week 1

Question 1

Main Agents of Biological Function

Answer 1

Catalysis
– enolase (in the glycolytic pathway)
– DNA polymerase (in DNA replication)

Transport
– hemoglobin (transports O2 in the blood)
– lactose permease (transports lactose across the cell membrane)

Structure
– collagen (connective tissue)
– keratin (hair, nails, feathers, horns)

Motion
– myosin (muscle tissue)
– actin (muscle tissue, cell motility)

Question 2

protein structure

Answer 2

primary structure: amino acid residues

secondary structure: a helix

tertiary structure: polypeptide chain

quaternary structure: assembled subunits

Question 3

Amino Acids: Building Blocks of Protein

Answer 3

Proteins are linear heteropolymers of a-amino acids
* Amino acids have properties that are well-suited to
carry out a variety of biological functions
– Capacity to polymerize
– Useful acid-base properties – Varied physical properties
– Varied chemical functionality
* When combined in various sequences, the functional groups contribute to the function.

Question 4

Most a-amino acids are chiral

Answer 4

• The a-carbon always has four
  substituents and is tetrahedral
• All(exceptproline)have:
  – an acidic carboxyl group
  – a basic amino group
  – an a-hydrogen connected to the a- carbon
• Thefourthsubstituent(R)is unique
  – In glycine, the fourth substituent is also hydrogen

Question 5

Amino Acids: Atom Naming

Answer 5

Organic nomenclature: start from one end * Biochemical designation:
– start from a-carbon and go down the R-group

Question 6

Amino Acids: Classification

Answer 6

Common amino acids can be placed in five basic groups depending on their R substituents:
* Nonpolar, aliphatic (7) * Aromatic (3)
* Polar, uncharged (5)
* Positively charged (3) * Negatively charged (2)

Question 7

Formation of Peptides

Answer 7

Peptides are small condensation products of amino acids
* They are “small” compared to proteins (Mw < 10 kDa)

Numbering (and naming) starts from the amino terminus

Usingfullaminoacidnames
– Serylglycyltyrosylalanylleucine
* Usingthethree-lettercodeabbreviation
– Ser-Gly-Tyr-Ala-Leu
* Forlongerpeptides(likeproteins)theone- letter code can be used
– SGYAL

Question 8

Peptides: A Variety of Functions

Answer 8

• Hormones and pheromones – insulin (think sugar)
  – oxytocin (think childbirth)
  – sex-peptide (think fruit fly mating)
• Neuropeptides
  – substance P (pain mediator)
• Antibiotics
  – polymyxin B (for Gram – bacteria) – bacitracin (for Gram + bacteria)
• Protection, e.g., toxins
  – amanitin (mushrooms) – conotoxin (cone snails) – chlorotoxin (scorpions)

Question 9

Structure of Proteins

Answer 9

Unlike most organic polymers,protein molecules adopt a specific three-dimensional conformation.
* Thisstructureisabletofulfillaspecific
biological function
* Thisstructureiscalledthenativefold
* The native fold has a large number of favorable interactions within the protein
* Thereisacostinconformationalentropyof folding the protein into one specific native fold

Question 10

Favorable Interactions in Proteins

Answer 10

• Hydrophobic effect
  – Release of water molecules from the structured solvation layer
  around the molecule as protein folds increases the net entropy
• Hydrogen bonds
  – Interaction of N-H and C=O of the peptide bond leads to local
  regular structures such as a-helices and b-sheets
• London dispersion
  – Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein
• Electrostatic interactions
  – Long-range strong interactions between permanently charged
  groups
  – Salt-bridges, esp. buried in the hydrophobic environment strongly stabilize the protein

Question 11

Structure of the Peptide Bond

Answer 11

Structureoftheproteinispartiallydictated by the properties of the peptide bond
* The peptide bond is a resonance hybrid of two canonical structures
* The resonance causes the peptide bonds
– to be less reactive compared to esters, for example
– to be quite rigid and nearly planar
– to exhibit a large dipole moment in the
favored trans configuration

Question 12

The Rigid Peptide Plane and the Partially Free Rotations

Answer 12

Rotationaroundthepeptidebondisnotpermitted
Rotation around bonds connected to the alpha carbon is permitted
f (phi): angle around the a-carbon—amide nitrogen bond
y (psi): angle around the a-carbon—carbonyl carbon bond
Inafullyextendedpolypeptide,both and are 180°

Question 13

Distribution of f and y Dihedral Angles

Answer 13

Some f and y combinations are very unfavorable because of steric crowding of backbone atoms with other atoms in the backbone or side chains
* Some f and y combinations are more favorable because of chance to form favorable H-bonding interactions along the backbone
* A Ramachandran plot shows the distribution of f and y dihedral angles that are found in a protein
* shows the common secondary structure elements
* reveals regions with unusual backbone structure

Question 14

Secondary Structures

Answer 14

Secondary structure refers to a local spatial arrangement of the polypeptide backbone
* Two regular arrangements are common:
* The a helix
– stabilized by hydrogen bonds between nearby residues
* The b sheet
– stabilized by hydrogen bonds between adjacent
segments that may not be nearby
* Irregular arrangement of the polypeptide chain
is called the random coil

Question 15

The a Helix

Answer 15

Helical backbone is held together by hydrogen bonds between the backbone amides of an n and n+4 amino acids
* Right-handed helix with 3.6 residues (5.4 Å) per turn
* Peptide bonds are aligned roughly parallel with the helical axis
* Side chains point out and are roughly perpendicular to the helical axis

Question 16

The a Helix: Top View

Answer 16

The inner diameter of the helix (no side chains) is about 4–5 Å
* Too small for anything to fit “inside”
* Theouterdiameterofthehelix(with sidechains) is 10–12 Å
* Happenstofitwellintothemajorgrooveof dsDNA
* Residues1and8alignnicelyontopofeachother

Question 17

The Helix Dipole

Answer 17

• Recallthatthepeptidebondhas a strong dipole moment
  – Carbonyl O negative – Amide H positive
• Allpeptidebondsintheahelix have a similar orientation
• Theahelixhasalarge macroscopic dipole moment
• Negativelychargedresidues often occur near the positive end of the helix dipole

Question 18

b Sheets

Answer 18

Theplanarityofthepeptidebondandtetrahedral geometry of the a-carbon create a pleated sheet-like structure
* Sheet-likearrangementofbackboneisheldtogetherby hydrogen bonds

Question 19

Parallel and antiparallel B Sheets

Answer 19

Parallelorantiparallel
orientation of two chains within a sheet are possible
* InparallelbsheetstheH- bonded strands run in the same direction
– Resulting in bent H-bonds (weaker) (> 5 residues)
* Inantiparallelbsheetsthe H-bonded strands run in opposite directions
– Resulting in linear H-bonds (stronger)

Question 20

b Turns

Answer 20

bturnsoccurfrequently whenever strands in b sheets change the direction
* The180°turnis accomplished over four amino acids
* Theturnisstabilizedbya hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence

Question 21

Circular Dichroism (CD) Analysis

Answer 21

CDmeasuresthemolar absorption difference De of left- and right-circularly polarized light: De = eL – eR
* Chromophoresinthechiral environment produce characteristic signals
* CDsignalsfrompeptide bonds depend on the chain conformation

Question 22

Protein Tertiary Structure

Answer 22

Tertiary structure refers to the overall spatial arrangement of atoms in a protein
* Stabilized by numerous weak interactions
between amino acid side chains.
- Largely hydrophobic and polar interactions
- Can be stabilized by disulfide bonds
* Interacting amino acids are not necessarily next to each other in the primary sequence.

Question 23

Quaternary Structure

Answer 23

Foundinsomeproteins:hemoglobin(4units)
* Results from interactions between two or more polypeptide chains.
* Interactions include hydrogen bonding and disulfide bonds. Locks the complex into a specific geometry.
Structural and Functional advantages of Quaternary Association:
* Stability:reductionofsurfacetovolumeratio.
* Geneticeconomyandefficiency.
* Bringingcatalyticsitestogether.
* Cooperativity