Class 2: Protein composition and structure

Question 1

What are the structural features and characteristics of amino acids?

Answer 1

A) free amino acids: @-carbon is between carboxyl and amino groups, side chain is distinctive

B) ‘polypeptide’ combined through peptide linkages: side gains determine properties of proteins

-protein folding
-binding to linkages
-interaction with environment

Question 2

Characteristics of peptide bonds in protein

Answer 2

-partial double-bond character
-rigid and planar
-trans configuration
-uncharged but polar

Question 3

Define Peptide Transferase

Answer 3

enzyme response for peptide bond formation

Question 4

Free amino acids in solution at neutral pH exist predominately as…

Answer 4

dipolar ions

Question 5

define zwitterions

Answer 5

An ion carrying both a positive and a negative charge

Question 6

What are the 4 amino acid groups

Answer 6

• Hydrophobic amino acids
• Polar amino acids
• Positively charged amino acids
• Negatively charged amino acids

Question 7

Hydrophobic amino acids

Answer 7

nonpolar R groups

- non polar: an even distribution of electrons
- side chains only consist of hydrogen and carbon
- does not gain or lose protons
- do NOT participate in hydrogen or ionic bonds
-oily or lipid like: promotes hydrophobic interactions, these amino acids prefer to remain inside protein molecules

Question 8

Define ambivalent and give two common examples

Answer 8

• that they can be inside or outside the protein molecule
• ex) alanine and glycine

Question 9

hydrophobicity increases as…

Answer 9

the number of carbon atoms on the hydrocarbon change increases

Question 10

What type of hydrophobic amino acids tend to cluster together inside the protein away from the aqueous environment of the cell

Answer 10

aliphatic and aromatic ones

Question 11

What is the location of non polar amino acids in soluble and membrane proteins

What about polar amino acids in soluble proteins

Answer 11

non polar membrane: cluster on the surface
nonpolar soluble: cluster in the interior
polar soluble: cluster on the surface
- known as the “hydrophobic effect”

Question 12

Hydrophobic Amino Acids Have Mainly Hydrocarbon Side Chains, what r their characteristic

Examples?

Answer 12

1) side chain is bonded to both the α-carbon and the nitrogen atom, limits the rotation, reduces structural flexibility of polypeptide regions.
2) often interrupts the a-helices found in globular proteins (a-helix breaker).
3) found in bends in protein chain, the formation of the fibrous structure of collagen.

Proline, methionine

Question 13

Polar amino acids

Answer 13

with neutral R groups but the charge is not evenly distributed


Question 14

Polar Amino Acids have side chains that contain…?

Answer 14

an Electrnegative Atom (Oxygen)
1) Hydroxyl groups(-OH)
2) -OH, -NH2, participate in hydrogen bonds
3) Phosphate group can be added to the OH (phosphorylation)

Question 15

The hydroxyl groups on serine, threonine, and tyrosine make them more…?

Answer 15

• hydrophilic (water loving) and reactive
• note: sulfzydrl (thiol) group is much more reactive than a hydroxyl group

Question 16

Positively charged amino acids

Answer 16

with R groups that have a positive charge at physiological pH (pH ≈ 7.4)

-hydrophilic (nitrogen)

Question 17

Negatively charged amino acids

Answer 17

with R groups that have a negative charge at physiological pH
- have acidic side chains, hydrophilic
- Second carboxylic acid group on side chain is deprotonated at neutral pH

Question 18

what do ASP (aspartate) and Glu (Glutamate) do

Answer 18

their ability to accept protons can be important in enzyme catalysis

Question 19

Glutamate Features

Answer 19

carries a negative charge on its side chain at physiologic pH and thus can engage in ionic bonds or hydrogen bonds with water or other side chains

Question 20

Is Valine hydrophobic or phyllic, what does this do

Answer 20

it is a hydrophobic amino acid and therefore tends to interact with other hydrophobic side chains to exclude water

Question 21

Protein Structures

Answer 21

Primary: amino acid residues - sequence of a chain of amino acids

Secondary: @ helix - local folding of the polypeptide chain into the helices or sheets

Tertiary: polypeptide chain - 3_D folding pattern of a protein due to side chain interaction

Quaternary: assembled subunits - proteins consisting of more than one amino acids chain

Question 22

Globular proteins

Answer 22

soluble and compact

• hydrophobic amino acid and therefore tends to interact with other hydrophobic side chains to exclude water.

Question 23

Fibrous Proteins

Answer 23

insoluble

• long strands or sheet repeating unit of 2-D structure, many similar polypeptides tightly packed, strong and structural proteins (Collagen, Keratin

Question 24

Membrane Proteins

Answer 24

embedded in membranes

• many have ≥ 1 a-helical stretches that span a membrane,
  hydrophobic residues

Question 25

Secondary structure of Proteins: @-helix

Answer 25

• common structural motif in proteins, in which a polypeptide main chain forms the inner part of a right-handed helix
• side chains extend outward
• the helix is stabilized by intrachain hydrogen bonds between amino and carboxyl groups of the main chain.

Question 26

Which amino acids prefer to adopt helical conformations

Answer 26

My Aunt Loves Good Laughs
- methionine, alanine, leucine, glutamate and lysine

Question 27

Where is rotation permitted in a secondary structure @-helix

Answer 27

about N-C@ and C@-C

Question 28

What type of Amino Acids disrupt an @-helix

Answer 28

-Proline: helix breaker. In Proline, rotation N-Ca bond not possible.

-Large numbers of charged amino acids: Serine, aspartate and asparagine

• amino acids with bulky side chains (tryptophan) or with branch side-chain (valine, isoleucine).

Question 29

Secondary Structure of Proteins: B-Sheet

Answer 29

• common structural motif in proteins, in which a number of β strands are associated as stacks of chains
• stabilized by interchain hydrogen bonds
• running in the same direction or opposite directions form an antiparallel pleated sheet.

Question 30

Which structures provide maximal hydrogen bonding for peptide bond components within the interior of polypeptides

Answer 30

@-helix and B-sheet

Question 31

Secondary Structure of Proteins: Non-repetitive

Answer 31

-bend, loop, turn

1) Turns and loops invariably lie on the surfaces of proteins

2) often participate in interactions between other proteins and the environment.

3) Loops exposed to an aqueous environment are usually composed of amino acids with hydrophilic R groups.

4) Turns and Loops facilitate the direction change of the polypeptide chains.

Question 32

Secondary Structure of Proteins: Super-secondary (motifs)

Answer 32

relatively small arrangements of secondary structure (side-chains) that are recognized in many different proteins.

Question 33

what is the driving force of globular proteins

Answer 33

Hydrophobic effect
covalent and non covalent interactions between side chains

Question 34

what interactions stabilize tertiary structures

Answer 34

1) dissulfide (S-S bonds)
2) hydrophobic interactions - stay aways from water buried inside protein
3) hydrogen and ionic bonds -

Question 35

what is the quaternary structure of a protein refer too

Answer 35

it refers to the association of individual polypeptide chain subunits in a geometrically and stoichiometrically specific manner: nonpolar side chains; hydrogen bonds; ionic bonds.

Question 36

what does protein denaturation do and how

Answer 36

• folded to non folded
• Denaturation involves transformation of a well-defined folded structure of a protein formed under physiological conditions, to an unfolded state under non-physiological conditions is called protein denaturation.
• -disrupts the weak forces responsible for 3-D structure, leading to loss of structure and
  protein function.

Question 37

Stabilization of a Protein Conformation

Answer 37

Question 38

What os the melting temp of a protein

Answer 38

is the temperature at which the transition from folded to unfolded happens (50% folded, 50% unfolded)

Question 39

denaturation by heat

Answer 39

affects the weak interactions in a protein
- primarily hydrogen bonds

Question 40

denaturation by low and high pH

Answer 40

Acids and bases disrupt salt bridges held together by ionic charges/bonds
- electrostatic repulsion between side chains that arise if no more neutralization by opposite charges

Question 41

Urea: a reversible denaturing agent

Answer 41

1) Form H-bonds to NH and C=O in peptide bonds,
blocks intramolecular H-bonding

2) interferes with the hydrophobic interactions
that normally stabilize the protein.

3) “Dissolves out” the peptide chain

4) Reversible: dialyze away urea, get refolding

Question 42

what is Protein misfolding and disease: amyloidosis

Answer 42

general term for diseases in which a protein becomes
misfolded and insoluble

Question 43

how can amyloidosis occur

Answer 43

a station (a.k.a. change)in the protein itself