Comprehensive Biochemistry and Organic Chemistry Review

Vocabulary flashcards covering amino acids, protein structure and folding, hemoglobin, lipids, enzyme kinetics, bioenergetics, metabolic pathways, and organic chemistry functional groups and mechanisms.

Zwitterion

The dipolar ionic form of an amino acid at physiological pH, carrying a positively charged amino group ($-NH_3^+$) and a negatively charged carboxyl group ($-COO^-$).

Peptide Bond

A covalent, planar bond with partial double-bond character formed between the carboxyl group of one amino acid and the amino group of another, eliminating a molecule of water ($H_2O$).

Primary Structure of Proteins

The specific linear sequence of amino acids in a polypeptide chain connected by peptide bonds, which determines all higher structural levels.

Secondary Structure of Proteins

Local, regular arrangements of the polypeptide backbone, primarily including $\text{α-helices}$ and $\text{β-sheets}$, stabilized mainly by hydrogen bonds involving the backbone.

Tertiary Structure of Proteins

The complete three-dimensional shape of a single polypeptide chain, resulting from interactions between side chain $-R$ groups such as hydrophobic interactions, hydrogen bonds, ionic bonds, van der Waals forces, and disulfide bonds.

Quaternary Structure of Proteins

The spatial arrangement and association of multiple distinct polypeptide subunits that assemble to form a single functional protein complex.

Denaturation

The disruption of a protein's normal secondary, tertiary, or quaternary three-dimensional structure without breaking its covalent peptide bonds.

Chaperone Proteins

Proteins (such as Hsp70 and Hsp90) that assist other proteins to fold correctly, maintain stability, prevent inappropriate aggregation, or refold after stress.

Chaperonins

Specialized multi-protein chaperone complexes (such as GroEL/GroES or Hsp60) that provide an enclosed, protected barrel-like environment favorable for protein folding.

Hemoglobin A (HbA)

An adult red blood cell protein composed of four polypeptide chains ($α_2β_2$) and four heme groups, capable of reversibly binding up to 4 $O_2$ molecules.

Bohr Effect

The reduction in hemoglobin's affinity for oxygen caused by increased $CO_2$ concentration and higher $H^+$ concentration (lower pH), favoring oxygen unloading in metabolically active tissues.

Methemoglobin

An altered form of hemoglobin in which the heme iron is oxidized from the functional ferrous state ($Fe^{2+}$) to the ferric state ($Fe^{3+}$), impairing oxygen binding.

Carboxyhemoglobin

Hemoglobin bound to carbon monoxide ($CO$), which binds with higher affinity than oxygen, occupying binding sites and impairing oxygen delivery to tissues.

Fetal Hemoglobin (HbF)

The tetrameric fetal oxygen-transport protein with an $α_2γ_2$ subunit structure that exhibits a higher affinity for $O_2$ than adult HbA due to weaker 2,3-BPG binding.

Myoglobin

A monomeric oxygen-binding protein found in skeletal and cardiac muscle consisting of 1 polypeptide chain and 1 heme group with a single $Fe^{2+}$ ion, displaying a hyperbolic oxygen dissociation curve.

Cytochromes

Heme-containing electron-transfer proteins in which the iron alternates between $Fe^{3+} ⇌ Fe^{2+}$, crucial for the mitochondrial electron transport chain.

Glycoproteins

Proteins containing carbohydrate groups covalently attached to their polypeptide chains, classified as N-linked (attached to Asn) or O-linked (attached to Ser or Thr).

Saturated Fatty Acids

Fatty acids containing no carbon-carbon double bonds, allowing hydrocarbon chains to pack tightly, resulting in higher melting points and solid consistency at room temperature.

Triacylglycerols

Biological lipids composed of a glycerol backbone esterified to three fatty acids, serving as the body's primary hydrophobic, energy-dense long-term energy storage form in adipose tissue.

Phospholipids

Amphipathic membrane lipids typically composed of glycerol, two fatty acid tails, a phosphate group, and a polar head group, which spontaneously form lipid bilayers in aqueous environments.

Gangliosides

Complex glycolipids containing one or more sialic acid residues, abundant in neuronal membranes; deficient degradation leads to lysosomal storage disorders like Tay-Sachs disease.

Cholesterol

The principal animal sterol containing four fused hydrocarbon rings and a hydroxyl group, serving as a membrane fluidity regulator and precursor for steroid hormones, bile acids, and vitamin D.

Enzymes

Biological catalysts, primarily globular proteins, that increase the rate of biochemical reactions by lowering activation energy ($E_a$) without being consumed or altering overall $ΔG$.

Induced-Fit Model

The model of enzyme-substrate interaction where the binding of the substrate induces a conformational change in the enzyme's active site to optimize catalytic fit and chemical reaction.

Activation Energy ($E_a$)

The minimum initial energy barrier that reactant molecules must overcome for a chemical transformation to occur.

Exergonic Reactions

Thermodynamically favorable reactions characterized by a negative change in Gibbs free energy ($ΔG < 0$) that release energy.

Endergonic Reactions

Thermodynamically non-spontaneous reactions characterized by a positive change in Gibbs free energy ($ΔG > 0$) that require an input of free energy.

Adenosine Triphosphate (ATP)

The primary energy currency of the cell, composed of adenine, ribose, and three phosphate groups, which drives endergonic cellular processes upon hydrolysis.

Catabolism

Metabolic pathways that break down complex molecules into simpler compounds, releasing free energy conserved as ATP and reduced electron carriers ($NADH$, $FADH_2$).

Anabolism

Biosynthetic metabolic pathways that construct complex cellular macromolecules from simpler precursors, requiring ATP and reducing power ($NADPH$).

Glycolysis

A 10-step cytosolic metabolic pathway that converts 1 molecule of glucose into 2 molecules of pyruvate, generating a net yield of 2 ATP and 2 NADH without requiring $O_2$ directly.

Phosphofructokinase-1 (PFK-1)

The key committed, rate-limiting regulatory enzyme of glycolysis that phosphorylates fructose-6-phosphate to fructose-1,6-bisphosphate; inhibited by ATP/citrate and activated by AMP/ADP/F-2,6-BP.

Pyruvate Dehydrogenase Complex (PDH)

A multi-enzyme mitochondrial matrix complex that oxidizes pyruvate to acetyl-CoA, producing 1 $NADH$ and 1 $CO_2$ per pyruvate molecule.

Citric Acid Cycle (Krebs Cycle)

An 8-step amphibolic metabolic pathway in the mitochondrial matrix that oxidizes acetyl-CoA to $CO_2$, producing 3 $NADH$, 1 $FADH_2$, and 1 GTP/ATP per acetyl-CoA.

Electron Transport Chain (ETC)

A series of inner mitochondrial membrane protein complexes (I–IV) and mobile carriers (CoQ, Cyt c) that transfer electrons to oxygen, pumping protons to establish a gradient.

Chemiosmosis

The process wherein the electrochemical proton gradient across the inner mitochondrial membrane drives protons through ATP synthase to catalyze ADP + $P_i → \text{ATP}$.

Lactic Acid Fermentation

An anaerobic pathway in cytosol catalyzed by lactate dehydrogenase, reducing pyruvate to lactate to regenerate $NAD^+$ so glycolysis can continue producing ATP.

Alcoholic Fermentation

An anaerobic two-step pathway in yeast converting pyruvate to acetaldehyde and then ethanol, releasing $CO_2$ and regenerating $NAD^+$.

Purine Salvage Pathway

A pathway that recycles free purine bases (hypoxanthine, guanine via HGPRT; adenine via APRT) into nucleotides, reducing de novo energy consumption.

Lesch-Nyhan Syndrome

An X-linked genetic disorder caused by severe HGPRT deficiency, leading to excessive de novo purine synthesis, hyperuricemia, gout, and severe neurological/behavioral symptoms.

Heme Synthesis

An 8-step pathway occurring partly in mitochondria and cytosol starting with glycine and succinyl-CoA; rate-limited by ALA synthase and finalized by ferrochelatase inserting $Fe^{2+}$.

Porphyrias

A group of metabolic disorders caused by enzymatic defects in the heme biosynthesis pathway, leading to accumulation of toxic porphyrin precursors.

Competitive Inhibition

Enzyme inhibition where the inhibitor competes directly with substrate for active site binding, increasing $K_m$ while leaving $V_{max}$ unchanged.

Non-competitive Inhibition

Enzyme inhibition where the inhibitor binds an allosteric site regardless of substrate presence, decreasing $V_{max}$ while leaving $K_m$ unchanged.

Uncompetitive Inhibition

Enzyme inhibition where the inhibitor binds exclusively to the enzyme-substrate ($ES$) complex, reducing both $V_{max}$ and $K_m$.

Zymogens

Inactive enzyme precursors (e.g., trypsinogen, pepsinogen) requiring selective proteolytic cleavage to become catalytically active.

Isoenzymes

Multiple structural forms of an enzyme that catalyze the same chemical reaction but differ in amino acid sequence, tissue distribution, and kinetic properties.

Reactive Oxygen Species (ROS)

Highly reactive oxygen derivatives (e.g., $O_2^{•-}$ superoxide, $H_2O_2$, $•OH$) that cause cellular damage to DNA, proteins, and lipids if not neutralized by antioxidant enzymes.

Glycogenesis

The pathway converting excess glucose into glycogen for storage in liver and muscle, catalyzed key step by glycogen synthase under insulin stimulation.

Glycogenolysis

The enzymatic breakdown of glycogen to glucose-1-phosphate in response to glucagon (liver) or epinephrine (muscle), rate-limited by glycogen phosphorylase.

Gluconeogenesis

The de novo synthesis of glucose from non-carbohydrate precursors (lactate, glycerol, amino acids) occurring primarily in the liver during fasting.

Pentose Phosphate Pathway (PPP)

A cytosolic glucose pathway that generates $NADPH$ for reductive biosynthesis/antioxidant defense and ribose-5-phosphate for nucleotide synthesis.

$$β-Oxidation$$

The mitochondrial catabolic pathway that sequentially breaks down fatty acyl-CoA molecules into acetyl-CoA, producing $NADH$ and $FADH_2$.

Ketone Bodies

Water-soluble fuel molecules (acetoacetate, $β-hydroxybutyrate$, acetone) produced by liver mitochondria from fatty-acid-derived acetyl-CoA during low carbohydrate availability.

Lipoproteins

Spherical lipid-protein complexes (Chylomicrons, VLDL, LDL, HDL) containing a hydrophobic core of TAGs/cholesteryl esters and an amphipathic coat for lipid transport in blood.

Transamination

The transfer of an $α-amino$ group from an amino acid to an $α-keto$ acid (typically $α-ketoglutarate$), catalyzed by aminotransferases requiring pyridoxal phosphate (PLP/Vitamin B6).

Urea Cycle

A hepatic pathway split between mitochondria and cytosol that converts toxic free ammonia ($NH_4^+$) into non-toxic urea for renal excretion.

Hydrocarbons

Organic compounds consisting entirely of carbon and hydrogen atoms, categorized into alkanes, alkenes, alkynes, and aromatic compounds.

Alkanes

Saturated hydrocarbons with general formula $C_n H_{2n+2}$ containing only $sp^3$-hybridized carbon single bonds ($σ$ bonds).

Alkenes

Unsaturated hydrocarbons with general formula $C_n H_{2n}$ containing a carbon-carbon double bond composed of 1 $σ$ bond and 1 $π$ bond between $sp^2$ carbons.

Alkynes

Unsaturated hydrocarbons with general formula $C_n H_{2n-2}$ containing a carbon-carbon triple bond composed of 1 $σ$ bond and 2 $π$ bonds between $sp$ carbons.

Markovnikov's Rule

Regioselectivity rule stating that in electrophilic addition of $HX$ to an unsymmetrical alkene, $H$ adds to the carbon with more hydrogen atoms to yield the more stable carbocation intermediate.

Benzene

A cyclic planar aromatic hydrocarbon ($C_6H_6$) possessing a delocalized system of 6 $π$ electrons across its ring.

Hückel's Rule

Rule stating that a planar, cyclic, continuously conjugated ring system is aromatic if it contains $4n + 2$ $π$ electrons (where $n$ is a non-negative integer).

Electrophilic Aromatic Substitution (EAS)

An organic reaction mechanism in which an electrophile replaces a hydrogen atom on an aromatic ring, passing through an arenium intermediate while preserving ring aromaticity.

Enantiomers

Stereoisomers that are non-superimposable mirror images of each other, having identical physical properties in achiral environments but opposite optical rotation.

Diastereomers

Stereoisomers that are not mirror images of one another and generally possess different physical and chemical properties.

$S_N2$ Mechanism

Bimolecular nucleophilic substitution occurring in a single concerted step via backside attack, causing complete inversion of stereochemical configuration at methyl or primary carbons.

$S_N1$ Mechanism

Unimolecular two-step nucleophilic substitution proceeding through a rate-limiting carbocation intermediate, favored by tertiary substrates.

E2 Elimination

Bimolecular concerted elimination requiring a strong base to abstract a $β-hydrogen$ while the leaving group departs, forming a C=C double bond.

E1 Elimination

Unimolecular two-step elimination proceeding through a carbocation intermediate from which a base abstracts a $β-hydrogen$ to yield an alkene.

Phenols

Aromatic compounds with a hydroxyl group directly bonded to a benzene ring ($C_6H_5OH$); substantially more acidic than alcohols due to resonance stabilization of the phenoxide ion.

Thiols

Sulfur analogues of alcohols ($R-SH$) containing a sulfhydryl group, capable of oxidation to form covalent disulfide bonds ($R-S-S-R$).

Nucleophilic Addition

The characteristic reaction of carbonyl compounds (aldehydes/ketones) where an electron-rich nucleophile attacks the electrophilic carbonyl carbon, breaking the C=O $π$ bond.

Hemiacetals

Compounds formed by nucleophilic addition of an alcohol to an aldehyde, featuring a carbon bound to $-OH$, $-OR'$, $-R$, and $-H$.

Keto-Enol Tautomerism

A constitutional isomerism equilibrium between a carbonyl compound with an $α-hydrogen$ (keto form) and an unsaturated alcohol (enol form).

Nucleophilic Acyl Substitution

The characteristic reaction of carboxylic acid derivatives ($R-CO-LG$) involving nucleophilic attack on the carbonyl carbon to form a tetrahedral intermediate followed by elimination of the leaving group.

Anomeric Carbon

The stereogenic carbon created during carbohydrate cyclization that was the electrophilic carbonyl carbon in the open-chain form.

Mutarotation

The change in specific optical rotation observed when $α$ and $β$ anomers interconvert via the open-chain form in aqueous solution until equilibrium is reached.

Reducing Sugars

Carbohydrates possessing a free hemiacetal or hemiketal anomeric carbon capable of opening to an aldehyde or ketone to act as a reducing agent.