Biochemistry Final Exam Review

Buffer pH

pH = pka + log (base/acid)

ΔE° using half-reactions

ΔE°= E° (reduction) - E° (oxidation)

ΔG° from half-reactions

ΔG° = 2.303 x RT x log ([Ain/Aout])

Alanine

Ala, A

Arginine

Arg, R

Asparagine

Asn, N

Aspartic acid

Asp, D

Cysteine

Cys, C

Glutamic acid

Glu, E

Glutamine

Gln, G

Glycine

Gly, G

Histidine

His, H

Isoleucine

Ile, I

Leucine

Leu, L

Lysine

Lys, K

Methionine

Met, M

Phenylalanine

Phe, F

Proline

Pro, P

Serine

Ser, S

Threonine

Thr, T

Tryptophan

Trp, W

Tyrosine

Tyr, Y

Valine

Val, V

Basic amino acids

Histidine, Lysine, Arginine

Acidic amino acids

Aspartate, Glutamate, Asparagine, Glutamine

Carboxyl group pKa

2 pKa

Amino group pKa

9.5 pKa

Disulfide bond reactions

Form between two Cystine residues (-SH groups)

Hydrophobic amino acids

Val, Leu, Ile, Met, Phe, Ala, Trp

Hydrophilic amino acids (polar)

Ser, Thr, Asn, Gln, Tyr

Hydrophilic amino acids (charged acidic)

Asp, Glu

Hydrophilic amino acids (charged basic)

Lys, Arg, His

Alpha helix protein structure

3.6 AA pre turn (allows for H-bonding between C=O of 1 AA and NH of AA 3-4 apart in primary sequence)

Reducing sugar

Where the anomeric carbon has an OH group attached that can reduce other compounds

Non-reducing sugar

Do not have an OH group attached to the anomeric carbon so they cannot reduce other compounds

SDS-PAGE

Separates by size; SDS denatures and gives uniform negative charge.

Cation Exchange

Binds positively charged proteins

Size Exclusion

Larger proteins elute first

Palindromic sequences

These are sequences that read the same 5' to 3' on both strands

EcoRI

Recognizes GAATTC and cuts between G and A

BamHI

Recognizes GGATCC

HaeIII

Recognizes GGCC and creates blunt ends

Hemoglobin-oxygen binding curve

Sigmoidal shape (s-curve): due to cooperative binding

P50 value

26 mmHg (lower P50 = high affinity; higher P50 = low affinity)

Shift right (Bohr effect)

Low pH, high CO2, high temperature

Shift left

High pH, low CO2

Competitive inhibitor

Binds to active site; increases Km

Noncompetitive inhibitor

Binds elsewhere; lowers Vmax

Uncompetitive inhibitor

Binds ES complex; lowers both Km and Vmax

Stabilizing force for DNA structure

In solution

Hydrogen Bonding

Base-pair specificity

Base stacking interactions

Major stabilizing force involving Van der Waals and Hydrophobic Effects

Electrostatic Interactions

Backbone stabilization via cations, reducing phosphate repulsion

Solvent effects

Stabilize via hydration and charge

Binding affinity

How tightly the enzyme binds to the substrate

Michaelis constant (Km)

Measured value indicating enzyme binding affinity; Low Km = High affinity, High Km = Low affinity

Catalytic Efficiency

Shows how well an enzyme binds its substrates and how quickly it converts it into product (CE = kcat/Km)

Kcal/Km

Measurement for catalytic efficiency; High kcat/Km means the enzyme is very efficient

Substrate binding

The substrate binds to the enzyme's active site, forming an enzyme-substrate complex using a lock and key mechanism

Transition state Formation

Enzymes stabilize the high-energy transition state, decreasing the activation energy

Catalysis

Enzyme facilitates the conversion of substrate to product, often by participating directly in the reaction

Product release

After product forms, it has low affinity for the enzyme and is released

Hexokinase/Glucokinase

Converts glucose to glucose-6-phosphate (G6P)

Phosphoglucomutase

Isomerizes G6P to glucose-1-phosphate (G1P)

UDP-glucose pyrophosphorylase

Activates G1P with UTP to form UDP-glucose and PPi

Glycogen synthase

Rate-limiting step that adds glucose from UDP-glucose to a pre-existing glycogen primer (alpha-1,4 linkages)

Branching enzyme

Transfers terminal 6-7 glucose residues to form alpha-1,6 branches

Glycosidic bond

A covalent bond that links a carbohydrate (sugar) molecule to another

Anomeric carbon configuration

Determines if the glycosidic bond is alpha or beta

Shared intermediates in citric acid cycle and gluconeogenesis

Includes Oxaloacetate, Malate, Fumarate, Succinate, and Alpha-Ketoglutarate

PCR

Amplifies specific DNA segments, requires forward and reverse primers

DNA sequencing

Uses a single primer to synthesize a complementary strand

Reverse Transcription

Synthesizes DNA from an RNA template

Molecular Cloning

Uses primers to amplify genes with restriction sites or tags for cloning into vectors

qPCR

Uses primer and fluorescent probes or dyes to quantify DNA in real time

Fatty acid nomenclature

Includes saturated (no double bonds) and unsaturated (one or more double bonds)

Cis

H atoms on the same side of a double bond, introducing a kink and fluidizing the membrane

Trans

H atoms on opposite sides of a double bond, making it more rigid, similar to saturated fats

Fatty acid chain length

Shorter = reduce Van der Waals interactions -> increases fluidity

Degree of unsaturation

Double bonds (especially cis) introduce kinks in fatty acid chains

Effect of unsaturation on fluidity

These prevent tight packing -> increase fluidity

Temperature

High temperature -> more kinetic energy -> increased fluidity

Effect of lower temperature on fluidity

Lower temperature -> decreased movement -> decreased fluidity

Cholesterol content

Acts as a fluidity buffer, helps maintain membrane integrity and consistency across temperature changes

Cholesterol at high temperatures

Decreased fluidity by restraining lipid movement

Cholesterol at low temperatures

Prevents tight packing -> increases fluidity

Lipid Composition (head groups)

Phosphatidylethanolamine: smaller head, allows tighter packing, lower fluidity

Phosphatidylcholine

Bulkier head group -> higher fluidity

Sphingolipids

Have long, saturated chains -> reduce fluidity

Presence of Proteins

High protein content can reduce lipid mobility

Environmental and Cellular factors

pH, ion concentration, and oxidative stress can alter membrane composition or protein-lipid interactions, affecting fluidity

Acetyl-CoA

Used in Circic Acid Cycle, Ketogenesis, Cholesterol synthesis, and Fatty acid synthesis

NADH and FADH2

Used in the Electron transport chain

Propionyl-CoA

Enters TCA cycle or used in gluconeogenesis

ATP and Reducing Equivalents

Used in Gluconeogenesis, Urea Cycle, Biosynthesis, Active transport and cell signaling

Primary Active transport

Directly used ATP, moved ions/molecules against their electrochemical gradient, driven by ATP hydrolysis

Secondary Active Transport

Does not use ATP directly, uses electrochemical gradients established by primary active transport to drive transport of another molecule.

Symport

Both molecules move same direction

Antiport

Molecules move in opposite directions

Enzyme regulation based on ΔG° level

Irreversible steps are regulation targets: reactions with large negative ΔG° are typically not at equilibrium in vivo