e2 cram

enzyme

alters a reaction rate by lowering activation energy

apoenzyme

enzyme without a cofactor

holoenzyme

enzyme with a cofactor

substrate

substance acted on by an enzyme

active site

location where substrate binds

cofactor

aids enzyme

coenzyme

organic molecule that associates with the enzyme

prosthetic group

organic molecule that covalently attaches to the enzyme

substrate level control

alters susbtrate concentrations based on Le Chatlier’s Principles

Feedback Control

accumulation of product can either increase or decrease the rate of the previous step

allosteric regulation

allosteric binding leads to conformational change of the active site

homotrophic effector

appears the same as the substrate and binds to the same site

heterotrophic effector

appears different than the substrate and binds to a site alternate to the active site

positive effector

enhances binding

negative effector

inhibits binding

6 enzyme classes

OTHLIL

oxidoreductase, transferase, hydrolase, lyase, isomerase, and ligase

oxidoreductase (1)

catalyzes oxidation/reduction reactions

A + B → C + D

transferase (2)

catalyzes the transfer of a functional group from one molecule to another

A-X + B → A + B-X

hydrolase (3)

catalyzes the hydrolysis of a chemical bond, typically involving the reaction of water with a substrate

AB + H2O → A-OH + H-B

lyase (4)

catalyzes the cleavage of chemical bonds by means other than hydrolysis or oxidation

B + C → A

isomerase (5)

catalyzes the conversion of a molecule from one isomer to another without the addition or removal of atoms

A-B → B-A

ligase (6)

catalyzes the joining of two molecules, typically using ATP

A + B + ATP → A-B + ADP + Pi

6 Reaction Mechanisms

(ACMEPT)

acid-base catalysis

covalent catalysis

metal ion catalysis

electrostatic catalysis

proximity

transition state catalysis

acid-base catalysis

a process where proton transfer facilitates the reaction mechanism by stabilizing charged intermediates.

• a. General Acid Catalysis: An amino acid side-chain of the enzyme donates $H^+$ to the substrate. Commonly used: Lys, Tyr, Arg, Cys.

• b. General Base Catalysis: An amino acid side-chain of the enzyme abstracts $H^+$ from the substrate. Commonly used: Glu, Asp, His.

covalent catalysis

an amino acid side-chain of the enzyme forms a covalent bond with the substrate

metal ion catalysis

metal ion binds substrate to stabilize negative charge

electrostatic catalysis

charged amino acid side-chain of enzyme stabilizes opposite charge on substrate

proximity and orientation effect

two substrates are brought close enough and properly oriented to each other to react

catalysis via preferential transition state binding

binding to the enzyme allows the substrate to adopt a transition state conformation, making the reaction easier

Michaelis-Menten Reaction Equation

$$[E]_t = [E] + [ES]$$

Types of Inhibition based on the Lineweaver-Burke Plot

Competitive, Uncompetitive, and Noncompetitive

Reaction Rate

the change in concentration per unit time

Competitive Inhibition

effector binds to the free enzyme and blocks the active site so that the substrate cannot bind

Uncompetitive Inhibition

effector binds at the allosteric site and slows down the reaction

Noncompetitive Inhibition

effector binds either the E or ES at an allosteric site, slowing the reaction

Carbohydrate

monomeric or polymeric polyhydroxylated aldehyde or ketone

aldose

sugar with an aldehyde group

ketose

sugar with a ketone group

sugar acids

sugar with a carboxylic acid group (two types: aldonic and uronic acids)

aldonic acid

Carboxylic acid at C1

uronic acid

Carboxylic acid at last carbon

Mutarotation

change of rotation of plane-polarized light during interconversion of anomeric forms in solution

pyranose

6-membered ring form

furanose

5-membered ring form

anomers

stereoisomers that differ in orientation about the anomeric carbon , where one is typically a carbohydrate's cyclic form and the other its open-chain form. e

epimers

steroisomers that differ at any non-anomeric carbon

monosaccharides are…

polar and capable of hydrogen bonding

Glycosylation

reaction of sugar with alcohols yielding glycosidic linkages

5 Key sugars

(GMRGF)

Glucose

Mannose

Ribose

Galactose

Fructose

Glucose

Mannose

Ribose

Galactose

Fructose

2 Classifications of Polysaccharides

Structural and Storage

(STORE SG, STRIKE CC)

Storage polysaccharides

starch and glycogen

Structural polysaccharides

Cellulose, Chitin, and acidic polysaccharides

Glycolysis

conversion of hexoses into trioses with ATP production

Glycogenolysis

degradation of glycogen into glucose for glycolysis, primarily in the muscles and liver

Pentose Phosphate Pathway

degradation of glycolytic metabolites yielding NADPH and carbohydrate byproducts

Gluconeogenesis

construction of glucose from small molecules

Glycogenesis

creation of glycogen

What are the 3 Catabolic Pathways in Carbohydrate Metabolism?

(LYSIS)

Glycolysis
Glucogenolysis
Pentose Phosphate Pathway

What are the 3 Anabolic Pathways in Carbohydrate Metabolism?

(GENESIS)

Gluconeogenesis

Glycogenesis

Pentose Phosphate Pathway

Of the methods of carbohydrate metabolism, which process can serve both anabolic and catabolic functions?

The Pentose Phosphate Pathway is unique as it can serve both anabolic functions, such as nucleotide synthesis, and catabolic functions, such as generating NADPH for cellular processes.

Glycolysis has ___ phases

2

Phase 1 of Glycolysis

glucose splits into two trioses, utilizing 2 ATP

Phase 2 of Glycolysis

conversion of two trioses into pyruvate, generating 4 ATP

What are the enzymes, in order, of Glycolysis?

(HPPATGPPEP)
(“Harry Potter Pirated All The Goods!” Pleaded Eunice Politely)

(2.7, 5.3, 2.7, 4.1, 5.3, 1.2, 2.7, 5.4, 4.2, 2.7)

Hexokinase - 2.7

Phosphoglucoisomerase -b 5.3

Phosphofructokinase - 2.7

Aldolase - 4.1

Triose Phosphate Isomerase - 5.3

Glyceraldehyde-3-phosphate dehydrogenase - 1.2

Phosphoglycerate kinase - 2.7

Phosphoglycerate mutase - 5.4

Enolase - 4.2

Pyruvate kinase - 2.7

Hexokinase

Enzyme 1 - costs 1 ATP to place phosphate on glucose via SN2

Phosphoglucoisomerase

Enzyme 2 - Catalyzes isomerization via enediol/enediolate intermediates

Phosphofructokinase-1

Enzyme 3 - adds a phosphate to F6P

Aldolase

Enzyme 4 - cleaved F-1,6-bisphosphate into DHAP and G3P

Triose Phosphate Isomerase

Enzyme 5 - interconverts DHAP to G3P

glyceraldedehyde-3-phosphate dehydrogenase

enzyme 6 - catalyzes the conversion of G3P to 1,3-bisphosphoglycerate, reducing NAD+ to NADH in the process.

phosphoglycerate kinase

enzyme 7 - produces ATP from 1,3-bisphosphoglycerate

phosphoglycerate mutase

enzyme 8 - catalyzes the conversion of 2-phosphoglycerate

Enolase

enzyme 9 - catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate, releasing water in the process.

pyruvate kinase

enzyme 10 - forms pyruvate and ATP.

3 Regulatory Enzymes in Glycolysis

Hexokinase, Phosphofructokinase-1, and Pyruvate Kinase

How does Hexokinase regulate Glycolysis?

prevents glucose from leaving the cell and inhibits its own activity when glucose-6-phosphate levels are high.

How does Pyruvate Kinase regulate Glycolysis?

it is inhibited by ATP and alanine and activated by F1,6BP via feedforward activation

Gluconeogenesis is the reverse of…

Glycolysis

what are the key enzymes of gluconeogenesis?

(PPFG)

(Power PuFf Girls!)

Pyruvate Carboxylase

Phosphoenolpyruvate Carboxykinase

Fructose 1,6 bisphosphate

Glucose-6-Phosphatase

Pyruvate Carboxylase in Gluconeogenesis

converts pyruvate into oxaloacetate; activated by acetyl-CoA

Phosphoenolpyruvate Carboxykinase in Gluconeogenesis

converts oxaloacetate to phosphoenolpyruvate

Fructose-1,6-Bisphosphate in Gluconeogenesis

critical regulatory step inhibited by AMP and F2,6BP

Glucose-6-Phosphatase in Gluconeogenesis

final step; high Km for G6P

What enzyme ensures that gluconeogenesis only occurs when G6P levels are high?

Glucose-6-Phosphatase

What are the important enzymes in Glycogenolysis?

(GPG)

(gloopy puppies glide)

Glycogen Phosphorylase

Phosphoglucomutase

Glycogen Debranching Enzyme

Draw out all of Glycolysis

see image