Post Midterms

Electron Transport Chain (ETC)

A series of protein complexes that transfer electrons from NADH and FADH2 to oxygen, creating a proton gradient that is used for ATP synthesis.

Oxidative Phosphorylation (OP)

The process through which ATP is produced using the proton gradient generated by the electron transport chain.

Proton Gradient

A concentration gradient of protons (H+) across the inner mitochondrial membrane, which is used to power ATP synthesis.

FADH2

Another high-energy electron carrier that contributes electrons to the electron transport chain, generated during the citric acid cycle.

Cofactors

Molecules that assist in biochemical reactions, such as NAD+ and FAD in the electron transport process.

ATP Synthase

A large membrane protein complex that synthesizes ATP from ADP and inorganic phosphate as protons flow through it.

REDOX Reactions

Chemical reactions involving the transfer of electrons, central to the function of the electron transport chain.

Proton Motive Force

The potential energy stored in the proton gradient that drives ATP synthesis.

Citric Acid Cycle

A key metabolic pathway that produces energy through the oxidation of acetyl-CoA, generating NADH and FADH2.

Nicotinamide Adenine Dinucleotide (NAD+)

Coenzyme of most dehydrogenases in glycolysis, pyruvate dehydrogenation and krebs cycle

Flavin Adenine Dinucleotide (FAS)

Coenzyme of succinate dehydrogenases (complex 2/enzyme in citric acid cycle)

Mitochondrion

Double-membrane structure, made up of an outer membrane, inter membrane space, inner membrane, and matrix

Pyruvate

End product of glycolysis that can enter the mitochondria under aerobic conditions.

Krebs Cycle (TCA Cycle)

Final common pathway for the oxidation of fuel molecules, operating in the mitochondrial matrix under aerobic conditions.

Acetyl-CoA

Product formed from the oxidation of pyruvate by the pyruvate dehydrogenase complex (PDH).

Pyruvate Dehydrogenase Complex (PDH)

Multi-enzyme complex responsible for the conversion of pyruvate into acetyl-CoA, involving oxidative decarboxylation. Includes pyruvate dehydrogenase, dihydrolipoly transacetylase, and dihydrolipoamide dehydrogenase.

Isocitrate Dehydrogenase

Enzyme that catalyzes the first oxidative decarboxylation in the Krebs cycle, converting isocitrate to α-ketoglutarate.

NADH

Reduced form of NAD+, produced during various metabolic reactions as an electron carrier.

GTP

High-energy compound formed during the hydrolysis of the thioester bond in the Krebs cycle.

Oxidative Decarboxylation

The process of removing a carboxyl group and producing CO2, while also generating NADH during metabolic reactions.

Fumarate

Intermediate in the Krebs cycle, converted from succinate by succinate dehydrogenase.

Substrate Level Phosphorylation

The formation of ATP or GTP by the direct transfer of a phosphate group to ADP or GDP.

Metabolism

A collection of all biochemical reactions present within a cell or organism, consisting of catabolism and anabolism.

Catabolism

The process of breaking down biochemical fuels to extract energy, involving energy-yielding reactions.

Anabolism

The process of building up biomolecules necessary for life, involving energy-requiring reactions.

Gibbs Free Energy (ΔG)

The available energy of a substance that can be used in a chemical transformation or reaction.

Exergonic Reaction

A reaction with a ΔG < 0, indicating a loss of free energy and is spontaneous.

Endergonic Reaction

A reaction with a ΔG > 0, indicating a gain of free energy and is non-spontaneous.

Standard Free Energy Change (ΔG°)

Values for different reactions available in literature, obtained experimentally at specified conditions.

Coupling Reactions

The process of linking non-spontaneous reactions with energetically favored reactions to achieve a negative net ΔG.

Cellular Respiration

The process of oxidizing food molecules like glucose to carbon dioxide and water, generating ATP.

Glycolysis

A series of reactions converting glucose to pyruvate, producing ATP and NADH, consisting of 10 enzymatic steps.

Substrate-level phosphorylation

A method of generating ATP by transferring a phosphate group to ADP from a phosphorylated intermediate.

Alcoholic Fermentation

The breakdown of pyruvate to alcohol and carbon dioxide in yeast and other microorganisms when oxygen is scarce.

ATP

A high-energy molecule that provides energy for cellular processes.

Biochemical Reaction

A chemical reaction that takes place inside living organisms, often involving the transformation of substrates into products.

Lactate

The product formed when pyruvate is converted in muscle cells under anaerobic conditions, causing muscle fatigue.

Stage one of glycolysis

Energy investment phase (reactions 1-5), glucose cleaved to yield 2 glyceraldehyde-3-phosphates, consumes 2 ATP

Stage two of glycolysis

Energy payoff phase (reactions 6-10), converts glyceraldehyde-3-phosphates to pyruvate, produces 4 ATP and 2 NADH.

Glycosidic Bond

The bond formed between monosaccharides to create disaccharides or polysaccharides.

Reducing Sugar

A sugar that can donate electrons to a chemical reaction, identified by the presence of a free anomeric carbon. Any sugar containing a hemiacetal

Maltose

A disaccharide formed from two glucose molecules linked by an α-1,4 glycosidic bond.

Lactose

A disaccharide composed of glucose and galactose, linked by a β-1,4 glycosidic bond.

Non-reducing Sugar

A sugar that does not have a free anomeric carbon and cannot act as a reducing agent. 2 sugars can be joined via a glycosidic bond between two anomeric carbons

Raffinose

A trisaccharide composed of galactose, glucose, and fructose.

Polysaccharides

Carbohydrates consisting of many monosaccharide units, can be homopolymers or heteropolymers.

Starch

A polysaccharide used as energy storage in plants, consisting of amylose and amylopectin.

Cellulose

A structural polysaccharide in plant cell walls, formed by β-1,4 glycosidic bonds and indigestible by humans.

Chitin

A polysaccharide that is a primary component of the exoskeletons of insects and crustaceans, rigid and stable

Glycosaminoglycans

Negatively charged heteropolysaccharides in the extracellular matrix, involved in joint lubrication and cell communication, form a meshwork with fibrous proteins to form extracellular matrix

Agar

A branched heteropolysaccharide used in laboratories for growing bacteria and separating DNA composed of agarose and agaropectin

Glycolipids

Lipids with a covalently bonded oligosaccharide component, important in cell membranes and blood group determination.

α-D-Glucose

A specific form of glucose used in the formation of various disaccharides and polysaccharides.

β-D-Glucose

Another form of glucose that participates in the formation of disaccharides like lactose.

Glycoside

The compound produced by a glycosidic bond

Glycogen

Polysaccharide that acts as energy storage in animals

Ganglioside carbohydrates

Composition determines blood groups in vertebrates

Carbohydrates

Most abundant biomolecules on earth, produced from CO2 and H2O via photosynthesis, frequently referred to as 'sugars'.

Monosaccharides

The simplest carbohydrates, consisting of a single polyhydroxy aldehyde or ketone unit.

Epimers

Two sugars that differ in configuration at one specific carbon atom.

Anomers

Stereoisomers that differ in configuration at the anomeric carbon.

Hemiacetal

A product formed when an aldehyde reacts with an alcohol.

Mutarotation

The change in optical rotation that occurs when an anomeric carbon converts between its alpha and beta forms.

Chirality

The property of a molecule having non-superimposable mirror images.

D- and L-Configuration

Configurations based on the orientation of the hydroxyl group on the penultimate carbon

Reducing sugars

Any sugar capable of acting as a reducing agent due to having a free aldehyde or ketone group.

Fischer Projection

A two-dimensional representation of a monosaccharide's stereochemistry, chiral carbs

Haworth Projection

A three-dimensional representation of a cyclic monosaccharide structure.

Diastereomers

Stereoisomers that are not mirror images of each other, differ at one or more chiral centers and have different physical properties

Disaccharides

2 units of monosaccharides

Oligosaccharides

Short chains (3-20) of monosaccharide units

Polysaccharides

Long chains of monosaccharide units

Aldose

Carb with aldehyde functionality

Ketose

Carb with ketone functionality

D-sugar configuration

OH group of the right of the penultimate carbon

L-sugar configuration

oh group of the left of the penultimate carbon

Stereoisomerism

Same atom connectivity, different spatial arrangements

D-aldoses

Retain the D-glyceraldehyde configuration at the penultimate carbon

Anomeric carbon

Carbonyl carbon in the linear form

Alpha-anomer

An anomer where the hydroxyl group on the anomeric carbon is positioned below the plane of the sugar ring.

Beta-anomer

The anomer where the hydroxyl group at the anomeric carbon is on the same side as the C6 carbon in the cyclic form.

Chymotrypsin

A digestive enzyme produced by the pancreas that hydrolyzes the carboxyl side of peptide bonds of certain amino acids.

Hydrophobic pocket

A region in the enzyme where nonpolar amino acids cluster to help stabilize the binding of substrates.

Acylation Phase

The first phase of chymotrypsin’s mechanism where the peptide bond is cleaved and an ester linkage is formed.

Deacylation Phase

The second phase of chymotrypsin’s mechanism where the ester linkage is hydrolyzed, regenerating the nonacylated enzyme.

Reversible Inhibitor

An inhibitor that binds reversibly to an enzyme and can dissociate from the enzyme-inhibitor complex.

Competitive Inhibitor

An inhibitor that structurally resembles the substrate and competes for binding at the active site.

Uncompetitive Inhibitor

An inhibitor that binds only to the enzyme-substrate complex, preventing product formation.

Mixed (Noncompetitive) Inhibitor

An inhibitor that can bind to either the free enzyme or the enzyme-substrate complex, preventing product formation.

Irreversible Inhibitor

A compound that binds permanently to the enzyme covalently or noncovalently, resulting in a long-term reduction of enzyme activity.

Enzyme Inhibitor Examples

Molecules like Ibuprofen, Penicillin, and Lovastatin that interfere with enzymatic reactions.

Covalent Catalysis

A mechanism of enzyme activity where a transient covalent bond forms between the enzyme and substrate.

Mechanism-Based Inhibitor

An inhibitor that binds in a manner similar to the substrate and undergoes a reaction to inactivate the enzyme.

Hexokinase

A glycolytic enzyme involved in the catabolism of glucose

Group-specific reagents

Reacts with particular R-groups of amino acids

Reactive substrate analogs aka affinity labels

Structurally similar to the enzymes substrate but inhibit the enzyme by covalently modifying an amino acid in the active site

Mechanism-based (suicide) inhibitors

Enzyme binds to the inhibitor as a substrate ie. very specific binding