Biochem Protein Lecture 8 Flashcards by michael perna

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

Tertiary Structure

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The arrangement of protein units into 3D complexes

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

Quaternary Structure

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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

Fibrous Proteins

Secondary

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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?

Globular proteins

Secondary

Enzymes and regulatory proteins

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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

α-Keratin

Intermediate filament (IF) proteins

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The α-Keratin helix is left or right handed?

Right handed

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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?

7 residue pseudorepeat

abcdefg

a and d are predominately non-polar

310

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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

Supertwisted coiled coil

nonpolar (a and d) residues

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

Hydrophobic residues

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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

Left handed

Left Handed superhelix

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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.

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

Quaternary Structure

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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

Dimers

Protofilament

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Protofilaments dimerize to form a

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

Protofibril

Microbfibril

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Microbfibrils are used to construct a

Macrofibril

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Hair cells are composed of many packed

Macrofibrils

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

Structure

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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

Extensible

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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

Hydrogen Bonds

Disulfide Bonds

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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

Stretched

H-bonds

β conformation

α-helical conformation

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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

Disulfide bonds

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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

Oxidizing agent

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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

α-helical

Disulfide bonds

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

Cys involved in disulfide bonds

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

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

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

Tertiary structure Left-handed superhelix

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

Quaternary structure

What provides hair resistance to stretching?

H bonds along α helices Numerous disulfide bonds between polypeptide chains within and and between protofilaments

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?

β sheet Silk Fibroin

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

Fibroin

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

Antiparallel β sheets Ala and Gly

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

To prevent steric interaction between chains in a sheet

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

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

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

Gly-ser-gly-ala-gly-ala Reflects 3:2:1: ratio

What is a single collagen molecule composed of? Approximately how many aa residues in a chain?

Three polypeptide chains? 1,000

A collagen helix is right or left handed? What are the φ and ψ values? n and p values?

Left Handed φ =-51 ψ = 153 n = 3.3 p=10

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

No, does not occur

Collagen tertiary and quaternary structure is called a the ___ chains are supertwisted about each other to form a right handed super helical structure

coiled coil

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

Right handed super helix

What stabilizes the superhelical structure of collagen?

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

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

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

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

An H on the peptide N

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

X=pro Y= hypro

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

Gly

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

Staggered array, crosslinked

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

Lys, Hylys, his

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

dehydrohydroxylysinonorleucine | LOL

How does age affect crosslinking?

Crosslinking increases, contributes to toughness of meat in older animals

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

Osteogenesis Imperfecta Ehlers-Danlos syndrome

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

Larger R group (cys, ser)

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

Vitamin C Cγ-exo conformation OH

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

Cγ-endo conformation Scurvy

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

Globular Proteins

Globular folding provides two things:

Compact form | Structural diversity for a range of biological functions

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

Human Serum Albumin

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

Myoglobin

This a relatively small oxygen oxygen binding protein in muscle cells

Myoglobin

What is the function of myoglobin? What else?

Store oxygen and facilitate oxygen diffusion in rapidly contracting muscle Oxygen storage and distribution enable animals to remain underwater for long periods of time

What is the composition of myoglobin?

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

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

Heme

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

α helix

Helix lengths in myoglobin vary from ___ residues to ____

7 to 23

All helices in myoglobin are ____ handed; greater than what percent of aa residues are in helical regions?

Right | >70%

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

Hydrophobic interactions

Where are the hydrophobic R groups in myoglobin's structure? Where are the polar ones?

Interior Surface (all but 2)

The globular shape of proteins can be compared to a

Micelle

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

Globular proteins tend to have a dense, hydrophobic core

! IN BOLD!

What other types of interactions contribute to the stability?

Weak interactions

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

van der Waals

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

Bends

3 of 4 _____ residues of myoglobin are found at bends

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

Where does the 4th pro occur in myoglobin thats not in bends? What does it do to this structure?

α helix Creates a kink for tight packing

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

Ser, Thr, Asn Destabilize the α helix

This rests in a hydrophobic pocket of myoglobin

Heme (the red part in the molecule diagram)

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

Fe His Oxygen

Accessibility of heme group to solvent is open or restricted in the pocket? How is this important for function?

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

Different AA sequences and different tertiary structure lead to different

Functions

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

Small

What are the three similarities in various single chain proteins?

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

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

Ask.

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

Metal-ligand interactions

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

Zn2+

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

Carboxypeptidase A

What three noncovalent interactions influence tertiary structure?

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

Biochem Protein Lecture 8 Flashcards

(85 cards)