Chapter 4: Proteins

Question 1

primary structure (3)

what it is+determines+can show

Answer 1

• The amino acid sequence
• determines the 3D structure of the protein, 3D structure determines function
• can show evolutionary history

Question 2

Explain the formation of a peptide bond

Answer 2

Question 3

In trans omega torsion is —— In Cis omega torsion angle is —-

Answer 3

• 180
• 0

Question 4

Peptides bonda are (2)

stability+what it is

Answer 4

• kinectically stable
• colvalent bond that links amino acids together

Question 5

Oligopeptide

Answer 5

a polypeptide with a small number of amino acid residues
ex: dipeptide, tripeptide, tetrapeptide (4- aa)

Question 6

Average weight for an AA residue is

Answer 6

• 110g/mol

Question 7

Proteins typically consist of —– amino acids

Answer 7

50 to 2000

Question 8

Secondary structure

Answer 8

The three dimensional structure resulting from a regular pattern of hydrogen bonds between the NH and the CO components of the amino acids in the polypeptide chain.

Question 9

Teriary Structure

Answer 9

When the R groups of amino acids that are far apart in the primary structure bond with one another.

Question 10

This level of structure is called —- structure and is the highest level of structure that an individual polypeptide can attain.

Answer 10

tertiary

Question 11

The final three-dimensional structure of a protein is determined simply by the —-.

Answer 11

amino acid sequence of the protein

Question 12

peptide bond (amide bond)

Answer 12

The linkage joining amino acids in a protein formed by linking the α carboxyl group of one amino acid to the α-amino group of another amino acid.

Question 13

The formation of a dipeptide from two amino acids is accompanied by —–

Answer 13

the loss of a water molecule

Question 14

Explain the biosynthesis of the peptide bonds

Answer 14

The equilibrium of this reaction lies on the side of hydrolysis rather than synthesis under most conditions. Hence, the biosynthesis of peptide bonds requires an input of free energy. Nonetheless, peptide bonds are quite stable kinetically because the rate of hydrolysis is extremely slow; the lifetime of a peptide bond in aqueous solution in the absence of a catalyst approaches 1000 years.

Question 15

a residue

Answer 15

each amino acid unit in a polypeptide

Question 16

By convention, the amino end is taken to be the beginning of a polypeptide chain, so the sequence of amino acids in a polypeptide chain is written starting with the —- terminal residue

Answer 16

amino

Question 17

Why is the polypeptide backbone rich in hydrogen-bonding potential?

Answer 17

Each residue contains a carbonyl group (C═O), which is a good hydrogen-bond acceptor, and, with the exception of proline, an amino group (N—H), which is a good hydrogen-bond donor. These groups interact with each other and with the functional groups of side chains to stabilize particular structures.

Question 18

a dalton

Answer 18

• Used to describe mass of protein

Question 19

Disulfide bond (2)

formed by+ can form btwn

Answer 19

• formed by the oxidation of a pair of cysteine residues.
• Disulfide bonds can form between cysteine residues in the same polypeptide chain, or they can link two separate chains together.

Question 20

The resulting unit of two linked cysteines is called .

Answer 20

cystine

Question 21

3D structure/ traits of peptide bonds (3):

struture+ resonance+ charge

Answer 21

• six atoms lie in the same plane (planar): the α-carbon atom and CO group of the first amino acid and the NH group and α-carbon atom of the second amino acid
• the peptide bond has considerable double-bond character owing to resonance structures: the electrons resonate between a pure single bond and a pure double bond. This partial double-bond character prevents rotation about this bond and thus constrains the conformation of the peptide backbone
• peptide bond is uncharged, allowing polymers (petide chains) of amino acids linked by peptide bonds to form tightly packed globular structures that would otherwise be inhibited by charge repulsion.

Question 22

Almost all peptide bonds in proteins are —. This preference can be explained by the fact that there are —- between R groups in the —– configuration but not in the —- configuration.

Answer 22

• trans
• steric clashes
• cis
• trans

Question 23

Steric exclusion

Answer 23

• the fact that two atoms cannot be in the same place at the same time, restricts the number of possible peptide conformations and is thus a powerful organizing principle

Question 24

Phi (ϕ) (2)

What the angle is between + comparing which?

Answer 24

• The angle of rotation about the bond between the nitrogen and the α-carbon atoms
• comparing angle between the 2 carbonyl atoms

Question 25

psi (ψ) (2) | What the angle is between + comparing which?

Answer 25

- the angle of rotation about the bond between the carbonyl carbon and the α-carbon atoms. - Comparing the angle between the two Nitrogen atoms

Question 26

In trans conformation the torsion angle is ----, in cis, omega torsion angle is ---- | omega torsion angle: the half double bond between Nh and Co

Answer 26

- 180 - 0 degrees (right ontop of eachother)

Question 27

Alpha helices, β pleated sheets, and turns are formed by

Answer 27

- a regular pattern of hydrogen bonds between the peptide NH and CO groups of amino acids that are often near one another in the linear sequence, or primary structure

Question 28

α helix (4) | the shape+ side chain+ residues+ chirality

Answer 28

- a rodlike structure with a tightly coiled backbone. - The side chains of the amino acids composing the structure extend outward in a helical array towards the amino end - The CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated four residues ahead in the sequence (same side of helix) *C=O pointed downwards to c terminal* - Helix are right handed due to chirality of the amino acids

Question 29

Proline in alpha helixes

Answer 29

No in the middle, maybe at end due to psi, phi angles

Question 30

In α helix each residue is related to the next one by a rise, also called translation, of ---- along the helix axis and a rotation of ----- degrees, which gives ----- amino acid residues per turn of helix.

Answer 30

- 1.5 A - 100 - 3.6

Question 31

amino acids spaced ---- apart in the sequence are situated on opposite sides of the helix and so are unlikely to make contact.

Answer 31

two

Question 32

The pitch of the α helix

Answer 32

the length of one complete turn along the helix axis and is equal to the product of the translation (1.5Å) and the number of residues per turn (3.6), or 5.4 Å

Question 33

α helix amino acid breakers:

Answer 33

Branching at the β-carbon atom, as in valine, threonine, and isoleucine, tends to destabilize α helices because of steric clashes. Serine, aspartate, and asparagine also tend to disrupt α helices because their side chains contain hydrogen-bond donors or acceptors in close proximity to the main chain, where they compete for main-chain NH and CO groups. Proline also is an α helix breaker because it lacks an NH group and because its ring structure prevents it from assuming the ϕ value to fit into an α helix.

Question 34

a helix 36 amino acids long would form ---- turns

Answer 34

10

Question 35

the rise

Answer 35

the distance between amino acids: it's a distance of 1.5 angstroms.

Question 36

β strand | extended....

Answer 36

is almost fully extended rather than tightly coiled as in the α helix

Question 37

The distance between adjacent amino acidnresidue along a β strand is approximately ---, in contrast with a distance of ---- along an α helix.

Answer 37

- 3.5 Å - 1.5 Å

Question 38

Instead of a single polypeptide strand, the β sheet is composed of ---- called β strands.

Answer 38

two or more polypeptide chains

Question 39

Beta strand R groups

Answer 39

The side chains of adjacent amino acids point in opposite directions (above and below the b sheet)

Question 40

Reverse turn

Answer 40

The carbonyl oxygen of residue i accepts a hydrogen bond from amide nitrogen of residue i+3

Question 41

Adjacent β strands run in opposite directions | tell me about the H bond

Answer 41

- Hydrogen bonds (green dashes) between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure

Question 42

Adjacent β strands run in the same direction.

Answer 42

Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.

Question 43

Mixed B sheet

Answer 43

- contains parallel and antiparallel segments

Question 44

Best conformation of phi and psi Beta sheet:

Answer 44

Question 45

Teritary structure are a result of.... such as....

Answer 45

- the result of interactions between the R groups of the peptide chain. - covalent bond- disulfide bonds - vanderwaals interactions - H-bond interactions - ionic interactions

Question 46

motifs or supersecondary structures (3) | what it is+ ex+ often the same motif.....

Answer 46

- particular combinations of secondary structure found in many proteins - ex: an α helix separated from another α helix by a turn, called a helix-turn-helix unit (DNA binding) - Often the same motif is found in proteins with similar functions (such as proteins that bind DNA, Ca2+, etc)

Question 47

A β-hairpin (3) | What is common+ what it consist of+in terms of i

Answer 47

- two consecutive hydrogen-bonded antiparallel β-strands connected by a loop region that typically comprises 1–5 amino acid residues. - glycine and proline are common - a hydrogen bond involving the carbonyl of residue i and the NH group of residue i+3

Question 48

domains (2) | What it is + size

Answer 48

- When polypeptide chains fold into two or more compact regions that may be connected by a flexible segment of polypeptide chain, rather like pearls on a string - range in size from about 30 to 400 amino acid residues

Question 49

subunit

Answer 49

Many proteins consist of more than one polypeptide chain in their functional states. Each polypeptide chain in such a protein is called a subunit

Question 50

The interactions among subunits of proteins displaying quaternary structure are usually the --- interactions discussed in Chapter 2: ----, -----, ------

Answer 50

- weak - hydrogen bonds, ionic bonds, and van der Waals interactions.

Question 51

dimer

Answer 51

two identical subunits

Question 52

In most cases, the subunits are held together by ---- bonds. | not peptide

Answer 52

noncovalent

Question 53

Dihedral angle is determined by -----.

Answer 53

4 atoms

Question 54

alpha helices have average phi angle of

Answer 54

-57

Question 55

alpha helices have average psi angle of

Answer 55

-47