Macromolecules: Nucleic acids & Proteins

Nucleic Acids

Store, transmit, and express genetic information (instructions for life)

Proteins

Do almost everything else that cells need

Genes

“Written in DNA.

Genome

(All genes in an organism) provide all of the instructions for making that organism

DNA

Stores and transmits biological information

RNA

Chemically similar to DNA, but used to ‘express’ genetic information

DNA composed of:

• Phosphate group

• Five-carbon sugar (ribose or deoxyribose)

• Nitrogen-containing aromatic base (purine or pyrimidine)

Types of Purines

Double ring

• Adenine

• Guanine

Types of Pyrimidines

Single rings

• Thymine

• Uracil

• Cytosine

Nucleoside

Are a base and a sugar

Adenosine monophosphate (AMP)

A base, sugar and one phosphate group

Adenosine diphosphate (ADP)

A base, sugar and two phosphate groups

Adenosine Triphosphate (ATP)

A base, sugar, and three phosphate group

3’5’ phosphodiester bonds

What nucleotides are linked by.

• 1 phosphate group is linked to 2 other groups of nucleotides via two phosphodiester bonds

5’ phosphate at one end and 3’ hydroxyl at the other end

To make nucleic acids what is needed

• Information about the preexisting template

• Energy, nucleotides enter as high energy triphosphates (RNA: nucleotide triphosphates)(DNA: deoxynucleotide triphosphates)

Hydrogen bonding between bases

• A forms 2 hydrogen bone with T

• G forms 3 hydrogen bonds with c

DNA strand is

Complementary - the two strands go in opposite directions

Antiparallel - Each DNA strand is the opposite of the other. (Each is a mechanism for DNA replication and acts as a template)

RNA (Characteristics)

• Normally single-stranded

• Depends on base pairing

• RNA base pairing usually occurs between bases in different regions of the same molecule and is less extensive than that in DNA.

Amino Acids (basic structure)

• 20 amino acids

Has a carboxyl group, an amino group, a hydrogen and an R group all bonded to an alpha carbon.

ONLY L-enantiomers is used for proteins

Polypeptide

Product of amino acid polymerization. This does not become a protein until folding has occurred and the protein is stable.

Protein synthesis

Process for elongating a chain of amino acids

Nonpolar Amino Acids

• Glycine

• Alanine

• Valine

• Leucine

• Isoleucine

• Methionine

• Phenylalanine

• Tryptophan

• Proline

Polar, uncharged amino acids

• Serine

• Threonine

• Cysteine

• Tyrosine

• Asparagine

• Glutamine

Polar, Charged amino acids

• Aspartic acid (-)

• Glutamic acid (-)

• Lysine (+)

• Arginine (+)

• Histidine (+)

Peptide Bonds

What amino acids are linked by in a polypeptide (they have directionality). To add to the amino acid chain you add to the C-terminus and NOT the N-terminus.

Amino acid Residue bonds and Interactions (covalent bonds: Disulfide bonds)

• very stable bond

• Formed between sulfur atoms in cystein residues (intra/inter-molecule)

Noncovalent bonds/interactions (Protein folding)

• Hydrogen bonds

• Ionic bonds

• Van De Waals interactions

• Hydrophobic interactions

Weak individually but strong as a whole

Primary structure (kind of structure and bonds/interactions)

Structure: Amino acid sequence

Interactions: Covalent peptide bonds

Secondary Structure (kind of structure and bonds/interactions)

Structure: Folding into alpha helix and beta sheet or random coiling

Interactions: Hydrogen bonds (NH and CO) in backbone

Tertiary Structure (kind of structure and bonds/interactions)

Structure: 3D folding of single polypeptide chain

Interactions: Disulfide bonds, hydrogen bonds, ionic bonds, van der waals interactions, hydrophobic interactions

Quaternary Structure (kind of structure and bonds/interactions)

Structure: Association of multiple polypeptides

Interactions: Same as tertiary

ONLY in multimeric proteins (consist of multiple identical subunits)

Alpha Helix (Characteristics)

• Spiral shape

• R groups jut-out from spiral

• Some amino acids have strong propensities toward forming helices; other amino acids disrupt helices.

Beta Sheet (characteristics)

• Sheet-like conformation formed by multiple polypeptide strands

• Extensive but variable hydrogen bonding (back bone)

• R groups jut-out on alternating sides

• Classified-based on relative directionalities (parallel - some direction)(antiparallel - opposite directions)

Tertiary structure (determined by)

1) Hydrophobic residue avoiding water

2) Hydophilic residues interacting with water

3) Repulsion of similarly charged residues

4) Attraction between oppositely charged residues.