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Flashcards in Protein Structure Deck (49):
1

What is the 3D structure of Proteins

1. Determined by amino acid sequence
2. determines function of protein
3. unique for each protein
4. maintained by non-covalent interactions
5. Has several recurring motifs

2

What are the 4 levels of protein architecture

1. Primary: Amino acid sequence + disulfide bond
2. Secondary: Regular recurring arrangements of adjacent amino acids.
3. Arrangements of the total protein, the complete 3D structure
4. Arrangement of multiple protein subunits

3

The primary structure can be derived from ____sequence

gene

4

The primary structure includes _____ and ____bonds

peptide; disulfide

5

The primary structure can give important clues to probable _____

protein function

6

Contigous regions of a protein with a distinct function or structure is called a

domain

7

Peptide bonds and disulfide bonds are both ____bonds

covalent

8

Peptide bonds are ____and ____

planar; rigid

9

What includes the secondary structure

1. alpha helix
2. beta sheet
3. beta turn

10

What do alpha helices consist of

1. Peptide bonds align along long axis
2. R groups stick out of sides
3. each turn -3.6 aa
4. every 3-4 aa in close proximity and stabilize through H bonding

11

What are alpha helix destabilizers

1. String of several basic or acidic aa's
2. String of several aa with bulky side groups
3. aa 3-4 residues apart which cannot interact
4. Proline residues ("helix breakers")
5. String of glycine residues

12

What are the characteristics of beta pleated sheets

1. Extended arrangement of polypeptides
2. H bonds hold adjacent chains together
3. Chains may be arranged in parallel or anti parallel fashion.

13

What are characteristics of Beta turn

Contain proline in the cis conformation; requires proline isomerase to convert it

14

What are characteristics of tertiary structure

1. 3D arrangement
2. Brings distant regions into close proximity

15

What are the two major groups of tertiary structure

1. Globular
2. Fibrous

16

What are fibrous proteins

1. Primarily water insoluble
2. Structural proteins
3. Simple arrangement
4. Usually long chains or sheets

17

What do fibrous proteins consist of

Alpha and beta keratin

18

What are fibrous proteins found in

Hair, nails, feathers

19

What are characteristics of fibrous proteins

1. Classic, right handed a helix
2. Many hydrophobic aa
3. 2 stranded superhelix= protofilament
4. Crosslinks via disulfide links
5. Permanent wave solution breaks, reforms disulfide bonds

20

How many types of keratin are found in the skin

18

21

What are cytokeratins

components of the intermediate filaments of the cytoskeleton

22

What are the characteristics of globular proteins

1. All other proteins
2. Most enzymes and protein hormones
3. Secondary structure is more complex
4. Multiple arrangements of folding into a "spherical" shape

23

How do water molecules arrange themselves

in an orderly manner to form "cages" around hydrophobic groups

24

____groups tend to be sequestered internally.

Hydrophobic

25

____regions interact with water.

Hydrophilic

26

What are the tertiary structure bond types

1. H bonds: an EN atom (usually O or N) acts as a H acceptor
2. Ionic bonds: Attraction bet oppositely charged atoms
3. Hydrophobic interactions
4. Van der Waals: Weak attractions resulting from transient dipole formation.

27

What is the tertiary structure folding

Proteins dont fold randomly. Most proteins use chaperone proteins to assist in folding

28

What are the most famous chaperone proteins

Heat shock proteins

29

What does Iatrogenic refer to

of or relating to illness caused by medical exam or treatment

30

What are prion diseases caused by

improper folding of Prp protein

31

What is Mad Cow Disease

Bovine spongiform Encephalitis

32

What is Scrapie

Spongiform encephalitis found in sheep

33

What is Kuru

human spongiform disease limited to Fore tribe of New Guinea

34

What is Creuzfeldt-Jacob

sporadic, hereditary, acquired

35

What is cystic fibrosis

Caused by defective protein folding
-chloride channel protein (CFTR) is missing a single amino acid (Phe- 508) due to a triplet deletion in the coding sequence of the gene.

36

What are the characteristics of quaternary structure

Only found in proteins with more than 1 protein subunit

37

What are some proteins with quaternary structure

1. pyruvate dehydrogenase
2. ribosomes
3. RNA polymerase

38

What is the best way to study proteins?

X-ray crystallography

39

What is protein denaturation

Disrupts weak interactions; destabilizes the structure and becomes less thermodynamically stable

40

Protein denaturation does NOT disrupt ____bonds

covalent (peptide and disulfide)

41

What are some protein denaturants

1. heat
2. pH extremes
3. detergents
4. organic solvents (alcohol, acetone, urea)

42

What is protein hydrolysis

Disruption of primary structure by hydrolysis to single aa by boiling in strong acid or base

43

What are proteases enzymatically?

enzymes that cleave proteins at specific dipeptide sites

44

T/F denatured proteins can be renatured

True

45

AA's critical for proper folding are _____ which means that mutations in codons for these aa are very deleterious (harmful_

invariant

46

Urea ____proteins

denatures

47

BME ____disulfide bonds

reduces

48

Primary structure dictates ____structure

tertiary

49

What two 3D protein structures are important in the progression of Eale's Disease and are current targets for drug design

retinal s antigen and interphotoreceptor retinoid binding protein