Biochemistry and Molecular Biology Review

Vocabulary flashcards summarizing major biochemical and molecular-biology concepts, enzymes, pathways and disease terms from the lecture notes.

Hyaluronic acid

Glycosaminoglycan composed of D-glucuronic acid and N-acetyl-D-glucosamine; major component of connective-tissue proteoglycans.

Citrate synthase

Krebs-cycle enzyme that catalyzes condensation of acetyl-CoA with oxaloacetate to form citrate.

α-Ketoglutarate

Five-carbon Krebs-cycle intermediate oxidatively decarboxylated to succinyl-CoA; key amino-group acceptor in transaminations.

NAD⁺

Nicotinamide adenine dinucleotide; oxidized coenzyme reduced in many dehydrogenase reactions to NADH.

Glutamate

Amino acid that donates amino groups in transamination; precursor of α-ketoglutarate via aminotransferases.

Tyrosine

Non-essential amino acid synthesized from phenylalanine by phenylalanine hydroxylase; precursor of catecholamines.

Phenylalanine hydroxylase

Tetrahydrobiopterin-dependent enzyme converting phenylalanine to tyrosine; deficiency causes phenylketonuria.

Carnitine

Quaternary amine that shuttles long-chain fatty acyl groups across the mitochondrial inner membrane.

Myoglobin

Monomeric heme protein in muscle; stores O₂ and has Svedberg coefficient ≈1.97S.

Svedberg coefficient (S)

Sedimentation coefficient expressing a particle’s velocity in a centrifugal field; larger S indicates faster sedimentation.

Chromophore

Part of a molecule responsible for light absorption, producing color or fluorescence.

Centrifugation

Method to fractionate organelles or macromolecules based on mass and density using centrifugal force.

Gel filtration chromatography

Size-exclusion method where molecular weight determines migration through porous beads.

Affinity chromatography

Separation technique exploiting specific interactions such as antibody–antigen binding.

Leader sequence

Short N-terminal peptide or 5′ UTR nucleotide segment directing protein/RNA trafficking.

Prion

Infectious, misfolded isoform (PrP⁽ˢᶜ⁾) of host protein PrP⁽ᶜ⁾; heat- and protease-resistant.

Lactate dehydrogenase

Enzyme that reduces pyruvate to lactate while oxidizing NADH to NAD⁺.

Glycolysis

Cytosolic pathway converting glucose to pyruvate; yields ATP and NADH anaerobically.

Glucokinase

Low-affinity liver enzyme phosphorylating glucose to glucose-6-phosphate; not product-inhibited.

Pyruvate carboxylase

Biotin-dependent mitochondrial enzyme converting pyruvate to oxaloacetate; first step of gluconeogenesis.

Acetoacetic acid

Primary ketone body; precursor of β-hydroxybutyrate and acetone; cerebral fuel during fasting.

β-Oxidation

Mitochondrial degradation of fatty acids producing acetyl-CoA, NADH and FADH₂.

Porphyria

Group of disorders caused by heme biosynthesis defects; some forms cause photosensitivity ("vampire disease").

Epigenetic carcinogen

Agent inducing cancer via DNA methylation or histone modification without direct DNA damage.

Visible light wavelength

Electromagnetic spectrum region around 4×10⁻⁷–7×10⁻⁷ m (~400–700 nm).

Monochromator

Prism or diffraction grating in spectrophotometer that isolates single wavelengths.

Dialysis

Technique that removes small molecules (e.g., NaCl) from macromolecular solutions via semipermeable membrane.

Isoelectric focusing

Electrophoretic method separating proteins by isoelectric point within a pH gradient.

UV absorption

Electronic transition of π or non-bonding electrons in C=C, C=O and heteroatoms upon UV irradiation.

Beer–Lambert law

Relates absorbance (A) to concentration and path length; A=0.3 when transmittance is 50 %.

Stokes shift

Difference between longer emitted and shorter absorbed wavelengths in fluorescence.

Spectrophotometer

Instrument measuring absorbance of light at specified wavelengths across UV/Vis range.

DEAE cellulose

Diethylaminoethyl anion-exchange resin binding negatively charged proteins at given pH.

Sephadex beads

Spherical porous matrix used as stationary phase in gel filtration.

Hypsochromic effect

Shift of absorption maximum to shorter wavelength with decreased intensity.

ATP synthase

Mitochondrial F₀F₁ complex that produces ATP using proton motive force; composed of rotor and stator.

Uncoupler

Compound that forms membrane pores allowing proton re-entry, dissipating gradient and inhibiting ATP synthesis.

Oxidative decarboxylation

Reaction where carboxyl group is removed as CO₂ while reducing NAD⁺ (e.g., isocitrate → α-KG).

Citric acid cycle

Mitochondrial pathway oxidizing acetyl-CoA to CO₂, generating NADH, FADH₂ and GTP/ATP.

Pyruvate dehydrogenase complex

Multienzyme assembly converting pyruvate to acetyl-CoA; requires TPP, lipoate, FAD, NAD⁺ and CoA.

Thiamine pyrophosphate (TPP)

Vitamin B₁-derived coenzyme for decarboxylations in PDH and α-KG dehydrogenase.

Coenzyme Q10

Lipid-soluble ubiquinone shuttling electrons between complexes I/II and III in ETC.

Electron transport chain

Series of mitochondrial inner-membrane oxidoreductases (I–IV) transferring electrons to O₂.

Succinyl-CoA synthetase

Citric-cycle enzyme generating GTP/ATP via substrate-level phosphorylation from succinyl-CoA.

Lipoic acid

Disulfide-containing cofactor covalently bound in PDH/α-KG dehydrogenase; carries acyl groups.

Carnitine shuttle

Mechanism importing long-chain acyl-CoA into mitochondria via carnitine acyltransferases I & II.

β-Oxidation products

Each cycle yields 1 FADH₂, 1 NADH and 1 acetyl-CoA, shortening acyl chain by two carbons.

α-Oxidation

Peroxisomal pathway removing one carbon from branched fatty acids like phytanic acid.

Very-long-chain fatty acid

Fatty acid ≥20 carbons; initial β-oxidation occurs in peroxisomes.

Malonyl-CoA

Three-carbon donor formed by acetyl-CoA carboxylase; inhibits carnitine acyltransferase I.

Fatty acid synthase

Cytosolic multienzyme complex synthesizing palmitate from acetyl-CoA and malonyl-CoA.

Acyl carrier protein (ACP)

Phosphopantetheine-containing domain that transports growing acyl chain in fatty acid synthase.

Ketogenesis

Hepatic pathway converting acetyl-CoA to acetoacetate, β-hydroxybutyrate and acetone during fasting.

Ketone bodies

Water-soluble fuels (acetoacetate, β-hydroxybutyrate, acetone) utilized by extrahepatic tissues.

Glutamine

Amide-nitrogen donor transporting ammonia from peripheral tissues to liver or kidney.

Alanine cycle

Transports amino nitrogen from muscle to liver as alanine, regenerating glucose via gluconeogenesis.

Transamination

Reversible transfer of amino groups between amino acids and α-ketoacids using aminotransferases.

Pyridoxal phosphate

Vitamin B₆ cofactor forming Schiff base in transaminases and other amino-acid enzymes.

Urea cycle

Hepatic pathway converting ammonia and CO₂ to urea; spans mitochondria and cytosol.

Ornithine transcarbamylase

Mitochondrial urea-cycle enzyme forming citrulline from ornithine and carbamoyl phosphate.

Carbamoyl phosphate synthetase I

Mitochondrial enzyme using NH₃, CO₂ and 2 ATP to produce carbamoyl phosphate; requires N-acetylglutamate.

Homocysteine

Intermediate in methionine metabolism; elevated levels linked to cardiovascular risk.

Maple syrup urine disease

Defect of branched-chain α-ketoacid dehydrogenase causing buildup of Leu, Ile, Val metabolites.

Phenylketonuria (PKU)

Autosomal-recessive phenylalanine hydroxylase deficiency leading to Phe accumulation and cognitive impairment.

Porphyrin

Macrocyclic compound forming heme upon iron insertion; synthesized via δ-ALA pathway.

δ-Aminolevulinic acid (ALA)

First committed precursor in heme biosynthesis; two molecules condense to porphobilinogen.

Purine

Double-ring nitrogenous base such as adenine or guanine.

Pyrimidine

Single-ring nitrogenous base such as cytosine, uracil or thymine.

Ribosomal RNA (rRNA)

Structural and catalytic RNA synthesized in nucleolus; forms ribosome together with proteins.

DNA polymerase

Enzyme that synthesizes new DNA strands using dNTPs in 5′→3′ direction.

Transfer RNA (tRNA)

Adaptor RNA that carries specific amino acids to ribosome during translation.

PRPP synthetase

Enzyme producing 5-phosphoribosyl-1-pyrophosphate, the activated ribose for nucleotide synthesis.

DNA hybridization

Formation of complementary base pairs between separate DNA or DNA/RNA strands.

Polymerase chain reaction (PCR)

In vitro amplification of specific DNA segments using primers, DNA polymerase and thermal cycling.

Quantitative PCR (qPCR)

PCR variant measuring amplification in real time via fluorescent dyes or probes.

Mg²⁺ in PCR

Cofactor stabilizing primer annealing and activating DNA polymerase’s catalytic site.

Taq polymerase

Thermostable DNA polymerase from Thermus aquaticus used in standard PCR.

Touchdown PCR

Protocol starting with high annealing temperature gradually lowered to enhance specificity.

Okazaki fragment

Short DNA segment synthesized discontinuously on lagging strand during replication.

DNA primer

Short oligonucleotide providing free 3′-OH for DNA polymerase initiation.

Exon

Coding sequence retained in mature mRNA after splicing.

Hot-start PCR

Technique using inactive polymerase activated by heat to reduce nonspecific amplification.

CpG island

GC-rich genomic region near promoters where cytosine methylation regulates gene expression.

DNA methylation

Addition of methyl group to 5-cytosine, often silencing gene transcription.

Histone acetylation

Covalent addition of acetyl groups to lysines, loosening chromatin and activating transcription.

MicroRNA (miRNA)

~22-nt regulatory RNA that binds mRNA to inhibit translation or promote degradation.

Enhancer

Distal DNA element binding activator proteins to increase transcription from a promoter.

Tumor suppressor gene

Gene whose loss-of-function promotes uncontrolled cell growth (e.g., TP53, RB1).

Oncogene

Mutated or overexpressed proto-oncogene that drives malignant transformation.

p53 protein

"Genome guardian" transcription factor triggering cell-cycle arrest or apoptosis after DNA damage.

Retinoblastoma protein (Rb)

Tumor suppressor controlling G₁→S transition by binding E2F transcription factors.

Aflatoxin

Mycotoxin from Aspergillus species; liver pro-carcinogen activated by CYP450 enzymes.

Benzo[a]pyrene

Polycyclic aromatic hydrocarbon; indirect carcinogen metabolically activated to DNA-binding epoxide.

Ionizing radiation

High-energy radiation (X-rays, γ-rays) causing DNA strand breaks and mutations; established carcinogen.

Proto-oncogene activation

Conversion to oncogene via point mutation, gene amplification, or promoter/ enhancer relocation by translocation.

Epigenetic (non-genotoxic) carcinogen

Agent inducing cancer through chromatin modification, not direct DNA adduct formation.

HPV E6/E7 proteins

Human papillomavirus oncoproteins that inactivate p53 and Rb, promoting cervical cancer.

Epidermal growth factor (EGF)

Peptide hormone that binds EGFR, stimulating cell proliferation via signal cascades.

Frameshift mutation

Insertion or deletion altering triplet reading frame downstream of the change.

Silent mutation

Base change that does not alter encoded amino acid (synonymous codon); usually neutral.