All Codon Vocab

Nucleotide

A molecule made up of a phosphate group and a nitrogenous base bonded to a 5-carbon sugar.

Nucleic acid

A molecule made up of nucleotides that are linked to form a “chain” or strand

Phosphodiester bond

A covalent bond between the phosphate group on the 5′ carbon of one nucleotide and the -OH group on the 3′ carbon of a second nucleotide.

Makes up the sugar-phosphate backbone.

Complementary base pairing

Hydrogen bonding between nucleotide bases (A to T, C to G) within a nucleic acid.

Ex. DNA and RNA

Primary structure (of a Nucleic acid)

The sequence of nucleotides within a nucleic acid, read 5’ to 3’ aka the “chain”

Ex.

5’ 3’

ATTCGCGCGATGCTACGAC

Secondary structure

The formation of a double helix (for DNA) or a stem and loop structure (for RNA). Based on complimentary base pairing; opposite bases want to connect with their compliments.

Sugar-phosphate backbone

The "spine" of 5-carbon sugars and phosphate groups in a nucleic acid (the nitrogenous bases project from this backbone).

Antiparallel strands

When strands of DNA or RNA are positioned in opposite 5’ to 3’ directions.

This allows for complimentary base pairing.

Monomer

A smaller molecule that can be considered as a subunit. When these are linked together via covalent bonds, they form polymers

Polymer

A larger molecule made up of linkages of smaller subunit molecules (aka the monomers)

Peptide bond

A covalent bond formed between the carboxyl group of one amino acid and the amino group of another.

Primary structure of protein

A sequence of amino acids, linked via peptide bonds.

Secondary structure of protein

When sequences of amino acids form larger structures, either alpha helixes or beta pleated sheets.

These are stabilized via hydrogen bonds between the “backbone” atoms.

Tertiary structure of protein

When alpha helices and beta pleated sheets are folded into 3d shapes.

These are stabilized by hydrogen bonds, ionic bonds, disulfide (sulfur to sulfur) bonds / bridges, and hydrophobic interactions.

Quaternary structure of protein

The assembly of multipart proteins, formed from folded subunits (smaller levels of organization), stabilized by hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.

Denaturing

When proteins begin to “unfold” / or lose 3d shape due to changes in environmental conditions (Ex. pH, temperature).

Damages quaternary, tertiary, and secondary structure; does NOT damage the individual amino acids.

Monosaccharide

Aka a “simple sugar”.

An organic molecule that includes a carbon chain, a C=O group, and C-OH groups. The carbon chain can be linear or form a ring structure.

Glycosidic linkage

The covalent bond that links monosaccharides together to form polymers.

Aka what binds sugars together.

Glycan

A polymer made up of many monosaccharides joined by glycosidic linkages.

(Same thing as a polysaccharide)

Carbohydrates

A group of molecules including glycans and polysaccharides.

Lipid

A type of organic molecule characterized by hydrophobia. (This molecule does not dissolve in water).

Saturated (lipids)

Lipids with hydrocarbon chains containing only single bonds. (No “kinks”.

Unsaturated (lipids)

Lipids with one or more hydrocarbon double bonds. These chains have “kinks”.

Fat

A lipid comprised of three fatty acids attached to glycerol.

The fatty acids have a COOH group on one end where the glycerol will attach.

Steroid

A lipid with a specific “four fused rings” structure. Bulky.

Phospholipid

A lipid that consists of 1) a hydrophilic "head" that includes a phosphate group and another polar group, and 2) a hydrophobic hydrocarbon tail.

They make up the plasma membrane.

Longer phospholipid tails have stronger hydrophobic reactions with one another

Amphipathic

When a molecule has both a hydrophobic and hydrophilic region.

Cell membrane / plasma membrane

The boundary of all Earth cells.

Made of a phospholipid bilayer, proteins, and lipids.

MEMBRANE PERMEABILITY

• Look at phospholipid tails ; longer tails = stronger hydrophobic reactions

• Saturated tails pack closer together

• Unsaturated tails pack more loosely

  • Cholesterol adds more space / more permeability as well as structure

• Temperature impacts membrane fluidity

• TL;DR: Longer, more saturated tails and more cholesterol make a less fluid membrane. Shorter, less saturated tails and less cholesterol make a more fluid membrane.

Oligosaccharides

Chains of sugars roughly 6-10 sugars long.

Peripheral membrane protein

Proteins tethered to the inner or outer surfaces of the cell membrane.

Integral membrane protein

A protein embedded, or integrated, into the cell membrane.

Transmembrane protein

A protein that spans across the lipid bilayer.

Kinetic energy

The energy of motion.

Diffusion

Movement of ions or molecules from an area of higher concentration to an area of lower concentration.

Concentration gradients.

Entropy

The tendency of systems to reach a higher state of disorder / randomness.