Molecules in Medicine 2 — MDSA 20210 Review Flashcards

Vocabulary-style flashcards covering Amino Acids, Protein Structure, DNA, Metabolism of Nitrogen and Lipids, based on exam MCQ concepts.

Glycine

The only achiral amino acid because its R group is $H$, meaning the $\alpha$-carbon has only 3 different groups.

Hydrophobic amino acids

Amino acids such as Valine, Leucine, Isoleucine, and Phenylalanine that are typically buried inside globular proteins away from aqueous solutions.

Cysteine

An amino acid containing a sulfhydryl ($-SH$) group that can form covalent disulphide bonds ($S-S$ bridges) to stabilize protein structure.

Asparagine and Glutamine

Amino acids characterized by having an amide group in their side chains ($Asn = -CH_2CONH_2$, $Gln = -CH_2CH_2CONH_2$).

Basic amino acids

Histidine, Lysine, and Arginine; Histidine is polar and basic because it can be protonated at physiological pH.

Peptide bond

A covalent linkage formed by condensation (loss of $H_2O$) between the carboxyl group of one amino acid and the $\alpha$-amino group of another.

$\alpha$-helix

A right-handed secondary protein structure with $3.6$ residues per turn, stabilized by H-bonds between backbone $-NH$ and $-C=O$ groups.

Tertiary structure

The three-dimensional folding of a protein driven primarily by hydrophobic interactions, burying nonpolar residues in the core.

Quaternary structure

The association of multiple polypeptide subunits through non-covalent bonds like H-bonds, ionic interactions, and hydrophobic forces.

$Glu \rightarrow Lys$ mutation

A drastic change in protein structure where an acidic (negatively charged) residue is replaced by a basic (positively charged) one.

Collagen stabilization

Stabilized by H-bonds and covalent cross-links between Lysine and hydroxyLysine, but notably contains no disulphide bridges.

DNA base pairing

Adenine pairs with Thymine via 2 H-bonds; Guanine pairs with Cytosine via 3 H-bonds.

Watson-Crick DNA model

Antiparallel strands with a sugar-phosphate backbone on the outside and nitrogenous bases stacked on the inside; 34\,\text{Å} per turn.

DNA Melting temperature ($T_m$)

The temperature at which DNA strands separate, which is linearly related to $G+C$ content due to having more H-bonds.

Semiconservative replication

Mode of DNA replication where each new duplex contains one parental strand and one newly synthesized strand.

DNA polymerase primer

A short RNA oligonucleotide with a $3'-OH$ group required for DNA polymerase to begin synthesis; synthesized by primase.

Okazaki fragments

Short fragments of DNA synthesized discontinuously on the lagging strand during DNA replication.

Telomerase

The enzyme responsible for extending the ends of linear chromosomes to solve the end-replication problem.

Introns

Non-coding sequences common in eukaryotes that are removed from nuclear RNA by splicing before translation.

Urea Cycle

A five-step process in the liver (2 steps in mitochondria, 3 in cytosol) that converts toxic ammonia into urea.

Hyperammonemia

The accumulation of toxic ammonia in the blood, which is the most serious consequence of urea cycle failure.

Carbamoyl phosphate synthetase I (CPS I)

The mitochondrial enzyme in the liver that catalyzes the synthesis of carbamoyl phosphate from free $NH_3$.

Pyridoxal phosphate (PLP)

The coenzyme derived from vitamin $B_6$ required for transamination, decarboxylation, and amino group transfers.

Glutamate dehydrogenase

The enzyme that incorporates free ammonia into $\alpha$-ketoglutarate to form glutamate, or releases it during oxidative deamination.

Phenylketonuria (PKU)

A deficiency in phenylalanine hydroxylase preventing the conversion of Phenylalanine to Tyrosine, leading to mental retardation.

Maple syrup urine disease

A deficiency in branched-chain $\alpha$-keto acid dehydrogenase affecting the breakdown of Valine, Leucine, and Isoleucine.

Negative nitrogen balance

A state where urinary nitrogen excretion exceeds dietary nitrogen intake, common in starvation or illness.

Heme Synthesis

A process starting with glycine and succinyl-CoA where iron is inserted into the porphyrin ring by ferrochelatase as the final step.

Bilirubin

A yellow-orange bile pigment produced by the reduction of biliverdin by biliverdin reductase.

Uric acid

The main urinary excretion product of purine degradation in humans, produced by xanthine oxidase.

Allopurinol

A drug that inhibits xanthine oxidase to reduce uric acid production, causing patients to excrete hypoxanthine and xanthine instead.

Methotrexate

A chemotherapy drug that inhibits dihydrofolate reductase (DHFR), blocking the regeneration of THF required for purine synthesis.

Adenosine Deaminase (ADA) Deficiency

A cause of Severe Combined Immunodeficiency (SCID) where the accumulation of $dATP$ is toxic to lymphocytes.

Essential fatty acids

Linoleic acid ($\omega-6$) and $\alpha$-linolenic acid ($\omega-3$), which humans cannot synthesize because we cannot insert double bonds beyond $C9$.

Gangliosides

Sialic-acid-containing glycosphingolipids composed of NANA, hexose, a fatty acid, and sphingosine; common in nerve tissue.

Tay-Sachs disease

A lipid storage disease caused by a deficiency of hexosaminidase A, leading to the accumulation of $GM2$ ganglioside.

Lipoprotein lipase (LPL)

An enzyme on capillary endothelium activated by $apoC-II$ that hydrolyzes triacylglycerols from chylomicrons and VLDL.

Reverse cholesterol transport

The process by which HDL acquires cholesterol from tissues and returns it to the liver for excretion.

Carnitine acyltransferase I (CPT1)

The rate-limiting enzyme for $\beta$-oxidation that transports long-chain acyl-CoA into the mitochondria and is inhibited by malonyl-CoA.

Ketone bodies

Water-soluble molecules (acetoacetate, $\beta$-hydroxybutyrate) produced in the liver that serve as fuel for the brain during starvation.

Hormone-sensitive lipase

An enzyme in adipose tissue activated by glucagon/epinephrine via phosphorylation that mobilizes fat into glycerol and free fatty acids.

Acetyl-CoA carboxylase (ACC)

The rate-limiting enzyme for fatty acid synthesis that converts acetyl-CoA to malonyl-CoA using biotin, $ATP$, and $CO_2$.

HMG-CoA reductase

The rate-limiting enzyme of cholesterol synthesis that converts HMG-CoA to mevalonate and is competitively inhibited by statins.

Cyclooxygenase (COX)

An enzyme inhibited by aspirin and indomethacin to block the synthesis of prostaglandins from arachidonic acid.