilic because aromatic ring bears a hydroxyl group 3. Tryptophan (Trp, W)

Describe the charge of an amino acid under these 3 conditions: 1. pH below its pI 2. pH equal to its pI 3. pH above its pI

1. Positive (both the acidic and the basic groups are protonated [acidic groups: neutral, basic groups: positive]) 2. Neutral (thats the definition of pI/ isoelectric point) 3. Negative (both the acidic and basic groups are deprotonated [acidic groups: negative, basic groups: neutral])

For most amino acids, L configuration means [1. Blank] stereochemistry and D configuration means [2. Blank] stereochemistry

1. S 2. R

Name 4 neutral, polar amino acids

1. Serine (Ser, S) 2. Threoine (Thr, T) 3. Asparagine (Asn, N) 4. Glutamine (Glu, Q)

Quaternary structure 1. What is it? 2. What types of bonds are important to this structure?

1. Side-chain (R-group) interactions between different polypeptide chains 2. The same types of bonds that are important in tertiary structure (Salt bridges (ionic), polar to polar, non-polar to non-polar and disulfide bridges)

Secondary structure 1. What is it? 2. What types of bonds are important to this structure? 3. Examples (2)

1. The interactions between backbone carboxylic acid and amino groups 2. Hydrogen bonds 3. Alpha helix, beta pleated sheet

Tertiary structure 1. What is it? 2. What types of bonds are important to this structure?

1. The interactions of R groups in a single polypeptide chain 2. Salt bridges (ionic), polar to polar, non-polar to non-polar and disulfide bridges

Primary structure 1. What is it? 2. What types of bonds are important to this structure?

1. The sequence of amino acid residues (N to C) 2. Peptide bonds

How many amino acids are encoded in DNA triplets (i.e. are naturally occurring)?

An amino acid that is not acidic or basic will have a pI (isoelectric point) close to:

What is the pI of histidine? Why is this important?

7.6 7.6 is extremely close to physiological pH (~7.4). That means histidine can be found in both protonated (charged) and deprotonated (neutral) states in the body

How many essential amino acids are there?

Zwitterion

A molecule that contains charges, but is neutral overall

Alanine

Ala

Alanine

Which amino acid category does alanine belong to?