DENT Fun. I - Amino Acids/Proteins

Functions of Proteins

- Enzymes

- Regulation of gene expression

- Transport

- Storage

- Structure

Peptide

Short polymer of amino acids

Protein is read from the ____ terminus to the ____ terminus.

amino/carboxyl

Amino Acid Structure

Amino Acids are ____.

weak polyprotic acids

L

Leucine (Leu)

I

Isoleucine (Ile)

P

Proline (Pro)

A

Alanine (Ala)

V

Valine (Val)

M

Methionine (Met)

W

Tryptophan (Trp)

F

Phenylalanine (F)

G

Glycine (Gly)

S

Serine (Ser)

N

Asparagine (Asn)

Q

Glutamine (Gln)

T

Threonine (Thr)

C

Cysteine (Cys)

Y

Tyrosine (Tyr)

D

Aspartic Acid (Asp)

E

Glutamic Acid (Glu)

K

Lysine (Lys)

R

Arginine (Arg)

H

Histidine (H)

Ka = ____

[H+][A-]/[HA]

Nonpolar Amino Acids

8

- L

- I

- P

- A

- V

- M

- W

- F

Polar Amino Acids

7

- G

- S

- N

- Q

- T

- C

- Y

Acidic Amino Acids

2

- D

- E

Basic Amino Acids

3

- K

- R

- H

What are the 6 rare amino acids that occur in proteins?

- Selenocysteine (U)

- Pyrrolysine (O)

- Hydroxylysine

- Hydroxyproline

- Carboxyglutamic Acid

- Pyroglutamic Acid

Chiral Center

Carbon with four different substituents and lack a plane of symmetry

Enantiomers

Isomers that are mirror images of each other

L-Amino Acid

Amino group on the left

D-Amino Acid

Amino group on the right

____-Amino Acids predominate in nature.

L

R, S System

R: clockwise

S: counterclockwise

Functional Group Priorities

(1) SH

(2) OH

(3) NH2

(4) COOH

(5) CHO

(6) CH2OH

(7) CH3

Peptide Backbone

N-C-C

Alpha Carbon

Central carbon atom of each amino acid

Peptide Bonds

- Covalent bonds between amino acids that release water when formed

- COO- (carboxyl) + NH3+ (amino)

- Has double-bond character due to Carboxyl

Trans-Conformation

Largest groups are opposite; Most stable

Syn-Conformation

Largest groups are eclipsed

Primary Structure

Amino acid sequence

What is the difference between conformation and configuration?

Conformation can be changed by rotating a bond while configuration requires breaking a bond to change

Secondary Structure

Noncovalent interactions of amino acids cause formation of sheets or helices

Tertiary Structure

3-D Shape of a polypeptide

Quaternary Structure

Association of 2 or more polypeptides, forming a functional protein

Proteins can be separated by ____ and ____.

size/charge

Proteins are least soluble at their ____.

isoelectric point

Isoelectric Point

The pH value at which the amino acid exists as a zwitterion (neutral)

Spectroscopy (NMR)

Use of infrared wavelengths to identify an amino acid

What is the best wavelength for absorbance?

280 nm

What amino acids can absorb UV light?

- Phe

- Tyr

- Trp

Determination of Protein Concentration via UV absorption depends on ____.

the presence of aromatic rings

What 2 methods can help sequence a Protein?

- Real Amino Acid Sequencing

- Sequencing the corresponding DNA

What are the 2 methods of "Real Amino Acid Sequencing"?

- Sanger Method

- Mass Spectrometry

Protein Sequencing Process

(1) Separate polypeptide

(2) Remove disulfide bonds

(3) Use proteolytic enzymes to make shorter polypeptides

(4) Determine sequence

(5) Use overlapping fragments to reconstruct the protein

a-Helix

Spiral

B-Sheet

The primary chain "zig-zags" back and forth forming a "pleated" sheet. Adjacent strands are held together by hydrogen bonds.

____ drive protein folding.

Hydrophobic interactions

Ionic interactions typically occur on the ____.

protein surface

phi angle (ϕ)

Angle around the alpha carbon-amide nitrogen bond

psi angle (Ψ)

Angle around the alpha carbon-carbonyl carbon bond

What combination of phi and psi angles are unfavorable?

(1) ϕ = 0*

Ψ = 180*

(2) ϕ = 180*

Ψ = 0*

(3) ϕ = 0*

Ψ = 0*

Cause orbital overlap and strain on the peptide bond

Ramachandran Map

List plotting the most favorable combinations of phi (ϕ) and psi (Ψ) angles for different structures

Secondary structures are stabilized by ____.

Hydrogen Bonds

What are the 4 Secondary Structures?

- Alpha-Helices

- Other Helices

- Beta-Sheet

- Tight Turns

Alpha-Helix

- Residues/Turn: 3.6

- Rise/Residue: 1.5

- Rise/Turn: 5.4

- ϕ = -60*

- Ψ = -45*

The arrangement of N-H and C=O groups along an Alpha-Helix creates a large net ____.

dipole moment

Helix Capping

- The formation of H-bonds with other nearby donor and acceptor groups

- Aids in the formation of the Alpha-Helix

Beta-Pleated Sheet

- A type of protein secondary structure; results from hydrogen bonding between polypeptide regions running antiparallel to each other

- Strands may be parallel or anti-parallel

Rise/Residue of Parallel Strands (B-Sheet)

3.25 Angstroms

Rise/Residue of Antiparallel Strands (B-Sheet)

3.47 Angstroms

Beta-Turn

- A type of protein secondary structure consisting of four amino acid residues arranged in a tight turn so that the polypeptide turns back on itself

- Carbonyl C is H-Bonded to an Amide 3 residues away

What 2 amino acids are prevalent in Beta-Turns?

- Proline

- Glycine

What are the 2 forms of Beta-Turns?

- Type 1: Proline in Pos.3

- Type 2: Proline in Pos.2, Glycine in Pos.3

X-Ray Crystallography

Technique used to study the three-dimensional structure of molecules. Utilizes the diffraction of X-Rays off of a crystal to create a protein model.

Proteins form into the most ____ structures possible.

stable

What 2 factors drive Protein Stability?

- Formation of many intramolecular H-Bonds

- The Hydrophobic amino acids cluster on the interior

What are the 2 Protein Tertiary Structures?

- Globular

- Fibrous

Globular Proteins

Spherical, water-soluble proteins that maximize internal bonds and minimize solvent contact

Fibrous Proteins

- Long, insoluble, structural proteins that maximize intermolecular bonds and molecule-molecule contact

- Mechanically strong

What are the 3 Fibrous Proteins?

- a-Keratin

- B-Keratin

- Collagen

a-Keratin

- Hard protein material found in the epidermis, hair, and nails

- Protein composed of a coiled-coil motif

Coiled-Coil Motif

Protein motif in which two alpha-helices twist around each other in a left-handed supercoil, interacting through hydrophobic contacts

B-Keratin

- Protein that composes the feathers of birds

- Forms extensive B-Sheets instead of fibers

Collagen

- Structural protein found in the skin and connective tissue

- Composed of a Triple Helix

What is the typical amino acid composition of Collagen?

Gly-Pro-Hydroxyproline

What are the 2 types of Collagen?

Right-Handed Helix

- 3.6 residues/turn

- 5.4 rise/turn

Left-Handed Helix

- 3.3 residues/turn

- 9.9 rise/turn

Globular Proteins mediate ____.

cellular function; more numerous than fibrous proteins

What are the 4 classes of Globular Proteins?

- Alpha: Alpha-Helices dominate

- Beta: Beta-Sheets dominate

- a/B: Helices and Sheets are intermingled

- a + B: Contain separate Helical and Sheet domains in one protein

What are the 5 advantages of Quaternary Structure?

- Stability: Surface/Volume Ratio

- Efficiency

- Assembly

- Cooperativity

- Regulation: Based on protein-protein interaction

There is a large amount of ____ in quaternary structure of Proteins.

symmetry

Proteins are purified by ____.

chromatography

The native structure of proteins are flexible under ____ conditions.

physiological