BFCP Lecture 1

What is DNA, and what is its role? [LO1]

Deoxyribonucleic acid (DNA) is a high-molecular-weight double-helix polymer of nucleotides that stores the structural blueprint of genetic instructions.

What is the central dogma of molecular biology? [LO1]

DNA → RNA → Protein; it describes the storage, retrieval, and translation of genetic information.

What three components make up a nucleotide? [LO1]

A nitrogen-containing base + a pentose sugar + a phosphate group.

Which nitrogenous bases are purines and which are pyrimidines? [LO1]

Purines: adenine (A) and guanine (G). Pyrimidines: cytosine (C), thymine (T), and uracil (U).

Which bases are found in DNA? [LO1]

Adenine (A), guanine (G), cytosine (C), and thymine (T).

Which bases are found in RNA? [LO1]

Adenine (A), guanine (G), cytosine (C), and uracil (U); RNA uses uracil instead of thymine.

What pentose sugar is found in DNA versus RNA? [LO1]

DNA contains deoxyribose; RNA contains ribose.

What structural feature distinguishes ribose from deoxyribose? [LO1]

Ribose has an -OH at the 2′ carbon; deoxyribose has an H at the 2′ carbon.

What is the difference between a nucleoside and a nucleotide? [LO1]

Nucleoside = base + sugar. Nucleotide = base + sugar + phosphate.

What bond links nucleotides within a nucleic acid strand? [LO1, LO2]

A phosphodiester bond links the 5′ phosphate of one nucleotide to the 3′-OH of the neighboring nucleotide.

What gives a nucleic acid strand polarity? [LO1, LO2]

One end has a 5′ phosphate and the other has a 3′ hydroxyl, giving the strand 5′ → 3′ directionality.

How do RNA and DNA compare structurally? [LO1]

Both use phosphodiester linkages and have 5′ → 3′ polarity. RNA contains ribose and U, is typically shorter, and is most often single-stranded; DNA contains deoxyribose and T and is double-stranded.

How does adenine pair in RNA? [LO1, LO3]

Adenine pairs with uracil (U), not thymine.

What are the major structural features of double-stranded DNA? [LO2]

Two polynucleotide chains form a double helix with antiparallel strands, sugar-phosphate backbones on the outside, and paired bases in the interior.

What does it mean that the two DNA strands are antiparallel? [LO2]

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

Where are the sugar-phosphate backbone and nitrogenous bases located in double-stranded DNA? [LO2]

The sugar-phosphate backbones are on the outside of the helix; the bases are paired in the interior.

In what direction is a DNA sequence conventionally read? [LO2]

5′ → 3′.

What are the major and minor grooves of DNA? [LO2]

They are the alternating larger and smaller grooves formed along the surface of the DNA double helix.

What are the complementary base-pairing rules in DNA? [LO3]

Adenine pairs with thymine (A-T), and guanine pairs with cytosine (G-C).

How many hydrogen bonds form in A-T versus G-C base pairs? [LO3]

A-T forms 2 hydrogen bonds; G-C forms 3 hydrogen bonds.

Why does a purine pair with a pyrimidine in double-stranded DNA? [LO3]

The bulkier purines (A or G) pair with the less bulky pyrimidines (C or T), maintaining the structure of the double helix.

How does G-C content affect double-stranded DNA stability? [LO3]

Greater G-C content increases stability because G-C pairs form 3 hydrogen bonds compared with 2 in A-T pairs.

During what phase of the cell cycle does DNA replication occur? [LO5]

The synthesis (S) phase.

Why is DNA replication necessary? [LO5]

It allows the genetic code to be passed to daughter cells.

What type of DNA template can DNA polymerase use? [LO4, LO5]

A single-stranded DNA template.

What four characteristics define eukaryotic DNA synthesis? [LO5]

It is semi-conservative, bidirectional with multiple origins of replication, primed by RNA, and semi-discontinuous.

What does semi-conservative DNA replication mean? [LO5]

Each daughter DNA double helix contains one original parental strand and one newly synthesized strand.

What does it mean that eukaryotic DNA replication is bidirectional with multiple origins? [LO5]

Replication begins at multiple origins and proceeds in both directions, allowing DNA synthesis to occur more rapidly.

In what direction does DNA polymerase read the template and synthesize the new strand? [LO4]

DNA polymerase reads the template 3′ → 5′ and synthesizes the new strand 5′ → 3′.

Where does DNA polymerase add each new nucleotide? [LO4]

To the 3′-OH end of the growing DNA chain.

Can DNA polymerase initiate DNA synthesis on a bare single-stranded template? [LO4, LO5]

No. DNA polymerase requires a pre-existing 3′-OH provided by an RNA primer.

How does DNA primase enable DNA polymerase to begin synthesis? [LO5, LO7]

Primase synthesizes a short RNA sequence complementary to the DNA template, providing a 3′-OH group for DNA polymerase to extend.

Why is DNA replication described as semi-discontinuous? [LO5]

The leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously as Okazaki fragments.

What is the difference between leading- and lagging-strand synthesis? [LO5]

The leading strand is synthesized continuously; the lagging strand is synthesized discontinuously in short DNA segments.

What are Okazaki fragments, and approximately how long are they in this lecture? [LO5]

Short DNA segments synthesized on the lagging strand; each is approximately 150 nucleotides long.

Approximately how fast does DNA polymerase add nucleotides? [LO4]

About 50 nucleotides per second.

How accurate is DNA polymerase according to the lecture? [LO4]

Exceptionally accurate, with an error rate of about 1 error per 10^9 nucleotides.

What proofreading activity does DNA polymerase possess? [LO4]

3′ → 5′ exonuclease activity, which allows incorrect nucleotides to be removed.

Does DNA polymerase proofread in the 5′ → 3′ direction? [LO4]

No. The lecture emphasizes that proofreading is only 3′ → 5′; DNA polymerase does not have 5′ → 3′ proofreading exonuclease activity.

Do multiple DNA polymerases participate in eukaryotic replication? [LO4, LO5]

Yes. Multiple DNA polymerases function as part of a replication complex.

What is the role of DNA helicase in replication? [LO7]

Helicase is a motor protein that hydrolyzes ATP to unwind short stretches of double-stranded DNA and create the replication fork.

What is the role of single-stranded DNA-binding proteins during replication? [LO5]

They stabilize the helicase-separated DNA strands and prevent them from re-annealing.

What is the role of DNA ligase in replication? [LO7]

Ligase seals nicks in DNA after gaps left by removed RNA primers are filled, creating phosphodiester bonds between adjacent nucleotides.

What is DNA supercoiling? [LO7]

The over-winding (positive supercoiling) or under-winding (negative supercoiling) of DNA, which affects torsional stress on the double helix.

Why must torsional stress be relieved during DNA replication? [LO7]

Increasing tension ahead of the replication machinery can slow and eventually stop movement of the replication fork and therefore replication.

What is the role of topoisomerases in DNA replication? [LO7]

They relieve torsional stress caused by replication-fork movement by creating reversible breaks in phosphodiester bonds and then resealing the DNA.

How do topoisomerase I and topoisomerase II differ? [LO7]

Topoisomerase I breaks and rejoins one DNA strand; topoisomerase II breaks and rejoins both DNA strands.

What is a telomere? [LO6]

A protective region made of repetitive stretches of DNA and proteins at the tips of chromosomes.

What is telomerase, and how does it maintain chromosome ends? [LO6]

Telomerase is an RNA-dependent DNA polymerase and ribonucleoprotein complex. It uses its own RNA template to add repeated deoxyribonucleotide sequences to chromosome ends, maintaining telomeres.

How does telomerase relate to the end-replication problem? [LO6]

By adding repeated DNA sequences to chromosome ends, telomerase overcomes the end-replication problem of linear chromosomes.