Amino Acids, Proteins & Associated Concepts

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Vocabulary flashcards covering amino-acid chemistry, protein structure, folding, functions, laboratory techniques, and related genetic diseases.

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86 Terms

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Central Dogma of Biology

Flow of genetic information: DNA → (transcription) mRNA → (translation) protein

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Amino Acid (AA)

Basic unit of proteins; contains central (α) carbon, amino group, carboxyl group, hydrogen, and variable R-group

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R-Group (Side Chain)

Variable chemical group of an amino acid that dictates its size, charge, polarity, and function

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Zwitterion

Molecule with both positive (NH3⁺) and negative (COO⁻) charges that exists at physiological pH

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Chiral α-Carbon

Four different substituents around the α-carbon; all amino acids are chiral except glycine

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L-Isomer

Naturally occurring stereochemistry of proteinogenic amino acids

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pKa (α-COOH)

≈ 2; pH where the carboxyl group is 50 % dissociated

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pKa (α-NH3⁺)

≈ 9–10; pH where the amino group is 50 % protonated

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Selenocysteine (Sec)

21st amino acid; Se-containing analogue of cysteine inserted at UGA codons via SECIS element; pKa ≈ 5.2

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Proteinogenic Amino Acids

The 20 standard α-amino acids encoded directly by the genetic code (plus Sec in special cases)

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Positively Charged AAs

Lysine, Arginine, Histidine (protonated side chains at pH 7.4)

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Negatively Charged AAs

Aspartic acid and Glutamic acid (deprotonated carboxylate side chains at pH 7.4)

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Polar Uncharged AAs

Serine, Threonine, Asparagine, Glutamine, Cysteine, Tyrosine

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Hydrophobic AAs

Non-polar side chains such as Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline, Glycine

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Neurotransmitter-Precursors

Glu, Gln, Trp (→ serotonin), Tyr (→ catecholamines) serve neuronal roles

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Non-protein Amino Acids

e.g., Ornithine, Citrulline (urea cycle) and GABA (neurotransmitter) not incorporated into proteins

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Physiological Plasma AA Level

0–750 µM; glutamine is most abundant (~500 µM in adults)

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Peptide Bond

Amide linkage between COOH of one AA and NH₂ of another; planar, partial double-bond character

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Primary Structure

Linear sequence of amino acids written N-terminus → C-terminus

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Conservative Substitution

A mutation replacing an AA with one of similar properties, generally retaining protein structure/function

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Missense Mutation

Point mutation changing one amino acid to another; may alter protein function

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Nonsense Mutation

Codon changed to stop signal, resulting in premature termination

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Frameshift Mutation

Insertion/deletion altering reading frame, generating abnormal protein

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Secondary Structure

Regular patterns (α-helix, β-sheet, β-turn) stabilized by backbone hydrogen bonds

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α-Helix

Right-handed coil; 3.6 AAs per turn; H-bond between C=O of residue i and NH of i+4

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β-Sheet

Extended strands linked by inter-strand H-bonds; can be parallel or antiparallel

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β-Turn (β-Bend)

Four-residue motif reversing polypeptide direction; often contains Pro and Gly

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Coiled-Coil

Super-secondary structure of 2–7 α-helices wound together; common in fibrous proteins

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Proline Effect

Cyclic AA that breaks α-helices when internal but can initiate/terminate helices or form turns

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Disulfide Bond

Covalent –S–S– link formed by oxidation of two cysteines; stabilizes tertiary/quaternary structure (cystine)

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Random Coil

Unordered peptide regions lacking stable secondary structure; common in flexible proteins

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Tertiary Structure

Three-dimensional folding of a single polypeptide driven by R-group interactions (hydrophobic, H-bonds, ionic, disulfide)

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Quaternary Structure

Association of multiple polypeptide chains (subunits) via non-covalent forces; e.g., hemoglobin

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Molecular Chaperone

Protein (e.g., HSP70/90) that assists folding/refolding and prevents aggregation

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Ubiquitin-Proteasome System

Pathway that tags misfolded proteins with ubiquitin for proteasomal degradation

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Post-translational Modification

Covalent change after translation (phosphorylation, acetylation, methylation, glycosylation, hydroxylation)

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Globular Protein

Compact, water-soluble proteins (enzymes, hemoglobin, albumin)

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Fibrous Protein

Elongated, structural proteins with repeating motifs (collagen, keratin, elastin)

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Integral Membrane Protein

Protein embedded in lipid bilayer; often α-helical or β-barrel domains

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Peripheral Membrane Protein

Protein loosely attached to membrane surface via non-covalent interactions

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GPI Anchor

Glycosylphosphatidylinositol lipid tether that attaches proteins to outer leaflet of plasma membrane

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Collagen

Triple-helical fibrous protein rich in Gly-Pro-(Hyp/Lys); major component of ECM and bone

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Myoglobin (Mb)

Monomeric oxygen-storage protein in muscle; 16 kDa, high O₂ affinity

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Hemoglobin (Hb)

Tetrameric protein in RBCs transporting O₂ & CO₂; exhibits cooperative binding (T↔R states)

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Sickle Cell Anemia

β-globin E6V mutation (HbS) causing Hb polymerization and RBC deformation

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Thalassemia

Reduced synthesis of α- or β-globin chains leading to anemia; severity depends on gene deletions

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Cystinuria

rBAT transporter mutations causing cystine accumulation and kidney stones

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Osteogenesis Imperfecta

COL1A1/COL1A2 mutations → defective collagen; brittle bones, blue sclera

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Ehlers-Danlos Syndrome

Mutations (often COL5A1/2) impair collagen crosslinking; hyperextensible skin & joints

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Marfan Syndrome

FBN1 mutations → abnormal fibrillin-1; tall stature, aortic aneurysm, lens dislocation

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Charcot–Marie–Tooth Disease

Peripheral neuropathy from mutations in myelin (PMP22) or axonal proteins; muscle weakness

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Lesch–Nyhan Syndrome

HPRT1 deficiency disrupting purine salvage → uric acid overproduction, self-mutilation

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Amyloid β (Aβ)

Peptide from APP that forms β-sheet fibrils deposited in tissues (amyloidosis, Alzheimer’s)

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Tau Protein

Microtubule-binding protein; hyperphosphorylation causes neurofibrillary tangles in Alzheimer’s

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Huntingtin (Htt)

Protein with poly-glutamine (poly-Q) tract; expansions >36 repeats cause Huntington’s disease

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α-Synuclein

Neuronal protein; aggregates into Lewy bodies in Parkinson disease

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Prion Protein (PrP)

Normal PrPᶜ converts to β-rich PrPˢᶜ, causing transmissible spongiform encephalopathies

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Misfolded Protein Aggregation

Improperly folded proteins form β-pleated fibrils leading to disease; can be stress-induced

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Salivary α-Amylase

496-AA (glycosylated) enzyme that initiates starch digestion; catalytic triad Asp197, Glu233, Asp300

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Mucins

Highly glycosylated PTS-rich salivary proteins providing lubrication and forming protective pellicle

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Statherin

Unstructured salivary protein that binds hydroxyapatite to inhibit enamel demineralization

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Histatins

Histidine-rich cationic salivary peptides with potent antifungal and antibacterial activity

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Nitric Oxide Synthesis

Arginine is substrate for NO production, promoting vasodilation and cardiovascular health

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Glutathione

Tripeptide (Glu-Cys-Gly) acting as major cellular antioxidant

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Proline-Rich Proteins

Salivary proteins and collagen segments where Pro promotes turns and helices initiation

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Denaturation

Loss of native protein conformation due to heat, pH, solvents; may be reversible (renaturation)

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SDS-PAGE

Lab technique that denatures proteins, masks charge, and separates them by size in polyacrylamide gel

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Western Blot

Method to detect specific proteins after SDS-PAGE using antibodies

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ELISA

Enzyme-linked immunosorbent assay for quantitative protein detection in solution

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Hydroxylation

Post-translational addition of –OH to Pro/Lys in collagen, enhancing tensile strength

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Phosphorylation

Addition of phosphate (Ser, Thr, Tyr) that often activates or deactivates enzymes

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Acetylation (Histones)

Addition of acetyl groups to Lys residues, loosening chromatin and promoting transcription

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Glycosylation

Attachment of sugar chains to Asn (N-linked) or Ser/Thr (O-linked) for folding and cell recognition

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Hydrophobic Interaction

Non-polar side chains cluster internally, driving protein folding

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Electrostatic (Salt Bridge)

Attraction between oppositely charged side chains stabilizing tertiary/quaternary structure

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Eero Mäntyranta Case

EPOR truncation increased RBC production, enhancing athletic endurance

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Hemoglobin R State

Relaxed conformation with high oxygen affinity

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Hemoglobin T State

Tense conformation with low oxygen affinity; stabilized by 2,3-BPG

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Proteasome

ATP-dependent complex that degrades ubiquitinated proteins into peptides

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Heat Shock Proteins (HSPs)

Stress-induced chaperones that refold proteins and maintain proteostasis

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β-Barrel

Transmembrane β-sheet cylinder forming channels in outer membranes

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G-Protein-Coupled Receptor (GPCR)

7-helix integral membrane protein that transduces extracellular signals via G-proteins

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Complement System

20-protein cascade activated during infection to destroy pathogens

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Immunoglobulins (IgG, IgA, IgM)

Antibodies constituting ~38 % of serum proteins, providing adaptive immunity

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Ferritin

Iron-storage protein releasing iron when needed

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Albumin

Major plasma protein (~55 %) maintaining oncotic pressure and transporting molecules