Biochem Module 1

What is biochemistry?

The study of the chemistry of life processes.

What are two examples of biological macromolecules?

Proteins and nucleic acids (like DNA).

What are two examples of low-molecular-weight metabolites?

Glucose and glycerol.

What are the three domains of life?

Eukarya, Bacteria, and Archaea.

What distinguishes eukaryotes from prokaryotes?

Eukaryotes have a nucleus; prokaryotes lack a nucleus.

What are the three components of a DNA monomer (nucleotide)?

A sugar (deoxyribose), a phosphate, and one of four nitrogenous bases.

What are the four nitrogenous bases in DNA?

Adenine (A), Cytosine (C), Guanine (G), and Thymine (T).

What forms the backbone of DNA?

Linked sugars and phosphates.

What holds the two strands of the DNA double helix together?

Hydrogen bonds between base pairs.

How are the two strands of DNA oriented relative to each other?

Antiparallel.

How many hydrogen bonds form between an A-T base pair?

Two hydrogen bonds.

How many hydrogen bonds form between a G-C base pair?

Three hydrogen bonds.

Why can each DNA strand serve as a template?

Because of specific base pairing, allowing two identical daughter helices to form from one parent strand.

What is the biochemical timescale?

The order of picoseconds to microseconds (10⁻¹²–10⁻⁶ s) for biological interactions and processes.

What are covalent bonds formed by?

Electron sharing between two adjacent atoms.

What is the typical bond distance and bond energy of a C–C covalent bond?

1.54 Å and 355 kJ/mol (85 kcal/mol).

What is 1 Angstrom (Å) equal to in meters?

10⁻¹⁰ m (0.1 nm).

What are resonance structures?

Multiple valid covalent structures that a molecule (like adenine) can exhibit.

What is an ionic interaction?

A noncovalent interaction between fully charged atoms or molecules.

What equation describes the energy of electrostatic attraction/repulsion?

The Coulomb energy equation: E = kq1q2/Dr.

What is the bond distance and energy of electrostatic interactions in water?

~3 Å and 5.86 kJ/mol (1.4 kcal/mol).

What causes an electric dipole in a molecule?

Uneven electron distribution in a molecule with no overall charge.

What is a hydrogen bond?

An interaction between an electronegative atom and a hydrogen covalently bonded to another electronegative atom.

What is the bond distance and energy range for hydrogen bonds?

1.5–2.6 Å and 4–20 kJ/mol (1–5 kcal/mol).

What is a hydrogen-bond donor?

The atom to which the hydrogen is covalently bonded, plus the hydrogen atom itself.

What is a hydrogen-bond acceptor?

The lone pair of electrons on the atom less tightly linked to the hydrogen atom.

When do van der Waals interactions occur?

When transient asymmetry in electron distribution in one atom induces complementary asymmetry in a neighboring atom.

What is the bond energy range of van der Waals interactions?

2–4 kJ/mol (0.5–1.0 kcal/mol).

What happens at distances shorter than the van der Waals contact distance?

Strong repulsive forces become dominant.

What powers the hydrophobic effect?

The increase in entropy of water.

List the five types of atomic interactions important in DNA structure.

Covalent bonds, ionic interactions, hydrogen bonds, van der Waals interactions, and the hydrophobic effect.

What reduces the charge repulsion between DNA's negatively charged phosphate backbone?

The high dielectric constant of water and interaction with positively charged ions.

Why does hydrogen bonding explain the specificity of DNA sequence pairing?

Because each base hydrogen bonds equally well with water as with its complementary base, so specific pairing depends on structural complementarity.

What interactions occur between stacked bases in the interior of the DNA helix?

Van der Waals interactions.

What is the First Law of Thermodynamics?

The total energy of a system and its surroundings is constant.

What is the Second Law of Thermodynamics?

The total entropy of a system plus its surroundings always increases.

Can entropy decrease locally in a system?

Yes, if there is a corresponding increase in entropy of the surroundings.

What is the equation for Gibbs free energy?

ΔG = ΔH(system) − TΔS(system).

For a biochemical reaction to occur spontaneously, what must be true of ΔG?

ΔG must be negative.

Why does double-helix formation not violate the Second Law of Thermodynamics?

Heat released by helix formation increases the entropy of the surroundings, offsetting the decreased entropy of the DNA.

What term describes unpredictable outcomes at the single-molecule level?

Stochastic.

How is pH defined?

pH = −log[H⁺].

What is the value of Kw, the ion constant of water?

Kw = [H⁺][OH⁻] = 10⁻¹⁴.

At pH 7.0, what are the concentrations of H⁺ and OH⁻?

Both equal 10⁻⁷ M.

What is pKa?

The negative logarithm of the acid dissociation constant (Ka), indicating susceptibility of a proton to removal.

What happens to base-pairing when pH is at or above guanine's N-1 proton pKa (9.7)?

Guanine loses its proton, preventing base-pairing with cytosine and denaturing the helix.

When pH equals pKa, what is the ratio of deprotonated to protonated forms?

The ratio is 1 ([A⁻] = [HA]).

What is the Henderson–Hasselbalch equation?

pH = pKa + log([A⁻]/[HA]).

At what pH are buffers most effective?

Near the pKa value of their acid component.

What is titration?

Gradually adding known amounts of reagent to a solution while monitoring the results.

Why is phosphoric acid an important physiological buffer?

Its second pKa (7.21) is close to physiological pH (~7.4), allowing nearly equal mixtures of H2PO4⁻ and HPO4²⁻.

How has the cost of DNA sequencing changed since 2001?

It has decreased dramatically, from about $100 million to under $1,000 per genome.

How does DNA sequence variation within populations compare to variation between populations?

Variation within a population is greater than the average difference between different populations.

How many amino acid building blocks are used to build proteins?

20.

What determines a protein's three-dimensional structure?

Almost exclusively its amino acid sequence.

What is comparative genomics?

The comparison of one organism's genome with the genomes of other organisms.

What is the molecular clock hypothesis?

The idea that sequence differences between the same protein in two organisms can measure time since their common ancestor.

What defines a virus structurally?

A nucleic acid genome (DNA or RNA) surrounded by a protein coat.

Why are viruses not considered alive?

They cannot grow or reproduce on their own.

What virus is the likely evolutionary source of both SARS-CoV and SARS-CoV-2?

Viruses found in horseshoe bats.

How many more microbial cells than human cells exist in an individual?

About 10-fold more.

What is the human microbiome?

The complex microbial communities living in and on human bodies.