Biochem - LUC Pine - Exam 1

bond associated with amino acids

peptides

bond associated with carbohydrates

glycosidic

bond associated with nucleotides

phosphodiester

acid (bronsted-lowry)

proton donor

base (bronsted-lowry)

proton accepter

lewis acid

electron pair acceptor

lewis base

electron pair donor

Kw=

[H3O+][OH-]

pkw=

pOH + pH

Ka=

[H3O+][A-]/[HA]

[H+]=

Ka x [HA]/[A-]

Henderson-Hasselbalch equation

pH = pKa + log [A-]/[HA]

pka=

-logKa

pH=

-log[H+]

buffer

weak base w/conj acid or weak acid w/conj base; neutralizes moderate amounts of added acid/base

buffering capacity

amount of acid or base a buffer can neutralize

buffering range

pH range the buffer can be effective

optimal pH=

pka (acid=base)

what range is a buffer effective

+/-1

buffers in the body

H2PO4 - /HPO4 2- is the principal buffer in cells H2CO3/HCO3 - is a major buffer in blood

hypoventilation

CO2 builds up in blood stream from slow breathing

build up of CO2 in blood causes

increase in H3O+

respiratory acidosis

caused by hypoventilation-low pH, high CO2

how do you treat respiratory acidosis

intravenous bicarbonate

hyperventillation

exhaling too much CO2, reduces H3O+ in blood

respiratory alkalosis

A rise in blood pH due to hyperventilation (excessive breathing) and a resulting decrease in CO2.

metabolic alkalosis

high pH, high HCO3 (excessive vomiting)

how to treat metabolic alkalosis

give ammonium chloride

metabolic acidosis

low pH, low HCO3 (diabetes)

how to treat metabolic acidosis

intravenous bicarbonate

primary protein structure

sequence of amino acids

secondary protein structure

coiling or folding of a polypeptide due to H-bonding between amino acids (alpha helix and beta sheets)

tertiary protein structure

3D folding pattern of a protein due to side chain interactions

quarternary protein structure

protein consisting of more than one amino acid chain

nonpolar hydrophobic amino acids

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline

polar hydrophilic neutral amino acids

serine, threonine, asparagine, glutamine, cysteine, tyrosine

polar hydrophilic acidic pos charged amino acids

glutamic acid and aspartic acid

polar hydrophilic basic neg charged amino acids

arginine, lysine, histidine

what amino acid uses disulfide bonds

cysteine

what amino acid restricts rotation of N-alpha carbon

proline

isoelectric point of pH=

pI

pI=

(pKa1 + pKa2)/2

oxytocin

stimulates smooth muscle contraction in the uterus during labor and in the mammary glands during lactation

vasopressin

stimulates resorption of water by the kidneys, thus raising blood pressure

alpha helix characteristics

3.6 residues per turn of the helix, and for every turn, the helix rises 0.54 nm along its axis. the carbonyl oxygen of each residue forms a hydrogen bond with the backbone NH group four residues ahead: an i+4 hydrogen bonding pattern

strong alpha helix formers

alanine, leucine, methionine, and glutamic acid

alpha helix breakers

proline and glycine

beta sheet characteristics

hydrogen bonds form between the carbonyl oxygen atoms and hydrogen atoms in the amide groups bending the polypeptide chain into a sheet; parallel or antiparallel

beta sheet formers

isoleucine, valine, phenylalanine

tertiary structure characteristics

Reduces the hydrophobic surface area, • Results from intramolecular non-covalent interactions (salt bridges and H bonds) and disulfide bonds

how do heat and organic compounds denature proteins

break apart H bonds and disrupt hydrophobic interactions

how do acids and bases denature proteins

break H bonds between polar R groups and disrupt ionic bonds

fibrous proteins

elongated, peptide chains are held together by strong intermolecular forces Usually are insoluble in water Examples: Keratin, Fibroin, Collagen

globular proteins

spherical, peptide chains are held together by relatively weak intramolecular bonds They are soluble in water Examples: Insulin, Casein, Egg albumin, myoglobin, antibodies

isoforms

related proteins encoded by the same genes

job of globular proteins

carry out synthesis, transport, and metabolism in the cells • transport and store oxygen in muscle

what do myoglobin and hemoglobin do

transport and store oxygen

heme

cofactor that allows a protein to carry out some function that amino acids alone cannot perform

hemoglobin and myoglobin affinities

One molecule of myoglobin binds one O2, Hemoglobin can bind up to four molecules of O2 • Binding of O2 to hemoglobin exhibits positive cooperativity

positive cooperativity

When one O2 is bound, it becomes easier for the next O2 to bind

allosteric regulation

Binding of an activator or inhibitor to one site (location) of a protein (or macromolecule) increases or decreases the activity of some other site

cooperative binding

A specific case of allosteric regulation in which the binding of a ligand at one site on a macromolecule affects the affinity of other sites for the same ligand

hemoglobin bohr effect

Increase in [H+] reduces O2 affinity of Hb and causes protonation of key amino acids

BPG and hemoglobin

metabolite that binds to and stabilizes T state of hemoglobin; His-143 makes salt bridge to BPG In the absence of BPG, oxygen-binding capacity of Hb would be higher

homogenization

Process of breaking cells open to release the organelles

salting out

Purification technique for proteins based on differential solubility in salt solutions using ammonium sulfate

column chromatography

-solution with mixture dripped down colum with solid phase.

-more polar=slower down column

column chromatography- stationary phase

Substance that selectively retards the flow of the sample, effecting the separation

column chromatography- mobile phase

Portion of the system in which the mixture to be separated moves

affinity chromatography

Powerful column separation procedure based on specific binding of molecules to a ligand

ion exchange chromatography

Method of separating substances on the basis of charge

cation exchanger

Resin that has a net negative charge and binds to positively charged molecules flowing through the column

anion exchanger

Resin that has a net positive charge and binds to negatively charged molecules flowing through it(poschargerwillelutefirst)

reverse phase high-performance liquid chromatography

Form of high-performance liquid chromatography in which the stationary phase is nonpolar and the mobile phase is a polar liquid » Uses high-resolution columns that take less time for separation than standard columns

High Performance Liquid Chromatography (HPLC)

chromatography technique that gives fast and clean purifications

isoelectric focusing

procedure used to determine the isoelectric point (pI) of a protein Method for separating substances on the basis of their isoelectric points

electrophoresis

Method for separating molecules on the basis of the ratio of charge to size

trypsin trypsin

Proteolytic enzyme specific for basic AA (Arg, Lys,His) residues as the site of hydrolysis

chymotrypsin

Proteolytic enzyme that preferentially hydrolyzes amide bonds adjacent to aromatic amino acid residues (Phe, Trp, Tyr)

cyanogen bromide

Reagent that cleaves proteins at internal methionine residues

enzyme-linked immunosorbent assay (ELISA)

Based on reactions between proteins and antibodies; used to detect antibodies or antigens

western blotting

Technique where proteins are separated using gel electrophoresis and then transferred to a nitrocellulose membrane for analysis and identification

guanidine hydrochloride is used to

break hydrogen bonds

when a protein is denatured

its secondary structure is dismantled but primary remains

Which histidine helps in promoting the O2 binding to myoglobin over other ligands?

distal

Which of these states of hemoglobin represents the low affinity binding O2 conformation of the hemoglobin?

T state

alternating hydrophobic and hydrophilic indicates

amphipathic beta sheet

nonionizable amino acids

lysine, glutamine

gel filtration elutes in order of

heaviest to lightest molecular weight

on a titration curve, inflection point is recognized by

the horizontal shift

on a titration curve, equivalence point is recognized by

the vertical shift