Amino Acids, Peptides and Proteins-Napper

Question 1

Amino Acids

Answer 1

• small biomolecules that are the building blocks for proteins
• all have amino group, carboxyl group, alpha carbon and R group
• cannot be super imposed on themselves, therefore they are enantiomers

Question 2

Gly, Ala, Pro, Val, Leu, Ile, Met

Answer 2

Nonpolar A.A., no potential for H bonding, found in the middle of peptide chains

Question 3

F, Y, W

Answer 3

Aromatic A.A. have phenyl rings.

Question 4

Ser, Thr, Cys, Asn, Gln

Answer 4

Polar AA, will H bond

Question 5

S, T, Y

Answer 5

Serine, Threonine and Tyrosine all have OH(hydroxyl) groups which allow them to undergo post-translation modification through phosphorylation

Question 6

Disulfide Bonds

Answer 6

-form through the oxidation of sulfhydryl groups of two cysteine AA, found in keratin

Question 7

K, R, H

Answer 7

Positively charged AA, Histidine can be both charged and neutral at the bodys pH(about 90% uncharged)

Question 8

D, E

Answer 8

Negatively charged AA, both have carboxyl COO- as part of side chain

Question 9

Zwitterion

Answer 9

carrying both a + and - charge, all AA are zwitterions, because of COO- group and NH3+ group

Question 10

Peptide Bonds

Answer 10

• formed between condensation reactions between carboxyl and amino groups
• rigid and planar with partial double bond characteristics
• almost always in trans configurations
• can accept and donate H bonds
• polar with permanent dipole moment

Question 11

Amino Acid Chains

Answer 11

• numbered from NH3 end to COO- end

- different AA in chain called residues

Question 12

How to approximate number of amino acids in a protein

Answer 12

-divide molecular weight by 110 to give approximate number of residues

Question 13

Native Conformation

Answer 13

• the natural folding state of a protein at physiological conditions. Biological function depends on native conformation.
• native proteins are only marginally stable(stability is defined as their tendency to maintain a native conformation)
• the conformation with the lowest free energy (most stable) is usually the one with the maximum number of weak interactions

Question 14

Weak interactions of a protein

Answer 14

• hydrogen bonds
• ionic interactions
• Van Der Waals forces
• hydrophobic interactions

Question 15

Hydrogen Bonds

Answer 15

• 2.0-20.0 kJ/mol in strength
• 0.2 nm in length
• electrostatic interaction between two electronegative atoms

Question 16

Ionic Interactions

Answer 16

• electrostatic interactions between charged particles(attraction or repulsion)
• strength of these interactions is greatly reduced by water
• important for molecular recognition and specificity of folding rather than stability

Question 17

Salt Bridge

Answer 17

-ionic interaction between oppositely charged functional groups

Question 18

Ion Pairs

Answer 18

-a salt bridge buried in hydrophobic interior of a protein. Stronger than surface salt bridge because not disrupted by water molecules.

Question 19

Van Der Waals

Answer 19

• interactions between permanent and induced dipoles

- short range, low magnitude forces

Question 20

Protein Denaturation

Answer 20

• the disruption of the native conformation of a protein, with loss of biological activity
• denaturing is cooperative(once some of it starts to go, the rest follows quickly and easily)
• some proteins can be renatured(refolded)

Question 21

Primary Structure

Answer 21

• sequence of AA in a protein

- tells nothing of three dimensional characeristics

Question 22

Secondary Structure

Answer 22

• formed mostly from hydrogen bonding
• major examples, alpha helix and beta sheet
• two key determinants 1) favoured conformation of peptide bond 2) optimization of hydrogen bonding potential

Question 23

Phi Bond

Answer 23

• bond between alpha carbon and N

- on LEFT side of alpha carbon, has + or - 180 rotation

Question 24

Psi Bond

Answer 24

• bond between alpha carbon and C

- on RIGHT side of alpha carbon, has + or - 180 rotation

Question 25

Ramachadran Plot

Answer 25

-shows the allowable conformations of peptide chains, along with those actually found in nature

Question 26

Alpha Helix

Answer 26

• right handed helix
• each carbonyl group hydrogen bonds with an amide group, carbonyl groups point towards the C-terminus
• 3.6 residues per turn, we use 4
• phi and psi bond angles are similar
• rarely see proline or glycine(helix breakers)
• helix has a net dipole, with N-terminus carrying partial positive and C-terminus a partial negative(body sometimes corrects for this, placing net negative AA at N-terminus and positives at C-terminus)
• hydrophobic side chains will bury themselves inside helix structure

Question 27

Beta Strands

Answer 27

• polypeptide chains that are almost fully extended

- stabilized by hydrogen bonds between COO- and NH3 when paired with adjacent strands(in Beta sheet)

Question 28

Beta Sheet

Answer 28

• made up of many beta strands
• side chains project above then below the plane, in an alternating fashion
• this could result in one side of beta sheet being hydrophobic, the other hydrophilic, (amphipathic beta sheet)
• can run in parallel or anti parallel with each other
• antiparallel Beta sheets are more stable because the hydrogen bonds are perpendicular to the side chains

Question 29

Keratin

Answer 29

• principle component of hair, wool, horns, and nails
• primary structure, pseudo 7 repeat (a,b,c,d,e,f,g) where a and d are hydrophobic
• secondary structure, forms right handed helices (a and d hydrophobicity will give helix a hydrophobic streak)
• tertiary, nearly the full length of the protein is helical
• quaternary, two right handed helices of keratin will make a “coiled coil” in a LEFT handed fashion, effectively burying the hydrophobic regions together
• quaternary keratin then forms disulphide bonds, the amount of disulphide bonds decides how tough the keratin will be (horn has more disulphide bonds than hair)

Question 30

Collagen

Answer 30

• major protein of vertebrates (25%of total protein) responsible for tendons and skin
• primary structure, multiple repeats of Gly-x-y where x is often proline and y is often hydroxyproline
• secondary structure, formation of left handed helices of THREE residues per turn(more like a zig zag look than helix to me)
• tertiary structure, same as keratin, nearly entire thing is helix
• quaternary structure, formation of “coiled coil” with three left handed helices coiling into a right handed helice
• structure of collagen is given when quaternary structures join together through covalent linkages, rather than disulphides, they occur from amino acid residues which undergo post translation modification (hydroxyproline and hydroxylysine)
• more of these cross linkages occur over time which makes connective tissue tougher

Question 31

Hydroxy proline and lysine

Answer 31

• formed by enzyme hydroxylation reactions that require vitamin c
• needed to stabilize collagen
• no vitamin c leads to scurvy

Question 32

Silk

Answer 32

• 200,000 psi strength
• primary structure, six residue repeat G,S,G,A,G,A
• fully extended polypeptide strength
• association of strands by hydrogen bonding(FLEXIBLE)
• association of sheets by Van Der Waals and hydrophobic interactions (flexible)