Biochem Exam 1

Properties of Water

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

• interacts electrostatically with charged solutes

• more than one state

Cohesion

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

Adhesion

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

Hydrogen Bonds

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

Properties of Hydrogen Bonds

• nearly tetrahedral arrangement of orbitals around oxygen

• bonds with 4 neighboring water molecules

H bonds in liquid state

each molecule forms H bond with only 3.4 other molecules

H bonds in solid state

each molecule forms bonds with 4 water molecules → lattice structure

Electronegativity

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

Polar Molecule

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

Electronegativity and Polarity

determines the polarity of a chemical bond by measuring how strongly an atom attracts shared electrons

Hydrophilic

• dissolves in water

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

Hydrophobic

• does not dissolve in water

• non-polar molecules: lipids and waxes

Amphiphilic

• part hydrophilic/hydrophobic

• surfactants, detergents, phospholipids, cholesterol, fatty acids

Solute

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

Solvent

a substance in which a solute is dissolved

Solution

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

• solute + solvent = solution

Stock Solution

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

Dilution of a stock solution

N1V1 = N2V2

pH Scale

• p = potential or power

• H = hydrogen ion concentration

• measures the amount of H+ ions in a solution

pH calculation

pH = -log[H+]

Acids

• more H+. ions

• few OH- ions

• can donate proton

Bases

• less H+ ions

• more OH- ions

• can accept a proton

Titration curve of acetic acid with NaOH

Henderson-Hasselbalch equation

pH = pKa + log[A-]/[HA]

Buffer

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

pKa

inherent property of a particular substance → a number that measures how acidic a molecule is

• pKa = -log(Ka)

Half-equivalence point

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

What are enzymes?

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

Oxidoreductase

• function: oxidation-reduction reactions

• examples: Dehydrogenase, Reductase, Oxidases

• analogy: chargers/batteries (move electrons)

Transferase

• function: transfers groups such as phosphate or methyl

• examples: Transaminases, Aminotransferase, Kinase

• analogy: delivery drivers (move packages/groups)

Hydrolase

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

• examples: Lipase (breaks down fatty acids), Peptidase (breaks down proteins), Nuclease, Phosphate, Amylase (breaks down starch)

• analogy: dish soap (cut with water)

Lyase

• function: non-hydrolytic removal or addition of a group to a substrate

• examples: Synthase, Synthetase

• analogy: balloon twisters (break without water)

Isomerase

• function: converts to isomers

• example: Glucose isomerase

• analogy: interior designer (rearranger)

Ligase

• function: that ligates

• example: DNA ligase

• analogy: superglue (join molecules together)

Holoenzyme

a complete, catalytically active enzyme composed of an inactive protein part (apoenzyme) combined with a non-protein component (cofactor)

Cofactor

small molecule including metals and coenzymes

• tightly bound coenzymes = prosthetic group

• loosely bound coenzymes = co-substrates

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 reactions

• does not change (or consumed)

• does not change the equilibrium position

• does not change the thermodynamics

• does not change the overall Δ G

Gibbs free energy (G)

measure of the amount of energy available to make or break chemical bonds

What is kcat

maximum velocity/enzyme concentration

• tells you how fast an enzyme works; it is the turnover number

Michaelis-Menten equation

What is Km

Michaelis-Menten constant

• tells you how well it binds to its substrate

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

Competitive inhibition

a process where a molecule blocks an enzyme's active site by competing directly with the normal substrate for binding

Non-competitive inhibition

a type of enzyme regulation where an inhibitor binds to an allosteric site (a spot other than the active site) with equal affinity, whether the substrate is already attached or not

Uncompetitve inhibition

a type of reversible enzyme inhibition where an inhibitor binds exclusively to the enzyme-substrate (ES) complex rather than to the free enzyme

Principle ways of enzyme regulation:

1. allosteric control

2. proteolytic activation

3. reversible covalent modification (Phosphorylation/Dephosphorylation)

4. multiple forms of enzymes - Isozymes

5. controlling by amount of enzyme present

Allosteric Enzymes

have a site for an effector to bind to, as well as the active site → larger and more complex than normal enzymes

Example of Allosteric Regulation

ATcase is inhibited by CTP (example of feedback inhibition)

Graph of Allosteric Enzymes

allosteric enzymes have sigmoidal kinetics

T state (“tense”)

• less active

• favored by CTP binding

• absence of substrate

• low affinity for substrate

• low catalytic activity

R state (“relaxed”)

• more active

• favored by substrate binding

• presence of substrate

• high affinity for substrate

Which is more energetically stable, T state or R state?

T state

Negative Allosteric Effector

• CTP

• decreases ATcase activity

Positive Allosteric Effector

• ATP

• increases ATcase activity

Zymogens

enzymes that start with the covered active site

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

Zymogens examples

trypsinogen, chymotrypsinogen, blood clotting

Trypsin

is the common activator of all the pancreatic zymogens

Trypsin Inhibitor

prevents severe damage to those tissues, which could lead to acute pancreatitis

Reversible Covalent Modification

phosphorylation and dephosphorylation

• enzymes controlled by this mechanism attach phosphate groups to amino acid side chains

Reversible Covalent Modification Examples

usually the polar but uncharged side chains of serine, threonine, or tyrosine

Isozymes

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

Isozymes Example

Lactate dehydrogenase - catalyses anaerobic glucose metabolism and glucose synthesis

Central Dogma

DNA Structure

double helix

RNA Structure

single helix

Deoxyribose

Ribose

Nucleotide

sugar + phosphate + nitrogenous base

Nucleoside

base + sugar

Purines

Adenine and Guanine

Pyrimidines

Cytosine, Thymine, Uracil

Adenine

Guanine

Cytosine

Thymine

Uracil

Phosphodiester Bond

between one sugar molecule’s 3’-OH group and the 5’-phosphate group on the adjacent sugar molecule

Base Pair Stacking

base pairs are stacked in a double helix which helps stabilize the double helix through van der waals forces

A DNA

dehydrated DNA, “right-handed”

B DNA

hydrated DNA, “right-handed”

Z DNA

forms upon methylation of deoxycytosine residues, the phosphoryl groups are zigzagged

Syn and Anti-forms of bases

• pyrimidines only allow anti-form

• purines allow both syn and anti

Tautomer

the ability of a molecule to exist in more than one chemical form

Messenger RNA (mRNA)

the template for protein synthesis or translation

Transfer RNA (tRNA)

two roles: carrying “activated” amino acids to the ribosomes for peptide bond formation and providing a decoder of the codons called anticodons

Ribosomal RNA (rRNA)

a major component of the ribosomes that provides a scaffolding where ribosomal proteins bind and form the overall structures

mRNA from DNA template

3’-CGCC GCTGCGCGTC AATTA TAC-5’ template strand DNA

5’-GCGG CGACGCGCAG UUAAU AUG-3’ mRNA

What are proteins?

the most versatile macromolecules in living systems that serve crucial functions in almost all biological processes

Amino Acid Structure

Peptide Bonds

are formed by condensation of carboxylic acids and amines; is accompanied by the loss of a water molecule

Amino Acids vary in: (due to their R groups)

• size

• charge

• shape

• Hydrogen-bonding capacity

• Hydrophobic character

• chemical reactivity

Non-polar Aliphatic R Groups

glycine, alanine, valine, leucine, isoleucine, methionine, proline

Non-polar Aromatic R Groups

phenylalanine, tyrosine, tryptophan

Glycine (G)

• simplest amino acid

• achiral

Alanine (A)

• has a CH3 methyl for its R group

Valine (V)

• branched-chain amino acid

• mostly metabolized in muscle tissues

Leucine (L)

• branched-chain amino acid

Isoleucine (I)

• branched-chain amino acid

Methionine (M)

• contains sulfur

Proline (P)

• R group bound directly to the alpha-amino group