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Flashcards in 8.1.16 Lecture Deck (48):
1

Name 3 functions of proteins (of 7 possible)

1. Enzymatic (catalysis) 2. Tissue and cell structure 3. Hormones and hormone receptors 4. Ion channels 5. Transporters 6. Transcription factors 7. Contraction in muscles

2

What is the central dogma?

1. In the nucleus, DNA/genes are transcribed to mRNA. 2. The mRNA is transported to the cytosol, where it is translated into a protein. 3. This protein may be modified further.

3

What is the proteome? Describe its makeup.

The proteome is the catalog of all proteins. The genome is composed of 20-25,000 genes. The genome is transcribed into 100,000 possible mRNA (transcripts) to make up the transcriptome. This occurs via alternative promoters, splicing, and mRNA editing. Finally, these are translated into the proteome, which is made up of over 1 million proteins.

4

Draw an amino acid in its original form.

5

Draw an amino acid in its Zwitterionic form. At what pH does this form occur?

Physiological pH = ~7.4

6

What is the only amino acid isomer found in proteins?

L-isomer

7

What are the characteristics of hydrophobic vs. hydrophilic amino acids?

Hydrophobic: non-polar, no water interactions, found in interior of proteins

Hydrophilic: polar and/or charged, interact with water via hydrogen bonds, found on the surface of a protein.

8

Glycine

Gly

pKa of R: n/a

9

Alanine

Ala

pKa of R: n/a

10

Valine

Val

pKa of R = n/a

11

Leucine

Leu

pKa of R = n/a

12

Isoleucine

Ile

pKa of R = n/a

13

Serine

Ser

pKa of R = n/a

14

Threonine

Thr

pKa of R = n/a

15

Cysteine

Cys

pKa = 8.37

16

Methionine

Met

pKa of R = n/a

17

Phenylalanine

Phe

pKa of R = n/a

18

Tyrosine

Tyr

pKa of R = 10.46

19

Tryptophan

Trp

pKa of R = n/a

 

20

Aspartate

Asp

pKa of R = 3.65

21

Asparagine

Asn

pKa of R = n/a

22

Glutamate

Glu

pKa of R = 4.3

23

Glutamine

Gln

pKa of R = n/a

24

Lysine

Lys

pKa of R = 10.8

25

Arginine

Arg

pKa of R = 12.5

26

Histidine

His

pKa of R = 6.0

27

Proline

Pro

pKa of R = n/a

28

Name the two amino acids categorized as small.

Glycine and Alanine

29

Name the three amino acids categorized as branched chain.

Valine, Leucine, and Isoleucine

30

Name the two amino acids categorized as hydroxyl.

Serine and Threonine

31

Name the two amino acids categorized as sulfuric.

Cysteine and Methionine

32

Name the three amino acids categorized as aromatic.

Phenylalanine, Tyrosine, and Tryptophan

33

Name the four acidic amino acids.

Aspartate, Asparagine, Glutamate, and Glutamine

34

Name the three basic amino acids.

Lysine, Arginine, and Histidine.

35

Name the amino acid categorized as imino.

Proline

36

What 5 amino acids are charged at physiological pH?

Aspartate, Glutamate, Lysine, Arginine, and Histidine

37

What are the characteristics of a peptide bond?

Amide, planar, trans

38

What is cystine?

A derived amino acid, created by oxidizing two cysteines; these two amino acids are joined by a covalent disulfide bond

39

What two proteins involve cystine?

Vasopressin (antidiuretic hormone) and insulin

40

Define acid and base.

Acid: H+ donor, Base: H+ receptor

41

What is Ka?

The acid dissociation equilibrium constant; it measures the strength of an acid.

42

Ka = ?

[H+][A-]/[HA]

43

Derive the Henderson-Hasselbach Equation.

44

A low pKa indicates ____. A high pKa indicates ____.

an acid; a base

45

On a titration curve, a flat portion (m~0) indicates ____.

pH = pKa; [A-] ~ [HA]

46

What is the isoelectric point (pI)? How can it be calculated?

The pH at which there are an equal number of + and - charges. It is calculated by averaging the pKa values that border the Zwitterion form. 

47

Describe 2-D electrophoresis.

First, run the specimen on a pH gradient. It will move to its pI and stop. Then, run the specimin on a second gel to separate it by size. 

48

After 2-D electrophoresis, how is a particular protein studied?

First, cut out the protein. Then, digest it with trypsin. Separate it by HPLC. Measure the mass and determine the amino acid sequence.