CheatSheetsHero

Catalog / Biochemistry Essentials Cheatsheet

Biochemistry Essentials Cheatsheet

A concise reference for key biochemical concepts, pathways, and reactions. This cheat sheet covers essential topics for students and professionals in biochemistry and related fields, providing a quick guide to metabolic processes, enzyme kinetics, and biomolecule structures.

Macromolecule Building Blocks

Amino Acids

General Structure:

Amino acids consist of a central carbon atom bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (-H), and a unique side chain (R).

Classification:

Amino acids are classified based on their R-group properties: nonpolar, polar uncharged, positively charged (basic), and negatively charged (acidic).

Peptide Bond:

Amino acids are linked by peptide bonds, formed through dehydration synthesis between the carboxyl group of one amino acid and the amino group of another.

Essential Amino Acids:

These cannot be synthesized by the body and must be obtained from the diet. Examples include leucine, isoleucine, valine, lysine, threonine, tryptophan, phenylalanine, and methionine.

Chirality:

All amino acids, except glycine, are chiral. Only L-amino acids are found in proteins.

pKa Values:

Each amino acid has at least two pKa values, corresponding to the protonation states of the amino and carboxyl groups. Some also have a pKa for their side chain.

Nucleotides

Structure:

Composed of a nitrogenous base (adenine, guanine, cytosine, thymine, or uracil), a pentose sugar (ribose or deoxyribose), and one or more phosphate groups.

Nitrogenous Bases:

Purines (adenine and guanine) have a double-ring structure, while pyrimidines (cytosine, thymine, and uracil) have a single-ring structure.

DNA vs. RNA:

DNA contains deoxyribose and thymine, while RNA contains ribose and uracil.

Phosphodiester Bond:

Nucleotides are linked by phosphodiester bonds between the 3’-hydroxyl group of one nucleotide and the 5’-phosphate group of another.

Base Pairing:

Adenine pairs with thymine (or uracil) via two hydrogen bonds, while guanine pairs with cytosine via three hydrogen bonds.

Nucleosides:

A nucleoside consists of a nitrogenous base and a pentose sugar, but without any phosphate groups.

Carbohydrates

Monosaccharides:

Simple sugars such as glucose, fructose, and galactose. They are the building blocks of complex carbohydrates.

Disaccharides:

Composed of two monosaccharides linked by a glycosidic bond. Examples include sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (glucose + glucose).

Polysaccharides:

Complex carbohydrates made up of many monosaccharides. Examples include starch, glycogen, and cellulose.

Glycosidic Bond:

The covalent bond that joins two monosaccharides. It is formed through dehydration synthesis.

Isomers:

Carbohydrates can exist as different isomers, such as D-glucose and L-glucose, which are mirror images of each other.

Functions:

Carbohydrates serve as energy sources, structural components (e.g., cellulose in plants), and signaling molecules.

Enzyme Kinetics and Mechanisms

Michaelis-Menten Kinetics

Equation:

v = \frac{V_{max}[S]}{K_M + [S]}
where:

  • v = reaction rate
  • V_{max} = maximum reaction rate
  • [S] = substrate concentration
  • K_M = Michaelis constant

K_M:

The substrate concentration at which the reaction rate is half of V_{max}. It is a measure of the affinity of the enzyme for its substrate. A lower K_M indicates higher affinity.

V_{max}:

The maximum rate of reaction when the enzyme is saturated with substrate. It is directly proportional to the enzyme concentration.

Lineweaver-Burk Plot:

A double reciprocal plot of the Michaelis-Menten equation: \frac{1}{v} = \frac{K_M}{V_{max}} \frac{1}{[S]} + \frac{1}{V_{max}}

  • x-intercept = -\frac{1}{K_M}
  • y-intercept = \frac{1}{V_{max}}

Catalytic Efficiency:

A measure of how efficiently an enzyme converts substrate to product. Given by k_{cat}/K_M, where k_{cat} is the turnover number.

Turnover Number (k_{cat}):

The number of substrate molecules converted to product per enzyme molecule per unit of time when the enzyme is saturated with substrate. k_{cat} = V_{max}/[E]_T, where [E]_T is the total enzyme concentration.

Enzyme Inhibition

Competitive Inhibition:

Inhibitor binds to the active site, preventing substrate binding. K_M increases, V_{max} remains unchanged.

Can be overcome by increasing substrate concentration.

Uncompetitive Inhibition:

Inhibitor binds only to the enzyme-substrate complex. Both K_M and V_{max} decrease.

Cannot be overcome by increasing substrate concentration.

Noncompetitive Inhibition:

Inhibitor binds to a site distinct from the active site, affecting enzyme conformation. V_{max} decreases, K_M remains unchanged.

Cannot be overcome by increasing substrate concentration.

Mixed Inhibition:

Inhibitor can bind to either the enzyme or the enzyme-substrate complex. V_{max} decreases, and K_M may increase or decrease.

Cannot be overcome by increasing substrate concentration.

Irreversible Inhibition:

Inhibitor binds covalently to the enzyme, permanently inactivating it. Examples include nerve gases and some drugs.

Allosteric Regulation:

Regulation of an enzyme by binding an effector molecule at a site other than the enzyme’s active site. Can be activating or inhibitory.

Enzyme Mechanisms

Acid-Base Catalysis:

Enzyme uses acidic or basic amino acid side chains to transfer protons, stabilizing transition states.

Covalent Catalysis:

Enzyme forms a transient covalent bond with the substrate, creating a reactive intermediate.

Metal Ion Catalysis:

Metal ions participate in catalysis by stabilizing charged intermediates, mediating redox reactions, or acting as Lewis acids.

Proximity and Orientation Effects:

Enzymes bring substrates together in the correct orientation, increasing the frequency of collisions and facilitating the reaction.

Transition State Stabilization:

Enzymes bind and stabilize the transition state of the reaction, lowering the activation energy and accelerating the reaction.

Serine Proteases:

A family of enzymes that use a serine residue in their active site to cleave peptide bonds. Examples include chymotrypsin, trypsin, and elastase.

Metabolic Pathways

Glycolysis

Overview:

The breakdown of glucose into pyruvate, producing ATP and NADH. Occurs in the cytoplasm.

Key Enzymes:

Hexokinase/Glucokinase, Phosphofructokinase-1 (PFK-1), Pyruvate Kinase.

Regulation:

PFK-1 is the major regulatory point. Activated by AMP and fructose-2,6-bisphosphate; inhibited by ATP and citrate.

Net Products:

2 ATP, 2 NADH, 2 Pyruvate per glucose molecule.

Anaerobic Fate of Pyruvate:

In the absence of oxygen, pyruvate is converted to lactate by lactate dehydrogenase, regenerating NAD+.

Aerobic Fate of Pyruvate:

In the presence of oxygen, pyruvate is converted to acetyl-CoA, which enters the citric acid cycle.

Citric Acid Cycle (Krebs Cycle)

Overview:

A series of reactions that oxidize acetyl-CoA to carbon dioxide, producing ATP, NADH, and FADH2. Occurs in the mitochondrial matrix.

Key Enzymes:

Citrate Synthase, Isocitrate Dehydrogenase, \alpha-Ketoglutarate Dehydrogenase Complex.

Regulation:

Isocitrate Dehydrogenase is activated by ADP and inhibited by ATP and NADH.
\alpha-Ketoglutarate Dehydrogenase is inhibited by ATP, NADH, and succinyl-CoA.

Net Products:

1 ATP, 3 NADH, 1 FADH2, 2 CO2 per acetyl-CoA molecule.

Entry Point:

Acetyl-CoA, derived from pyruvate, fatty acids, and amino acids.

Intermediates:

Citrate, Isocitrate, \alpha-Ketoglutarate, Succinyl-CoA, Succinate, Fumarate, Malate, Oxaloacetate.

Oxidative Phosphorylation

Overview:

The process by which ATP is synthesized using the energy released from the electron transport chain. Occurs in the inner mitochondrial membrane.

Electron Transport Chain (ETC):

A series of protein complexes (Complex I-IV) that transfer electrons from NADH and FADH2 to oxygen, creating a proton gradient.

ATP Synthase:

An enzyme that uses the proton gradient to drive the synthesis of ATP from ADP and inorganic phosphate.

Uncouplers:

Molecules that disrupt the proton gradient, uncoupling electron transport from ATP synthesis. Examples include DNP.

Inhibitors:

Substances that block the electron transport chain at various points. Examples include cyanide (Complex IV) and rotenone (Complex I).

Net ATP Yield:

Approximately 32 ATP per glucose molecule, depending on the efficiency of the proton gradient and ATP synthase.

Lipid Metabolism

Fatty Acid Synthesis

Location:

Cytosol

Precursor:

Acetyl-CoA (transported from mitochondria via citrate shuttle)

Key Enzyme:

Acetyl-CoA Carboxylase (ACC)

Regulation:

ACC is activated by citrate and insulin, inhibited by palmitoyl-CoA and glucagon/epinephrine

Process:

Repeated addition of two-carbon units from malonyl-CoA to a growing fatty acid chain

Product:

Palmitate (C16:0), which can be further elongated and desaturated

Fatty Acid Oxidation (Beta-Oxidation)

Location:

Mitochondrial matrix

Process:

Sequential removal of two-carbon units (acetyl-CoA) from the fatty acid chain

Activation:

Fatty acids are activated by attachment to CoA, forming fatty acyl-CoA

Carnitine Shuttle:

Transports fatty acyl-CoA from the cytosol into the mitochondrial matrix

Products:

Acetyl-CoA, FADH2, NADH

Regulation:

Inhibited by malonyl-CoA (ensures that fatty acid synthesis and oxidation do not occur simultaneously)

Ketone Body Metabolism

Ketone Bodies:

Acetoacetate, 3-hydroxybutyrate, and acetone

Synthesis:

Occurs in the liver mitochondria during prolonged fasting or starvation

Precursor:

Acetyl-CoA (derived from fatty acid oxidation)

Utilization:

Used as an alternative fuel source by the brain, heart, and muscle during glucose deprivation

Ketogenesis:

The process of ketone body synthesis

Ketoacidosis:

Excessive production of ketone bodies, leading to a decrease in blood pH (occurs in uncontrolled diabetes)
Download PDF