Biology CH4

Glycine

is different from the other amino acids because its R group is hydrogen, exactly like the hydrogen on the other side, and therefore it is not asymmetric.

Translation

is the process by which sequence of bases in mRNA specifies the order of successive amino acids in a newly synthesized protein.

Quaternary structure

made up of several polypeptide subunits

Tertiary structure

3D shape, results from long range interactions of amino acid side chains

Formation of a peptide bond

A peptide bond forms between the carboxyl group of one amino acid and the amino group of another.

Role of base pairing

Base pairing determines the relationship between a three-base triplet in double-stranded DNA to a codon in mRNA, and between a codon in mRNA to an anticodon in tRNA.

Chaperones

Cells have evolved proteins that help protect slow-folding or denatured proteins until they can attain their proper three-dimensional structure. Chaperones bind with hydrophobic groups and nonpolar side chains to shield them from inappropriate aggregation, and in repeated cycles of binding and release they give the polypeptide time to find its correct shape.

αlpha helix

Hydrogen bonding between carbonyl and amide groups in the backbone stabilize the helix.

βeta sheet

Hydrogen bonds between neighboring strands stabilize the structure.

Amino acid Structure

It consists of a central carbon atom, called the alpha (α) carbon, connected by covalent bonds to four different chemical groups: an amino group (-NH2 shown in blue), a carboxyl group (-COOH shown in brown), a hydrogen atom (-H shown in gray), and a side chain or R group (shown in green).

Proline

Note how its R group is linked back to the amino group. This linkage creates a kink or bend in the polypeptide chain and restricts rotation of the C-N bond, thereby imposing constraints on protein folding in its vicinity, an effect the very opposite of glycine's.

Peptide Bond

The bond formed between the two amino acids

polypeptide

a polymer of amino acids connected by peptide bonds

Folding Domain

a region of a protein that folds in a way and that carries put a specific function.

First step of Translation: Initiation

in which the initiator AUG codon is recognized and Met is established as the first amino acid in the new polypeptide chain.

Primary structure of a protein

determines how a protein folds, which in turn determines how it functions

Function of Glycine

glycine is nonpolar and small enough to tuck into spaces where other R groups would not fit. The small size of glycine's R group also allows for freer rotation around the C-N bond since its R group will not get in the way of the R groups of neighboring amino acids. Thus, glycine increases the flexibility of the polypeptide backbone, which can be important in the folding of the protein.

Transfer RNA (tRNA)

have an anticolon that base pairs with the codon in the mRNA and carries a specific amino acid

The second process is elongation

in which successive amino acids are added one by one to the growing chain.

Cysteine

makes a special contribution to protein folding through its -SH group. When two cysteine side chains in the same or different polypeptides come into proximity, they can react to form an S-S disulfide bond, which covalently joins the side chains. Such disulfide bonds form cross-bridges that can connect different parts of the same protein or even different proteins. This property contributes to the overall structure of single proteins or combinations of proteins.

What are proteins

proteins are linear polymers of amino acids that form 3D structures with specific functions

Secondary structure

results from the interactions of a nearby amino acids. Results from hydrogen bonding in a polypeptide backbone. ex: a helix, and Bsheet

Aminoacyl tRNA

synthetases attach apecific amino acids to tRNAs

Transcription

the sequence of bases along part of a DNA strand is used as a template in the synthesis of a complementary sequence of bases in a molecule of RNA.

messenger RNA (mRNA) is

used to specify the order in which successive amino acids are added to a newly synthesized polypeptide chain.

Termination

when the addition of amino acids stops and the completed polypeptide chain is released from the ribosome.

Ribosomes

which are complex structures of RNA and protein. Ribosomes bind with mRNA, and it is on ribosomes that translation takes place.