OPTO 5344: DNA Structure and Replication Review

Comprehensive 90-card practice flashcard set covering DNA chemical structure, nitrogenous bases, Chargaff's rules, history of discovery, chromatin packaging, prokaryotic and eukaryotic DNA replication mechanics, telomerase, and related pharmacological agents.

What is the main sequence of information flow described by the Central Dogma of gene expression?

DNA replication produces DNA, transcription synthesizes RNA from DNA, and translation synthesizes protein from RNA.

What process do RNA viruses such as HIV use to synthesize DNA from an RNA genome?

Reverse transcription.

Who delivered the lecture on DNA structure and replication for OPTO 5344 Physiology & Molecular Biology?

John O’Brien, Ph.D.

In what year did Frederick Griffith perform his transformation experiment on Streptococcus pneumoniae?

1928.

Which bacterium was used in Frederick Griffith's 1928 transformation experiment?

Streptococcus pneumoniae.

In Griffith's experiment, what were the outcomes of injecting live S strain versus live R strain Streptococcus pneumoniae into mice?

Injecting live S strain killed the mouse (virulent), whereas injecting live R strain allowed the mouse to live (non-virulent).

What happened to the mouse when heat-killed S strain Streptococcus pneumoniae cells were injected alone?

The mouse lived because heat-killing the S strain rendered it non-infectious.

What was the result when heat-killed S strain cells were mixed with live R strain cells and injected into mice?

The mouse died, and live, virulent S strain bacteria were recovered from the animal.

What primary conclusion was drawn from Frederick Griffith's 1928 experiment?

Characteristics of dead bacteria could be passed to live bacteria by a transforming substance that remains in cell extracts.

Which researchers demonstrated in 1944 that DNA is the genetic material carrying the virulence factor?

Oswald Avery, Colin MacLeod, and Maclyn McCarty.

How did Avery, MacLeod, and McCarty prove that DNA was the virulence factor?

Only the selective destruction of DNA eliminated the virulence factor, whereas destroying proteins, lipids, RNA, or polysaccharides did not.

In the experimental diagram shown, which treatment specifically prevented the transformation of non-virulent R strain into live S strain bacteria?

The destruction of DNA (DNA destroyed).

What three chemical components make up a nucleotide?

A deoxyribose sugar, a nitrogen-containing base, and a phosphate group.

How does a nucleoside differ structurally from a nucleotide?

A nucleoside consists of deoxyribose sugar and a base, but lacks a phosphate group.

What full chemical name corresponds to the nucleotide abbreviation dAMP?

Deoxyadenosine 5'-monophosphate.

What component attaches to the 1' carbon of deoxyribose in a nucleotide?

The nitrogen-containing base.

How does the 2' carbon of deoxyribose differ from the 2' carbon of ribose?

Deoxyribose has a hydrogen atom ($-H$) at the 2' carbon instead of a hydroxyl group ($-OH$), meaning it lacks oxygen.

Why is the hydroxyl group ($-OH$) at the 3' carbon of deoxyribose essential for DNA synthesis?

It provides the functional group required for DNA polymerization to add subsequent nucleotides.

What functional group attaches to the 5' carbon of deoxyribose?

The phosphate group.

Which two specific carbon positions on adjacent deoxyribose molecules are linked together during DNA synthesis?

The 5' and 3' carbons.

How many ring structures characterize purine bases versus pyrimidine bases?

Purine bases have a two-ring structure, whereas pyrimidine bases have a single-ring structure.

Around what year were purine bases first synthesized in the laboratory?

~1888.

Around what year were pyrimidine bases first synthesized in the laboratory?

~1879.

What are the two purine bases found in DNA and their corresponding nucleoside triphosphates?

Adenine (dATP) and Guanine (dGTP).

What are the two pyrimidine bases found in DNA and their corresponding nucleoside triphosphates?

Cytosine (dCTP) and Thymine (dTTP).

What does Chargaff's Rule state regarding the base composition of DNA?

In DNA of a given species, percentage of adenine equals percentage of thymine ($\%A = \%T$) and percentage of cytosine equals percentage of guanine ($\%C = \%G$).

If a sample of double-stranded DNA contains 20% Adenine, what are the percentages of Thymine, Cytosine, and Guanine?

Thymine = 20%, Cytosine = 30%, Guanine = 30%.

If double-stranded DNA contains 50% Adenine, what are the percentages of the remaining three bases?

Thymine = 50%, Cytosine = 0%, Guanine = 0%.

Why is a double-stranded DNA sample containing 55% Adenine mathematically impossible?

Because Adenine equals Thymine, 55% A plus 55% T would equal 110%, exceeding the 100% total base capacity.

Why does Chargaff's Rule NOT apply to RNA molecules?

Because RNA is single-stranded.

Does the percentage of GC ($\%GC$) vary between different individuals of the same species?

No, $\%GC$ is the same in all members of a species, but differs between different species.

Who published a one-page paper in Nature in 1953 proposing the double helix structure of DNA?

James Watson and Francis Crick.

Whose X-ray crystallography data was essential for Watson and Crick to deduce the structure of DNA?

Rosalind Franklin and Maurice Wilkins.

Which researchers shared the 1962 Nobel Prize in Physiology or Medicine for discovering the structure of DNA?

Francis Crick, James Watson, and Maurice Wilkins.

Why was Rosalind Franklin not awarded a share of the 1962 Nobel Prize for the discovery of DNA structure?

She passed away four years earlier in 1958, and Nobel Prizes are not awarded posthumously.

How many hydrogen bonds form between Cytosine and Guanine, and how many between Adenine and Thymine?

Cytosine and Guanine form 3 hydrogen bonds; Adenine and Thymine form 2 hydrogen bonds.

Which base pair provides greater thermal and structural stability in DNA: A-T or G-C?

G-C, because it is joined by 3 hydrogen bonds instead of 2.

What are the physical dimensions and base pair content of one full turn of a DNA double helix?

One full turn contains ~10 base pairs and spans $34\,\text{\AA}$ ($3.4\,\text{nm}$).

Why do regulatory proteins preferentially bind to the major groove of DNA rather than the minor groove?

Because DNA base pairs are more exposed in the major groove.

What type of chemical bond connects the deoxyribose sugars along the DNA backbone?

Phosphodiester bonds.

What term describes the opposite directional alignment of the two sugar-phosphate backbones in a DNA double helix?

Anti-parallel.

In the chemical structure diagram shown, which base pair is held together by three hydrogen bonds?

Cytosine and Guanine.

How many genes and base pairs are contained in human nuclear DNA per cell?

20,000-25,000 genes and $6 \times 10^9$ base pairs.

What is the total length of nuclear DNA in a single human cell if fully stretched out?

Approximately 2 meters.

Assuming a human body contains over 10 trillion cells, what is the combined length of all nuclear DNA in meters and kilometers?

~20 trillion meters (~20 billion km).

Given an Earth-to-Sun distance of ~150 million km, how many round trips could a single person's combined nuclear DNA make?

Approximately 66.7 times.

What is a nucleosome?

The basic unit of chromatin, consisting of DNA wrapped 2.5 times around an octameric histone core.

How many histone protein subunits form a mature histone octamer, and which histones compose it?

8 subunits, composed of two molecules each of histones H2A, H2B, H3, and H4.

What is the structural diameter of open chromatin ('beads-on-a-string') compared to condensed chromatin fibers?

Open chromatin has a diameter of $11\,\text{nm}$, whereas condensed chromatin forms $30\,\text{nm}$ fibers.

What is the length of the smallest human chromosome when fully condensed during mitosis?

2 micrometers ($2\,\mu\text{m}$).

What components constitute chromatin?

DNA combined with histone proteins.

In the diagram of chromatin organization, what fiber thickness represents condensed chromatin coiled from nucleosomes?

$30\,\text{nm}$ fibers.

What is meant by the semiconservative model of DNA replication?

Each parent DNA strand serves as a template for a new daughter strand, resulting in double helices containing one original parent strand and one newly synthesized strand.

Who experimentally proved the semiconservative mechanism of DNA replication, and in what year?

Matthew Meselson and Franklin Stahl in 1958.

What specific chemical structure must be present at the 3' end of a growing DNA strand for DNA polymerase to add a new nucleotide?

A free 3'-OH (hydroxyl) group.

What occurs during DNA synthesis if the 3' end of the growing strand lacks a free 3'-OH group?

A new nucleotide cannot be added, and DNA synthesis stops.

How does DNA polymerase catalyze chain elongation when adding a nucleoside triphosphate?

It forms a phosphodiester bond between the phosphate attached to the 5' carbon of the incoming dNTP and the 3'-OH at the end of the growing DNA strand.

In what directional orientation does DNA polymerase perform new DNA strand synthesis?

Always in the 5' to 3' direction.

In what direction is the parent DNA template strand read during replication?

From 3' to 5'.

What structure forms when double-stranded DNA unwinds to allow bidirectional replication starting at an origin of replication?

A replication bubble containing two active replication forks.

What is the primary enzymatic activity of DNA polymerases?

Synthesizing DNA by adding new bases to the growing strand end and generating phosphodiester bonds between adjacent deoxyribonucleotides.

How do naming conventions for DNA polymerases differ between prokaryotes and eukaryotes?

Prokaryotic DNA polymerases are named with Roman numerals (I, II, III), whereas eukaryotic DNA polymerases are named with letters (A, B, D, G, etc.).

How do chromosome structure and replication origins compare between prokaryotes and eukaryotes?

Prokaryotes have circular DNA with a single origin of replication; eukaryotes have linear DNA with multiple origins of replication per chromosome.

Which DNA polymerase synthesizes the continuous leading strand in prokaryotes?

DNA Polymerase III (Pol III).

Which enzyme synthesizes RNA primers required for lagging strand replication in prokaryotes?

Primase.

What are Okazaki fragments?

Short stretches of newly synthesized DNA generated discontinuously on the lagging strand during DNA replication.

Which prokaryotic enzyme removes RNA primers from Okazaki fragments and fills the resulting gaps with DNA?

DNA Polymerase I (Pol I).

What specific enzymatic activity allows DNA Pol I to remove RNA primers in prokaryotes?

Exonuclease activity.

Which enzyme forms phosphodiester bonds to join adjacent Okazaki fragments together in both prokaryotes and eukaryotes?

DNA ligase.

Which DNA polymerase synthesizes the continuous leading strand in eukaryotes?

DNA Polymerase D (Pol D).

What dual roles does DNA Polymerase A (Pol A) perform on the lagging strand in eukaryotic DNA replication?

It synthesizes the RNA primer and the first 20 base pairs of DNA on the lagging strand.

Which eukaryotic enzyme is responsible for removing RNA primers from Okazaki fragments?

RNase H.

Which DNA polymerase fills in the gaps between Okazaki fragments after primer removal in eukaryotic replication?

DNA Polymerase D (Pol D).

Which eukaryotic DNA polymerase is specialized for replicating mitochondrial DNA (mtDNA)?

DNA Polymerase G (Pol G).

What is the function of Helicase at the replication fork?

It unwinds the double helix and separates the two DNA strands by breaking hydrogen bonds.

What is the primary function of Topoisomerase (DNA Gyrase in prokaryotes)?

It relieves supercoiling caused by DNA unwinding by cleaving phosphodiester bonds in supercoiled regions, allowing untwisting, and re-ligating the DNA.

According to the provided diagram, what are the three steps DNA gyrase performs to relieve supercoiling ahead of a replication fork?

1. DNA gyrase cuts DNA strands; 2. DNA rotates to remove the coils; 3. DNA gyrase rejoins the DNA strands.

Which two proteins are required for eukaryotic histone re-assembly immediately following DNA replication?

CAF-1 (Chromatin Assembly Factor 1) and PCNA (Proliferating Cell Nuclear Antigen).

What are the specific functions of CAF-1 and PCNA during eukaryotic chromatin re-assembly?

CAF-1 assembles the histone octamer, and PCNA wraps the DNA around the octamers to form nucleosomes.

Why does lagging strand synthesis create a terminal gap problem at the ends of linear eukaryotic chromosomes?

Removal of the final RNA primer at the 5' end leaves an unreplicated gap on the 3' overhang strand that standard DNA polymerases cannot fill.

What enzyme maintains linear chromosome length in eukaryotes by synthesizing repetitive DNA at chromosome ends (telomeres)?

Telomerase.

Who received the 2009 Nobel Prize in Physiology or Medicine for discovering how chromosomes are protected by telomeres and telomerase?

Elizabeth H. Blackburn, Carol W. Greider, and Jack W. Szostak.

What rare inherited condition characterized by premature aging, mucocutaneous abnormalities, and bone marrow failure is linked to telomerase defects?

Dyskeratosis congenita.

How does the antiviral drug Trifluridine (Viroptic) disrupt viral DNA replication?

It functions as a nucleoside analog that incorporates into DNA and blocks base pairing.

How do fluoroquinolone antibiotics (such as Cipro, Ofloxacin, Levofloxacin, and Gatifloxacin) block prokaryotic DNA replication?

They inhibit DNA gyrase, blocking DNA replication.

Which specific clinical condition is Cipro highlighted for treating?

Corneal ulcers.

How do sulfonamide drugs like sulfacetamide inhibit bacterial DNA synthesis?

They block DNA synthesis by preventing the production of folate needed for nucleotide synthesis.

How do Rifamycins inhibit prokaryotic RNA synthesis?

They bind to RNA polymerase and block transcription elongation.

How do Aminoglycosides (tobramycin, gentamicin) and Macrolides (erythromycin) differ in their mechanisms of blocking protein synthesis?

Aminoglycosides bind to the A site of the 30S ribosomal subunit, whereas Macrolides bind to the 50S subunit of ribosomes.

Which classes of antibacterial drugs target bacterial cell wall synthesis versus cell membrane integrity?

Beta-lactams (penicillin, ampicillin) and Glycopeptides (vancomycin) inhibit cell wall synthesis; Polypeptide antibiotics (polymyxin, bacitracin) disrupt the cell membrane.