Protein composition and structure

Question 1

Primary protein structure

Answer 1

AA sequence, linked by peptide bonds (a type of amide bond) formed between carboxyl group of 1 AA and amino group of next.

Question 2

Secondary protein structure

Answer 2

Conformation adopted by local regions of the polypeptide chain. Chains can fold into alpha helix, beta sheet and turns and loops.

Question 3

Tertiary protein structure

Answer 3

Overall folding of the polypeptide chain. Water-soluble proteins fold into compact, asymmetric structures with nonpolar cores.

Question 4

quaternary protein structure

Answer 4

Specific association of multiple (more than 1) polypeptide chains to form multi-subunit complexes. Can be as simple as 2 identical subunits or complex as dozens of diff subunits.

Question 5

Proteins

Answer 5

Linear polymers of AA’s. Built from repertoire of 20 AA’s. Written from amino to carboxyl terminus. They make possible most of the key processes of life through their structural stability, diversity and chemical reactivity.

Question 6

Amino Acid (AA)

Answer 6

Consists of - a central tetrahedral carbon atom linked to an amino group, a carboxylic acid group, a distinctive side chain, a hydrogen atom.

Question 7

Tetrahedral centre of AA’s

Answer 7

All chiral except for glycine. Only L isomer exists in natural proteins

Question 8

4 side chain groups

Answer 8

1. Hydrophobic (the aliphatic AA’s and aromatic side chains)
2. Polar (hydroxyl-, sulfhydryl-, and carboxamide-containing side chains)
3. Basic
4. Acidic

Question 9

4 important properties of peptide bonds

Answer 9

1. Resistant to hydrolysis, so proteins kinetically stable
2. Peptide group is planar because C-N bond has considerable double-bond character
3. Each pep bond has hydrogen-bond donor (NH group) and acceptor (CO group). Hydrogen bonding between these backbone groups unique feature of proteins
4. Pep bond uncharged, so proteins can form tightly packed globular structures with lots of backbone buried in protein interior.

Question 10

2 major elements of secondary structure

Answer 10

alpha helix and beta strand.

Question 11

Alpha helix

Answer 11

Polypeptide chain twists into tightly packed rod. Within, the CO group of each AA is hydrogen bonded to NH group of AA four residues farther along chain.

Question 12

Beta strand

Answer 12

Poly chain nearly fully extended. 2 or more strands connected by NH-CO hydrogen bonds form beta sheets. Strands in sheets can be antiparallel, parallel or mixed.

Question 13

Common features of tertiary structures of water-soluble proteins

Answer 13

1. Interior formed of AA’s with hydrophobic side chains.
2. Surface formed mainly of hydrophilic AA’s that interact with aqueous environment.

Driving force of tertiary structure formation is hydrophobic interactions between interior residues

Question 14

Tertiary structure of protein in hydrophobic environment, such as membranes

Answer 14

Display inverse distribution of hydrophobic and hydrophilic AA’s. So hydrophobic AA’s on surface to interact with environment, hydrophilic in interior so shielded from environment.

Question 15

Subunit

Answer 15

Each individual polypep chain in quaternary structure is called a subunit. In most cases, subunits held together by noncovalent bonds

Question 16

AA sequence

Answer 16

Determines 3d structure and so determines all other properties of protein. Sequence is determined by sequences of bases in DNA molecule.

Question 17

Protein folding

Answer 17

1d DNA base sequence info extended into 3d world by ability of proteins to spontaneously fold. Some can be unfolded completely but then refold under stable conditions.

Question 18

Intrinsically unstructured proteins and metamorphic proteins

Answer 18

Do not strictly adhere to 1-sequence 1-structure paradigm. They are versatile, so expand the protein encoding capacity of the genome.

Question 19

Covalent modifications

Answer 19

Can include functional groups not present in the 20 AA’s, so enhance the versatility of proteins. Other modifications important to regulation of protein activity.