2A- Amino acids and proteins

Question 1

Give the general structure of an amino acid

Answer 1

i. All 20 amino acids in the body are α-amino acids, which means the amino group is attached to the α-carbon (the 1 next to the carboxylate group) ii. The α-carbon also has a H and a side chain (-R). The side chain makes each amino acid different.

Question 2

At physiological pH, what charge does the amino and carboxylic group have?

Answer 2

Amino has + Carboxylic has -

Question 3

What is the pKa of the primary carboxylic group of an AA?

Answer 3

~2

Question 4

What is the pKa of the primary amino group of an AA?

Answer 4

~9.5

Question 5

Name the 3 amino acids which are postively charged

Answer 5

Arg, His, Lys

Question 6

What are the 2 amino acids which are negatively charged?

Answer 6

Asp, Glu

Question 7

What are the 4 amino acids that are polar uncharged?

Answer 7

Ser, Thr, Asn, Gln

Question 8

What are the 3 “special” amino acids?

Answer 8

Cys (has an SH) Gly (just an H) Pro (has a N ring)

Question 9

What are the 8 hydrophobic amino acids?

Answer 9

Ala Val Ile Met Phe Tyr Trp

Question 10

Name the 5 true nonpolar amino acids

Answer 10

Ala Ile Leu Pro Val

Question 11

Name the 3 aromatic amino acids

Answer 11

Phe Tyr Trp

Question 12

Name the 2 acidic amino acids

Answer 12

Glu

Asp

Question 13

Name the 3 basic amino acids

Answer 13

His

Arg

Lys

Question 14

Name the 3 alcoholic amino acids

Answer 14

Tyr, Ser, Thr

Question 15

Name the 4 amide amino acids

Answer 15

Arg Lys Asn Glu

Question 16

What is glycosylation and what is it’s function?

Answer 16

Oligosaccharides (small carbohydrate chains) are bound to proteins by N or O linkages N-linked oligo’s are on cell surface proteins, where they protects the cell from proteolysis or an immune attack O-linked oligo’s is a common way of attacking ologo;s to the Ser or Thr OH groups in secreted proteins.

Question 17

What is fatty acylation and it’s function?

Answer 17

Fatty acids are often attached to plasma membrane proteins or to intracellular vesicles.

Question 18

What is phosphorylation of amino acids and its function?

Answer 18

Phosphorylation is adding a PO4 group to an end of an AA. It introduces a large, bulky, negatively charged group thatt can alter the acitivity of the protein

Question 19

What is ribosylation and its function?

Answer 19

ADP-ribosylation is the trasnfer of an ADP-ribose from the NAD+ to an Arg, Glu, or Cys residue on a target protein in the membrane This regulates the activity of the proteins

Question 20

What is carboxylation modification of amino acids and what is its function?

Answer 20

It is the addition of -COO to the AA its important for attachment by binding a blood clot to the surface of a vessel in certain blood-clotting proteins.

Question 21

What is a peptide bond and its characteristics?

Answer 21

It’s the bond between the carboxylic acid of 1 AA and the amino group of another AA This process has water as a byproduct

Question 22

What are the chemical forces that govern protein structure?

Answer 22

The peptide bond forms the backbone of the protein structure the side chains extend outwards and interact with the backbone or sidechains of other proteins (or the same protein) This forms hydrophobic regions, electrostatic bonds, H bonds, or disulfide bonds.

Question 23

What is the primary structure?

Answer 23

The peptide backbone of the protein showing the molecules involved with the sidechains and everything

Question 24

What are secondary structures?

Answer 24

Regions within polypeptide chains that form recurring, localized structures. Forms either a alpha-helix or a beta-sheet

Question 25

What are alpha-helixes?

Answer 25

2o structure Formed by strong H-bonds between each carbonyl O atom and the amide H of an AA located 4 resudies down the chain. Proline can’t form a-helixes because it has a weird cyclic structure that doesnt promote H-bonding.

Question 26

What are beta-sheets?

Answer 26

2o structure H-bonding between peptide backbones while maintaining the allowed torsion angles. Usually occurs between regions of separate strands alligned parallel to each other running in opposite direction (usually).

Question 27

What are tertiary structures?

Answer 27

it’s the folding pattern of the 2o structural elements into 3D conformation it creates specific and flexible binding sites for ligands

Question 28

What are quatenary structures?

Answer 28

It refers to the association of subunits

Question 29

What occurs during protein folding?

Answer 29

the primary structure of a protein dictates the way that it folds into its tertiary structure, which is a stable conformation. chaperons act as templates to overcome kinetetic barrier to reach a stable conformation prion proteins cause neurodegerative diseases by acting as a template for misfolding. Heat, acid and other agents misfold proteins.

Question 30

What are some protein denaturation processes through nonenzymatic modification?

Answer 30

It can be either nonenzymatic glycosylation or oxidation such modifications leads to a loss of fxn and denaturation of the protein, sometimes into a form that cannot be degraded in the cell

Question 31

What does changes in pH do to protein folding?

Answer 31

at low pH, ionic bonds and H-bonds formed by carboxylate groups would be disrupted At a high pH, hydrogen and ionic bonds formed by basic amino acids would be disrupted. This commonly occurs by stomach acid when we eat food.

Question 32

What are prions and how do they work?

Answer 32

Prion proteins act as a template to misfold other cellular prion proteins that cannot be degraded. Our normal prion protein, PrP(c), gets misfolded into our brain into a form called PrP(sc). The (sc) has 3 more beta sheets even though it has the same AA sequence. Ex: CJD/mad cow, Kuru

Question 33

What are the structural differences between myoglobin and hemoglobin?

Answer 33

Both are very similiar, however: -Myoglobin is a globular protein with 1 O2 binding site -Hemoglobin is a tetramer somposed of 2 different subtypes (alpha and beta)

Question 34

How does the oxygenation saturation curve compare between myoglobin and hemoglobin?

Answer 34

Myoglobin has a much smaller P50 than Hb. This means they are 50% saturated with O2 at a much lower partial pressure of O2.

Question 35

What are 3 things that will shift the O2-binding curve of Hb to the left?

Answer 35

Basically, it’s increasing the affinity to O2 at a lower partial pressure of O2.

The P50 will decrease.

Decrease CO2

Decrease 2,3-BPG

Increase pH

Question 36

What are 3 things that would cause a larger P50 for Hb and O2?

Answer 36

Basically, things that will cause a decrease in association of Hb and O2. The Hb will need a higher partial pressure of O2 to become saturated, thus shifting the P50 to the right of graph. Increase in CO2 (competitive for binding spot) Increase 2,3-BPG (competitive for binding spot) Decrease in pH (Bohr effect)

Question 37

How does CO2 get transported in the blood?

Answer 37

Question 38

Label 1-6

Answer 38

1 and 4 = pH

2 and 5 = CO2

3 and 6 = 2,3-BPG

Question 39

What are the differences between adult and fetal Hb?

Answer 39

Fetal have a different type of subunit which has a higher affinity for O2, thus making the P50 for fetal Hb lower than adult Hb