Chem1050 Unit 2

Difference between myoglobin and hemoglobin is

quaternary structure

What stabilizes O2 binding in myoglobin/hemoglobin

histidine residues

What type of structure is the heme ring

porphyrin

What is the heme ring stabilized by

proximal histidine

What are the quaternary structures stabilized by?

hydrophobic interactoins, H-bonds, salt bridges

Apoprotein

protein without ligand

Haloprotein

protein with its ligand for functionality

Myoglobin has

8 alpha helices with alpha turns and is monomeric.

What holds the heme in myoglobin?

Hydrophobic pocket

Does myoglobin have a low oxygen affinity

No, it’s high, allowing it be good for storage

How many oxygens can hemoglobin bind to?

4

How does cooperativity in hemoglobin work?

When the oxygen binds the iron in a heme, it moves the iron into the plane of the heme’s ring, pulling on the histidine which shifts the alpha helix in a conformational way to allow for more O2 to bind

T-configuration has

low oxygen affinity and is stabilized by salt bridges and allosteric inhibitors —> good for unloading

R-configuration has

high oxygen affinity & is stabilized by oxygen binding and allosteric activators, good for loading

Salt bridges need to ____ in order to go from R to T config

form

Low pH’s effect

low oxygen affinity because there are more H+’s to bind so the O2 will bind to the hemoglobin and push it into T-state

Low CO2 means

R-state

High PO2 means

R state

high amounts of BPG means hemoglobin is in

T-state

Where is myoglobin?

Cardiac and skeletal muscle

A decrease in pH causes a _____ in hemoglobin saturation

decrease

Where are the functional groups that participate in catalysis located?

Active site

Do enzymes affect reaction rate?

Yes

General classes of enzymes

oxidoreductase, transferase, hydrolases, lyases, isomerase, ligase

Oxidoreductase

Catalyzes redox reactions

Transferases

Catalyze transfer of a functional group from one molecule to another

hydrolase

Cleaving a C-O, C-N, or C-S bond by adding in water via OH- and H+

Chymotrypsin is an example of

a hydrolase

Lyases

Cleave C-C, C-O, C-N, C-S bonds through means other than hydrolysis or oxidation

Aldolase B cleaving fructose 1,6 biphosphate into dihydroxyacetone and G3P is an example of

lyase

Give an example of lyase

Fructose 1, 6 biphosphate being cleaved into G3P and dehydroxyacetone by aldolase b

Isomerase

rearranging the existing atoms of a molecule to create an isomer

Ligase

Synthesizes CC, CS, CO, CN bonds in reactions using ATP cleavage

Amylase

Involved with carbohydrate digestion —> used to diagnose acute pancreatitis

Alanine aminotransferase

Uses to transfer amino groups from an amino acid to a ketoacid —> viral hepatitis

Lipase

On endothelial cells —> hydrolyses triacylglycerol into free fatty acids to be stored in adipose —> acute pancreatitis

Lactase dehydrogenase

Anerobic glycolysis to convert glucose to lactate —> liver diseases/skeletal muscle damage

Beta-glucocerebrosidase

Involved in complex liver metabolism —> leads to gaucher’s disease

Troponin

Muscle found in heart —> heart attack

Transketolase

Participates in nonoxidative portion of the pentose phosphate pathway and needs thiamine as a cofactor —> reduced activity = thiamine deficiency

Panthenic acid

acetyl coa —> acyl group carriers

Thiamine pyrophosphate

decarboxylation reactions

pyridoxal phosphate

transamination

Biotin

Carboxylation reactions

Cobalamin

Carbon transfers

Heme

Oxygen carrying

What part of catalysis is there the most free energy?

Transition states

Specific acid base catalysis

Reactions are only modified by chagnes in the concentratio of theacid or base participating in the reaction

Covalent catalysis

Enzyme is modified by a cofactor —> becomes a reactant that can reduce activation energy

What is an example of a covalent catalysis

Transamination using pyridoxal phosphate

Covalent catalysis is facilitated by amino acids that can act as

nucleophiles: histidine, serine, aspartate, and cysteine

Three categories of cofactors

Coenzymes (Typically inert when not bound to enzyme; organic), prosthetic groups, metal ions

Michaelis-Menten Equation

Vi = Vmax[S]/Km[S]

Vmax

Maximal velocity a reaction can achieve at an infinite concentration of substrate

Km

Substrate concentration at which the reaction rate is at half maximum and is a measure of the substrate’s affinity for the enzyme

Small km means _____ affinity

higher —> Vmax is met at lower concentrations of substrate

Km and Vi are _____ related

inversely

What can affect the rate of reactions

Temperature, hydrogen ion concentration

Competitive inhibitors

Bind to the active site; Km increases (substrate concentration has to be increased to compete with the competitive inhibitor) while Vmax remains the same (if the concentration of the substrate is high enough, there is little chance of the competitive inhibitor binding to the active site)

The impact of ________ can be overcome by an increase in substrate concentration

Competitive inhibition

Noncompetitive inhibitor will

decrease Vmax, not affect Km

Allosteric effectors will

stabilize the conformation of a protein —> R state

Example of allosteric effector:

AMP can bind phosphofructokinase I and increase its activity

Allosteric inhibitors do this

stabilize the conformation of a protein that decreases binding of substrate and reaction rate by inducing T-state

What AA’s have phosphorylation done

Serine and Tyrosine and sometimes threonine

What hydrolyzes the phospho-ester bonds of phosphor-seryl and phosphor-tyrosyl residues?

Protein phosphatases

What does dephosphoryation require

Water and mg+2

Examples of cleavage to ensure a protein is active

chymotrypsin to chymotrypsin and proinsulin to insulin

First law of thermodynamics

Total energy remains constant

Second law of thermodynamics

In all spontaneous reactions, entropy increases

Enthalpy

Internal energy of a system; heat being given off is a decrease

Endergonic

Requires the absorption of energy

Exergonic

Gives off energy

Energonic reactions have a ____ Delta G

Positive

Exergonic reactions have a ____ Delta G

negative

catabolic reactions are

exergonic

Anabolic reactions have a ____ Delta G

Positive

Energy in ATP is stored in the

phosphoanhydride bonds

Which complex is not needed for oxidative phosphorylation

Complex 2, because it does not span the mitochondrial membrane

Three forms of CoQ

Quinol = fully reduced with 2 e- and 2 protons, then semiquinone than quinone which is fully oxidized

Complex 1 name, substrate

NADH Q Oxidoreductase, NADH

Complex 1 inhibitor

Rotenone

Coenzyme Q is a

quinone derivative

Complex 2 name and substrate

Succinate Q Reductase, FADH2

Complex 3 name

Q cytochrome c oxidoreductase

Complex 3 inhibitor

Antimycin A

Complex 4 name

Cytochrome c oxidase

cytochrome 4 inhibitor

Cyanide and carbon monoxide

Complex 5 name and inhibitor

ATP synthase and oligomycin

Do inhibitors increase oxygen consumption

No

Do inhibitors block reduction?

No

Do uncouplers increase ATP Product and o2 consumption

No and yes

Examples of uncouplers

Dinitrophenol and UCP protein

What is important about the inner mitochondrial membrane where the ETC is?

Impermeable; H+ can’t pass through —> keeps the gradient for aTP Production

Glycerol-3-phosphate shuttle

NADH from cytosol gets moved into an FAD in the mitochondrion ;

Cystolic dihydroxyacetate phosphate is reduced to G3P which moves into the mitochondria and gives the e- to FAD bound to a dehydrogenase

Malata Aspartate Shuttle

Oxaloacetate is reduced to malate by cystolic malate dehydrogenase that goes into the mitochondria where it gets oxidized back to oxaloacetate by mitochondrial malate dehydrogenase. Then a transamination reaction occurs with glutamate tomove an amine from glutamate into oxaloacetate to generate alpha ketoglutarate and aspartate which can move in and out of the mitochondria, being converted to oxaloacetate