Biochemistry Test 1 – Flashcards

a discipline in biochemistry; is the description of molecules in biology/chemistry of proteins

a discipline in biochemistry; the manipulation of DNA, genetics

a discipline in biochemistry; larger scale, functions and mechanisms within a cell/cell energetics

a natural polymer; found in plants for storage

a natural polymer; found in animals for storage

a natural polymer; tightly linked bonds

a natural polymer; covalent bonds

chemical elements commonly found in biochemistry

an element commonly found in biochemistry, creates strong single or double bonds with very little rotation

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

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

4 types of non-covalent interactions

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

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

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

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

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

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

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

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

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

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

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)

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

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

the concentration of water (molar)

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

relating to pH; a substance that releases a proton

relating to pH; a substance that accepts a proton

relating to pH; = ([H⁺][A⁻])/[HA]

relating to pH; = -log[Ka]

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

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

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

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

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

two natural buffers

a synthetic buffer; the pKa of TRIS

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

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)

the pH of blood

an organ that regulates blood pH

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

also known as the R-group

the 4 general constituents of an AA

short form for Amino Acid

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

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)

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

a form of stereochemistry; used mainly in organic chemistry

total number of AA's

the carboxyl pKa

the amino pKa

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

the point on a titration curve where the [zwitterion] concentration is the highest

during AA titrations, the ______ of the AA changes

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

oxidized S-S bonded aa usually outside the cell

reduced S, single cysteine usually found inside the cell

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

the name of the reaction when 2 AA's join their amino and carboxyl terminus (water is removed)

1 to 10 AA's together

10 to 100 AA's together

greater than 100 AA's together

another name for the side chain of an AA

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

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

specialized proteins that break peptide bonds (trypsin and chymotrypsin are examples)

equivalent mass of 1 Da (Dalton)

the average mass of an AA

protein composition; protein consists of a single polypeptide chain

protein composition; same as oligiomeric; protein consists of two or more polypeptide chains (chains can be identical or different)

protein composition; 2 or more polypeptide chains together

protein composition; single pieces of a multisubunit protein

protein composition; a protein is said to be this if it is only composed of AA's (no other groups)

protein composition; a protein is said to be this if it contains AA's and other chemical groups (such as organics or metal ions)

protein composition; names of non AA groups found on conjugated proteins, cofactors/coenzymes covalently linked to protein

protein composition; a protein is said to be this if it is water soluble and found in the cytoplasm of cells

protein composition; a protein is said to be this if it is water soluble and found in the cell structure

first step in protein isolation and purification

second step step in protein isolation and purification

a protein isolation technique that separates the supernatant from the pellet

the liquid component left from a fractional centrifugation

the more solid component separated from a fractional centrifugation

a protein isolation technique that separates proteins based on many characteristics

a method of chromatography; separation based on size, large proteins elute first, small proteins elute later,

a method of chromatography; separates proteins based on charge (PI); gel is usually agarose or cellulose

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)

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

total activity/total protein

total activity(current)/total activity(original)

specific activity(current)/specific activity(original)

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

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

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

reducing agent for cistiene that breaks S-S bonds

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

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

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

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

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

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

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

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

a level of protein structure; interactions between 2 protein chains

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

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

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

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

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

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

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

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

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

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

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

a supersecondary structure; usually deals with DNA

a supersecondary structure; a more common structure

a supersecondary structure; 4 adjacent beta strands

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

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

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

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

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

a biological process that occurs in it's natural environment

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

a folding accessory protein; ensures that proteins do not de-nature at high temperatures

the 4 causes of protein unfolding

the loss of protein function (as well as structure), can be renatured "in vitro"

a protein in which all the subunits are the same

a protein in which the subunits are different

the number of AA's on one alpha chain in hemoglobin

the number of AA's on one beta chain in hemoglobin

a prosthetic group (polypyrole ring) that binds Fe, has 4 bonding points

the number of bonding points that Fe requires

interacts with Fe in hemoglobin

shields the Fe in hemoglobin in the +2 state of oxygen uptake

an oxygen carrying molecule, forms a sigmoidal oxygen binding curve, found in the vascular system, 50% saturation @ 3kPa

an oxygen carrying molecule, forms a hyperbolic oxygen binding curve, found in the musculature for uptake, 50% saturation @ .2kPa

the binding of one site affects binding at another site

the co-operative binding of hemoglobin and its dependency on protons and carbon dioxide concentrations (allosteric effectors)

the T(tense) state of hemoglobin, central cavity is larger

the R(relaxed) state of hemoglobin, central cavity is smaller

the physical form hemoglobin helix assumes when in the unbound state

the physical form hemoglobin helix assumes when in the bound state

a molecule present in high concentrations in RBC, binds to the T state of Hb, and allows for the better release of all oxygen molecules, is an allosteric effector, negatively charged

found in fetal Hb, replaces the two beta subunits, difference between the beta is that it has a serine at 143 instead of a histidine, higher affinity for oxygen than maternal Hb

a Hb mutation; a mutation from Glu6-->Val in the beta subunit decreases the solubility, causing fibrous aggregations

a Hb mutation; the loss or substantial reduction of a single Hb chain

a Hb mutation; no alpha subunits in Hb, 4 beta subunits (HbH)

a Hb mutation; no beta subunits, 4 alpha subunits; this condition is more common

structures involved in immune response

an immunoglobulin that is most common

an immunoglobulin that is usually found in secretions (such as saliva)

an immunoglobulin that is usually related to allergenic responses

the number of domains in IgG

a region on an antibody that changes, allowing the recognition of different antigens

a region on an antibody that does not change

a structure found in the beta chains of immunoglobulin folds that allows for the recognition of different antigens

a waste product which is detrimental to cells, it degrades on its own slowly and requires a high activation energy

an unfavored state at the peak of the activation energy between reactants and products

enzymes; a second chemical entity (organic or inorganic)

enzymes; usually organic or organometallic, does not a form a permanent part of the enzyme

enzymes; a complete complex of protein and cofactor

enzymes; just the protein component in a holoenzyme

enzyme kinetics; initial velocity, ([P]/time) at start of reaction, =(Vmax[S])/(Km+[S])

enzyme kinetics; the maximum velocity for an enzyme

enzyme kinetics; Michaelis constant

when Vo=Kmax/2

when Km=[S]

enzyme kinetics; is an utight bond between enzyme and substrate, low affinity

enzyme kinetics; is a tight bond between enzyme and substrate, high affinity

Vmax/[E]

enzymes mediated by a modulator or effector, or substrate

a region on an enzyme where the substrate binds

the 3 characteristics of active sites

ES complex theory; the enzyme and substrate are rigid structures

ES complex theory; enzyme active site is similar to substrate, the enzyme "stretches" a conformational change occurs and the substrate binds

ES complex theory; enzyme stabilizes the substrate, which can lead to products

mechanisms of enzyme activity; assists in proton transfer reactions, functional groups act as acids or bases

mechanisms of enzyme activity; (30% of all enzymes) hold a substrate properly, stabilizes negative intermediates to polarize scissile bonds, participate in redox reactions

mechanisms of enzyme activity; nucleophilic groups on enzyme reacts and forms covalent bonds with substrate, usually interacts with carbonyl in serine

a bond in a substrate that is to be broken

substances high in electrons/lone pairs

an enzymatic process where an effector shuts down or reduces an enzymes activity; drugs and toxins exert their effects through this mechanism

enzymatic inhibition; covalent bonds permanantly change an enzyme

enzymatic inhibition; non-covalent bonding effectors stop enzymatic processes, the three general forms are competative, non-competative (pure and mixed), and uncompetative

enzymatic inhibition; where the effector resembles the substrate, binds to the active site, high [S] lessens the effect of the inhibitor, Vmax stays the same, Km is altered

enzymatic inhibition; inhibitor and substrate bind to different sites; Km stays the same, Vmax changes

enzymatic inhibition; inhibitor and substrate bind to different sites; Vmax and Km changes

enzymatic inhibition; inhibitor binds to the ES complex, Km decreases and Vmax increases, locks the substrate in position

regulatory pathways are usually controlled by these class of enzymes; in addition, the first enzyme in the pathway is usually the regulatory one and of this type

in enzymes, binding or catalytic changes cause a conformational change elsewhere

enzymatic allosterism; where the substrate and the effector molecule are identical

enzymatic allosterism; where the substrate and the effector are different

allosteric regulation; enzymes can either be found in the TT or RR state, the effector molecule shifts the enzyme to one state (hybrid TR not possible)

allosteric regulation; enzymes can either be found going from TT->TR->RR, the TR hybrid is possible

cellular enzyme regulation; modification via phosphorylation of Ser, Thr, Tyr or ubiquitination of Lys

cellular enzyme regulation; some enzymes are synthesized in the inactive form, the zymogen is cleaved into the active state, this is a irreversible process

cellular enzyme regulation; enzymes that carry out the same reaction but have different kinetics, regulatory properties, forms of coenzymes, and distribution

cellular enzyme regulation; the term used to describle an enzyme formed in an inactive state that has to be cleaved in order to work