Biochem

chemical compositions

covalent

a chemical bond in biology; a pair of shared electrons, very strong, bonds between polymers, >1 bond per atom, flexible and alternate re-arrangement

non-covalent

a chemical bond in biology; weaker bonds, but additive, creates specificity, highly dynamic/transient bonds, required for molecular recognition

electrostatic, hydrogen, van der waals, hydrophobic

4 types of non-covalent interactions

electrostatic

a non-covalent interaction; such as ionic bonds Na⁺ + Cl⁻ -> NaCl

hydrogen

a non-covalent interaction; a H is shared between two electronegative atoms such as F,O, or N; the more electronegative atom pulls the electron closer, creating a dipole

donor acceptor

the H bond _____ becomes more tightly linked, the H bond_____becomes less tightly linked (two answers separated by a space please)

Van Der Waals

a non-covalent interaction; the interaction between molecules with temporary dipoles from fluctuating electrons, are weak but additive

hydrophobic interaction

a non-covalent interaction; the clustering of these molecules in polar substances i.e. water interacts with itself and causes other non-polar residues to cluster

biological solvent

roles of water; many organic and biological materials are able to dissolve in water

part of reaction

roles of water; water is a common substance in biochemical reactions such as the cleavage of bonds

regulation

roles of water; water is essential in regulating temperature and pH (the ideal temperature of water with the highest heat capacity is 37°C)

water

a substance found in nearly all biological reactions and organisms; has a bond angle between H's of 104.5°, has a dipole, H-bonds with itself, cohesive and dissolves polar or charged compounds

hydrophilic

water as a solvent; types of bonding in water "loving" compounds are dipole-dipole, H-bonding, and dipole-ion

hydrophobic aliphatic

water as a solvent; types of bonds formed with water "fearing" compounds are called______. Non-polar/apolar compounds that usually fall in this category are long chained molecules composed of C and H called______molecules (two answers separated by a space please)

amphiphilic

water as a solvent; water "loving and fearing" compounds that contain both polar and non polar regions

micelle

a conformation formed by amphiphilic substances in water that usually serve to sequester different regions in the cell

55.5

the concentration of water (molar)

pH

the power of hydrogen (acidity) of a solution, = -log[H⁺]

acid

relating to pH; a substance that releases a proton

base

relating to pH; a substance that accepts a proton

Ka

relating to pH; = ([H⁺][A⁻])/[HA]

pKa

relating to pH; = -log[Ka]

monoprotic

an acid is said to be this if it is capable of releasing 1 H⁺ ion

inflection point

the point on a titration curve that is ½ the way to neutralization, where pH=pKa

polyprotic

an acid is said to be this if it is capable of releasing more than 1 H⁺ ion

HH equation

the name of the following equation(remember equation too): pH=pKa+log([base]/[acid])

buffer

a substance that significantly (to ±1 pH unit) can control molecular structure and activity

acetate and citrate

two natural buffers

8.3

a synthetic buffer; the pKa of TRIS

7.5

a synthetic buffer; the pKa of HEPES(a zwitterion)

phosphate, proteins, carbonate

3 cellular buffers (hint: first can be found at 1mM in blood, examples of the second are hemoglobin and albumen, the third is the most common)

7.4

the pH of blood

lungs

an organ that regulates blood pH

zwitterion

compounds that have both a positive and negative charge on the same molecule but are neutral overall

side chain

also known as the R-group

amino, carboxyl, alpha carbon, r-group

the 4 general constituents of an AA

AA

short form for Amino Acid

chiral

the ∝-carbon is said to be this (it has 4 groups attached)

enantiomers

also known as stereo isomers, the only AA that is not is glycine, where R=H

+

the charge of NH₃ (symbol)

-

the charge of COO (symbol)

D and L

a form of stereochemistry; polarization of light; nearly all biological AA's are in the "L" form when produced, "D" is rare

R and S

a form of stereochemistry; used mainly in organic chemistry

20

total number of

2.3

the carboxyl

9.7

the amino

7

the pH if the R-group has no net charge. ie. charge is 0

equivalence

the point on a titration curve where the [zwitterion]

structure

during AA titrations, the ______

Isoelectric pH

defined as the pH were the structure of an AA or peptide has no net charge; the average of the pKa's

cystine

oxidized S-S bonded aa usually

cysteine

reduced S, single cysteine usually found inside

histidine

an AA that usually regulates the active sites of an enzyme in response to pH

condensation

the name of the reaction when 2 AA's join their amino and carboxyl terminus

multiple

1 to 10 AA's

polypeptide

10 to 100 AA's together

protein

greater than 100 AA's together

residue

another name for the side chain of an AA

left right

directionality of drawn peptides; ______side is the N terminus, ______side is the C terminus (two answers please, separated by a space)

hydrolysis

the name of the reaction when 2 AA's break their amino and carboxyl terminus (water, 6M HCl and heat are added)

affinity chromatography

a method of chromatography; separation based on ligand attachment; protein attaches to ligand in gel; excess ligand is then poured in, eluting the protein (due to entriopic processes)

HPLC

a method of chromatography; separation based on hydrophobic interactions, works well with peptides, resin is small, slow flow, high pressure

specific activity

total activity/total protein

Yield

total activity(current)/total activity(original)

purification level

specific activity(current)/specific activity(original)

SDS-PAGE

a gel used to determine the molecular size and purity of a protein, smaller proteins migrate faster, charge does not matter, blue dye stains basic residues

SDS

sodium dodecyl sulfate, a negatively charged detergent used to coat proteins in molecular size and weight assay (used with PAGE)

PAGE

polyacrylamide gel electrophoresis, gel used in molecular size and weight assay (used with SDS)

beta-mercaptoethanol

reducing agent for cistiene that breaks S-S bonds

acrylamide

a neurotoxic component of PAGE gel, it forms a 3-D mesh/pores in the gel

bis-acrylamide

causes acrylamide to crosslink in PAGE gel, the higher the concentration, the more crosslinking and the smaller the pores

isoelectric focusing

used to determine the size for unknown proteins, separation based purely on charge (pH gradient)

ampholytes

the name of the group of compounds that create the pH gradient in isoelectric focusing

2-d electrophoresis

a handy molecular technique that first employs IEF in one direction and SDS-PAGE in the other

primary

a level of protein structure; the AA sequence of the protein

secondary

a level of protein structure; how AA sequences form small structures such as ∝-helices or þ-sheets

tertiary

a level of protein structure; the interaction of ∝-helices or þ-sheets, globular forlds

quaternary

a level of protein structure; interactions between 2 protein chains

Edman degeneration

method to determine primary structure; reagent binds to first N terminus stripping of AA, AA then identified by HPLC, cycle repeated and good for proteins up to 50AA's long

two enzymatic digestions

method to determine primary structure; first, trypsin recognizes ARG and LYS and cleaves after the bond, second chymotrypsin recognises PHE, TRP and TYR, cleaving after each

DNA sequencing

method to determine primary structure; low quantities of sample required, high speed, examples are the Human Genome Project

native conformation

this refers to a protein that is properly folded (functional) in structure and is in its natural environment

alpha helix

a secondary structure; rod-like, with R-chains branching out, stabilized by H bonds between N-H and C=O groups. 3.6 residues per turn with H bonding every 4 aa. 10-20 residues per turn is average, proline disrupts steric interactions and is usually found at the ends to prevent bonding

beta sheet

a secondary structure; sheet-like, 2 or more interactions, small AA's are favored

anti parallel

the configuration of the more common beta sheets which form tighter H-bonds, which leads to smaller loops

bends or loops

a secondary structure; reverses in the direction of the main chain, usually connects an alpha helix and beta sheet

common bend

a secondary structure; known as a beta turn, connects different anti parallel sheets

bend

a secondary structure; 4 residues with H-bonding between AA 1 and AA 4

loop

a secondary structure; longer bends which are usually >6 AAs

alpha alpha motif

a supersecondary structure; usually deals with DNA

beta beta motif

a supersecondary structure; a more common structure

greek key

a supersecondary structure; 4 adjacent beta strands

beta barrel

a supersecondary structure; parallel beta strands connected with an alpha helix

collagen

a supersecondary structure; a fibrous protein that contains a triple helix(superhelix) high in proline and hydroxyproline, a non-conventional helix

early events

first part of the protein folding pathway; the formation of secondary structure

intermediate

second part of the protein folding pathway; formation of ionic bonds

final

last part of the protein folding pathway; compaction of the protein

in vivo

a biological process that occurs in it's natural environment

molecular chaperone

a folding accessory protein; binds unfolded proteins by "sheltering" exposed non-polar regions