MTC Module 1: Amino Acids and Proteins

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What does NPH stand for?

Neutral Protein Hagadore


What's the basic structure of an amino acid?

1. Amino group (NH3+)
2. Carboxyl Group (COO-)
3. Alpha-Carbon at center (chiral)
4. Side Chain (Differs, gives properties)


What catalyzes the dehydration synthesis that binds amino acids together?

Ribozymes (RNA enzymes)


Describe the formation of a peptide bond.



What is the implication of chiral amino acids.

All amino acids except Glyciene are chiral. They have D and L versions. All human proteins are L.

-The proteins that are used to form bacterial cell walls are D.


List the Aliphatic Amino Acids.

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


What are the properties of an Aliphatic Amino Acid?

1. Hydrophobic
2. Mainly CH side chains
3. The bigger the CH side chain, the more hydrophobic


Describe the structures of the Aliphatic Amino Acids.

1. Gly (H side chain)


List the aromatic amino acids

1. Phenylalanine (Phe, F)
2. Tyrosine (Tyr, T)
3. Tryptophan (Trp, W)


What are the properties of the aromatic amino acids?

1. Absorbs UV light
2. Hydrophobic
3. Ability to stack
4. Can be identified easily by other enzymes


List the polar amino acids.

1. Asparagine (Recognized for glycosylation) (Asn, N)
2. Glutamine (Gln, Q)
3. Serine (Ser, S)
4. Threonine (The, T)


What are the properties of the polar amino acids?

1. Hydrophilic
2. Some can be targeted for addition of sugar


List the sulfur-containing amino acids.

1. Methionine (Met, M)
2. Cysteine (Cys, C)


What are the properties of the sulfur amino acids?

1. They can donate sulfur
2. They can form disulfide bonds (stabilize proteins in an oxidative environment)


List the Positive (Basic) Amino Acids.

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


What are the properties of the Basic Amino Acids?

1. Act as a base.
2. Can act as a buffer
3. Acid base chemistry


What are the properties of the Negative (Acidic) Amino Acids?

1. Aspartate (Asp, D)
2. Glutamate (Glu, E)


What are the properties of the Acid Amino Acids?

1. Form salt bridges
2. Act as an acid.
3. Act as a buffer.
4. Acid base chemistry.


What is pKa?

The point at which the number of protonated and unprotonated are equal.


What is PI?

-The point during a titration at which the solution becomes natural.


What are some the important amino acid interactions important for protein folding?

1. Hydrophobic interaction: Aromatics have the ability to stack
2. Hydrogen Bonds: Side chains and peptide backbones can form hydrogen bonds because of the C double bond O and N bond H on the peptide backbone.
3. Disulfide bonds can form between Sulfur side groups in order to stabilize proteins (good in oxidative environments)
4. Salt Bridges can form between acid and base side chains


What can disrupt a salt bridge?

-Changes in pH
-Changes in ion concentration


What is the primary structure of a protein?

The sequence/order of amino acids in a chain
-Determined by the sequence of codons in the mRNA


What causes variation in primary structure?

1. Forward to backwards does not equal backwards to forwards
2. DNA mutations


What are the two types of variations in protein primary structure?

1. Non critical: Sam Structure, Same Function
2. Critical: Different Structure, Different Function (Could increase or decrease activity. Could alter structural integrity)


What should one consider when thinking about variation in primary structure of a protein?

-What group is being substituted for what?
-Do they two groups come from the same Properties Group
- IF so, they probably won't change interaction.
-If they don't come from the same group, ask where it is in the molecule, what did the past residue do, how could this change thing?


What is a polymorphism?

Polymorphisms = sequence variations in an allele within a population


What is developmental variation?

-Certain variants of a protein family are differentially expressed based on the developmental stage of the organism.
-The variant proteins are called isoforms or isozymes


Describe the developmental variations in hemoglobin.

Different forms of hemoglobin are associated with different affinities for O2. HbF has a higher affinity for O2 than HbA Thus, O2 can be exchanged at the placenta and then released in the embryonic tissues where the oxygen tension is very low. Subunit composition:
-Hemoglobin α2ζ2 - Embryonic Hb
-Hemoglobin α2γ2 - HbF
-Adult Hemoglobin α2β2 - HbA


Describe Cell/Tissue Specific Variations in protein.

Different protein sequences are associated with slightly different functions and thus cell-type specific expression of particular isoforms are made.
• Isoforms are differentially expressed through tissue specific transcription, alternate splicing unique targeting or differential degradation.
• E.g., Adenylyl cyclase, ATP cAMP- 9 different isoforms are derived from 9 different genes.


Describe the application of variations to insulin.

-Bovine insulin differs from human insulin in simple amino acid substitutions.
-Threonine goes to Alanine... etc.
-However, these changes can be recognized by the immune system. They can lead to auto-immunity. Therefore human insulin is better.


How do we create injectable human insulin?

1. A residue that was once Pro-Lys was switched to Lys-Pro through genetic engineering.
2. This makes the insulin less likely to aggregate with zinc and settle, and it creates a more fast acting insulin (better than old forms)
3. Insulin mixes (like 75:25) describe the amount of fast acting to slow acting.


Where are carbohydrates added on proteins?

O-glycosylation: OH of Ser, Thr, Tyr
N-glycosylation: NH2 of Asn


Where are lipids added on proteins?

Palmitoylation: Internal SH of Cys
Myristoylation: NH of N-terminal Gly
Prenylation: SH of Cys


How are proteins modified for regulation?

Phosphorylation: OH of Ser, Thr, Tyr
Acetylation: NH2 of Lys terminus
ADP-ribosylation: N of Arg, Gln; S of Cys


How are proteins oxidized?

Occurs on the carbon of Pro, Lys


How are proteins carboxylyzed?

Occurs on the carbon of Glu


What are the levels of protein structure?

Primary: Amino Acid Sequence
Secondary: Regular Sub Structures
Tertiary: Three dimensional folding of regular substructures
Quaternary: Complex of multiple tertiary structures


Can peptide bonds spin?

No, peptide bonds are planar, and have restricted rotation.


Describe the location of R groups across a peptide backbone.

-R groups tend to alternate from side to side


What is the main stabilizing force of the alpha helix?

-There is a hydrogen bond between the NH group and the COO group of the peptide backbone. This causes the protein to twirl, and places the R groups on the outside.
-The characteristics of the R groups can become important. For example, you can arrange alpha helices in a lipid bilayer with hydrophobic R groups that interact with the bilayer and hydrophilic R groups facing one another in order to create a pore.


What is the main stabilizing force of the Beta Pleated Sheet?

-Hydrogen bonds form between the peptide backbone of two proteins strands that run parallel. The R groups now alternate going "up" and "down" on the sheet.
-One side of the sheet tends to be hydrophobic, and the other tends to be hydrophilic
-This allows for the stacking of sheets


What is a common structural motif in Beta Pleated Sheet?

Beta Turn


What are the patterns of secondary structure that eventually lead to protein tertiary structure?

Structural Motif-->Subdomain-->Domain-->Fold

-Several domains may be joined by a "hinge region". The fold may have a "cleft" that binds the substrate.


Give some examples of a tertiary structure.

Nucleotide Binding Fold
-Used in lactate dehydrogenase domain 1

Actin Fold
-Binds ATP


What is quaternary structure?

• Thespecificinteractionofdistinct polypeptide chain subunits.
- Geometrically
- Stoichiometrically
• Meanstoproducefullyfunctional highly stable proteins
EXAMPLE: Hemoglobin


What factors influence protein folding?

• Mutations
• Environment-solvent, pH, salt, temperature, oxidizers, etc.
• Chemical modification
- Enzymatic
- Non-Enzymatic
• Protein-protein interactions
- Chaperones
- Abnormal proteins


Where are hydrophobic residues on Globular, Fibrous, and Membrane proteins?

Globular: On the inside
Fibrous: Less hydrophobic because filamentous
Membrane: In contact with membrane


What is a great example of a variety of protein folding?

Beta-adrenergic receptor


What proteins assist the folding of other proteins in vivo?

Chaperones, Heat Shock Proteins, Isomerases


What are examples of protein folding diseases?

Prions (cause), ALS, Alzheimers


What leaks into the blood after muscular injury, or during a myocardial infarction?

•Myoglobin appears in the blood most rapidly, however, it is relatively nonspecific for cardiac injury.