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Flashcards in Protein Structure and Function Deck (62):
1

What is the diagnostic test for CF? What is a normal value?

Sweat test Normal = < 40

2

How do uncharged polar amino acids behave?

Zero net charge at physiologic pH (7.4) R groups form hydrogen bonds with water

3

How do proteins fold?

Naturally, to reach lowest energy state With the help of chaperone proteins

4

When is an amino acid a zwitterion?

At pH 7 charge is balanced between + and - forms

5

Which amino acids tend to cluster stabilizing proteins through hydrophobic interactions?

Alanine Valine Leucine Isoleucine (last 3 are branched chain AAs)

6

How is pI calculated for nonionizable R groups?

= (pka1 + pka2) / 2

7

What is a "motif"? Does it have function?

Classified as (recognizable) folding patterns which may include multiple secondary structures e.g. helix-turn-helix Motifs do not have inherent function

8

Which AAs can act as attachment sites for oligosaccharides and glycoproteins? What group do they attach to?

Asn - amide group

Ser - hydroxyl group

Thr - hydroxyl group

9

What is an example of a "disordered" protein? What does this mean?

p53 tumor suppressor Is disorganized and flexible, usually means it can bind to multiple things

10

What are stabilizing influences to protein structure?

Most important: sequence! Chemical properties Covalent and disulfide bonds Hydrophobic interactions Van der Waals forces Electrostatic forces

11

What indicates a strong acid?

Small pKa

12

Do proteins play a major role in the buffering system of cells and plasma?

yes

13

Which AAs have ionizable side chains?

 

Lysine

Arginine

Tyrosine

Cysteine

Histidine

14

What AAs promote the alpha helix? Which ones do not?

Promote: Met, Ala, Leu Destabilize: Asp, His, Lys (charged) Pro Glu

15

Describe the beta sheet:

Composed of 2 or more regions of one OR MORE polypeptide chains R groups can be above or below plane of sheet

16

What is the isoelectric point (pI)?

The point at which proteins and some amino acids are electrically neutral

17

What is the quaternary structure of proteins?

Arrangement of 2 or more polypeptide chains/subunits

18

What are three new CF drugs?

Ivacaftor Dornase alfa Orkambi (helps deltaF508 patients!)

19

What is the bond between amino acids?

Peptide bond

20

What is the basic structure of an amino acid?

Carbon with 1 H, a Carboxyl group, an amino group + VARIABLE R group

21

What is the secondary structure of amino acids?

Alpha helix Beta sheet Loops Coils

22

Which AAs cause MSUD when they fail to be broken down? What do they have in common with one another?

Branched chain AAs! Valine Leucine Isoleucine

23

What are two general categories of proteins?

Fibrous, Globular

24

What do globular proteins do?

Enzymes, regulatory proteins, immunoglobulins, transport proteins, motor proteins, etc.

25

Which amino acid forms disulfide (S-S) bonds? Are these especially strong bonds?

Cysteine YES! Can be formed between 1 or 2 polypeptides

26

What elevated protein is indicative (but not diagnostic) of cystic fibrosis? Where is it produced?

Immunoreactive Trypsinogen (IRT) Produced by the pancreas

27

Which AA is barely charged and what is it good for?

Histidine is weakly basic and thus makes a good buffer

28

Which AAs have polar hydroxyl groups that can be attachment sites for groups (e.g. phosphate)?

Serine Threonine Tyrosine

29

What is a protein domain? Does it have function?

Regions of polypeptide chains that can fold stably and independently with respect to the protein. Has function even outside of the protein as a whole!

30

Describe the structure of globular proteins

Polypeptide strands folded into globular shape, tend to have complex tertiary structures e.g. myoglobin and hemoglobin

31

How is Ka calculated? pKa?

Ka = [H][A]/ [HA] pKa = - log Ka

32

What is the unique feature of proline?

It is large and bulky and thus not flexible

33

How are peptide bonds form?

Carboxyl group attacks amino group, water is formed

34

What is Maple Syrup Urine Disease (MSUD)?

Build up of alpha-keto acids due to failure of branched chain alpha-keto acid DH complex (enzyme that breaks down branched chain amino acids)

35

Can beta sheets be parallel or antiparallel?

Yes!

36

What are the 4 groupings of amino acids?

Non polar Polar uncharged Positively charged Negatively charged

37

Describe structure of fibrous proteins

Tend to contain one form of secondary structure and little tertiary structure Tend to be hydrophobic (e.g. collagen)

38

What is unique about glycine?

It is very small (R group is just a hydrogen) and thus tiny and can make tight turns/is flexible

39

What are uncharged polar amino acids?

Asparagine Glutamine Cysteine Serine Threonine Tyrosine

40

How many classes of CF are there? What is the most common (85%)?

6 Class II - (delta)F508 phenylalanine deletion

41

What determines the primary structure of amino acids?

Sequence (which includes all covalent bonds: peptide and disulfide)

42

What are characteristics of nonpolar amino acids?

1. Hydrophobic 2. Do not participate in hydrogen bonding or ionic bonding? 3. Do not accept or donate protons

43

How is pI calculated for ionizable R groups?

= (pKaNH31 + pKaNH32) / 2 OR = (pKaCOO1 + pKaCOO2) / 2

44

What does pKa mean functionally?

The pH at which points the molecule is 50% in the acid form and 50% in the base form

45

What are the positively charged polar AAs?

Lysine Arginine Histidine (BARELY basic)

46

What causes CF?

Single mutation in Cystic Fibrosis Transmembrane conductance Regulator (CTFR) gene Causes malfunction in chloride transport and an increase sodium (and thus water) absorption across epithelial cells. This leaves behind a viscous/dry medium in the airway This is also a very favorable environment for bacterial growth

47

What does pKa indicate?

The relative strength of a weak acid or base

48

What is a common AA in enzyme active sites?

Cysteine

49

Is the carboxyl group a stronger acid than the amino group?

Yes

50

What are the branched chain amino acids?

Valine Leucine Isoleucine

51

What do fibrous proteins do?

Provide structural support, external protection, shape, flexibility, etc.

52

Describe the alpha helix:

Secondary structure 3.6 AA residues per turn R groups stick out from helix

53

What are the nonpolar amino acids?

Glycine Alanine Valine Leucine Isoleucine Proline Phenylalanine Tryptophan Methionine GAV LIPPTM

54

What are the negatively charged polar AAs?

Aspartic acid Glutamic Acid

55

What is the tertiary structure of proteins?

Folding to give 3D form Net effect of many weak interactions and disulfide bonds Hydrophobic residues get buried

56

What occurs at point A?

Both amino and carboxyl group are protonated

57

What happens at point B?

pKa of the carboxyl group

58

What happens at point C?

Isoelectric point

59

What happens at point D?

pKa of amino group

60

What happens at point E?

Neither amino nor carboxyl groups are protonated

61

The proteasome consists of two 19S caps and one 20S core, where are the catalytic subunits contained?

Inner surface of the 20s core

62

The glycine residue of ubiquitin attaches to which amino acid on the target protein?

Lysine