Introduction to Amino Acids - lecture 9

Biochemistry

the scientific discipline that seeks to explain life at the molecular level

Proteins

are true polymers comprised of amino acids (_______ monomers)

3D structure

water solubility of proteins depends on this

physical properties

amino acids within proteins differ in ________ properties, like polarity

enzymes, histones and peptide derived hormones

water soluble components of proteins

collagen and lamina (within nuclear membrane)

water insoluble components of proteins

lipids (proteolipids) or carbohydrates (glycoproteins)

things proteins may be attached to

Proteins have a variety of biochemical roles

serve as signaling molecules, transporters and receptors

Serve as enzyme catalysts; enhancing rate of chemical reactions

Maintain cell shape/provide structural support

General structure of amino acid in neutral pH

Central atom (α carbon) atom

primary / α carboxyl group (COO-)

primary / α amine group (NH3+)

Hydrogen atom (H)

Side chain (R)

Tetrahedral structure

what shaped molecule an amino acid is

carboxyl and amine

at neutral pH these protein structures are ionizable groups

- can gain or lose electrons, which alters charge of free amino acid

20 standard proteinogenic amino acids

these amino acids differ by side chain, whether humans can synthesize, etc.

3 letter code

1 letter code

how each amino acid can be abbreviated

Glycine

abbreviation is Fly or G

chemical characteristics

what classification and categorization of amino acids relies on

Group 1

hydrophobic amino acids

hydrophobic amino acids

have non polar R groups that mainly consist of hydrocarbon side chains

differ in length of side chains; may have aromatic side chains (like phenylalanine)

group with most members (10 our of 20)

hydrophobic amino acid charge

overall neutral charge at physiological pH (approximately 7.4)

Group 2

polar amino acids

polar amino acids

have polar R groups as electron distribution uneven; overall neutral charge

some (i.e. serine, threonine and tyrosine) can be phosphorylated - a post-translational modification

polar amino acids - cytosines thiol (SH) group

this group can form covalent disulfide bonds, which help stabilize protein structure

Groups 3 & 4

charged amino acids

charged amino acids

hydrophilic with R groups that retain a charge at physiological pH

- often involved in protein ion channels

charged amino acids group 3

positively charged (basic)

side chain contains amine group

*Histone only charged when pH is ~6.1 or below

charged amino acids group 4

negatively charged (acidic)

side chain contains carboxyl group

Ionic form of amino acids - acid-base behavior of glycine

Why do charge states of amino acids change?

pKa values of the ionizable groups (α-COOH, α-NH3+ and R group)

pKa

negative base-10 logarithm of the acid dissociation constant (Ka) of a solution

lower pKa = stronger acid

lower pKa = (stronger or weaker) the acid

Ka equation

__ = 10^-pKa

pKa equation

___ = -logKa

How are amino acids connected to one another

linked by covalent peptide bond between the carboxyl group and amino group, formed in condensation reaction by a ribosome

polypeptide

longliner chain made of many amino acids

amino acid residues

name for amino acids within a molecule

Directionality of a polypeptide chain

Beginning: α-amine group (N-terminus)

End: α-carboxyl group (C-terminus)

Groups of proteins based on shape

Fibrous (simple shaped)

Globular (complex shape)

Fibrous proteins

have structural roles and assist with spatial organization

- form sytoskeleton in a cell or anchoring junctions between cells

Globular proteins

have functional or chemical roles

- serve as enzymes, signaling moleciles, transporters and receptors

Proteins based on compositions

Simple (only amino acids)

Conjugated (have non-protein portion)

SImple proteins

include albumin (transports fatty acids) and histones

- (involved in DNA compaction)

Conjugated proteins

include glycoproteins, chromoproteins (hemoglobin, chlorophyll, etc.) and phosphoproteins (tooth dentin , milk casein, etc.)

Hydrophobic effect

drives protein folding