MCAT Biochemistry Review

glycine, alanine, valine, leucine, isoleucine, methionine, proline

Nonpolar nonaromatic side chains

isoelectric point

Point at which a compound is electrically neutral.

heterogenous nuclear RNA (hnRNA)

Primary transcript formed Precursor to mRNA - produces mRNA via posttranscriptional modifications

methylation

a biochemical process that influences behavior by suppressing gene activity and expression. addition of a methyl group

operon

a cluster of genes transcribed as a single mRNA

purine

a nitrogenous base that has a double-ring structure; one of the two general categories of nitrogenous bases found in DNA and RNA; either adenine or guanine

pyrimidine

a nitrogenous base that has a single-ring structure; one of the two general categories of nitrogenous bases found in DNA and RNA; thymine, cytosine, or uracil

Tollen's reagent

-detects presence of reducing sugar -uses Ag(NH3)2+ as oxidizing agent *in a + test, aldehydes reduce Ag+ to metallic silver

saponification

-ester hydrolysis of TAG using a strong base -Based used is typically lye: common name for sodium or potassium hydroxide -Ester bonds are broken

waxes

esters of long-chain fatty acids with long-chain alcohols

cofactor

generally inorganic molecules/metal ions don't generally bind the enzyme Ca+2 or Mg+2

oncogenes

genes that cause cancer by blocking the normal controls on cell reproduction

structural genes

genes that code for proteins in an operon

keratin

intermediate filament proteins found in epithelial cells. coiled coil structure

DNA libraries

large collections of known DNA sequences

voltage-gated ion channels

regulated by membrane potential change near the channel. ie: neurons

Glycerophospholipids

phospholipids that contain a glycerol backbone bonded by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head group

9.6

pka of amino group

2.3

pka of carboxyl group

Serine, Threonine, Asparagine, Glutamine, Cysteine

polar amino acids

arginine, lysine, histidine

positively charged amino acids

myosin

primary motor protein that interacts with actin

proto-oncogenes

the corresponding normal cellular genes that are responsible for normal cell growth and division

E site

the exit site, where discharged tRNAs leave the ribosome

vitamin E

tocopherols and tocotrienols. substituted aromatic ring with long isoprenoid side chain, hydrophobic - antioxidant

RNA polymerase II

transcribes mRNA

DNA methylase

adds a methyl group to cytosine and adenine nucleotides. linked with silencing of gene expression

reducing sugar

any monosaccharide with a hemiacetal ring

surfactant

any substance that interferes with the hydrogen bonding between water molecules and thereby reduces surface tension

holoenzyme

apoenzyme + cofactor

DNA polymerase δ, ε

are assisted by the PCNA protein which assembles into a trimer to form the sliding clamp The clamp helps to strengthen the interaction between these DNA polymerases and the template strand

tryptophan, phenylalanine, tyrosine

aromatic amino acids

chaperone proteins

assist in folding other proteins

affinity chromatography

creating a column with a high affinity for a particular protein - coat beads with receptor or antibody - elute using competitive inhibitor for receptor/antibody

acetylation

decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA, resulting in an open chromatin that allows for easier access of the transcriptional machinery to the DNA

DNA polymerase δ

- adds DNA nucleotides where the primer had been (eukaryotes)

Benedict's reagent

-detects presence of reducing sugar -aldehyde group of an aldose is readily oxidized indicated by a red precipitate of Cu2O

DNA polymerase β, ε

- participate in DNA repair

inducible systems

- the repressor is bound tightly to the operator system and thereby acts as a roadblock - an inducer must bind to the repressor inhibiting it from binding to the operator so the structural genes can be transcribed - positive control mechanism - lac operon

repressible system

- transcribed under normal conditions - can be turned off by a corepressor coupling with the repressor and the binding of this complex to the operator site - trp operon

terpenoids

-derivatives of terpenes -have undergone oxygenation & rearrangement of the carbon skeleton -contribute to steroid biosynthesis -similar characteristics w/ terpenes

nucleosides

-a 5 carbon sugar (pentose) linked to a nitrogenous base - formed by covalently linking the base to C-1' of the sugar

Native PAGE

-a method for analyzing proteins in their native states -maintains the protein's shape, but results are difficult to compare because the mass-to-charge ratio differs for each protein -most useful to compare the molecular size or the charge of proteins known to be similar in size from other analytic methods

vitamin A

-carotene -unsaturated - important in vision, growth, development, & immune function -Important metabolite of [answer] is retinal: component of light sensing molecular system in the human eye -Retinol (the storage form of [answer]) is oxidized to retinoic acid --> hormone that regulates gene expression during epithelial development

vitamin D

-cholecalciferol -consumed or formed in a UV light driven reaction in the skin -converted to calcitriol which increases calcium and phosphate intake in intestines (promotes bone production) -Regulates calcium so it is added to milk to aid in absorption of calcium

genomic libraries

-contain large fragments of DNA - include both coding (exon) and non-coding (intron) regions of DNA

cDNA libraries

-contain smaller fragments of DNA, and only include exons of genes expressed by the sample tissue -can be used to make recombinant proteins or for gene therapy

terpenes

-metabolic precursors to steroids and other lipid signaling molecules -odiferous chemicals -class of lipids built from isoprene - carbons are grouped in multiples of 5 -grouped according to the # of isoprene units present -a single terpene consists of 2 isoprene units

polyacrylamide gel

-porous matrix mixture used in electrophoresis -particles move faster if they are small, highly charged, or placed in large electric field -proteins move slower if they are bigger, electrically neutral, or placed in small electric field

ion exchange chromatography

-stationary phase is made of either negatively or positively charged beads (attract & bind compounds that have opposite charge) -salt is added to elute proteins stuck to column

Edman degradation

-used to analyze small proteins - selectively & sequentially removes the N terminal AA of the protein which is analyzed by mass spectroscopy

Huckel's Rule of Aromaticity

4n+2 pi electrons

southern blot

A DNA sample is electrophoresed on a gel and then transferred to a filter. The filter is then soaked in a denaturant and subsequently exposed to a labeled DNA probe that recognizes and anneals to its complementary strand. The resulting ds labeled piece of DNA is visualized when the filter is exposed to film.

enhancer

A DNA segment containing multiple control elements that can recognize certain transcription factors that stimulate the transcription of nearby genes.

Bradford protein assay

A colorimetric method of determining the concentration of protein in an isolate against a protein standard; relies on a transition of absorption between bound and unbound Coomassie Brilliant Blue dye

tumor suppressor genes

A gene whose protein product inhibits cell division, thereby preventing the uncontrolled cell growth that contributes to cancer.

actin

A globular protein that links into chains, two of which twist helically about each other, forming microfilaments in muscle and other contractile elements in cells.

spliceosome

A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex.

elastin

A protein that is similar to collagen and is the chief constituent of elastic fibers.

Hill's Coefficient

A quantitative measure of cooperative binding effects in enzymes

Amphoteric species

A species capable of reacting as either an acid or base, depending on the nature of the reactants

chromatography

A technique that is used to separate the components of a mixture based on the tendency of each component to travel or be drawn across the surface of another material. - sample placed on solid medium called the "stationary phase" or "absorbent" - a mobile phase, the "elute", is sent through

glycerol

A three-carbon alcohol to which fatty acids are covalently bonded to make fats and oils.

activation domain

Allows for binding of several transcription factors and other important regulatory proteins

telomerase

An enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells.

aminoacyl-tRNA synthetase

An enzyme that joins each amino acid to the appropriate tRNA.

ss DNA binding proteins

Bind unraveled strands to prevent reassociation and degradation by nucleases

transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription. transcription-activating proteins that search the DNA looking for specific DNA-binding motifs

recombinant DNA

DNA produced by combining DNA from different sources

restriction enzymes

Enzyme that cuts DNA at a specific sequence of nucleotides - palindromic sequences - protect bacteria from viruses

Gangliosides

Glycolipids with a head group composed of oligosaccharides with a terminal sialic acid (NANA) molecule.

DNA polymerase α, δ, ε

In charge of synthesizing nucleotides onto the leading end in the classic 5' to 3' direction in eukaryotes

DNA polymerase III

In charge of synthesizing nucleotides onto the leading end in the classic 5' to 3' direction in prokaryotes

Sphingolipids

Lipids with a sphingosine backbone: ceramide, sphingomyelins, glycosphingolipids, gangliosides

primase

Synthesizes RNA primers needed to start replication

DNA methylation

The addition of methyl groups to bases of DNA after DNA synthesis; may serve as a long-term control of gene expression.

Jacob-Monod Model

The description of the structure and function of operons in prokaryotes, in which operons have structural genes, an operator site, a promoter site, and a regulator gene

Tautomerization

The rearrangement of bonds within a compound, usually by moving a hydrogen and forming a double bond

Shine-Dalgarno sequence

The prokaryotic ribosome-binding site on mRNA, found 10 nucleotides 5' to the start codon.

esterification

The reaction of an alcohol with a carboxylic acid to produce an ester and water.

DNA-binding domain

The site on a DNA-binding protein that directly interacts with specific DNA sequences.

triacylglycerol

Three fatty acids linked to one glycerol molecule; also called a fat or a triglyceride. carbons are more reduced than in sugars, oxidation yields twice as much energy hydrophobic, don't draw in water, reduces their weight

DNA topoisomerase

allows relaxation of torsional strain from supercoiling by working ahead of helicase and nicking one or both strands

ungated ion channel

always open. unregulated ion channel that allow leak flow of ions

retention time

amount of time a compound spends in stationary phase

Uncompetitive Inhibition

bind only to the enzyme-substrate complex and essentially lock the substrate in the enzyme, preventing its release decreases Vmax decreases Km

selectins

bind to carbohydrate molecules that project from other cells -expressed in white blood cells & endothelial cells that line blood vessels -role in host defense (inflammation & white blood cell migration)

ligand-gated ion channel

binding of a specific substance or ligand to channel causes open/close. ie: neurotransmitters

glycolipids

carbohydrates covalently bonded to lipids

hydrolase

catalyze a hydrolytic cleavage reaction

ligases

catalyze addition or synthesis reactions, generally between large similar molecules, and often require ATP

oxidoreductases

catalyze oxidation-reduction reactions

lyase

catalyze the cleavage of a molecule into 2 products without water as a substrate

transferase

catalyze the movement of a functional group from one molecule to another

Isomerases

catalyze the rearrangement of bonds within a molecule

collagen

characteristic trihelical fiber

column chromatography

column filled w/ beads (stationary phase), gravity moves the solvent & compounds down the column - the less polar the compound the faster it elutes - solvent polarity, pH, and salinity can be changed to help elute protein of interest -different particles that leave the column are collected over time

nucleotide excision repair

eliminates thymine dimers, cut and patch process. 1) proteins scan DNA molecule and recognize the lesion because of bulge 2) excision endonuclease makes nicks in the backbone on both sides of the dimer and removes defective oligonucleotide 3) DNA pol fills gap using undamaged strand as template 4) DNA ligase seals the nick

helicase

enzymes responsible for unwinding DNA, generating ss template strands ahead of the polymerase

apoenzymes

enzymes without their cofactors

G-protein coupled receptors

family of integral membrane proteins involved in signal transduction

Cell adhesion molecules

found on the surface of most cells and aid in binding the cell to EM matrix or other cells

cadherins

group of glycoproteins that mediate calcium-dependent cell adhesion. often hold similar cell types together

integrins

group of proteins that all have two membrane spanning chains call a and b or alpha and beta can promote cell division, apoptosis, or other processes

P site

in a ribosome, holds the tRNA carrying the growing polypeptide chain

A site

in a ribosome, holds the tRNA carrying the next amino acid to be added to the chain

monocistronic

in eukaryotes, each mRNA molecule translates into only one protein product

polycistronic

in prokaryotes, starting the process of translation at different location in the mRNA can result in different proteins

zymogen

inactive form of an enzyme

vitamin K

includes phylloquinone and menaquinones, vital to post translational modifications required to form prothrombin, an important clotting factor in blood

Noncompetitive Inhibition

inhibitor binds elsewhere on the enzyme; alters active site so that the substrate cannot bind cannot be overcome by adding more substrate binds to E and ES complex with the same affinity Decreases Vmax because less enzyme available to bind Does not alter Km because enzymes that are still active maintain same affinity

Steroids

lipids characterized by a carbon skeleton consisting of four fused rings

tubulin

makes up microtubules, which provide structure, also helps in chromosome separation in mitosis and meiosis

kinesins

motor proteins associated with microtubules. Align chromosomes and depolarize microtubules. Bring vesicles towards positive end of microtubule

dyneins

motor proteins associated with microtubules. Involved in movement of cilia and flagella. Bring vesicles towards negative end of microtubule.

aspartate, glutamate

negatively charged amino acids

promoter region

region of DNA that RNA polymerase attaches to to begin transcription.

DNA cloning

produces large amounts of a desired sequence - ligate the DNA of interest into a vector, forms a recombinant vector - vector inserted into a bacterium - bacteria grown in colonies, colony containing water is isolated - recombinant colony replicates

antigen

proteins produced by beta cells that function to neutralize targets in the body. made up of 2 identical heavy chains and 2 identical light chains linked by disulfide bonds neutralize the antigen, making pathogen/toxin unable to exert their effect marking pathogen for destruction clumping together (agglutination) antigen to be eaten by macrophages

histone acetylases

proteins that are involved in chromatin remodeling can be recruited due to transcription factors they acetylate (CH3C=O) lysine residues found on the N terminal of the histone tail region acetylation of the histone proteins decreases the positive charge on the lysine residues and weakens the interaction between DNA and the histone proteins - the chromatin starts to open and allows for easier access of the transcription machinery to the DNA it increases the space between the histones, allowing for better access to DNA for other transcription factors

histone deacetylases

proteins that function to remove the acetyl groups from histones make the chromatin in a more closed conformation overal decreases the gene expression levels of the cell

enzyme-linked receptors

receptors that display catalytic activity in response to ligand binding. has a membrane-spanning domain, a ligand-binding domain, and a second messenger cascade

size exclusion chromatography

relies on porous beads; larger molecules elute first because they are not trapped in small pores

RNAase H

removes RNA primers in eukaryotes

DNA polymerase I

removes the RNA primer and replaces it with DNA in prokaryotes

Base excision repair

repairs small, non helix distorting mutations 1) affected base recognized and removed by glycosylase enzyme, leaving behind an apurinic/apyrimidic site 2) AP site recognized by an AP endonuclease that removes damaged sequence from the DNA 3) DNA polymerase and DNA ligase can fill gap and seal the strand

motif

repetitive organization of secondary structural elements

DNA Polymerase γ

replicates mitochondrial DNA

Mixed inhibition

results when an inhibitor can bind to either the enzyme or the E-S complex, but has different affinity for each; binds to allosteric alters Km depending on affinity decreased Vmax

sliding clamp

ring-shaped protein that holds the DNA pol on the DNA strand

Isoelectric focusing

separates on basis of isoelectric point (pI) - gel has a pH gradient - electric field applied to gel - protein migrates through gel into reaching point of gradient where pH= pI, becomes neutral and stops migrating

SDS PAGE

separates proteins based on their mass alone; SDS disrupts all noncovalent interactions to bind proteins and creates large chains with net negative charge, thus neutralizing the protein's original charge and denaturing it

replication complex

set of specialized proteins that assist DNA polymerases

coenzyme

small organic molecule, such as a vitamin or its derivative, which is required to enhance the activity of an enzyme loosely bind to the enzyme

competitive inhibition

substance that resembles the normal substrate competes with the substrate for the active site Doesn't alter Vmax Alters Km

Euchromatin

the looser, less-dense collections of DNA that appear light-colored under a microscope; transcriptionally active

pI

the pH at which the average charge of all of the amino acid species in solution is zero

Heterochromatin

the tightly coiled DNA that appears dark-colored under a microscope; transcriptionally inactive

small nuclear ribonucleoproteins (snRNPs)

these enzymes cut out introns and splice together eons in the pre-RNA to create a functional mRNA

promoter site

upstream of operator site, provides place for RNA polymerase to bind

regulator gene

upstream of promoter site codes for the repressor protein

operator site

upstream of structural gene, nontranscribable region of DNA that is capable of binding a repressor protein

migration velocity

velocity at which the protein will move to the anode (+) or move to the cathode (-) directly proportional to the electric fields strength (E) and the net charge of the molecule (z) and inversely proportional to the frictional coefficient (f) v = E/f

supercoiling

wrapping of DNA on itself as its helical structure is pushed ever further toward the telomeres during replication