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Biochemistry > Biochem Protein Lecture 8 > Flashcards

Biochem Protein Lecture 8 Flashcards

1
Q

The 3D arrangement of all atoms in a protein. It includes longer range interactions of AA sequence. AAs far apart in different types of secondary structure can interact with each other within the completely folded protein structure

A

Tertiary Structure

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2
Q

The arrangement of protein units into 3D complexes

Some proteins contain 2 or more polypeptide chains or subunits. They can be identical or different.

A

Quaternary Structure

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3
Q

This major group of proteins is polypeptide chains arranged in long strands or sheets. They provide support, shape and external protection. A clear relationship between structure and function is observed

They consist largely of a single type of ______ structure

A

Fibrous Proteins

Secondary

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4
Q

In this major group of proteins, polypeptides are folded in spherical or globular shapes.

Often contain several groups of ____ structure

What are some examples of these?

A

Globular proteins

Secondary

Enzymes and regulatory proteins

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5
Q

These proteins are abundant in hair, wool, nails, claws, quills, horns, hooves, and much of the outer layer of skin

They are composed of ________ proteins

A

α-Keratin

Intermediate filament (IF) proteins

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6
Q

The α-Keratin helix is left or right handed?

A

Right handed

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7
Q

α-Keratins contain a central segment of a polypeptide chain which has a ___ residue pseudorepeat, how is the sequence represented? Which residues are predominately nonpolar?

How many residues is this central segment?

A

7 residue pseudorepeat

abcdefg

a and d are predominately non-polar

310

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8
Q

In α-Keratin, the central 310 residue segments of two polypeptide chains form α-helices which coil around eachother to form dimers. They form a _______ like the strands of a rope

The strands interact with eachother between the ________ residues. Their R groups interact in a regular pattern-permitting a close packing

A

Supertwisted coiled coil

nonpolar (a and d) residues

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9
Q

α-Keratin is rich in _______ residues: ala, val, leu, ile, met, phe

A

Hydrophobic residues

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10
Q

The helical path of α-Keratin supertwists is left or right handed?

thus, the tertiary structure of an individual polypeptide in the α-Keratin coiled coil is the helical axis of the α-helical polypeptide twisted in a ___ handed superhelix

A

Left handed

Left Handed superhelix

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11
Q

The twisting of the axis of an α-helix in keratin to form a coiled coil explains the discrepancy between predicted (5.4 A per turn) and observed (5.1-5.2 per turn) repeating structure in the X-ray diffraction of hair.

A

!

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12
Q

This structure of α-Keratin is the intertwining of two α-helical polypeptides

A

Quaternary Structure

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13
Q

The quaternary structure of hair can be quite complex. The _____ are arranged in two staggered rows with the non helical ends of the chains arranged in a head to tail manner. A _____ is formed

A

Dimers

Protofilament

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14
Q

Protofilaments dimerize to form a

About 4 protofibrils (32 strands of α-Keratin) make up a

A

Protofibril

Microbfibril

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15
Q

Microbfibrils are used to construct a

A

Macrofibril

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16
Q

Hair cells are composed of many packed

A

Macrofibrils

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17
Q

We can relate the properties of hair and wool to protein _____

A

Structure

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18
Q

Wool is very ____; it can be stretched out to almost twice its length because it’s composed of α-helices that are not fully extended

A

Extensible

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19
Q

Hair is resistant to stretching because _______ bonds along the α-helices provide some resistance to stretching. The α helices are not fully extended.

Hair also has numerous _____ bonds between polypeptides within and between protofilaments which provide resistance to stretching and enhanced fiber strength

A

Hydrogen Bonds

Disulfide Bonds

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20
Q

When hair is exposed to moist heat, in can be

The moist heat breaks ___ bonds, causing the α-helical structure of the polypeptide chains to uncoil

The α-helices are stretched out until they are at the fully extended ___ conformation

Upon cooling, the α-Keratin spontaneously returns to the __ helical conformation

A

Stretched

H-bonds

β conformation

α-helical conformation

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21
Q

When hair is subjected to a permanent waving process, it is first bent around a roller and then a reducing agent is applied with heat

The reducing agent breaks ___ bonds by reducing each bond to form two cys residues

A

Disulfide bonds

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22
Q

After a reducing agent is applied to hair, after some time period the reducing solution is removed and an _______ is added to establish new disulfide bonds between different pairs of cys residues of adjacent polypeptides

A

Oxidizing agent

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23
Q

After applying the oxidizing agent, hair is washed and cooled, and the polypeptide chains revert to ______ conformation. Hair is now curled because the new ___ bonds exert some twist of the α-helical bundles of hair fibers

A

α-helical

Disulfide bonds

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24
Q

In the hardest, toughest α keratins, (horns and nails), 18% of the amino acid residues are _____ involved in disulfide bonds

A

Cys involved in disulfide bonds

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25
Q

Is the permanent wave process that is made by the reducing/oxidizing process permanent? Why or why not?

A

It is not permanent because as new hair grows, the α keratin has the natural nonwavy pattern of disulfide bonds

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26
Q

In sum,

An individual polypeptide in α keratin has ____ structure, the helical axis of the α helix is twisted in a _____ handed superhelix

A

Tertiary structure

Left-handed superhelix

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27
Q

In sum, the intertwining of two α helical polypeptides (coiled coils) represents ____

A

Quaternary structure

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28
Q

What provides hair resistance to stretching?

A

H bonds along α helices

Numerous disulfide bonds between polypeptide chains within and and between protofilaments

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29
Q

What is the normal form of keratin with structures other than hair and wool? Examples include feathers, skin, claws, and beaks

What is the structure similar to?

A

β sheet

Silk Fibroin

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30
Q

This is the protein of silk that is produced by insects and spiders

A

Fibroin

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31
Q

In silk fibroin, polypeptide chains are layers of closely packed ________ β sheets rich in ___ and ____ residues

A

Antiparallel β sheets

Ala and Gly

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32
Q

Why are R groups small (ala and gly) in closely packed β sheets?

A

To prevent steric interaction between chains in a sheet

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33
Q

What 3 amino acids comprise 86% of the aa in silk fibroin?

A

Gly (45%), ala (29%), ser (12%)

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34
Q

What is the repeating sequence in the primary structure of β sheets?

A

Gly-ser-gly-ala-gly-ala

Reflects 3:2:1: ratio

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35
Q

What is a single collagen molecule composed of?

Approximately how many aa residues in a chain?

A

Three polypeptide chains?

1,000

36
Q

A collagen helix is right or left handed?

What are the φ and ψ values?

n and p values?

A

Left Handed

φ =-51
ψ = 153

n = 3.3 p=10

37
Q

Is the left handed helix of collagen stabilized by intrapeptide H bonds?

A

No, does not occur

38
Q

Collagen tertiary and quaternary structure is called a

the ___ chains are supertwisted about each other to form a right handed super helical structure

A

coiled coil

39
Q

Is the tertiary and quaternary structure of collagen right or left handed?

A

Right handed super helix

40
Q

What stabilizes the superhelical structure of collagen?

A

H bonds between carbonyl O atoms in one chains and peptide N-H groups in the other chains

41
Q

There are many types of collgaen, what are the four aas it contains

A

Gly (35%), pro (21%) ala (11%), and 4Hyp (4-hydroxyproline)

42
Q

What do pro and 4-hyp lack that limits the number of H bonds they can form?

A

An H on the peptide N

43
Q

The AA sequence in collagen is generally a repeating tripeptide unit, Gly-X-Y where X is often ____ and Y is often _____

A

X=pro

Y= hypro

44
Q

What one residue can be accommodated in the tight junctions between individual alpha chains of collagen?

A

Gly

45
Q

Collagen fibrils consist of triple helical collagen molecules aligned in a ______ array and _____ for increased tensile strength

A

Staggered array, crosslinked

46
Q

The α chains of collagen molecules and the collagen molecules of fibrils are cross linked by unusual types of covalent bonds involving ____, _____ or ____ residues that are present at a few of the X and Y positions in collagens

A

Lys, Hylys, his

47
Q

The unusual covalent bonds that cross link α chains of collagen molecules and the collagen molecules of fibers create uncommon amino residues such as

A

dehydrohydroxylysinonorleucine

LOL

48
Q

How does age affect crosslinking?

A

Crosslinking increases, contributes to toughness of meat in older animals

49
Q

A number of human diseases are linked with genetic defects in collagen structure

This when is characterized by abnormal bone formation in babies

This one is characterized by loose joints

A

Osteogenesis Imperfecta

Ehlers-Danlos syndrome

50
Q

Both osteogenesis imperfecta and ehlers-danlos syndrome can be lethal and result from the substitution of an AA residue with a ________ for a single gly residue in each α chain, disrupting the gly-X-Y repeat that gives collagen its unique structure

A

Larger R group (cys, ser)

51
Q

What vitamin has an important role in the formation of collagen?

The collagen helix structure requires the pro residue in the Y positions to be in the _______ conformation

This conformation is enforced by the ____ substitution at C4 in 4-hydroxyproline

A

Vitamin C

Cγ-exo conformation

OH

52
Q

Collagen structure requires the the pro residue in the X position to have the ____ conformation, introduction of 4-hyp here can destabilize the helix

The inability to hydrozylate pro at the Y positions when vitamins C is absent results in collagen instability and connective tissue problems seen in

A

Cγ-endo conformation

Scurvy

53
Q

In ____ proteins, different segments of the polypeptide chains fold back on each other. This group includes enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobins

A

Globular Proteins

54
Q

Globular folding provides two things:

A

Compact form

Structural diversity for a range of biological functions

55
Q

This globular protein in its native globular form is 100 X 60 A

In an entirely β conformation it would be 2000 x 5 A

In an entirely α conformation it would be 900x11A

A

Human Serum Albumin

56
Q

An understanding of 3-D structure of globular proteins came about through X-ray diffraction studies of ______ in the 1950s

A

Myoglobin

57
Q

This a relatively small oxygen oxygen binding protein in muscle cells

A

Myoglobin

58
Q

What is the function of myoglobin?

What else?

A

Store oxygen and facilitate oxygen diffusion in rapidly contracting muscle

Oxygen storage and distribution enable animals to remain underwater for long periods of time

59
Q

What is the composition of myoglobin?

A

A single polypeptide chain of 153 aa residues of known sequence and a single Fe protoporphyrin group

60
Q

What is the other name of the singe Fe protoporphyrin group in myoglobin?

A

Heme

61
Q

The backbone of myoglobin consists of either segments of _____ interrupted by bends (some β turns)

A

α helix

62
Q

Helix lengths in myoglobin vary from ___ residues to ____

A

7 to 23

63
Q

All helices in myoglobin are ____ handed;

greater than what percent of aa residues are in helical regions?

A

Right

>70%

64
Q

What type of interactions greatly contribute to the stability of the myoglobin structure?

A

Hydrophobic interactions

65
Q

Where are the hydrophobic R groups in myoglobin’s structure?

Where are the polar ones?

A

Interior

Surface (all but 2)

66
Q

The globular shape of proteins can be compared to a

A

Micelle

67
Q

The myoglobin molecule is very compact, the interior only has room for __ water molecules

A

4

68
Q

Globular proteins tend to have a dense, hydrophobic core

A

! IN BOLD!

69
Q

What other types of interactions contribute to the stability?

A

Weak interactions

70
Q

Due to the close packing of the side chains in myoglobin’s core, ________ interactions of nonpolar side chains stabilize hydrophobic interactions

A

van der Waals

71
Q

In addition to the 8 alpha helical segments dominating the myoglobin structure, there are ___ in the myoglobin 3D structure. Certain AAs are found in them

A

Bends

72
Q

3 of 4 _____ residues of myoglobin are found at bends

A

Pro (Pro has fixed φ bond angle and no peptide bond N-H group

73
Q

Where does the 4th pro occur in myoglobin thats not in bends?

What does it do to this structure?

A

α helix

Creates a kink for tight packing

74
Q

These AAs are also found in bends (not pro) if they are together in the sequence, bulk and shape STABILIZE/DESTABILIZE the α helix

A

Ser, Thr, Asn

Destabilize the α helix

75
Q

This rests in a hydrophobic pocket of myoglobin

A

Heme (the red part in the molecule diagram)

76
Q

This atom in myoglobin has two bonding positions perpendicular to the heme plan

One is bound to R group of ____ at position 93

Another is open, it is a binding site for

A

Fe

His

Oxygen

77
Q

Accessibility of heme group to solvent is open or restricted in the pocket?

How is this important for function?

A

Restricted

Free heme groups rapidly oxidize from ferrous form (Fe2+), which reversibly binds to )2, to ferric form (Fe3+) which does not bind O2

78
Q

Different AA sequences and different tertiary structure lead to different

A

Functions

79
Q

Covalent bonds are needed to help stabilize large or small globular proteins?

A

Small

80
Q

What are the three similarities in various single chain proteins?

A

1) They fold compactly
2) Their hydrophobic aa side chains are oriented toward the interior, away from water
3) Hydrophilic side chains are predominantly on the surface

81
Q

Should you know about the proteins in the table on slide 32?

A

Ask.

82
Q

What type of interactions are impt to the tertiary structure of metalloproteins?

A

Metal-ligand interactions

83
Q

What metal participates in an impt metal ligand interaction in carboxypeptidase A?

A

Zn2+

84
Q

FOr this structure, the polypeptide chain has 307 aa folded in a spherical shape. Zn2+ is tetrahedrally coordinated to the side chains of his 69, glu 72, his 156, and H2O molecule

A

Carboxypeptidase A

85
Q

What three noncovalent interactions influence tertiary structure?

A

H-bonding between side chains
Salt Bonds between side chains of aa or carboxy amino termini and aa side chains
Hydrophobic Interactions

Biochemistry (27 decks)

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