BIOL 2500 - Topic 2 (part 8)

Amino acid components

1.) Central ⍺-carbon

2.) A 5’ amino group

3.) A 3’ carboxyl group

4.) An R group, which is what differentiates each amino acid from each other

Linkage of amino acids

They are joined together by covalent peptide bonds, specifically between the amino group of AA and the carboxyl group of another AA, thereby forming polypeptides

Non-polar AA (9)

1.) Glycine

2.) Alanine

3.) Valine

4.) Proline

5.) Leucine

6.) Isoleucine

7.) Methionine

8.) Tryptophan

9.) Phenylalanine

Polar uncharged AA (6)

1.) Serine

2.) Threonine

3.) Tyrosine

4.) Cysteine

5.) Asparagine

6.) Glutamine

Positively charged AA (basic)

1.) Lysine

2.) Arginine

3.) Histidine

Negatively charged AA (acidic)

1.) Aspartate

2.) Glutamate

Primary protein structure

The sequence of amino acids, synthesized by the ribosomes

What do ribosomes make?

They make polypeptides which then become proteins

Secondary protein structure

Local regions that fold to create alpha helices and beta-pleated sheets, as a result of hydrogen bonds, van der waals interactions, and the hydrophobic effect

R-groups of alpha-helices

1.) It depends on their location in the protein and the location of the protein itself

2.) Non-polar R-groups will usually fold into the helix, unless the protein is in a non-polar environment, in which case the R-groups will primarily be pointing outwards

R-groups of beta-pleated sheets

They R-groups are sticking right up or down, therefore they are usually the polar or charged R-groups

Tertiary structure

1.) The 3D shape of the protein, as a result of the interactions between the R-groups

2.) It is stabilized by disulfide bridges and noncovalent interactions

Significance of cysteine

It is the only amino acid that can make covalent bonds

Quaternary structure

Multi-peptide protein sequences, where each subunit in the complex is a polypeptide

Tertiary vs. quaternary structure

Most proteins only go up to tertiary structure

Beadle and Tatum

In 1942, they proposed the one-gene-one-polypeptide hypothesis, using the fungi Neurospora crassa to determine that genes controlled the production of proteins

Neurospora crassa

A haploid model organism for fungi

The genetic code

Refers to the 3 nucleotide sequences called codons transcribed from DNA, each of which code for a specific amino acid

DNA sequence =

Amino acid sequence

Synonymous codons

Refers to codons that code for the same amino acid

Genetic code is…

Degenerate/redundant

The genetic code being redundant

There are 64 codons, but only 20 amino acids

Why are there so much more codons than amino acids

This is because in addition to being degenerate, it is also non-ambiguous, such that an amino acid can be encoded by multiple codons, but each codon only codes for one amino acid