2-Proteins

Question 1

What is the size of a typical protein?

Answer 1

• Typical protein ~20-40K Da

- Average aa in a protein ~110 Da

Question 2

What are the main 2 shapes of proteins?

Answer 2

1. Globular: dominant; enzymes are globular

2. Structural: elongated (fibrous); collegen, elastin, keratin

Question 3

Where do charges arise from in proteins?

Answer 3

1. amino terminal +
2. carbonyl terminal -
3. side chains of aa (D, E, H, K, R) at ph7
4. covalent modification (phosphorylation)
5. metal ions

Question 4

What is a zwitterion?

Answer 4

It’s a neutral molecule that carries two distinct ionizable groups, (a positive and a negative electrical charge).

Question 5

What is pKa?

Answer 5

The pH oat which an amino acid is half protonated and half unprotonated. Determines the charge state of the amino acid.

Question 6

what is the pKa of the amino acids with ionizable chains?

Answer 6

Asp 3, Glu 4, His 6, Cys 8,

Tyr 11, Lys 11, Arg 12.5

Question 7

Why aren’t proteins good buffers?

Answer 7

pKa values of most aa side chains are not useful for physiological buffering. Only histidine and amino groups have a pKa in the righ range, but they are too sparse in serum proteins.
*Blood buffering: by carbonic acid and bicarbonate

Question 8

What are peripheral proteins?

Answer 8

Those are proteins associated with membrane proteins. No direct contact with plasma membrane.

Question 9

What are integral proteins?

Answer 9

Proteins embedded in the membrane either directly or indirectly via a lipid anchor.

Question 10

What are some characteristics of transmembrane proteins?

Answer 10

• Single and multiple pass structures
• External domain: glycosyation & disulfide bonds (cysteines oxidized)
• Transmembrane segment: highly hydrophobic alpha helix
• Internal domain: reduced sulfhydryl groups (cysteines reduced), phosphorylation, no complex carbohydrate.

Question 11

What are the 2 major types of protein glycosylation?

Answer 11

N-linked: sugar is linked to the side chain N of asparagine

O-linked: sugar is linked to the OH group of serine or threonine.

Question 12

What is glycosylation?

Answer 12

Modification of proteins that include the addition of carbohydrate chains. Most common in proteins that are secreted or exposed to the environment.

Question 13

What is Leri-Weill dyschondrosteosis disease?

Answer 13

• Disorder of bone growth, shortening of bones of the arms and legs
• Due to improper localization because of a mutation in SHOX transcription factor.

Question 14

What are some protein destinations within the cell?

Answer 14

1. ER
2. Nucleus (reversible)
3. mitochondrion
4. cytoplasm (“default”)
5. peroxisome

Question 15

Explain how proteins destined for secretion enter the ER:

Answer 15

• Signal peptide is immediately degraded
• S-S bonds formed
• Initial N-linked carbohydrate attachment
• Chaperons assist in folding
• They go to Golgi for packaging
• Secretory granules are released

Question 16

How do proteins destined for mitochondiral matrix get there?

Answer 16

• Signals (MSF) and many proteins (Tom 37/40/70) get proteins through the first membrane
• Another machinery including chaperone proteins (Tim 17/23/44) allow crossing into 2nd membrane

Question 17

What allows proteins to go to the proper locations?

Answer 17

• Targeting sequences, essentially molecular mailing addresses for proteins.
• Two types of nuclear localization signals, monopartite and bipartite
• Nuclear localization signal has to be in the surface because it is hydrophilic (has basic aa)

Question 18

Where can proteins be extracted from?

Answer 18

Tissues and from recombinant systems (yeast, bacteria, insect cells in culture, mammalian cells in culture)

Question 19

What are some protein isolation methods?

Answer 19

• Ion exchange chromatography (based on charge)
• Gel filtration chromatography (based on size)
• Absorption chromatography (based on hydrophobicity)
• Affinity chromatography (based on interaction with other molecules)

Question 20

What is the relationship between protein structure and function?

Answer 20

• Same function in different species -> related sequences
• Similar function -> similar sequences
• 3ry structure may be more conserved than 1ry
• Similar function proteins with little structural similarity ma be due to convergent evolution

Question 21

What are the structural and sequence similaritiesbetween myoglobin and Hb?

Answer 21

• Alpha chain of these two have many identical & similar aa’s in other positions (~30% homology)
• Structures are almost indistinguishable
• Along with leghemoglobin, they have origins in a single gene that underwent duplication

Question 22

What are paralog proteins?

Answer 22

These are proteins that share evolutionary history and that evolved to have very different functions.

Question 23

What is Hb’s structure? What is wrong with sickle cell anemia Hb?

Answer 23

• Hb is a tetramer : 2 alpha and 2 beta chains.
• In sickle cell anemia, HbS, the E (charged) at position 6 in beta chain is changed to a V (hydrophobic).
• This causes Hb aggregation due to hydrophobic interactions with F85 and V88 on 2nd beta chain
• Aggregation forms fibers and sickle shape in cell

Question 24

Based on what does electrophoresis separate proteins?

Answer 24

Size, charge, or both

Question 25

What are allozymes?

Answer 25

Form of a protein encoded by different alleles of a gene

Question 26

What are isozymes?

Answer 26

Forms of a protein encoded by different genes, but catalyzing the same reaction (often with different kinetics)

Question 27

What is the structure of creatine kinase?

Answer 27

• It has 2 subunits (M and B); isozymes:
• CK1 (BB)
• CK2 (MB): heart
• CK3 (MM): skeletal muscle
• CK2 is released after myocardial infarction

Question 28

What is cardiac troponin?

Answer 28

It’s a cardiac regulatory protein. It’s an even better marker than CK2 for myocardial infarction because its specific and remains elevated longer.