Biochemistry Unit 1

Aqueous enviornment

containing water

water

• medium of life

• 70% of the human body

• universal solvent

• can act as both an acid and base

  • hydronium ion gives up a proton and water accepts proton and becomes hydronium

• neutral pH of 7

dehydration

loss of 4% of body’s water

fatal dehydration

loss of 15% of body’s water

properties of water

• interacts electrostatically with charged solutes

• high melting point, boiling point, and heat of vaporization

electronegativity

a measure of an atom’s ability to attract shared electrons to itself

• increases with a positive slope on the periodic table

  • most electronegative element = fluoride

polar molecule

part of the molecule is slightly positive while the other part is slightly negative

water polarity

• polar molecule

• oxygen “hogs” electrons from H

• Oxygen— 8 e- ; Hydrogen—1e-

hydrogen bond

electrostatic forces of attractions caused by the difference in charge between hydrogen and oxygen atoms

• bond angle between O and H is 104.5

hydrogen bond properties

• nearly tetrahedral arrangement of orbitals around oxygen — bonds with 4 neighboring water molecules

• in liquid, each molecule forms H-bond with only 3.4 other molecules

• In ice, each molecule forms bond with 4 water molecules → lattice structure

hydrophilic

• dissolves in water

• polar compounds: glucose, glycine, aspartate, lactate, glycerol

hydrophobic

• does not dissolve in water

• non-polar molecules- lipid, waxes

amphiphilic

• part hydrophilic/hydrophobic

• surfactants, detergents, phospholipids, cholesterol, fatty acids

cohesion

property of water molecules to be attracted to each other, which causes them to stick together

adhesion

property of water molecules to be attracted to molecules other than water

• meniscus

solutions

• homogenous mixture of one or more solutes dissolved in a solvent

• Solute + Solvent = Solution

• ex: blood

solute

a substance that can be dissolved into a solution by a solvent

solvent

a substance in which a solute is dissolved

stock solution

concentrated solution of a chemical substance that is used to make more dilute solutions

• N1V1 = N2V2

pH scale

• measures the amount of H+ ions in a solution

  • = -log(H+)

acid

• more H+ ions

• Few OH- ions

• Can donate a proton

base

• Less H+ ions

• More OH- ions

• Can accept a proton

buffer

a solution that resists changes in pH when an acid or base is added, even in small amounts

strong acids

completely dissociate in water

weak acids

do not ionize readily; do not completely dissociate in water

acid dissociation constant

measure of how readily an acid dissociates into ions in a solution

• higher Ka = more acidic

• lower ka= less acidic

(H3O+)(A-)/(HA)

pKa

Inherent property of a particular substance;

• a number that measures how acidic a molecule is, or provides a convenient way to compare the strengths of different acids

= -log Ka

• lower value = more acidic

• higher value = less acidic

Henderson-Hasselbach Equation

• relationship between pH and pKa

pH= pKa + log(A-/HA)

half-equivalence point

the point at which the acid and conjugate base are in balance, the pH of the solution is equal to the pKa of the acid

diastase

• mixture of amylases

• first enzyme to be discovered (1833)

enzyme

• coined by Wilhelm Kuhne (1877)

• proteins that help speed up metabolism, or the chemical reactions in our bodies

  • Catalytic power and specificity

• typically end in -ase

  • old enzymes for digestion: trypsin, chymotrypsin, pepsin

• can catalyze one reaction (urease)

• can catalyze group of reaction (chymotrypsin)

apoenzyme

enzyme without cofactor

cofactor

small molecules including metals and coenzymes

prosthetic group

tightly bound coenzymes

co-substrates

loosely bound coenzymes

oxidoreductase

• category of enzymes

• function: oxidation-reduction reactions

• ex: dehydrogenase, reductase, oxidases

• analogy: chargers/batteries (move electrons)

transferase

• category of enzymes

• function: transfers groups such as phosphate or methyl

• ex: transaminases, aminotransferase, kinase

• analogy: delivery drivers (move packages/groups)

hydrolase

• category of enzymes

• function: hydrolysis of substrate; breaks down in presence of water

• ex: lipase (breakdown fatty acids), peptidase (breakdown proteins), nuclease, phosphatase, amylase (breakdown starch)

• analogy: dish soap (cut with water)

lyase

• category of enzymes

• function: nonhydrolytic removal or addition of a group to a substrate

• ex: synthase or synthetase

• analogy: balloon twisters (break without water)

isomerase

• category of enzymes

• function: converts to isomers

• ex: glucose isomers

• analogy: interior decorators (rearrange)

ligase

• category of enzymes

• function: ligates

• ex: DNA ligase

• analogy: superglue (join molecules together)

properties of enzymes

• increases speed of reaction

• decreases activation energy

• sensitive to changes in pH and temperature

• specific for a particular reaction or class of reaction s

• does not change (or consumed)

• does not change the equilibrium position

• does not change the thermodynamics

• does not change the overall delta G

gibbs free energy

• measures the amount of energy available to make or break bonds

catalyzed reaction

• the reaction rate increases with increasing substrate concentration until a maximal velocity is reached

uncatalyzed reaction

• no saturation effect

  • would be a straight line graph

active site

a 3D cleft formed by amino acid sequence where the substrate fits and where the chemical reaction occurs

• induced fit model

kinetics

the study of rate of chemical reactions

Michaelis Menten equation

• Vo = Vmax times (S)/[(S)+(Km)]

kcat

• turnover number

• the maximum number of substrate molecules converted to product per active site per unit time

• tells how fast an enzyme works

= Vmax/enzyme concentration

Km

• how well the enzyme binds to its substrate

• the amount of substrate necessary to allow an enzyme to function at half its maximal velocity

Vmax

the maximum velocity achieved by the system, at saturating substrate concentrations

reversible enzyme inhibition

• rapid dissociation of the enzyme-inhibitor complex

• contains subgroups

  • competitive

  • uncompetitive

  • noncompetitive

irreversible enzyme inhibition

dissociates slowly from its target enzyme

• ex: drugs, penicillin, aspirin

competitive inhibitor

• a process where a molecule blocks an enzyme's active site. This inhibitor looks like the real substrate. It fights with the substrate to bind to the site.

uncompetitive inhibitor

a type of enzyme regulation where an inhibitor molecule binds only to the already formed enzyme-substrate (ES) complex, rather than to the free enzyme.

• blocks the release of substrate

noncompetitive inhibition

a type of enzyme regulation where an inhibitor binds to an allosteric site

• changes the shape of the active site

hypothyroidism

example of regulated enzyme activity.

Symptoms: fatigue, unexplained weight gain, increased sensitivity to cold, dry skin and hair

hyperthyroidism

example of regulated enzyme activity.

Symptoms: sped up metabolism, rapid heartbeat, weight loss, tremors, and heat sensitivity.

cell fear response

• cell must sense levels of molecules and adjust to actions on the fly

• ex: such as when running away from something

  • something must turn on an enzyme that breaks down stored glycogen to release glucose

  • the glycogen breakdown enzyme must be active long enough to provide necessary amount of glucose

  • then STOP, or reserves will be depleted.

enzymatic regulation

principle ways:

• allosteric control

• proteolytic activation

• reversible covalent modification—phosphorylation/dephosphorylation

• multiple forms of enzymes—isozymes

• controlling by amount of enzyme present

feedback inhibition

a cellular control mechanism where the end product of a metabolic pathway binds to an enzyme early in that same pathway to slow or stop further production.

• prevents waste

• prevents depletion (ex: production of ATP from glucose)

• prevents dangerous build-up (ex: cholesterol)

• Maintains homeostasis:

allosteric enzymes

• regulatory molecule in one part of the enzyme that can adjust the enzyme’s behavior

• have a site for an effector to bind, as well as an active site

• larger and more complex than normal enzymes

• do not follow Michaelis-Menten kinetics- SIGMOIDAL KINETICS

  • results from cooperation between enzyme subunits (time delay)

effectors

regulatory molecule that can bind reversibly, allowing them to exert/remove control as needed

ATCase

• allosterically inhibited by CTP

• Made of Aspartate and Carbamoyl

• Function: makes building blocks for DNA

• catalyzes the first step in the pyrimidine synthesis pathway that makes cytidine triphosphate (CTP)

• Activity depends on levels of different nucleotides and increasing/decreasing enzyme activity.

• inhibited by the end product of the pathway, CTP, an example of feedback inhibition

• made up of 12 polypeptide subunits (6 catalytic trimers (C) and 6 regulatory dimers (R))

  • R subunits have allosteric binding site

    • this site bind to CTP for pyrimidines or ATP for purines

T state

• less active site

• favored by CTP binding

• absence of substrate

• low affinity for substrate

• low catalytic activity

• reduces catalysis

R state

• more active state

• favored by substrate binding

• presence of substrate

• high affinity for substrate

• favors catalysis

cooperativity

a phenomenon where the binding of a ligand (like a substrate or oxygen) to one active site on a macromolecule with multiple binding sites influences the affinity of the remaining sites

negative allosteric effector

• decreases ATCase activity

• high levels of pyrimidine CTP → latches to R subunit → shifts enzyme to T state → reduces enzyme affinity for substrate

positive allosteric effector

• increases ATCase activity

• high levels of purine ATP → ATP binds to enzyme → C subunit → shifts enzyme to R-state → increases enzyme affinity for substrate

Proteolytic activation

• lysis of the peptide bond

• substrates get access to the active site only after one or more peptide bonds in the zymogen are broken

• ex: digestive proteases

  • Chymotrypsin, a protease in teh intestines, will attack the pancreas if activated too soon (if not, chronic pancreatitis)

  • Chymotrypsinogen → Trypsin (only active when active site is exposed by active site cleavage)

zymogen

enzymes that start with the covered active site

• also called proenzymes

activation of Trypsin

• pathway of digestion in the duodenum requires concurrent action of several enzymes

• zymogens must be switched on at the same time

• coordinated control by activation of this enzyme

• Enteropeptidase → trypsinogen → X → more zymogens

  • formation by enteropeptidase is the master activation step

Trypsin inhibitor

• binds so tightly to the active site that it cant progress to the transition state

• binds to any prematurely activated trypsin molecules in the pancreas or pancreatic ducts

• prevents severe damage to those tissues, which could leads to acute pancreatitis

blood clotting

• cascade of zymogen activations

• may form within the blood supply system and stop blood flow if the system is too active

  • thrombophlebitis

• Pathway: convert inactive protein (fibrinogen) → active form (fibrin)

• final product due to intrinsic and extrinsic pathway

• intrinsic- activation of factor XII

• extrinsic- by trauma, whcih releases tissue factor

phosphorylation

• kinases covalently link a phosphate group to the appropriate side

  • changes sidechain to negative

• can only be reversed by removing phosphate group by phosphatases (dephosphorylation)

Isozymes

• enzymes that differ in amino acid sequence, yet catalyze the same reaction

  • ex: Lactate dehydrogenase (LDH)

    • enzyme that catalyzes a step in anaerobic glucose metabolism + glucose synthesis

      • humans have 2 polypeptide chains for this enzyme

        • H isozyme- in heart

        • M isozyme - in muscles (skeletal)

    • increases in serum levels of H4 relative to H3M is an indication that a myocardial infarction has damaged heart muscle cells, leading to the release of cellular material

• important for diagnostics

DNA discovery

• knowledge of DNA came from its structure

• 1953, James Watson and Francis Crick through the use of Rosalind Franklin’s data

• DNA crystals, the central cross is diagnostic of a helical structure

Central Dogma

DNA → RNA → PROTEIN

• DNA strand → transcription → messenger RNA → translation → protein

Nucleotide

• 5 Carbon Sugar, a nitrogenous base, and 1+ phosphates

• 3 hydrophilic regions:

  • Phosphate group

  • sugar molecule

  • hydrophilic base edge

DNA

• lacking a 2’C OH group

• bases:

  • adenine

  • guanine

  • thymine

  • cytosine

RNA

• has a 2’C OH group

• bases:

  • adenine

  • guanine

  • uracil

  • cytosine

Purine

• adenine

• guanine

• 2 membered ring- 9’C chain

pyrimidine

• cytosine

• uracil

• thymine

• 1 membered ring- 6’C

cytosine

pyrimidine

thymine

pyrimidine

uracil

pyrimidine

adenine

purine

guanine

purine

imidazole

5 membered heterocyclic aromatic ring containing 2 nitrogen atoms

phosphodiester bond

bond between 1 sugar 3’OH and the 5’Phosphate of adjacent sugar

DNA backbone

consist of sugar and phosphate

Nucleoside

base + sugar

glycosidic bond

• N-9 of purine or N-1 of pyrimidine is attached to C’1 of sugar

nucleoside monophosphate

nucleoside diphosphate

nucleoside triphosphate

deoxyadenosine

• nucleoside nomenclature

  • can add phosphate groups after

• found in DNA

• adenine base

adenosine

• nucleoside nomenclature

  • can add phosphate groups after

• found in RNA

• adenine base

deoxyguanosine

• nucleoside nomenclature

  • can add phosphate groups after

• found in DNA

• guanine base

guanosine

• nucleoside nomenclature

  • can add phosphate groups after

• found in RNA

• guanine base