BBL Lecture Series: Amino Acids to Clinical Case Presentations

Comprehensive vocabulary flashcards covering basic biochemistry, metabolism, molecular biology, and clinical dental applications based on the lecture transcripts.

Essential Amino Acids

Amino acids that the body cannot biochemically produce and must be obtained through the diet.

Proline

The only amino acid with an irregular cyclic structure; its nitrogen is a secondary amine, making it a rigid structure that acts as a helix breaker and cannot be a hydrogen bond donor.

Chiral

A property of molecules having four different groups covalently bonded to an alpha carbon; all naturally occurring amino acids are chiral except glycine.

Zwitterion

A molecule that contains both a positive and negative charge, such as an amino acid at physiological $pH \text{ 7.4}$, resulting in a net charge of zero.

Peptide Bond

A covalent bond formed through dehydration synthesis between the carboxylic acid of one amino acid and the amine of another; it is a rigid, resonance-stabilized hybrid that usually exists in the trans configuration.

Hydrophobic Effect

The primary force for protein folding where non-polar amino acids are sequestered into the protein interior to exclude water, thereby increasing net entropy.

Primary Structure

The linear sequence of amino acids linked by covalent peptide bonds, as dictated by the genetic code.

Ramachandran Plot

A graphic distribution of the dihedral angles $\text{phi (Φ)}$ and $\text{psi (Ψ)}$ that identifies favorable secondary structures within a protein.

Alpha Helix

A secondary structure stabilized by hydrogen bonds between the carbonyl oxygen of residue $n$ and the amide hydrogen of residue $n+4$, featuring $3.6$ residues per turn.

Tertiary Structure

The overall three-dimensional spatial arrangement of atoms in a single polypeptide chain, stabilized by weak interactions and disulfide bonds.

Quaternary Structure

The functional assembly of multiple individual polypeptide subunits held together by non-covalent forces or disulfide bonds.

Active Site

A specific crevice in an enzyme's globular structure where substrates bind via weak interactions and the catalytic biochemical reaction occurs.

Activation Energy ($E_A$)

The energy barrier required to reach the transition state of a reaction; enzymes increase reaction rates by lowering this value.

$K_M$ (Michaelis Constant)

The substrate concentration at which the reaction velocity is half of its maximum ($1/2V_{max}$), representing the apparent affinity of an enzyme for its substrate.

Competitive Inhibition

A type of inhibition where an inhibitor binds to the active site, preventing substrate binding; it increases the apparent $K_M$ while keeping $V_{max}$ constant.

Epimers

Diastereoisomers that differ in the spatial orientation of only one specific chiral center, such as D-glucose and D-galactose.

Mutarotation

The spontaneous interconversion between the alpha and beta anomers of a monosaccharide when dissolved in water to reach an equilibrium.

Glycosaminoglycans (GAGs)

Highly hydrophilic heteropolysaccharides found in the extracellular matrix that attract water to provide hydration and structural support.

Phosphofructokinase (PFK)

The key regulatory enzyme of glycolysis that catalyzes the irreversible committed step: the conversion of fructose-6-phosphate to fructose-1,6-bisphosphate.

Substrate-level Phosphorylation

The formation of ATP from ADP by the direct transfer of a phosphate group from a high-energy metabolic intermediate.

Cori Cycle

The metabolic pathway where lactate produced in muscles or RBCs is transported to the liver, converted to pyruvate, and then regenerated into glucose via gluconeogenesis.

Pyruvate Dehydrogenase Complex

A large multienzyme complex that oxidatively decarboxylates pyruvate into acetyl-CoA in the mitochondrial matrix to link glycolysis to the TCA cycle.

TCA Cycle (Citric Acid Cycle)

A sequence of reactions in the mitochondria that oxidizes acetyl-CoA into two molecules of $CO_2$, producing high-energy electron carriers (NADH and $FADH_2$) and one ATP/GTP.

Glyoxylate Cycle

A metabolic pathway found in plants and microorganisms that bypasses the decarboxylation steps of the TCA cycle to allow the net conversion of acetyl-CoA into glucose.

Proton-motive Force

The electrochemical gradient generated by the pumping of protons across the inner mitochondrial membrane, used to power ATP synthesis.

ATP Synthase

A membrane-bound enzyme (Complex V) that uses the flow of protons down their concentration gradient to catalyze the phosphorylation of ADP to ATP.

Beta Oxidation

The four-step mitochondrial pathway (oxidation, hydration, oxidation, thiolysis) that breaks down fatty acids into acetyl-CoA, NADH, and $FADH_2$.

Ketone Bodies

Water-soluble fuels (acetoacetate and hydroxybutyrate) produced by the liver from acetyl-CoA during fasting that can cross the blood-brain barrier for energy.

Lipoproteins

Complexes that transport hydrophobic lipids in the blood; LDL carries cholesterol to peripheral tissues, while HDL scavenges cholesterol to return it to the liver.

Urea Cycle

A nitrogen disposal pathway in the liver that converts toxic ammonia, derived from amino acid deamination, into non-toxic urea for excretion.

Purines

Double-ringed nitrogenous bases used in nucleic acids, specifically adenine (A) and guanine (G).

Pyrimidines

Single-ringed nitrogenous bases used in nucleic acids, specifically cytosine (C), thymine (T), and uracil (U).

Okazaki Fragments

Short DNA sequences synthesized discontinuously on the lagging strand during DNA replication because synthesis only occurs in the $5' \rightarrow 3'$ direction.

Telomerase

A specialized enzyme that extends the telomeres at the ends of linear chromosomes, preventing the loss of essential genetic information during replication.

Promoter

A specific DNA sequence, such as the TATA box in eukaryotes, that directs RNA polymerase to the site of transcription initiation.

Codon

A sequence of three nucleotides in mRNA that specifies a particular amino acid or a stop signal during translation.

Southern Blot

A laboratory technique used to detect specific DNA sequences by separating fragments via gel electrophoresis and transferring them to a solid membrane for probe hybridization.

PCR (Polymerase Chain Reaction)

A technique used to amplify specific DNA sequences through repeated cycles of denaturation, primer annealing, and elongation by DNA polymerase.

Hydroxyapatite (HAP)

The highly crystalline calcium phosphate mineral ($Ca_{10}(PO_4)_6(OH)_2$) that provides hardness to bone, enamel, and dentin.

Amelogenin

The primary protein in the enamel matrix that assembles into nanospheres to provide a scaffold for the growth and orientation of hydroxyapatite crystals.

Sjögren’s Syndrome

An autoimmune disorder characterized by the dysfunction of salivary and lacrimal glands, leading to chronic dry mouth (xerostomia) and dry eyes.

Trimethylaminuria (TMAU)

A metabolic disorder, often caused by a mutation in the $FMO3$ gene, resulting in the failure to oxidize odorous trimethylamine, causing a primary symptom of a rotting fish body odor.