Lecture 9: The Structure of Proteins

Question 1

the sequence of amino acids is specified by the __ sequence encoding the protein

Answer 1

gene

Question 2

amino acid polymers of less than 50 amino acids are called __

Answer 2

peptide

Question 3

a peptide bond is formed between which two groups in a peptide chain?

Answer 3

carboxyl group of the first and the amino group of the second

Question 4

the H and R groups are opposite the ___ in a peptide bond to avoid steric clash

Answer 4

o in the carbonyl

Question 5

the equilibrium of making a peptide bond favours the ___ side

Answer 5

left (hydrolysis)

Question 6

why does the peptide equilibrium favour the hydrolysis rather than synthesis?

Answer 6

because the synthesis requires free energy

Question 7

the alpha carbon can always be identified because it has the ___ attached to it

Answer 7

R group

Question 8

each amino acid in a peptide chain is called a __

Answer 8

residue

Question 9

every peptide chain begins with a ___ residue and ends in a __ residue

Answer 9

amino, carboxyl

Question 10

the amino acid at the beginning of the chain is called the __

Answer 10

amino / N terminus

Question 11

the amino acid at the end of the chain is called the __-

Answer 11

carboxly / C terminus

Question 12

the geometry of an aa about a peptide bond is __

Answer 12

planar

Question 13

what makes the peptide bond rigid? (not free to rotate)

Answer 13

resonance from the carboxyl makes the bond not purely single and therefore unable to freely rotate

Question 14

the psi and phi bonds flank the ___ of each amino acid

Answer 14

alpha carbon

Question 15

what bonds are free to rotate in amino acids?

Answer 15

the phi and psi bonds

Question 16

the phi bond forms between the alpha carbon and the

Answer 16

amino group

Question 17

the psi bond forms between the alpha carbon and the

Answer 17

carbonyl group

Question 18

what does a Ramachandron plot show?

Answer 18

the permissible phi and psi bond angles allowed in a polypeptide backbone

Question 19

the range of permissible angle combinations reflect the ___ and ___structure of proteins

Answer 19

secondary and tertiary

Question 20

the polypeptide structure will have inherent __ and ___ within the constraints dictated by the permissible angles

Answer 20

flexibility and mobility

Question 21

the secondary structure of proteins is stabilized by __ bonds between N and carboxyl groups in linear squence

Answer 21

H bonds

Question 22

due to combination of bond angles and H bonding effects, certain aa segments ____ form secondary structures

Answer 22

spontaneously

Question 23

what are the 3 types of secondary structures?

Answer 23

aplha helix , beta sheets, turns and loops

Question 24

proteins can be made exclusively of alpha helix/beta sheets, or a mix of both (T/F)

Answer 24

true

Question 25

turns and loops function to __

Answer 25

connect helices or sheets together

Question 26

alpha helixes are segments of amino acids that form ___ handed helical structure (rotates ___ (cw.ccw)

Answer 26

right; clockwise

Question 27

what is the average length of an alpha helix?

Answer 27

10 amino acids

Question 28

there are about ___ amino acids per complete turn along the the alpha helix

Answer 28

3.6

Question 29

in the alpha helix, every ___ amino acid interacts via hydrogen bonding

Answer 29

4

Question 30

side chains extend in what direction with respect to the helix?

Answer 30

outwards

Question 31

what makes some amino acids unsuited for helix formation?

Answer 31

geometry or size of side chains

Question 32

about ___ % of all soluble proteins are composed of alpha helices

Answer 32

25

Question 33

the B sheets are made by multiple __ of amino acids in a ___ sequence rather than coiled in a helix

Answer 33

adjacent segments; fully extended

Question 34

adjacent segments in a B sheet interact by __ interactions

Answer 34

hydrogen bonding

Question 35

adjacent B strands can be in anti-parallel or parallel (T/F)

Answer 35

true

Question 36

in antiparallel B sheets, each amino acid is bonded to __ on the other strand

Answer 36

one amino acid

Question 37

in parallel B sheets, each amino acid is bonded to __ on the other strand

Answer 37

2 different amino acids

Question 38

in parallel B sheets, the two strands run in the ___ direction

Answer 38

same

Question 39

in antiparallel b sheets, the two strands run in the ___ direction

Answer 39

opposite

Question 40

B strands associate to become __

Answer 40

B sheets

Question 41

B sheets are stabilized by intracellular ___ bonds

Answer 41

H

Question 42

arrows representing B sheets point in the direction of the ___ terminal end

Answer 42

carboxyl

Question 43

Beta sheets can be flat, but most adopt a ___ shape

Answer 43

twisted

Question 44

what two amino acids participate in forming turns?

Answer 44

proline and glycine

Question 45

there is open space in the interior of a protein (T/F)

Answer 45

no; little to none

Question 46

name 5 things that stabilize tertiary structure

Answer 46

1. charge interactions 2. H bonding 3. van der waal between side chains 4. hydrophobic effect 5. disulphide bonds b tween cysteine side chains

Question 47

myoglobin is an example of a __ protein

Answer 47

globular

Question 48

myoglobin is an extremely compact molecule made of __ polypeptide chain(s) of ___ (#) amino acids

Answer 48

1; 153

Question 49

about 70% of the myoglobin structure is made of __

Answer 49

alpha helices

Question 50

tertiary structures of many proteins can be divided into __ and ___ units

Answer 50

structural and functional

Question 51

some proteins fold into multiple tertiary structures called __

Answer 51

domains

Question 52

each domain may posses a unique ___ that may be quite functional even id separated from the protein

Answer 52

enzymatic function

Question 53

discrete sub-structures in a protein with special structural/functional significance are called __

Answer 53

motifs

Question 54

what motif is typically found in proteins that bind double-stranded DNA?

Answer 54

helix--turn--helix

Question 55

each polypeptide chain in a protein complex is called a __

Answer 55

subunit

Question 56

quaternary structure refers to the arrangement of ___ and the nature of their interactions

Answer 56

subunits

Question 57

what is homotypic association?

Answer 57

proteins assemble within each other

Question 58

what is heterotypic association?

Answer 58

different proteins assemble into multi-subunit complexes

Question 59

example of a heterotypic protein

Answer 59

DNA polymerase