Biochemistry - Lecture 2 - Structure Of Proteins

Front 1

Which amino acid does not have a chiral alpha carbon

Back 1

Glycine

Front 2

Which type of amino acids can be found in mammalian proteins?

Back 2

Ls

Front 3

Alpha carbon is bonded to:

Back 3

amine group (ionized at pka 9-10), H, R group (protonated at 7), COOH (ionized pka 9-10)

Front 4

Name the non-polar aliphatic (hydrophobic) amino acids

Back 4

Alanine (ALA)
Glycine (GLY)
Isolucine (ILE)
Leucine (LEU)
Methionione (MET)
Proline (PRO)
Valine (VAL)

Front 5

What are the characteristics of the hydrophobic amino acids (aliphatic)

Back 5

1. found in interior of globular proteins
2. Glycine does not have asymmetric alpha carbon because H (R) group
3. Proline is a secondary alpha amide, generating a ring. Has great impact on structure - restricting conformation.
4. Methionine - sulfur containing

Front 6

1. definition of Aromatic amino acids

Back 6

found in interior of water soluable proteins - shielded in interior so form bonds with other polar genes.
2. Tyrosine some polarity because of OH group
3. OH can be phosporylated by protein tyrosine kinases
4. Tryptophan slightly polar because of ring nitrogen

Front 7

Aromatic Amino Acids

Back 7

1. Phenyalanine (PHE)
2. Tryptophan (TRP)
3. Tyrosine (TYR)

Front 8

Polar, Uncharged Amino Acid Definition

Back 8

1. Found in interior and exterior of proteins
2. Form H bonds - imp. for structure
3. OH group of SER and THR serve as phosphate acceptors in protein kinases reactions
4. Cysteine is the second containing sulfur amino acid
5. Cysteine dimer (cystine) found in cross linking polypeptide chains

Front 9

Ionizable side chains

Back 9

1. R groups donate/accept prot

Front 10

Acidic amino acids

Back 10

Aspartate (ASP) and Glutamate (GLU)

Front 11

Basic Amino Acids

Back 11

Lysine (LYS), Arginine (ARG) and Histadine (HIS)

Front 12

Peptide bonds

Back 12

1. dehydration reaction
2. blanar bond - double bond character, and free rotation between alpha carbons and their respective amino groups and carbonyl groups

Front 13

Primary Structure
Secondary Structure

Back 13

Amino Acid sequence
alpha and beta sheets

Front 14

b sheets

Back 14

2 polypeptide chains or segments lined up and held together by H bonds of the backbone C=0 and N-H. R groups project above/below

Front 15

Alpha helix

Back 15

shot shaped spiral. each =0 is H bonded to the H-N group of 4 amino acid down chain. Each turn = 3. 6 amino acids. R groups protrude outward.

Front 16

Disruptions to structural features

Back 16

1. proline residues - disrupt H bonding of alpha helix by putting sharp bend in chain
2. bulky R groups - block formation of alpha helix - steric hinderance/e repulsion

Front 17

Reverse Turns

Back 17

allow polypeptide chain to change directions and loop back on self. STablize H bonds between c=O (first) and N-H bonds (4th) of the loop often found on b antiparallel sheets. Proline (ring) and glycine (H R group)

Front 18

Various interactions stablizing a native protein structure

Back 18

1. reverse turns
2. salt bridges
3. metal ions
4. disulfide bonds