BIOL 2P02 Exam

Last minute hoping and praying.

What is the central dogma?

DNA is transcribed into RNA, and RNA is translated into protein.

What is molecular biology?

The study of essential cellular macromolecules and the processes that store, transmit, and express biological information.

What is electronegativity?

An atom's relative affinity for shared electrons in a chemical bond.

When is a bond considered nonpolar covalent by electronegativity difference?

When the electronegativity difference is approximately zero and electrons are shared nearly equally.

When is a bond considered polar covalent?

When electrons are shared unequally, producing partial positive and partial negative charges.

When is a bond considered ionic in these lectures?

When the electronegativity difference is greater than about 1.67 and electrons are effectively transferred.

What is an electric dipole moment?

A separation of positive and negative charge within a bond or molecule.

Why are salt bridges important in biology?

They are flexible, noncovalent electrostatic interactions that help stabilize biomolecular structures.

What are van der Waals forces?

Weak attractions caused by temporary or induced fluctuations in electron distribution.

What is a hydrogen bond?

An attractive interaction between a hydrogen covalently attached to an electronegative atom and another electronegative atom with a lone pair.

Why does hydrogen-bond geometry matter?

Hydrogen bonds are strongest at specific distances and orientations rather than being simple nonspecific attractions.

What is the hydrophobic effect?

The tendency of nonpolar molecules or groups to cluster away from water, increasing the entropy of surrounding water.

What are the three components of a nucleotide?

A nitrogenous base, a pentose sugar, and one or more phosphate groups.

What is the difference between a nucleoside and a nucleotide?

A nucleoside is a base plus sugar; a nucleotide is a nucleoside plus one or more phosphate groups.

Which bases are purines?

Adenine and guanine.

Which bases are pyrimidines?

Cytosine, thymine, and uracil.

Which sugar is present in DNA?

Deoxyribose.

Which sugar is present in RNA?

Ribose.

What structural difference distinguishes ribose from deoxyribose?

Ribose has a 2′-OH group, whereas deoxyribose has a 2′-H.

What is a phosphodiester bond?

The covalent linkage between the 3′ carbon of one sugar and the 5′ phosphate of the next nucleotide.

What gives a nucleic-acid strand directionality?

The chemically distinct 5′ phosphate end and 3′ hydroxyl end.

What does antiparallel mean in DNA?

The two strands run in opposite directions, one 5′→3′ and the other 3′→5′.

How many hydrogen bonds form between A and T?

Two.

How many hydrogen bonds form between G and C?

Three.

Why are GC-rich DNA regions generally more stable than AT-rich regions?

G-C base pairs form three hydrogen bonds and have strong stacking interactions, so more energy is usually required to separate them.

What is Chargaff's rule for double-stranded DNA?

The amount of A equals T and the amount of G equals C; total purines equal total pyrimidines.

What is base stacking?

Stabilizing interactions between adjacent aromatic bases within the DNA helix.

Why can bases flip out of the DNA helix?

Rotation around bonds can expose a base so enzymes can scan, modify, remove, or repair it.

What information can proteins read in DNA grooves?

Patterns of hydrogen-bond donors, acceptors, nonpolar groups, and methyl groups on base-pair edges.

Why is the major groove more sequence-informative than the minor groove?

The major groove displays a more distinct chemical pattern for each base pair, allowing exact sequence recognition.

What is the most common DNA conformation in cells?

B-DNA.

What are key features of B-DNA?

A right-handed helix about 2 nm wide, approximately 10-10.5 base pairs per turn, and a rise of about 0.34 nm per base pair.

What is A-DNA?

A more compact right-handed helix with about 11 base pairs per turn, often favoured under dehydrating conditions or in some protein-bound nucleic acids.

What is Z-DNA?

A left-handed DNA helix with a zig-zag sugar-phosphate backbone.

What is a chromosome?

One continuous DNA molecule associated with proteins and containing genes and other sequences.

What is a karyotype?

An organized image of stained chromosomes arranged into homologous pairs.

What is the human haploid chromosome number?

n = 23.

What is the human diploid chromosome number?

2n = 46.

What do human gametes contain?

22 autosomes and one sex chromosome.

What do p and q denote in chromosome nomenclature?

p is the short arm and q is the long arm.

What does 4q21 indicate?

Chromosome 4, long arm, region 2, band 1.

What is a metacentric chromosome?

A chromosome with a centromere near the centre.

What is a submetacentric chromosome?

A chromosome with an off-centre centromere.

What is an acrocentric chromosome?

A chromosome with a centromere near one end.

What is a telocentric chromosome?

A chromosome with a centromere at the end; normal humans do not have telocentric chromosomes.

What is chromatin?

DNA associated with histone and nonhistone proteins.

What are the major purposes of chromatin organization?

To compact DNA, organize it, protect it, and regulate access for processes such as transcription and replication.

What is a nucleosome core particle?

About 147 base pairs of DNA wrapped around a histone octamer.

Which histones form the nucleosome octamer?

Two copies each of H2A, H2B, H3, and H4.

What is linker DNA?

The DNA segment connecting adjacent nucleosome core particles.

What is histone H1?

A linker histone that binds near DNA entry and exit sites and promotes higher-order chromatin compaction.

What are histone tails?

Flexible N-terminal extensions that contact DNA and can be covalently modified to regulate chromatin.

What is euchromatin?

Relatively open, less condensed chromatin that is generally more transcriptionally active.

What is heterochromatin?

Highly condensed chromatin that is generally transcriptionally inactive.

What is constitutive heterochromatin?

Chromatin that remains densely packed, is gene-poor and repeat-rich, and is commonly found at centromeres and telomeres.

What is facultative heterochromatin?

Chromatin that can switch between condensed and active states during development or differentiation.

What are chromosome territories?

Preferred, nonrandom regions of the nucleus occupied by particular chromosomes.

What is an SMC protein?

A structural-maintenance-of-chromosomes ATPase involved in chromosome organization, cohesion, and condensation.

Approximately how large is the human genome?

About 3.2 × 10^9 base pairs, or 3.2 gigabases.

Approximately what percentage of the human genome is protein-coding?

About 1.2%.

Why can noncoding DNA still be functional?

It can contain promoters, enhancers, structural sequences, and genes for functional noncoding RNAs.

What were major goals of the Human Genome Project?

Develop mapping and sequencing technologies, sequence the human genome, sequence model organisms, and examine ethical, legal, and social implications.

What are LINEs and SINEs?

Common classes of human retrotransposons; LINEs can encode proteins needed for movement, whereas SINEs generally depend on LINE machinery.

During which cell-cycle phase is DNA replicated?

S phase.

What happens during G1?

The cell grows and performs normal functions before DNA synthesis; some cells may exit into G0.

What happens during G2?

The cell grows and prepares for mitosis after DNA replication.

What is semiconservative DNA replication?

Each daughter DNA molecule contains one parental strand and one newly synthesized strand.

What enzyme unwinds the DNA double helix at the replication fork?

Helicase.

In what direction does DNA polymerase synthesize DNA?

5′→3′.

Why can DNA polymerase not begin a strand de novo?

It requires an existing primer with a free 3′-OH to which nucleotides can be added.

What serves as the template during DNA replication?

Each parental DNA strand directs synthesis of a complementary daughter strand.

What is bidirectional replication?

Replication proceeds away from an origin in both directions, creating two oppositely moving forks.

What is a replication bubble?

The locally unwound region around an origin bounded by two replication forks.

Why do eukaryotic chromosomes require multiple origins of replication?

Their DNA molecules are too long to be copied in time from a single origin.

What is the leading strand?

The daughter strand synthesized continuously in the same overall direction as fork movement.

What is the lagging strand?

The daughter strand synthesized discontinuously away from fork movement as Okazaki fragments.

Why is DNA replication called semidiscontinuous?

The leading strand is continuous, while the lagging strand is synthesized in fragments.

What is an Okazaki fragment?

A short DNA segment synthesized on the lagging strand and later joined to neighbouring fragments.

What five components were identified as necessary for DNA synthesis?

A DNA template, a primer, DNA polymerase, dNTPs, and Mg2+.

What role does Mg2+ play in DNA polymerase reactions?

It acts as a catalytic divalent cation that helps activate the 3′-OH and stabilize negative charges.

What is the energy source for DNA-chain elongation?

Cleavage of the incoming dNTP's high-energy phosphoanhydride bonds and release of pyrophosphate.

What is exonuclease activity?

Removal of nucleotides from the end of a nucleic-acid strand.

What is endonuclease activity?

Cleavage of phosphodiester bonds within a nucleic-acid strand.

What is the purpose of 3′→5′ exonuclease activity in DNA polymerase?

Proofreading newly added nucleotides and removing mispaired bases.

What is the purpose of DNA polymerase I's 5′→3′ exonuclease activity?

Removal of RNA primers or nucleotides ahead of the polymerase during nick translation.

What is processivity?

The number of nucleotides a polymerase adds each time it binds the template.

What is the sliding clamp?

A ring-shaped protein that encircles DNA and keeps a polymerase attached, greatly increasing processivity.

What is a point mutation?

A small-scale sequence change involving one or a few base pairs.

What is a base substitution?

Replacement of one base pair with another.

What is an indel?

Insertion or deletion of one or more nucleotides.

What is a frameshift mutation?

An insertion or deletion not divisible by three that changes the downstream translational reading frame.

What is a silent mutation?

A nucleotide substitution that does not change the encoded amino acid.

What is a missense mutation?

A nucleotide substitution that changes one amino acid to another.

What is a nonsense mutation?

A nucleotide substitution that converts an amino-acid codon into a stop codon.

What is a conservative missense mutation?

A substitution that replaces an amino acid with another having similar chemical properties.

What is a nonconservative missense mutation?

A substitution that replaces an amino acid with one having substantially different chemical properties.

What large-scale mutations were emphasized?

Deletion, duplication, inversion, insertion, and translocation.

What is deamination?

Removal of an amino group from a base, potentially changing its base-pairing properties.

What is depurination?

Spontaneous loss of a purine base from DNA, leaving an abasic site.

What are reactive oxygen species?

Highly reactive oxygen-containing molecules that can oxidize DNA bases and damage the backbone.