amino acids

exam 1

Amino acids

Basic building blocks for proteins; there are 20 common amino acids.

Amino acid anatomy

Contains an α-amino group, α-carboxyl group, α-carbon (chiral center), R-group (sidechain)

L-form vs D-form amino acids

L-form is in most proteins; D-form is rare.

Amino acid charges at neutral pH

The amine is protonated and the acid is deprotonated.

Zwitterion

An amino acid with both positive and negative charge.

Amino acid abbreviations

Each amino acid has a 3-letter and 1-letter abbreviation.

Amino acid categories

Amino acids can have nonpolar

pKa

The negative base-10 logarithm of the acid dissociation constant (Ka) of the molecule; pKa = -log10 Ka.

pI

Isoelectric point; the pH at which the molecule is electrically neutral.

Peptide bond

The α-carboxyl of one amino acid is joined to the α-amino of a second amino acid with removal of water; only α-carboxyl and α-amino groups are used

Amide bond

The bond formed when amino acids are joined by a peptide bond.

N-terminus and C-terminus

The ends of a protein chain; amino acid sequence is written N → C.

Protein amino acid sequence

Written N → C; example: Met – Asp – Leu – Tyr.

Peptide

2 or more amino acids linked together.

Polypeptide

Fewer than 50 amino acids; insulin is an example.

Proteins

Longer peptide chains; 100–500 amino acids.

Peptide bond structure

Peptide bonds are planar due to resonance; chain rotations are restricted to φ and ψ.

Protein functions

Enzymes catalyze reactions

structural proteins maintain cell shape and bind tissues

recognition proteins include cell surface receptors and antibodies

transport proteins shuttle nutrients or oxygen in and waste or CO₂ out

locomotion includes flagellum

signaling includes some hormones such as insulin.

Protein abundance

30–70% of a cell’s dry weight is protein.

Protein diversity

A single cell contains ~2000 different types of proteins.

Protein building blocks

Amino acids are the basic building blocks for proteins.

Primary structure

The linear arrangement of amino acids in a protein; due to peptide bonds.

Secondary structure

One of the four levels of protein structure.

Tertiary structure

One of the four levels of protein structure.

Quaternary structure

One of the four levels of protein structure.

Primary structure conservation

Amino acids that are important to protein structure and function are conserved across species.

Homologs

Multiple versions of a particular protein that have highly conserved regions important for function.

Motifs

Clusters of conserved residues; motifs carry out a particular function or form a particular structure that is important for the conserved protein.

Amino acid sidechain properties

Sidechains can be small hydrophobic

Non-Polar AA

Glycine, Proline, Leucine, Alanine, Phenylalanine, Methionine, Valine, Tryptophan, isoleucine

Glycine

Gly/G

Proline

Pro/P

Leucine

Leu/L

Alanine

Ala/A

Phenylalanine

Phe/F

Methionine

Met/M

Valine

Val/V

Tryptophan

Trp/W

Isoleucine

lle/I

Polar, Non-charged AA

Serine, Threonine, Asparagine, Cysteine, Tyrosine, Glutamine

Serine

Ser/S

Threonine

Thr/T

Asparagine

Asn/N

Cysteine

Cys/C

Tyrosine

Tyr/Y

Glutamine

Gln/Q

Negatively-Charged AA

Aspartate, Glutamate

Aspartate

Asp/D

Glutamate

Glu/E

Positively-Charged AA

Arginine. Histidine, Lysine

Arginine

Arg/R

Histidine

His/H

Lysine

Lys/K