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Biochem Exam 2 > Ch 4 > Flashcards

Ch 4 Flashcards

1
Q

The spatial arrangement of a 3-D strutcture is known as

A

conformation

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2
Q

True or false: the native (folded) conformation of a 3-D structure has the lowest free energy (G) meaning it is the least stable conformation

A

False, it is the MOST stable

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3
Q

What are the two ways 3-D conformation is stabilized?

A

‘burying’ hydrophobic groups

maximizing H-bonding

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4
Q

A peptide bond can twist. True or false?

A

False, the nitrogen pulls electrons for partial double bond characteristics, when there is a partial double bond, no twisting

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5
Q

How many atoms are there in a plane of a peptide bond?

A

6 atoms

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6
Q

Is 360 degree rotation about the N-C and C-C bonds possible?

A

yes, it is what makes peptides and proteins more flexible, but certain angles are more stable than others

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7
Q

What is the most comon example of a secondary structure

A

alpha helix

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8
Q

how are secondary structures stabilized?

A

by hydrogen bonds

and by R groups on the outside

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9
Q

With what molecule (amino acid) can an alpha helix not be formed?

A

proline - disrupts any alpha helix “proline kink”

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10
Q

What type of structure is a beta sheet?

A

a secondary structure

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11
Q

what is an antiparallel beta sheet?

A

the beta sheet is where at least to parts of a peptide are linked together, in an antiparallel beta sheet the polypeptides alternate directions they are moving in

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12
Q

True or false, parallel beta sheet strands alternate the directions they are moving in?

A

False, they all go in the same direction

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13
Q

In globular proteins how much of the amino acid residues are in turns or loops between beta sheets and/or alpha helices?

A

1/3 of the aa residues

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14
Q

2/3 of the amino acids are part of what?

A

alpha helices or beta sheets (the other 1/3 are connectors)

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15
Q

Secondary structure involves what?

a. the spatial arrangement of adjacent amino acids
b. the 3-d structure involving long-range interactions

A

A

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16
Q

tertiary structure involves what?

a. the spatial arrangement of adjacent amino acids
b. the 3-d structure involving long-range interactions

A

B

17
Q

What are the two major groups of proteins (tertiary structures)?

A

fibrous and globular

18
Q

What are the three major types of fibrous proteins?

A

alpha keratin
collagen
silk fibroin

19
Q

What are the defining characteristics of fibrous proteins?

A

they are elongated, and structural proteins

long amino acid pieces

20
Q

All are true about alpha keratin, except:

a. strong
b. right handed alpha helix (primary structure)
c. the secondary structure is a left handed alpha helix
d. it is strengthened by cross-links
e. it is in tendons, cartilage and bone

A

E.

alpha keratin is in hair, nails, hooves, horns, and outer skin layers

21
Q

What stabilizes the structure of keratin?

A

cross links ***cysteine forms cross links

22
Q

What part of the body does collagen make up?

A

tendons, cartilage, bone

23
Q

True or false: collagen can be pulled apart.

A

False, collagen has high tensile strength

24
Q

What is unique/significant about collagen?

A

it has hypro and hylys cross links which are not part of the normal 20 amino acids

25
Q

True or false: the left handed helix in collagen is an alpha helix.

A

False, it is a single strand, it is the alpha chain but not an alpha helix

26
Q

What does the right handed form of collagen create?

A

A superhelix (3 helices)

27
Q

What inactivates the enzyme required to convert Pro to Hypro?

A

the absence of vitamin C

28
Q

The absence of vitamin c can lead to collagen instability and connective tissue problems, what can this cause?

A

Scurvy

29
Q

We need vitamin C to make what for collagen?

A

vitamin C is needed to make hypro for collagen

30
Q

What two amino acids are rich in silk fibroin?

A

Ala and Gly (small, compact)

31
Q

What structure predominates in silk fibroin?

A

Beta sheets (antiparallel)

32
Q

True or false: silk fibroin can be stretched.

A

False, it is fully extended

33
Q

What is important about silk fibroin?

A

There is extensive hydrogen binding and van der waals interactions between sheets, but no covalent cross links making it flexible
(Long sheet, no cross links, very flexible)

34
Q

How are alpha helices cross linked?

A

by disulfide bonds

35
Q

Match the following

a. alpha helix, cross linked by disulfide bonds
b. beta conformation
c. collagen triple helix

  1. collagen of tendons, bone matrix
  2. alpha keratin of hair, feathers, nails
  3. silk fibroin
A

a, 2
b, 3
c, 1

36
Q

What is important about intrinsically disordered proteins or protein segments?

A

They may include up to 1/3 human proteins

  • flexibility allows interaction with many diff. partner molecules
  • some wrap around each and inhibit targets

Biochem Exam 2 (1 decks)

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