Proteins and their Building Blocks General Structure of Amino acid

Proteins

- class of biomolecules

- they are polymers made of building blocks known as

amino acids

Importance

- Structure, support, movement, and external

protection

- Storage and transport

- Energy Source

- Nitrogen Source

- Regulation/Balance
• Nonpolar side chains
- Internal protection

- Catalysis

Ex. Hemoglobin

Levels of Structure in Proteins

• Aromatic side chains

Primary Level

- Identity of polypeptide chains in terms of its building

block sequence

- amino acids are the building blocks

- sequence is usually read from N-terminal to

C-terminal
 • Polar side chains, uncharged Stereochemistry

- organic compounds can have the same molecular

formula but entirely different identities

- Isomers

Ex. Ethanol

CH3Ch2OH -------- C2H6O -------- H3C-O-CH3

• Polar side chains, charged Constitutional isomers

- compounds that differ in the connection of atoms

- C2H6O

• Negative charged R groups

Stereoisomers or Configurational Isomers

- cis-trans isomers

AMINO ACIDS - Isomers with chiral centers

- all protein-derived amino acids have at least 1 chiral - Chirality
carbon – (chirality)

- Except for G

- This is usually the α-carbon

- These α-amino acids are usually present in the

L-configuration

- Except for P, which is usually D

enantiomers
Amino acids usually have chiral centers, too.

Ex. Alanine

Naming of Peptides

- Peptide names vary depending on the sequence of the

AA residues

- each amino is read starting from the amino

terminal to the carboxyl terminal

• Amino terminal (N-terminal) is the end

containing α-amino group

• Carboxyl terminal (C-terminal) is the end with a

free carboxyl group
PEPTIDE BONDS
- If amino acid sequence is written and structure is not
- Have partial double bond character shown, the N-terminal is generally considered to be the
Covalent bond between amino acids in forming one on the left end and the C-terminal is the one at the
polypeptides right end

- formation of peptide bonds remove the ionizable

components

- the -COOH group of the AA in the left

- the -NH2 group of the AA in the right

- The affects the pI of the polypeptide compared with

the initial AAs

pH 0 not charge

isoelectric point

pI
- For peptide names, you simply consider the N-side AA
residues to be an alkyl substituent to the next AA

e.g

- phe-trp

- Phenylalanyltryptophan

- FW

Secondary (2°) structure

- the 3-dimensional arrangement of a small region of

amino acids in a single polypeptide chain

- Key factor is H-bonding

- can be one of either

Y
ser-gly-tyr-ala-leu
L

S G A

Peptide name: seryglycyltyrosylalanylleucine

Ex.

1. α-helix

L-aspartyl-L-phenylalanine methyl ester (aspartame) Some α-helix features

Some other commonly known peptides - Coil of the helix is clockwise or right-handed

- There are 3.6 amino acids per turn

- C=O of each peptide bond is hydrogen bonded to the

N-H of the fourth amino acid away

- C=O----H-N hydrogen bonds are parallel to helical axis

- All R groups point outward from helix

How to check for helix handedness? 2. β-pleated sheet

Some β-pleated sheet features

- polypeptide chains lie adjacent to one another; may be

parallel or antiparallel

Factors affecting the helical structure

- Proline

- electrostatic repulsion

- steric strain

- I, V, T

- R groups alternate, first above and then below plane

- O and N-H groups of each peptide bond are

perpendicular to axis of the sheet

- C=O---H-N hydrogen bonds are between adjacent

- substituents of molecules are big enough to sheets and perpendicular to the direction of the sheet
cause electron cloud interference with one Antiparallel
another
Reverse Turns

- a small substructure found in β-sheets, facilitating the

change in the direction of the polypeptide

- can include gly (small) and pro (bulky)

Tertiary (3°) structure

- overall 3D structure of a polypeptide chain

Fibrous proteins
- H-bonding
-Polypeptide chains are usually arranged in parallel
- electrostatic attraction along a single axis

- electrostatic repulsion - Keratin

- Collagen
- Includes longer-range interaction between
residues

- Many are classified as either fibrous or globular

Supersecondary structures

- combinations of α and β structures

• Βαβ unit
• Αα unit
• β-meander
• Greek key
• β-barrel
Globular Proteins

- Structure folds into a somewhat spherical shape

- usually influenced by its environment

- hydrophobic residues go inside the

globular proteins

- hydrophilic residues are exposed,

interacting with the aqueous
environment

- Can introduce pockets in the globular proteins

Summary of Interactions Influencing Protein Structure Heme

- Covalent interactions - prosthetic group

- Disulfide bridges

- Noncovalent interactions

- H-bonding

- Hydrophobic interactions

- Electrostatic attraction and repulsion

- residue to residue

- ligand to residue

Protein Denaturation

- the loss of the native structure of a protein to the loss

of biological activity

- Factors that disrupt protein structure:

Quaternary structures
- Heat
- The association of multiple polypeptide chains into
aggregations that have a particular function - pH change

- Leads to the formation of multisubunit - Detergents

proteins
- Mercaptoethanol
- Dimers
- Urea
- Trimers

- Tetramers

Ex. of tetramers
β-thalassemia

anemia

Factors that affect protein function

- Presence of prosthetic group/cofactors

- Apoenzyme/apoprotein

- holoenzyme

-Denaturation

- Inhibitors