Lecture 2- Enzymes To Glycolysis Flashcards by Nicholas Poovey

RNA with catalytic activity is called

Ribozyme

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The 6 major classes of enzymes

Oxidoreductase
Transferase
Hydrolase
Lyase
Isomerase
Ligase

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Difference between Lyase and Ligase?

Lyase lyses and ligase joins together

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Synthetase vs Synthase

Synthetase requires ATP

Synthase does not require ATP

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What does phosphatase do?

Removes a phosphate group

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Difference between phosphorylase and kinase

Phosphorylase adds a phosphate group using Pi,

Kinase uses ATP

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What does Oxidase do and how?

Catalyze redox rxns using O2 as the electron acceptor but oxygen atoms are not incorporated into the substrate

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Oxygenase- what and how it works

Oxidizes a substrate by transferring oxygen atoms to do it

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What is an enzyme?

A protein catalyst that increases the rate of a rxn without being consumed by the rxn

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Holoenzyme vs apoenzyme

Holoenzyme- enzyme with its nonprotein component (active)

Apoenzyme- enzyme without its nonprotein component (inactive)

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Cofactor vs coenzyme, and examples

Cofactor tends to be inorganic nonprotein moeity (metals)

Coenzyme is a subfactor of cofactor and are small organic, frequently derived from vitamins (NAD+ and FAD)

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What is a prosthetic group?

Refers to a coenzyme that is permanently associated with the enzyme

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What is a cosubstrate?

Refers to a coenzyme that only transiently associate with the enzyme

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What is an allosteric enzyme?

An enzyme that changes its conformation when bound by an effector at a site other than the active site. (Enzyme can then become activated or inhibited)

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What does an enzyme do?

Lowers the activation energy

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Factors that affect the reaction velocity in enzymes

Substrate concentration
Temperature
pH

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Difference in graph shape between enzymes following Michaelis-Menten kinetics vs allosteric enzymes

Michaelis-Menten show a hyperbolic curve

Allosteric enzymes show a sigmoidal curve

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Explain effects that occur in enzyme activity with increased temperature

Increased reaction velocity as it is easier for molecules to reach activation energy.
Begins to decrease once temperature gets too high and begins to denature the enzyme

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Explain pH and enzymes

Specific enzymes tend to have a specific pH at the which they have optimal function.
Too high or low could lead to denaturation, or
a specific AA may need to be protonated or deprotonated in order to function

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Michaelis-Menten equation (simple idea and actual equation)

E + S ES –> E + P k1/k-1 and k2 respectively

V0 = (Vmax [S]) / (Km + [S]). Km = (k-1 + k2)/k1

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What does the Michaelis-Menten equation describe?

How the reaction velocity varies with respect to substrate concentration

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If Km is high, this means that the affinity of the substrate to the enzyme is…?

Low affinity

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Simply put, Km is equal to what?

Half of Vmax

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Where on the Michaelis-Menten graph do we see first and zero orders? And what do they mean?

First order before Km (V is proportional to [S], zero order after Km (V is constant and independent of [S].

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What is the Lineweaver-Burk plot equation?

1/V0 = (Km/Vmax [S]) + (1/Vmax)

Lineweaver-Burk plot, X-axis intercept =? Y-axis intercept =?

``` X-axis = -1/Km Y-axis = 1/Vmax ```

Substance that can diminish the velocity of an enzyme-catalyzed reaction is called...

An inhibitor

What type of bonds are typically made to enzymes by reversible inhibitors?

Noncovalent bonds

What Bond is made to enzymes typically by irreversible inhibitors?

Covalent bonds

Competitive vs noncompetitive inhibitors

Competitive competes with substrate for active site | Noncompetitive binds the E or E-S at a different site other than the active site

What happens to Km in the presence of a competitive inhibitor?

Km is increased, (lower affinity)

What happens to Vmax during competitive inhibition?

Vmax stays unchanged

What happens to Km during noncompetitive inhibition?

Km remains unchanged

What happens to Vmax in presence of a noncompetitive inhibitor?

Vmax decreases (moves higher on lineweaver-burk plot)

Homotropic effectors....?

When the substrate itself serves as an effector

Heterotropic effectors...?

Effectors that are different than the substrate

Regulation of enzymes by covalent modification is most frequently done by addition or removal of phosphate groups from which 3 AA residues of the enzyme?

Serine Threonine Tyrosine

What type of enzyme is involved in phosphorylation?

Protein kinase

What type of enzyme is involved with dephosphorylation?

Phosphoprotein phosphatases

Bioenergetics

The study of energy transfer in biological systems

Free energy equation and what each variable represents

``` ^G= ^H - T^S G energy available to do chemical work and a measure of the spontaneity of chemical rxns H enthalpy, total heat content T temperature S entropy, measure of disorder ```

What is equation for ^G for rxn A+B --> C+D Incorporating ^G0

^G = ^G0 + RT ln [C][D]/[A][B] R= 1.987 cal/mol x degK

What is the standard free energy of hydrolysis of ATP, ^G0?

-7.3 kcal/mol

Final products of the electron transport chain?

CO2 and water

The two energy rich coenzymes in he electron transport chain are?

NADH and FADH2

Oxidative phosphorylation results in the formation of what?

ATP

Where does glycolysis take place?

Cytoplasm

Where does the TCA cycle take place?

Matrix of mitochondria

Where does the electron transport chain take place?

Inner membrane of the mitochondria

1 NADH allows how many H+ to pass through in the ETC?

FADH allows how many H+ to pass through during ETC?

In the ETC, electrons from complex I and II are transferred to what?

Coenzyme Q

In which complex is O2 reduced to water?

Complex IV

Incomplete reduction of oxygen to water can produce?

Reactive oxygen species | Ex superoxide or hydroxyl radical

Example of an enzyme to combat the production of reactive oxygen species

Superoxide dismutase Catalase Glutathione peroxidase

What determines the direction of electron flow in the ETC?

Standard reduction potential, E0 | Electrons flow from the pair with the more negative E0 to the more positive E0

^G0 for the phosphorylation of ADP to ATP is how much?

+7.3 kcal/mol

What happens at complex V?

Protons are pumped into the matrix, coupled with the phosphorylation of ADP to ATP and pumped into the intermembrane space

Complex V has how many domains and what are the names?

2 | F0 at the base and F1 on the matrix side

Where are uncoupling proteins (UCPs) found in humans?

Inner mitochondrial membrane

What do UCPs do and what is the process called?

Allow protons to re-enter the matrix without energy being captured as ATP and instead releases heat Nonshivering Thermogenesis

Isomer vs epimer

Isomers are compounds that have the same chemical formula but different structures Epimers are isomers that differ in configuration around only one specific carbon atom

Where is the location of the determining -OH group on a sugar that is a D and L isomer?

L is on the left | D is on the right

Anomeric carbons in ring: What position is the determining OH group when in the alpha position?

Pointing DOWN, or whichever is TRANS to the projecting CH2OH group

If the hydroxyl group of the anomeric carbon of the cyclized sugar is not linked to another compound by a glycosidic bond, the ring can open and is then termed...?

A reducing sugar

The bond that links sugars is called

Glycosidic bond

What enzymes are used to bind sugars?

Glycosyltransferases

Enzymes that rapidly digest carbohydrates are called

Glycosidases

What is the glycosidic bond formed in cellulose that humans cannot digest?

B(1->4)

Where in the body does the digestion of carbohydrates occur?

In the mouth and the small intestines

In the small intestine, what transport system is used to transport glucose, galactose and fructose across the mucosal lining into the blood vessels? (Not into the mucosal layer from the lumen)

GLUT-2

What is the result of undigested disaccharides reaching the large intestine?

Water is drawn into the large intestine leading to Diarrhea Bacterial fermentation of the remaining carbohydrate plus large volumes of CO2 and H2 gas causing abdominal cramps and flatulence

What two monosaccharides make up lactose?

Glucose + galactose

What percentage of the world adult population are lactose intolerant?

75%

What enzyme breaks down lactose?

Lactase

The sum of all the chemical changes occurring in a cell...

Metabolism

Which specific tissues employ the glycolytic pathway?

ALL tissues

What is the end product of glycolysis?

Pyruvate

GLUT-1 through 4; | What type of transport system and where each is located

All Na+ independent facilitated diffusion transports for glucose GLUT-1 - erythrocytes, blood brain barrier GLUT-2 - pancriatic B-cells, liver, kidney GLUT-3 - neurons GLUT-4 - adipose tissue, skeletal muscle

In the gut, what transport system is used to transport glucose, and what type of transport is it?

It is a Na+ dependent co-transporter system called Sodium Dependent Glucose Transporter (SGLT) Occurs in the epithelial cells of the intestine

Two main phases of glycolysis

Energy investment phase | Energy generation phase

First step of glycolysis

Glucose is phosphorylated by hexokinase (glucokinase in liver and pancreas) to produce glucose-6-phosphate (G6P) *Irreversible step

In glycolysis, G6P is converted to fructose-6-phosphate (F6P) via what enzyme?

Phosphoglucose isomerase

What is the most important control point in glycolysis and what exactly is happening?

3rd step in glycolysis where F6P is converted to fructose-1,6-bisphosphate (F1,6BP) via phosphofructokinase-1 (PFK-1) *first committed step to overall pathway

In glycolysis, a 6 carbon molecule is cleaved into two 3 carbon molecules. What molecules are involved and enzyme used

4th step; Fructose 1,6-bisphosphate is cleaved by ALDOLASE to produce Glyceraldehyde-3-phosphate (G3P) and Dihydroxyacetone phosphate (DHAP)

What happens to DHAP? What enzyme used?

DHAP isomerized to G3P via | Triose Phosphate Isomerase

What happens to glyceraldehyde-3-phosphate (G3P) in glycolysis?

G3P is oxidized by glyceraldehyde-3-phosphate dehydrogenase, using NAD+ and an organic Pi to produce 1,3-bisphosphoglycerate (1,3BPG)

Overall concept of Arsenic poisoning

Competes with Pi for G3P dehydrogenase leading to 3-phosphoglycerate formation directly therefore bypassing the ATP making step

What happens next to 1,3-bisphosphoglycerate (1,3BPG) in glycolysis?

1,3BPG is converted to 3-phosphoglycerate (3BPG) by Phosphoglycerate kinase *the removed phosphate group synthesizes an ATP in this step

Step 8 in glycolysis, what happens to 3-phosphoglycerate?

3-phosphoglycerate is converted to 2-phosphoglycerate via | Phosphoglycerate mutase

Step 9 of glycolysis, what happens to 2-phosphoglycerate?

2-phosphoglycerate is dehydrated to phosphoenolpyruvate (PEP) by Enolase

What can inhibit enolase?

Fluoride

Step 10 in glycolysis, | What happens to phosphoenolpyruvate (PEP) and why is this step significant?

PEP is converted to pyruvate by Pyruvate kinase Producing an ATP *the third irreversible step in glycolysis

What is the NET equation of glycolysis?

Glucose + 2 Pi + 2ADP + 2 NAD+ = 2 pyruvate + 2 NADH + 2 ATP (net)

Lecture 2- Enzymes To Glycolysis Flashcards

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