Comprehensive Biochemistry: From Foundational Chemistry to Macromolecules

Comprehensive practice flashcards covering foundational chemistry, nucleotides, nucleic acids, mutations, protein structure, enzyme kinetics, carbohydrates, and lipid biochemistry.

What are the four most abundant chemical elements in biological matter, making up over $99\%$ of cell mass?

Carbon ($\text{C}$), hydrogen ($\text{H}$), nitrogen ($\text{N}$), and oxygen ($\text{O}$).

How do the lengths of a hydrogen bond and a covalent bond compare in liquid water?

A hydrogen bond between water molecules is approximately $0.177\,\text{nm}$, which is significantly longer and weaker than the intramolecular covalent bond length of $0.0965\,\text{nm}$.

According to Le Chatelier's principle, how does the physiological bicarbonate buffer system ($\text{HCO}_3^- + \text{H}^+ \rightleftharpoons \text{H}_2\text{CO}_3 \rightleftharpoons \text{CO}_2 + \text{H}_2\text{O}$) shift in peripheral tissues versus in the lungs?

In peripheral tissues, $\text{CO}_2$ release into the blood shifts the equilibrium toward carbonic acid and bicarbonate (to the left), whereas in the lungs, $\text{CO}_2$ exhalation shifts the equilibrium toward $\text{CO}_2$ and $\text{H}_2\text{O}$ (to the right).

What defines the buffering region on a weak acid titration curve?

The buffering region extends approximately $1\,\text{pH}$ unit above and below the weak acid's $\text{p}K_a$ (for acetic acid, between $\text{pH } 3.76$ and $\text{pH } 5.76$, centered at $\text{p}K_a = 4.76$ where $[\text{CH}_3\text{COOH}] = [\text{CH}_3\text{COO}^-]$).

What is the torsional energy difference between the staggered and eclipsed conformations of ethane?

The eclipsed conformation is $12\,\text{kJ/mol}$ higher in energy than the staggered conformation, making the staggered conformation significantly more stable.

How do configuration and conformation differ in organic stereochemistry?

Conformation describes the spatial shape of a molecule that can be altered by rotation around single bonds without breaking covalent bonds, whereas configuration describes the spatial arrangement of atoms that can only be interconverted by breaking one or more covalent bonds.

How does pharmacological activity differ between the two enantiomers of citalopram?

$(S)\text{-Citalopram}$ is therapeutically active, whereas $(R)\text{-Citalopram}$ is therapeutically inactive.

What are the three core structural components of a nucleotide, and how are their atoms numbered?

A nucleotide consists of a pentose sugar (ribose or deoxyribose), a nitrogenous base (purine or pyrimidine), and $1$ to $3$ phosphate groups. Base ring atoms use standard numbers ($1, 2, 3, \dots$), while pentose carbons are designated with prime numbers ($1', 2', 3', \dots$).

Which nitrogenous bases are classified as pyrimidines?

Cytosine, thymine (specific to DNA), and uracil (specific to RNA), each possessing a single six-membered heterocyclic aromatic ring.

What two primary physical interactions stabilize the double-stranded structure of DNA?

Hydrogen bonding between complementary bases ($\text{A}$ pairs with $\text{T}$, and $\text{G}$ pairs with $\text{C}$) and base stacking through $\pi\text{-}\pi$ interactions among adjacent aromatic rings sharing electron density.

Which scientists were awarded the 1962 Nobel Prize for discovering the structure of DNA?

James Watson, Francis Crick, and Maurice Wilkins (following the 1953 structural model published in Nature, which utilized key X-ray diffraction data collected by Rosalind Franklin).

What primary photoproducts are formed in DNA following exposure to ultraviolet (UV) radiation?

UV radiation promotes the formation of cyclobutane thymine dimers and 6-4 photoproducts between adjacent thymine bases, producing an abnormal kink in the double helix.

What chemical bases are produced when cytosine, 5-methylcytosine, adenine, and guanine undergo spontaneous deamination?

Cytosine deaminates to uracil, 5-methylcytosine deaminates to thymine, adenine deaminates to hypoxanthine, and guanine deaminates to xanthine.

What are the three fundamental rules governing DNA replication?

1. Replication is semiconservative; 2. Replication is bidirectional, originating at specific base sequence origins; 3. Synthesis proceeds strictly in the $5' \rightarrow 3'$ direction, forming a continuous leading strand and discontinuous Okazaki fragments on the lagging strand.

How do bacterial and eukaryotic ribosomes differ in their overall sedimentation coefficients and subunit compositions?

Bacterial ribosomes sediment at $70\text{S}$ (composed of $50\text{S}$ and $30\text{S}$ subunits), whereas eukaryotic ribosomes sediment at $80\text{S}$ (composed of $60\text{S}$ and $40\text{S}$ subunits).

What distinguishes conservative from non-conservative missense point mutations?

A conservative missense mutation replaces an amino acid with another from the same chemical group (likely maintaining conformation and function), while a non-conservative missense mutation replaces an amino acid with one from a different group (likely disrupting conformation and function).

What is the universal stereochemical configuration of naturally occurring standard $\alpha$-amino acids built into proteins?

They exist in the $\text{L-configuration}$ at the $\alpha$-carbon.

Which standard amino acid is achiral, and which contains an aliphatic ring bonded directly to its $\alpha$-amino nitrogen?

Glycine is the only achiral standard amino acid; proline is the only standard amino acid whose side chain forms a covalent ring with its $\alpha$-amino group.

How is cystine formed, and what role does it play in protein architecture?

Two cysteine residues undergo enzymatic oxidation of their sulfhydryl ($-\text{SH}$) groups to yield cystine linked by a covalent disulfide ($-\text{S}-\text{S}-$) bond, releasing $2\text{H}^+ + 2\text{e}^-$ to structurally cross-link and stabilize polypeptide chains.

What is a conjugated protein, and what is its non-amino acid component called?

A conjugated protein is a functional protein containing non-amino acid chemical components; each non-amino acid component is termed a prosthetic group (e.g., lipids in lipoproteins, carbohydrates in glycoproteins, heme in hemoproteins).

What are the structural dimensions and stabilization characteristics of a standard protein $\alpha$-helix?

An $\alpha$-helix completes one turn every $5.4\,\text{Å}$, encompassing $3.6$ residues per pitch, and is stabilized by intrachain hydrogen bonds aligned parallel to the helical axis.

What are the six sequential stages of collagen biosynthesis?

1. Synthesis of pro-$\alpha$ chains on rough ER ribosomes; 2. Vitamin C-dependent enzymatic hydroxylation of proline and lysine; 3. Glycosylation of hydroxylysine/hydroxyproline/threonine residues; 4. Assembly of three chains into a triple-helical procollagen via C-terminal disulfide cross-links; 5. Transport in secretory vesicles to the extracellular matrix; 6. Cleavage of terminal extensions by procollagen peptidases to yield tropocollagen, which self-assembles into cross-striated fibrils.

How do the oxygen-binding curves of myoglobin and hemoglobin reflect their distinct physiological roles?

Myoglobin exhibits a hyperbolic curve indicating high oxygen affinity at low $\text{pO}_2$ (ideal for muscle oxygen storage), whereas hemoglobin exhibits a sigmoidal curve demonstrating positive cooperativity and lower affinity at low $\text{pO}_2$ (ideal for oxygen loading in the lungs and delivery to tissues).

How does an enzyme accelerate the rate of a chemical reaction?

An enzyme lowers the activation energy ($\Delta G^\ddagger$) for reaching the transition state ($\Delta G^\ddagger_{cat} < \Delta G^\ddagger_{uncat}$) without altering the ground states of substrate or product or shifting the overall equilibrium ($\Delta G^{\circ\prime}$).

In Michaelis-Menten kinetics, what does the constant $K_m$ signify?

$K_m$ is the substrate concentration at which the initial velocity is half of the maximal velocity ($\frac{1}{2}V_{max}$); a lower $K_m$ value indicates a higher binding affinity of the enzyme for its substrate.

Which aldoses are the C-2 and C-4 epimers of D-glucose?

D-Mannose is the C-2 epimer of D-glucose, differing solely in the configuration at carbon 2, while D-galactose is the C-4 epimer of D-glucose, differing solely at carbon 4.

What chemical reaction produces the cyclic $\alpha$ and $\beta$ anomers of D-glucose?

An intramolecular nucleophilic attack of the C-5 hydroxyl group on the C-1 aldehyde carbon forms a cyclic hemiacetal, converting C-1 into a new chiral anomeric carbon with either an $\alpha$ (hydroxyl facing down) or $\beta$ (hydroxyl facing up) orientation.

What are the monomeric components and glycosidic linkage of sucrose?

Sucrose ($\alpha\text{-D-glucopyranosyl } \beta\text{-D-fructofuranoside}$) consists of glucose and fructose linked by an $\alpha 1 \leftrightarrow 2 \beta$ glycosidic bond joining both anomeric carbons.

Why is sucrose a non-reducing sugar, whereas maltose and lactose are reducing sugars?

In maltose and lactose, one sugar retains a free hemiacetal anomeric carbon capable of mutarotating to an open chain with an oxidizable aldehyde that reduces $\text{Cu}^{2+}$. In sucrose, both anomeric carbons are engaged in the $\alpha 1 \leftrightarrow 2 \beta$ glycosidic bond, preventing ring opening.

How do the linkages in cellulose compare to those in amylose, and how does this affect structural function?

Amylose contains $\alpha 1 \rightarrow 4$ linkages that cause the glucose polymer to adopt a compact, flexible helical coil optimized for fuel storage, whereas cellulose contains $\beta 1 \rightarrow 4$ linkages that force an extended, linear chair conformation capable of interchain hydrogen bonding into rigid, insoluble plant cell wall fibers.

What are the four architectural regions of bacterial lipopolysaccharide (LPS), and which part acts as the endotoxin?

LPS consists of the O antigen, outer core, inner core, and Lipid A; the hydrophobic Lipid A anchor serves as the toxic endotoxin that activates immune responses.

What determines whether a polyunsaturated fatty acid belongs to the $\omega\text{-}3$ or $\omega\text{-}6$ family?

The classification depends on the distance of the first double bond from the terminal methyl ($\omega$) carbon: at carbon 3 for $\omega\text{-}3$ and carbon 6 for $\omega\text{-}6$.

How do cis and trans double bonds influence fatty acid packing and fluidity?

A natural cis double bond introduces a rigid bend/kink in the hydrocarbon chain that impedes tight van der Waals packing, lowering melting points (liquid at room temperature). Trans double bonds maintain an extended, linear conformation that packs tightly like saturated chains, resulting in higher melting points (solid or semi-solid).

What energetic and physiological advantages do triacylglycerols (TAGs) have over glycogen for energy storage?

TAGs are more chemically reduced and provide more energy per gram than carbohydrates, and because they are completely hydrophobic, they are stored anhydrously without associating with water, unlike glycogen which binds approximately $2\,\text{g of } \text{H}_2\text{O}$ per gram.

What are the head groups and net charges at $\text{pH } 7$ for the four principal glycerophospholipids?

1. Phosphatidic acid (head: $-\text{H}$, charge: $-2$); 2. Phosphatidylethanolamine (head: ethanolamine, charge: $0$); 3. Phosphatidylcholine/lecithin (head: choline, charge: $0$); 4. Phosphatidylserine (head: serine, charge: $-1$).

What structural ring system defines sterols, and what is the primary sterol in animals?

Sterols are characterized by a rigid, planar steroid nucleus composed of four fused carbon rings (three six-membered rings and one five-membered ring); cholesterol is the primary sterol in animal cell membranes and the precursor to steroid hormones, bile acids, and vitamin D.

What terminal carbohydrate residues differentiate human ABO blood group antigens on glycosphingolipids?

All three types possess a common ceramide-oligosaccharide core; the O antigen has no additional terminal sugar, the A antigen possesses an added terminal N-acetylgalactosamine, and the B antigen possesses an added terminal galactose.