BIOL10212 Biochemistry

amphipathic

molecules having both a hydrophilic region and a hydrophobic region

Aliphatic

The group of amino acid including glycine, alanine, valine, leucine and isoleucine. Only contrains hydrocarbon side chains

Aromatic

The group of amino acids including phenylalanine, tyrosine, tryptophan and histidine

Hydroxyl

Amino acid group containing tyrosine, serine and threonine

Sulphur containing

The amino acid groups containing cysteine and methionine

Acidic

The amino acid group containing aspartate and glutamate

Amide

The amino acid group containing asparagine and glutamine

Basic

The amino acid group containing lysine and arginine

Alanine, Ala, A

Arginine, Arg, R

Asparagine, Asn, N

Aspartic acid, Asp, D

Cysteine, Cys, C

Glutamic acid, Glu, E

Glutamine, Gln, Q

Glycine, Gly, G

Histidine, His, H

Isoleucine, Ile, I

Leucine, Leu, L

Lysine, Lys, K

Methionine, Met, M

Phenylalanine, Phe, F

Proline, Pro, P

This is a unique amino acid as the R group forms a bond with the amide group to create a ring called a heterocycle.

Serine, Ser, S

Threonine, Thr, T

Tryptophan, Trp, W

Tyrosine, Tyr, Y

Valine, Val, V

Primary structure

The sequence of amino acids in a protein

Bioinformatics

A database of the primary sequences of proteins

Peptide bond

The bond formed between the alpha-carboxyl and alpha-amino of two amino acids in a condensation reaction

N-terminus

The start of a protein

Secondary structure

Regular repeats in folding patterns like alpha helices and beta pleated sheets

Native conformation

The single stable shape a protein folds to under physiological conditions.

Rotation

This is restricted in the amide bond due to double bond characteristic. It causes all backbone atoms to lie in one plane

Trans

The conformation preferred by amide bonds - the other conformation is less favoured due to steric interference of alpha carbon chains

Phi bond

The N-C(alpha) bond in a peptide chain. Rotation is possible around this

Psi bond

The C(alpha)-C bond in peptides. Rotation around this is possible too

Alpha helices

A right handed corkscrew in the secondary structure of a protein. Each carboxyl group of amino acid (n) forms a hydrogen bond with the amide group of amino acid n+4. All carboxyl groups point towards the C terminus which creates a dipole moment

3.6

The number of amino acids per turn in an alpha helix.

Beta strands

A polypeptide chain that is alost fully extended but not stable by itself

Beta sheets

Multiple beta strands running next to each other that are stabilized by hydrogen bonds. Part of secondary structure. Side chains project above and below. One side is hydrophilic and the other is hydrophobic.

Antiparallel beta sheets

Secondary structure where strands run in opposite directions with hydrogen bonds between. These are closer and straighter so more strong than the other form

Parallel beta sheet

Secondary structure where strands run in the same direction and are stabilized by hydrogen bonds

Loops and turns

The short section of a protein that connect beta strands and alpha helices and allow the protein to fold back on itself. Often only 5 or less residues.

Tertiary structure

The 3D shape of a protein which is what makes the protein specific for its particular biological function. It is stabilized by non-covalent interactions - mainly hydrophobic ones. Also disulphide brdiges

Motifs

Reoccurring folding patterns in tertiary structures. Also known as supersecondary structures

Helix-turn-helix

A motif that is common in proteins that bind to DNA

Coiled coil

A motif Where two alpha helices wrap around each other. Found in some proteins that bind to DNA and structural proteins.

Beta-alpha-beta

A motif found in metabolic proteins - a beta sheet followed by an alpha helix and then another beta sheet.

Helix bundle

A motif with mutiple alpha helices pressed together

Beta-hairpin

A motif with two beta strips together

Greek key

A motif that is a variation of the anti parallel beta sheet where the strips don't need to form hydrogen bonds with their adjacent strip

Domain

An independently folded, compact unit in proteins that can be 25-300 amino acids in length. Proteins often have 3 domains with each having a different function. Domains can be shared between proteins that bind to the same ligand or catalyses the same reaction

Folding pattern

A part of tertiary structure that helps us identify This has 4 categories - all alpha, all beta, mixed alpha beta and alpha + beta

Quaternary strucuture

The organisation of subunits in a protein with multiple. These associate through weak noncovalent interactions and disulphide bonds.

Monosacharides (simple sugars)

A single unit of a carbohydrate - one monomer. They are in two forms: aldoses or ketoses

Triose

A monosaccharide with 3 carbons

Tetrose

A monosaccharide with 4 carbons

Pentose

A monosaccharide with 5 carbons. Forms a ring

Hexose

A monosaccharide with 6 carbons. Forms a ring

Heptose

A monosaccharide with 7 carbons

Oligiosaccharides

2-20 monosaccharides joined together

Polysaccharides

20+ monosaccharides joined together

Glycoconjugates

Carbohydrates that are covalently liked to proteins or lipids

Aldose

A monosaccharide with an aldehyde group

Ketose

A monosaccharide with a ketone group

D

The stereoisomer of sugars that are much more common in nature

hemiacetal

Forms when the aldehyde of aldose reacts with an alcohol

Acetal

Forms when a hemiacetal reacts with another alcohol in a condensation reaction

Hemiketal

Ketone reacts with an alcohol to form this.

Ketal

A hemiketal reacts with an alcohol to form this in a condensation reaction

Pryranoses

A sugar with a 6 membered ring - 5 carbons and 1 oxygen

Furanoses

Sugars with a 5 membered ring - 4 carbons and oxygen

Disaccharides

Two monosaccharides linked by a glycosidic bond. Hemiacetal/ketals become acetals/ketals when this occurs

Homoglycans

Polysaccharides with only 1 monomer

Heteroglycans

Polysaccharides with more than one monomer

Glycogen

The way anials and fungi store glucose. Joined by a1-4 glycosidic bonds. Also branching at a1-6 glycosidic bonds every 8-12 residues

Starch

The way plants store glucose - a mixture of amylose and amylopectin

Amylose

Glucose joined by a1-4 glycosidic bonds to form a spiral chain but with no branches

Amylopectin

Glucose joined by a1-4 glycosidic bonds to form a spiral chain. Also a1-6 glycosidic bonds every 24-30 residues

cellulose

The most abundant biopolymer on earth. B glucose linked by b1-4 glycosidic bonds and little branches. Strong hydrogen bonds between strands.

Glycoproteins

Carbohydrates linked to proteins usually by an O-glycosidic linkage to the -OH group of Ser or Thr

Deoxyribose

The 5 membered ring carbohydrate monomer in DNA

Ribose

The 5 membered ring carbohydrate monomer in RNA.

Triacylglycerol

A lipid composed of a a glycerol backbone and 3 fatty acids. Used as a fuel source in the cell. Stored as fat droplets

Glycerophospholipids

A lipid composed of a glycerol backbone, a phosphate molecule connected to a polar head group and 2 fatty acids. The most abundant lipid in the ell membrane

Sphingolipids

A lipid built on a sphingosine backbone. They have 2 nonpolar tails and a polar head. Sphingosine is similar to an amino acid

Isoprenoids

A group of lipids including steroids, lipid vitamins and hormones

Fatty acids

Have 12-22 carbons with a carboxyl group at C1. Can be saturated or unsaturated.

Steroids

A class of isoprenoids that are derived from isoprene.

Cholesterol

An amphipathic molecule with a fused ring system that makes it less flexible than a fatty acid. Acts a fluidity buffer for membranes

Biological membranes

Defines boundaries between cells and subcellular compartments. Made up of proteins and lipids

25-50%

The percentage by mass of lipids in a membrane

50-75%

The percentage of proteins by mass in a membrane

Integral membrane proteins

proteins found in the lipid bilayer than span the entire bilayer. Must contain hydrophobic regions. Membrane spanning alpha helices are the most common motifs. Beta sheets can act as a channels through the membrane .

Peripheral membrane proteins

Associated with the membrane face with charge-charge or hydrogen bonding interactions. They can readily disociate

Lipid anchored membrane proteins

Proteins tethered to the membrane though a protein-lipid covalent bond.

Channels/pores

A passage that allows molecules and ions to move through the membrane passively. Molecules/ions must be the right size, charge and molecular structure

Induced fit

Where an active site of an enzyme fits better to the substrate after it has bound