BMSC 200 Chapter 4

Peptide bonds are:

a. hydrogen bonds between amino acids

b. covalent linkages between amino acids

c. protein blocks between amino acids

d. hydrophilic interactions between amino acids

b. covalent linkages

How do peptide bonds form?

dehydration synthesis

- condensation reaction involving the loss of a water molecule

What is eliminated in the formation of peptide bonds?

alpha carboxyl and alpha amino charged groups - important for protein folding

peptide bonds are __________, _________ of the amino acids being joined

a. different, dependent

b. same, dependent

c. different, independent

d. same, independent

d.

True or false:

Due to the conserved nature of peptide bonds, there is a repeating pattern within the main chain.

True

The main chain has a ________ portion of the polypeptide, the side chains are ____________

a. inconsistent, the same

b. contant, variable

c. inconsistent, variable

d. constant, the same

constant, variable

Within the main chain there is a repeating pattern of?

NCCNCC

partial double bond character

caused by resonance due to delocalizable pi electrons and lone pair electrons

- rotation around C-N peptide bond is restricted due to its partial double bond characteristic

Consequence of the partial double bond:

the six atoms of the peptide group are rigid and planar

configuration

a shape or outline; a method of arrangement

Partial double bond of the peptide bond creates?

cis-trans isomers

The ____________ of the carbonyl group and the ________________ of the amide group are usually trans to each other

a. nitrogen, hydrogen

b. hydrogen, oxygen

c. oxygen, hydrogen

d. oxygen, nitrogen

c. oxygen, hydrogen

The ________ configuration is favored over the _______ configuration.

a. cis

b. trans

b. trans

why is the trans configuration favored

the cis configuration causes steric interference between side chain groups

What does steric exclusion mean?

two groups can't occupy the same space at the same time

primary structure

linear sequence of amino acids

secondary structure

localized interactions within a polypeptide

Tertiary structure:

the final folding pattern of a single polypeptide

quaternary structure

the folding pattern when multiple polypeptides are involved

assembled subunits

quaternary structure

polypeptide chain

tertiary structure

alpha helix

secondary structure

amino acid residues

primary structures

Primary structures have what kind of arrangement?

linear

Primary structure is presented from the

a. C terminus to the N terminus

b. R terminus to the C terminus

c. N terminus to the C terminus

d. N terminus to the R terminus

c. N amino to the C carboxyl terminus

Where is the information specifying correct folding contained?

a. within the secondary structure

b. within the primary structure

c. within the tertiary structure

d. within the quaternary structure

b. primary

can you predict the three dimensional structure based on the primary structure?

no

what structure represents localized patterns of folding in a polypeptide?

secondary

secondary structures are maintained by hydrogen bonds between the __________ and _________ carbonyl groups

a. amine and carboxyl

b. amide and carboxyl

c. amide and carbonyl

d. amine and carbonyl

c. amide and carbonyl

beta sheets and alpha helices

secondary structures

What structure is conserved across proteins?

secondary

True or false:

elements of secondary structures are found in different proteins

true

Viable forms of secondary structures must include:

- optimize hydrogen bonding potential of main chain carbonyl and amide groups

- represent favoured conformation of the polypeptide chain

Each peptide has:

hydrogen bond donor and acceptor group

There is ________ number of hydrogen bond donors and acceptors within the polypeptide main-chain

a. equal

b. different

a equal

The alpha carbon in a secondary structure is held within the main-chain through __________ about which there is complete freedom of rotation

a. double bonds

b. single bonds

c. triple bonds

d. all of the above

b. single bonds

phi bond

N-Calpha

psi bond

Calpha-C

Phi and Psi range from:

-180-180

What prevents the formation of most conformations?

steric interference

What is a Ramachandran plot?

A plot of the angles of phi and psi angles

Who is Linus Pauling?

a chemist who won two noble prizes, one for peace and one for chemistry

alpha helix

right handed helix with 3.6 residues/turn

an alpha helix is stabilized by?

hydrogen bonds which run parallel to the axis of the helix

in the alpha helix the carbonyl groups point toward the ____ terminus amide groups to the ___ terminus

a. C, N

b. N, C

c. N, R

d. R, C

a. C, N

phi bond

carbon nitrogen

Psi bond

carbonyl carbon bond

amphiphatic helix

- residues separated by three or four positions in the primary sequence will be on the same side

In an amphipathic helix separated by two residues where will they be located?

a. same side

b opposite side

b. opposite sides

residues that are separated by 3 or 4 positions where will they be located?

a. same side

b opposite side

a. same side

Beta sheets are

stronger, more rigid/structural

how many strands are beta sheets made up of?

a. 3

b. 2-3

c. 3-4

d. 4-5

d. 4-5

conformation of beta sheets

fully extended polypeptide chains

beta sheets are stabilized by

hydrogen bonds between C=O and -NH on adjacent strands

True or false:

Beta sheets can only be parallel

false - they can be anti-parallel as well

Anti-parallel beta sheets run

a. same direction

b. many directions

c. different directions

c different directions

Parallel beta sheet run:

a. same direction

b. many directions

c. different directions

a. same direction

Which beta-sheet is more stable?

a. anti-parallel

b. parallel

c. mixeed

a. anti-parallel due to better geometry hydrogen bonding

in what beta-sheet do the side chains alternate above and below the polypeptide chain?

a. parallel

b. anti-parallel

c. mixed

d. amphipathic

d. amphipathic

tertiary structure

the final folding pattern of a single peptide

The biological active folding pattern is the _________ conformation

a. regular

b. native

c. changed

d. tertiary

native

True or false: the amino acid sequence determines tertiary structure

true

Protein conformation is stabilized by

a. strong interaction

b. weak interactions

c. secure interactions

d. average interactions

b. weak interactions

Stability is defined as

the tendency to maintain a native conformation

the protein conformation with the lowest free energy - most stable is usually the one with the

a. minimum number of weak interactions

b. maximum number of weak interactions

c. minimum number of strong interactions

d. maximum number of strong interactions

maximum number of weak interactions

The stability of the protein reflects the _________ in the free energies of the folded and unfolded states

a. difference

b. bonds

c. interactions

a. difference

Folded proteins occupy a ____________ state of the _____________ stability

a. low energy, greatest stability

b. high energy, greatest stability

c. low energy, lowest stability

d. high energy, lowest stability

a. low energy - greatest stability

true or false: the low energy state is fully stable

false - it is only marginally stable

Is protein folding a slow developing or rapid process?

rapid

Denaturation

disruption of native conformation with loss of biological activity - unfolding

True or false- a large amount of energy is required for denaturation and many hydrogen bonds

False - only a small amount of energy and few hydrogen bonds

Protein folding and denaturation is what kind of process?

cooperative

Is denaturation reversible?

sometimes

quaternary structure of a protein

multiple polypeptide chains - subunits in a separate polypeptide

Biological advantages of quaternary structure

- stabilize subunits and prolong life of protein

- active sites produced at the interfaces between subunits

- hemoglobin

Biological roles of proteins:

- enzymes

- storage and transport

- physical cell support and shape

- mechanical movement

- decoding cell information

- hormones and hormone receptors

How many protein's do bacteria have?

a. 5000

b. 16000

c. 25000

a. 5000

how many proteins do fruit flies have?

a. 5000

b. 16000

c. 25000

b. 16000

how many organisms do human beings have?

a. 5000

b. 16000

c. 25000

c. 25000 - million different protein isoforms

How many amino acids in length are proteins?

a. 100-100000

b. 100 - 1000

c. 1000 - 10000

d. 100000 - 1000000

b 100 - 1000

How many amino acids does insulin have?

a. 54

b. 73

c. 51

d. 23

c. 51

How many amino acids in the protien titin?

a. 4000

b. 34350

c. 87000

d. 3420

b. 34350

The number of amino acids is calculated by:

dividing the proteins molecular by 110

The function of a protein depends on

its structure

the three dimensional structure of a protein is determined by

amino acid sequence

What are the three fibrous proteins?

1. keratin

2. collagen

3. silk

What are the 2 globular proteins?

1. myoglobin

2. hemoglobin

Keratin

hair, wool, and nails

Keratin contains?

pseudo-seven repeat where positions a and d are hydrophobic residues

Keratin in the secondary structure forms a

alpha helix

• Two amphipathic helices of keratin interact to bury their hydrophobic faces together. this results in the formation of:

2 right hand helices coiled-coil in a left-handed fashion

What is a coiled coil?

intertwined alpha helices

Strength of keratin comes from:

covalent linkages - individual units are linked together through disulphide bonds

1st and 4th position end up on the same face, hydrophobic strip

a. keratin

b. collagen

c. silk

a. keratin

Collagen

primary protein in connective tissue

What is the repeating pattern in collagen?

- three Gly-X-Y often Pro Y often hydroxypro

NO alphahelicies

What kind of helix is collagen?

a. right hand

b. left hand

- left hand 3.0

What is the coiled coil structure of collagen?

3 left handed helices wrap around in a right handed fashion

What is the collagen dietary deficiency?

scurvy - vit C

What are the genetic defects associated with collagen?

- osteogenesis imperfecta

- marfan's syndrome

stickler syndrome

ehlers-danlos syndrome