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Vocabulary flashcards covering amino-acid chemistry, protein structure, folding, functions, laboratory techniques, and related genetic diseases.
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Central Dogma of Biology
Flow of genetic information: DNA → (transcription) mRNA → (translation) protein
Amino Acid (AA)
Basic unit of proteins; contains central (α) carbon, amino group, carboxyl group, hydrogen, and variable R-group
R-Group (Side Chain)
Variable chemical group of an amino acid that dictates its size, charge, polarity, and function
Zwitterion
Molecule with both positive (NH3⁺) and negative (COO⁻) charges that exists at physiological pH
Chiral α-Carbon
Four different substituents around the α-carbon; all amino acids are chiral except glycine
L-Isomer
Naturally occurring stereochemistry of proteinogenic amino acids
pKa (α-COOH)
≈ 2; pH where the carboxyl group is 50 % dissociated
pKa (α-NH3⁺)
≈ 9–10; pH where the amino group is 50 % protonated
Selenocysteine (Sec)
21st amino acid; Se-containing analogue of cysteine inserted at UGA codons via SECIS element; pKa ≈ 5.2
Proteinogenic Amino Acids
The 20 standard α-amino acids encoded directly by the genetic code (plus Sec in special cases)
Positively Charged AAs
Lysine, Arginine, Histidine (protonated side chains at pH 7.4)
Negatively Charged AAs
Aspartic acid and Glutamic acid (deprotonated carboxylate side chains at pH 7.4)
Polar Uncharged AAs
Serine, Threonine, Asparagine, Glutamine, Cysteine, Tyrosine
Hydrophobic AAs
Non-polar side chains such as Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline, Glycine
Neurotransmitter-Precursors
Glu, Gln, Trp (→ serotonin), Tyr (→ catecholamines) serve neuronal roles
Non-protein Amino Acids
e.g., Ornithine, Citrulline (urea cycle) and GABA (neurotransmitter) not incorporated into proteins
Physiological Plasma AA Level
0–750 µM; glutamine is most abundant (~500 µM in adults)
Peptide Bond
Amide linkage between COOH of one AA and NH₂ of another; planar, partial double-bond character
Primary Structure
Linear sequence of amino acids written N-terminus → C-terminus
Conservative Substitution
A mutation replacing an AA with one of similar properties, generally retaining protein structure/function
Missense Mutation
Point mutation changing one amino acid to another; may alter protein function
Nonsense Mutation
Codon changed to stop signal, resulting in premature termination
Frameshift Mutation
Insertion/deletion altering reading frame, generating abnormal protein
Secondary Structure
Regular patterns (α-helix, β-sheet, β-turn) stabilized by backbone hydrogen bonds
α-Helix
Right-handed coil; 3.6 AAs per turn; H-bond between C=O of residue i and NH of i+4
β-Sheet
Extended strands linked by inter-strand H-bonds; can be parallel or antiparallel
β-Turn (β-Bend)
Four-residue motif reversing polypeptide direction; often contains Pro and Gly
Coiled-Coil
Super-secondary structure of 2–7 α-helices wound together; common in fibrous proteins
Proline Effect
Cyclic AA that breaks α-helices when internal but can initiate/terminate helices or form turns
Disulfide Bond
Covalent –S–S– link formed by oxidation of two cysteines; stabilizes tertiary/quaternary structure (cystine)
Random Coil
Unordered peptide regions lacking stable secondary structure; common in flexible proteins
Tertiary Structure
Three-dimensional folding of a single polypeptide driven by R-group interactions (hydrophobic, H-bonds, ionic, disulfide)
Quaternary Structure
Association of multiple polypeptide chains (subunits) via non-covalent forces; e.g., hemoglobin
Molecular Chaperone
Protein (e.g., HSP70/90) that assists folding/refolding and prevents aggregation
Ubiquitin-Proteasome System
Pathway that tags misfolded proteins with ubiquitin for proteasomal degradation
Post-translational Modification
Covalent change after translation (phosphorylation, acetylation, methylation, glycosylation, hydroxylation)
Globular Protein
Compact, water-soluble proteins (enzymes, hemoglobin, albumin)
Fibrous Protein
Elongated, structural proteins with repeating motifs (collagen, keratin, elastin)
Integral Membrane Protein
Protein embedded in lipid bilayer; often α-helical or β-barrel domains
Peripheral Membrane Protein
Protein loosely attached to membrane surface via non-covalent interactions
GPI Anchor
Glycosylphosphatidylinositol lipid tether that attaches proteins to outer leaflet of plasma membrane
Collagen
Triple-helical fibrous protein rich in Gly-Pro-(Hyp/Lys); major component of ECM and bone
Myoglobin (Mb)
Monomeric oxygen-storage protein in muscle; 16 kDa, high O₂ affinity
Hemoglobin (Hb)
Tetrameric protein in RBCs transporting O₂ & CO₂; exhibits cooperative binding (T↔R states)
Sickle Cell Anemia
β-globin E6V mutation (HbS) causing Hb polymerization and RBC deformation
Thalassemia
Reduced synthesis of α- or β-globin chains leading to anemia; severity depends on gene deletions
Cystinuria
rBAT transporter mutations causing cystine accumulation and kidney stones
Osteogenesis Imperfecta
COL1A1/COL1A2 mutations → defective collagen; brittle bones, blue sclera
Ehlers-Danlos Syndrome
Mutations (often COL5A1/2) impair collagen crosslinking; hyperextensible skin & joints
Marfan Syndrome
FBN1 mutations → abnormal fibrillin-1; tall stature, aortic aneurysm, lens dislocation
Charcot–Marie–Tooth Disease
Peripheral neuropathy from mutations in myelin (PMP22) or axonal proteins; muscle weakness
Lesch–Nyhan Syndrome
HPRT1 deficiency disrupting purine salvage → uric acid overproduction, self-mutilation
Amyloid β (Aβ)
Peptide from APP that forms β-sheet fibrils deposited in tissues (amyloidosis, Alzheimer’s)
Tau Protein
Microtubule-binding protein; hyperphosphorylation causes neurofibrillary tangles in Alzheimer’s
Huntingtin (Htt)
Protein with poly-glutamine (poly-Q) tract; expansions >36 repeats cause Huntington’s disease
α-Synuclein
Neuronal protein; aggregates into Lewy bodies in Parkinson disease
Prion Protein (PrP)
Normal PrPᶜ converts to β-rich PrPˢᶜ, causing transmissible spongiform encephalopathies
Misfolded Protein Aggregation
Improperly folded proteins form β-pleated fibrils leading to disease; can be stress-induced
Salivary α-Amylase
496-AA (glycosylated) enzyme that initiates starch digestion; catalytic triad Asp197, Glu233, Asp300
Mucins
Highly glycosylated PTS-rich salivary proteins providing lubrication and forming protective pellicle
Statherin
Unstructured salivary protein that binds hydroxyapatite to inhibit enamel demineralization
Histatins
Histidine-rich cationic salivary peptides with potent antifungal and antibacterial activity
Nitric Oxide Synthesis
Arginine is substrate for NO production, promoting vasodilation and cardiovascular health
Glutathione
Tripeptide (Glu-Cys-Gly) acting as major cellular antioxidant
Proline-Rich Proteins
Salivary proteins and collagen segments where Pro promotes turns and helices initiation
Denaturation
Loss of native protein conformation due to heat, pH, solvents; may be reversible (renaturation)
SDS-PAGE
Lab technique that denatures proteins, masks charge, and separates them by size in polyacrylamide gel
Western Blot
Method to detect specific proteins after SDS-PAGE using antibodies
ELISA
Enzyme-linked immunosorbent assay for quantitative protein detection in solution
Hydroxylation
Post-translational addition of –OH to Pro/Lys in collagen, enhancing tensile strength
Phosphorylation
Addition of phosphate (Ser, Thr, Tyr) that often activates or deactivates enzymes
Acetylation (Histones)
Addition of acetyl groups to Lys residues, loosening chromatin and promoting transcription
Glycosylation
Attachment of sugar chains to Asn (N-linked) or Ser/Thr (O-linked) for folding and cell recognition
Hydrophobic Interaction
Non-polar side chains cluster internally, driving protein folding
Electrostatic (Salt Bridge)
Attraction between oppositely charged side chains stabilizing tertiary/quaternary structure
Eero Mäntyranta Case
EPOR truncation increased RBC production, enhancing athletic endurance
Hemoglobin R State
Relaxed conformation with high oxygen affinity
Hemoglobin T State
Tense conformation with low oxygen affinity; stabilized by 2,3-BPG
Proteasome
ATP-dependent complex that degrades ubiquitinated proteins into peptides
Heat Shock Proteins (HSPs)
Stress-induced chaperones that refold proteins and maintain proteostasis
β-Barrel
Transmembrane β-sheet cylinder forming channels in outer membranes
G-Protein-Coupled Receptor (GPCR)
7-helix integral membrane protein that transduces extracellular signals via G-proteins
Complement System
20-protein cascade activated during infection to destroy pathogens
Immunoglobulins (IgG, IgA, IgM)
Antibodies constituting ~38 % of serum proteins, providing adaptive immunity
Ferritin
Iron-storage protein releasing iron when needed
Albumin
Major plasma protein (~55 %) maintaining oncotic pressure and transporting molecules