Biochemistry 100 UCSC

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Midterm 2 - enzymes, etc..

enzyme

any of several complex proteins that are produced by cells and act as catalysts in specific biochemical reactions

substrate

the reactant being catalyzed

cofactor

Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis.

apoenzyme

An enzyme that requires a cofactor to become catalytically active.

holoenzyme

an enzyme that consists of an apoenzyme and a cofactor

coenzyme

An organic molecule serving as a cofactor. Most vitamins function as coenzymes in important metabolic reactions

free energy

energy that is available to do work

free energy of activation

The amount of energy that reactants must absorb before a chemical reaction will start; also called activation energy.

transition state

High energy complex in which old bonds are partially broken and new bonds are partially formed. Charges existing only prior to or after the formation of the complex are designated as partial charges.

enzyme-substrate complex

A temporary complex formed when an enzyme binds to its substrate molecule(s).

active site

The specific portion of an enzyme that attaches to the substrate by means of weak chemical bonds.

induced fit

The change in shape of the active site of an enzyme so that it binds more snugly to the substrate, induced by entry of the substrate.

proteolytic enzyme

enzyme that breaks protein down into smaller fragments called polypeptides

enzyme specificity

each enzyme catalyzes only one kind of reaction

catalysis

the acceleration of a chemical reaction by a catalyst

transition state analog

A compound that resembles a transition state. These analogs characteristically bind extremely tightly to the active sites of appropriate enzymes and thus act as potent inhibitors.

trigonal

A molecular geometric shape comprising of a central atom with Three legs, one of which is double bonded. Bond angle 120°.

kinetics

the study of reaction rates

michaelis-menten equation

A rate equation relating the initial velocity (v0) of an enzymatic reaction to the substrate concentration ([S]), the maximum velocity (Vmax), and the Michaelis constant (Km); v0=Vmax([S])/Km + [S]

lineweaver burk equation

affords a line with a slope of Km/Vmax and y-intercept of 1/Vmax. The x-intercept, a theoretical point since 1/[S] cannot be negative, is -1/Km. Inverted so it looks like y=mx+b

turnover number

number of substrate molecules one enzyme active site 'can con- vert to product in a given unit of time when an enzyme solution is saturated with substrate.

kcat/km

Kcat/Km= ratio compares one enzyme with two different substrates
Higher the ratio the better the substrate.

sequential reaction

An enzymatic reaction in which all the substrates must be bound to the enzyme before and product is released.

ping-pong reaction

A reaction in which an enzyme binds one substrate and releases a product, leaving a substituted enzyme thaat then binds a second substrate and releases a second product, thereby restoring the enzyme to its original form.

allosteric enzyme

an enzyme containing an active site plus an allosteric site for binding an effector molecule, an enzyme which contains a region to which small regulatory molecules may bind in addition to and separate from the substrate binding site, thereby affecting catalytic activity

What is the maximum rate possible with a given amount of enzyme?

Vmax

kcat

Turnover number

catalytic efficiency

The catalytic constant is defined as above
This is also known as the turnover number because it is the number of catalytic reactions per active site per unit time.
How many reactions can be created with each enzyme
As [E] increases, so does Vmax.
How many porductions you can get per enzyme
When k₂>>k₋₁, the
k₁k₂
k¹ + k₂
is maximal

Rate limiting step

feedback inhibition

Also called negative feedback, the inhibition of an early step in a series of events by the product of a later step in the series. This has the effect of stopping the series of events when the products are plentiful and the series is unnecesseary. Feedback inhibition is the most common form of regulation in the body, controllin such things as enzyme reactions, hormone levels, blood pressure, body temperature, etc.

mwc model

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), , concerted model
- all subunits switch at once, oxygen binds to both high and low affinity forms, but oxygen binding shifts the equilibrium to the high affinity form, , Each subunit exists in a conformational state that has either a low affinity (T or tight state) or a high affinity (R or relaxed state) for ligand.

heterotropic effects

Allosteric interactions that occur when different substances are bound to the protein; e.g., inhibition of ATCase by CTP and activation by ATP, effects of regulatory molecules on allosteric enzymes.

homotropic effects

Allosteric interactions that occur when several identical molecules are bound to the protein; e.g., the binding of asparate to ATCase, effect of substrates on allosteric enzymes.

sequential model

model of allosteric subunit interaction in which subunits of allosteric enzyme convert from T state to R state with each substrate binding reaction

Competitive Inhibitor

An enzyme inhibitor that competes with substrate for binding at the active site of the enzyme. When the inhibitor is bound, no product can be made.

Uncompetitive Inhibitor

reversible enzyme inhibitor that binds only to the enzyme-substrate complex

Noncompetitive Inhibitor

A substance that impedes the activity of an enzyme without entering an active site and thus without competing directly with the normal substrate. By binding elsewhere on the enzyme, a noncompetitive inhibitor changes the shape of the enzyme so that the active site no longer functions.

suicide inhibitor

Binds to an enzyme covalently at an active site thereby destroying the enzyme

beta lactam ring

Core molecule in penicillin, cephalosporin, and other antimicrobials that block peptidoglycan synthesis (cell wall synthesis), all contain a highly reactive 3 carbon, 1 nitrogen ring, Penicillin acts by covalently modifying the enzyme transpeptidase, thereby preventing the synthesis of bacterial cell walls and thus killing the bacteria.

chymotrypsin

Secreted by the pancreas; chymotrysinogen when inactive; is activated by trypsin and breaks down proteins into peptides

ser 195

Together with His57 and Asp102, these constitute the charge relay system. The system is in place in the zymogen. Universally conserved chief catalytic residue

dipf

inactivates many proteolytic enzymes (ex chemotrypsin) by reacting w/a specific serine residue at the active site. although such enzymes contain many serine residues, the "active site" serine reacts w/DIPF much more rapidly than with these other serine residues. these enyzmes are called "serine proteases"

catalytic triad

-found in active site of serine proteases
-aspartic acid induces histidine to act as a base and remove the proton from serine's hydroxyl group
-activated serine (RO-) can bond with substrate and hydrolize a peptide bond, , Asp 102, His 57, Ser195

oxyanion hole

The __________ stabilizes the intermediate of the hydrolysis of a peptide bond by chymotrypsin

covalent modification

Enzyme's activity is affected by addition or removal of specific chemical groups via covalent bonding

binding energy

The energy required to break a nucleus apart into its constituent neutrons and protons, at a max when enzyme binds to the transition state, favors transition state and thereby promotes catalysis.

hemoglobin

Iron-containing protein in red blood cells that transports oxygen from the lungs to the tissues of the body

myoglobin

A hemoprotein that receives oxygen from hemoglobin and stores it in the tissues until needed.

cooperative effect

When hemoglobin binds to O2 and it makes it easier to bind additional O2 to the other sites

sigmoidal curve

Shows cooperative behavior, less pO2 in tissues than lungs, because of coop hemoglobin delivers more O2 to tissues than would myoglobin

Heme

contained in a single molecule of subunit, which holds an iron ion that can reversibly bind an oxygen molecule, O binding changes position of iron, deoxygenated is nonplanar.

protoporphyrin

Molecule that joins w/Fe to make heme. Will build up in blood if Fe is low.

T R state

Hb has only two stable conformation states, the T state (deoxyHb) and R state (oxyHb). Oxygen binding causes the T state to shift to the R state, which has greater affinity for O2. The T to R shift is triggered by O binding to the heme iron, which pulls the heme iron atom into the heme plane. This movement is transmitted to the F helix through His F8, which ligands the iron atom. Conformational changes in one subunit are transmitted across the α1-β2 and α2-β1 interfaces. Due to the conformational constraints at these interfaces, the conformational shift of one subunit must be accompanied by the conformational shift of all subunits, thereby increasing the O affinity of the unoccupied subunits

2,3-BPG

Binds to T state of Hb and lowers its affinity for O2. fetal HB binds less 2,3 bpg and bings O2 with higher affinity

Fetal Hb

Has lower affinity for 2,3 Bisphosphate-D-glycerate thus a higher affinity for O2 so it can absorb it through the placenta

sickle cell anemia

disease where red blood cells become crescent shaped because they contain defective hemoglobin; the sickle cell hemoglobin carries less O2; caused by a single substitution of valine for glutamic acid, Mutation of a nonpolar Valine on outside of Hb S reduces the solubility of deoxy form of Hb.. so they can aggregate and clump together, sickling results when there is a high concentration of deoxy form of Hb S.

Bohr effect

The tendency of certain factors to stabilize the hemoglobin in the tense conformation, thus reducing its affinity for oxygen and enhancing the release of oxygen to the tissues. The factors include increased PCO2, increase temperature, increased bisphosphoglycerate (BPG), and decreased pH. Note that the Bohr effect shifts the oxy-hemolobin saturation curve to the right.

CO2 transport

Function of Hemoglobin
Indirect transport
Predominant mechanism
CO2 diffuses into RBC
Transformed into carbonic acid
H2O + CO2 = H2CO3
H2CO3 → H+ + HCO3-

(hydrogen carbonate ion)
Hydrogen is accepted by deoxyhemoglobin
Bicarbonate diffuses into plasma and is exchanged for a Cl- (Chloride shift)
H2CO3 → H2O + CO2 (In the lungs)

carbamate

15% of CO2 transported as this molecule.
CO2 is attached to N-terminal amino group of Hb
stabilizes low affinity T state

carbonic anhydrase

An enzyme abundant in RBCs that catalyzes the conversion of CO2 and H2O into carbonic acid (H2CO3).

Carbohydrate

a class of molecules that includes sugars, starches, and fiber; contains carbon, hydrogen, and oxygen

Monosaccharide

a sugar (like sucrose or fructose) that does not hydrolyse to give other sugars, simple carb.

Ketose

Sugar containing a ketone group R-C=O-R'

Aldose

Sugar containing an aldehyde group -CH=O

Isomer

Compounds with the same simple formula but different three-dimensional structures resulting in different physical and chemical properties, two types: stereoisomers, constitutional isomers

stereoisomer (2 types)

Isomers with the same structural formula but different spatial arrangements of atoms

Diastereoisomer

Stereoisomers that are optically active (chiral) isomers that are not mirror images

Enantiomers

Stereoisomers that are mirror images of each other

Constitutional isomer

Compounds with the same molecular formula but connected differently, nonsuperimposable mirror images

Epimer

diastereomers that differ in configuration of only one stereogenic center.

Anomer

Diastereomers that are cyclic carbs that differ in configuration only at the anomeric carbon and can freely interconvert(alpha and beta) through Mutarotation.

glycosidic bond

Bond between two monosaccharides

Oligosaccharide

Short chain carbohydrate of two or more covalently bonded sugar monomers (e.g., disaccharides).

Sucrose

glucose + fructose

Lactose

glucose + galactose

Maltose

glucose + glucose

Glycogen

An extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch.

Starch

Polysaccharide in plant cells that consists entirely of glucose monomers

Cellulose

Polysaccharide consisting of glucose monomers that reinforces plant-cell walls, the most abundant organic compound in the biosphere

Pectin

Molecule that serves to bind cellulose molecules together in a cell wall

Hurler disease

Disease caused by mutations in alpha-L-iduronidase. Lysosome is not functioning properly. Will cause a mucus build up in the lysosome.

glycoprotein

A protein with one or more carbohydrates covalently attached to it.

glycosyltransferase

Attaches one or more sugars (glucose, mannose) to a protein in the process of glycosylation

Lectin

Proteins that bind carbs and increase delivery of drug to receptor, carb binding protein, linked by weak noncovalent interactions, facilitate embryonic development by selectins that are made by embryo and attach to mother's uterus

reducing sugar

A sugar that can be oxydized by Cu2+ solutions (weak oxidizing agents...All monosccharides are reducing sugars)

nonreducing sugar

Don't react

Fatty acid

Unbranched carbon chains that make up most lipids

Steroid

A lipid molecule in which the carbon skeleton forms four fused rings, most common is cholestoral, differ from other lipids because of ring structure

Glycolipid

A lipid covalently attached to a carbohydrate.

Phospholipid

A lipid that contains phosphorus and that is a structural component in cell membranes, polar head and np tail

degree of unsaturation

the more unsaturated, the more fluid the fat will be at room temp; saturated are solid fats from animal sources, polyunsaturated are liquid oils from plant sources; the tropical oils are solid at room temp; can be mono -> one unsaturated point or poly -> more than one unsaturated point

Triacylglycerol

Three fatty acids linked to one glycerol molecule; also called a fat or a triglyceride, Fatty Acids stored as _____________.

lipid bilayer

Structure of membrane, two sheets of lipid molcules with tails pointed inward, proteins embedded in bilayer (serve as channels) along with carbohydrate molecules

liposome

Vesicle formed spontaneously from lipid bilayer. surrounded by 2 phospholipid layers

secondary transport

Form of active transport which does not use ATP as an energy source; rather, transport is coupled to ion diffusion down a concentration gradient established by primary active transport.

antiporter

A carrier protein that transports two molecules acrss the plasma membrane in opposite directions.

symporter

A carrier protein that transports two molecules across the plasma membrane in the same direction. For example, the Na+-glucose cotransporter in intestinal cells is a symporter.

ion channel

A complex of protein molecules in a cell membrane that form a pore through which ions can pass

selectivity filter

The narrowest part of the ion channel

ATP-binding cassette

ATP-powered pump. Has 2 halves each with 6 transmembrane a-helices. Has 2 NBDs (cytoplasmic nucleotide binding domains) -- bind to a specific substrate. Can be both importers or exporters. Transport sugars, ions, amino acids, phospholipids and HYDROPHOBIC drugs.

p-type ATPase

Type of transport ATPase that is reversibly phosphorylated by ATP as part of the transport mechanism.

lipid raft

An area of decreased membrane fluidity (has much more cholesterol than rest of bilayer)

Micelle

Small particle formed by aggregates of detergent like molecules; the polar ends of these molecules will arrange themselves externally and the non-polar ends will arrange themselves internally.

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