Chapter 11: DNA Structure and Replication

DNA Structure and Replication

In 1869…?

Friedrich Miescher discovers “nuclein”

In 1928…?

Frederick Griffith discovers “transformation” of bacteria

In 1944…?

Avery, MacLeod, and McCarty demonstrate “transformation” of bacteria was transfer of DNA

In 1950…?

Erwin Chargoff determines nucleotide “rules”

In 1952…?

Hershey and Chase demonstrate bacteriophage genetic material is DNA

In 1953…?

Watson and Crick published their model of DNA based on Rosalind Franklin’s X-ray diffraction images of DNA

In 1958…?

Messelson Stahl demonstrate replication is semi-conservation

In 1977…?

Sanger Sequencing

In 1990…?

Human genome project begins

Nucleic Acids are Assembled from Nucleotides

True

DNA is a ____

nucleic acid

Nucleotides consist of what?

5-carbon sugar called deoxyribose, a nitrogenous base, and a phosphate group

Type of nitrogenous bases?

Adenine, Thymine, Cytosine, and Guanine

Where is the phosphate group attached to?

The 5’ carbon of sugar

What are the names of the two chemical group attached to the 2’ carbon of the sugar is associated with the identity of nucleic acids

OH in RNA and H in DNA

The #’ carbon of sugar is

Bound to a different functional group

Types of Double-Ringed Nitrogenous Base (purines)

Adenine and Guanine

Types of Single Ringed Nitrogenous Base (pyrimidines)

Cytosine, Thymine (DNA only), and Uracil (RNA only)

What is attracted to the 5’ carbon of sugar?

Phosphate group

What is attracted to the 3’ carbon of sugar?

A free hydroxyl group (-OH)

What is attracted to the 1’ carbon of sugar?

A nitrogenous base

Phosphodiester Bonds don’t link Nucleotides

False

Phosphodiester Bonds are formed between?

The phosphate group of one nucleotide and the 3’ -OH of another nucleotide through a dehydration synthesis reaction

The chain of nucleotides has intrinsic polarity (5’ to 3’ orientation)

True

What is intrinsic polarity?

Cell polarity refers to the intrinsic asymmetry observed in cells, either in their shape, structure, or organization of cellular components

Phosphodiester Bonds are?

ester bonds linking sugars and a phosphate group

Chargaff’s Rule

Amount of Adenine = Amount of Thymine

Amount of Cytosine = Amount of Guanine

The proportion of purines (A and G) = the proportion of pyrimidines (C and T)

The ration of G-C to A-T varies between species

Maurice Wilkins and Rosalind Franklin discovered what?

DNA is helical

Maurice Wilkins and Rosalind Franklin performed X-Ray diffraction studies to identify 3-D structure

True

DNA has a diameter of ____ nm and makes a complete turn of the helix every ____ nm

2 ; 3.4

The Watson-Crick Model of DNA

proposed a double helix structure

G forms __ H bonds with C

3

A forms __ H bonds with T

2

Strands aren’t antiparallel

False

The Watson-Crick Model of DNA

Deduced the structure of DNA using evidence from Franklin, Chargaff, and others

Conservative Model

both strands of parent molecule remain intact

Semiconservative model

one strand of parent molecule remains intact

Dispersive model

parts of parental molecule. are dispersed throughout

In 1958, Meselson and Stahl experiment provided evidence disproving both ______ and _____ model and supporting the _____ model

conservative, dispersive; semiconservative

DNA replication requires?

Something to copy, Something to do the copying, Building Blocks to Make New Copy

Something to copy example?

Parental DNA molecule (template)

Something to do the copying example?

Enzymes (DNA polymerase)

Building Blocks to Make New Copy example?

Nucleoside Triphosphates

DNA replication occurs in three stages. What are the three stages?

Initiation, Elongation, and Termindation

Initiation

The process of replication start

Elongation

New DNA strands are synthesized

Termination

The process of replication ends

DNA Polymerase is?

an enzyme matches template bases with complementary nucleotides and link incoming nucleotide to daughter strand

Although DNA Polymerase has several types. They have several common features, what are the three features?

Adds new bases to 3’ end of existing strands, synthesize in 5’ to 3’ direction, and require a primer of RNA

Reads in 3’ to 5’ and synthesizes to 5’ to 3’

True

Prokaryotic Replication contains a ______ ________ molecule of DNA (chromsome)

Single Circular

Replication Steps in Prokaryotic

Begins at one orgin

Replication Step Two in Prokaryotic

Is catalyzed by replisomes

Replication Step Three in Prokaryotic

Proceeds in both directions around the chromosome

The E.coli chromosome contains a signle region of DNA controlled by an origin. The origin is also called.

Replicon

E.Coli is a type of _____

Prokaryotic

E.Coli has multiple DNA polymerases

True

The three main multiple DNA polymerases in E.Coli

DNA polymerase I, DNA polymerase II, DNA polymerase III

DNA polymerase I

Replaces RNA primers w/ DNA

DNA polymerase II

Involved in DNA repair processes

DNA polymerase III

Main replication enzyme

All have 3’ to 5’ exonuclease activity (proofreading)

True

All synthesize DNA in the 5’ to 3’ direction

True

DNA is composed of ____ antiparallel strands

2

DNA polymerase can only ______ in 5’ to 3’ direction

synthesize

Semi-discontinuous is?

One of the strands is synthesized continuously, while the other strand, is discontinuously by the formation of Okazaki fragments

Okazaki fragments are created by?

Lagging strand synthesized discontinuously with multiple priming and synthesis events

The lagging strand is synthesized in ______ direction as replication fork move

opposite

Leading strand synthesized continuously from an initial primer

True

Lagging Strand Synthesis: DNA Ligase

seals “nick” in backbone

Lagging Strand Synthesis: DNA polymerase III

Synthesizes fragment

Lagging Strand Synthesis: DNA polymerase I

Replaces RNA with DNA

Lagging Strand Synthesis: Primase

Makes RNA Primer

Primer RNA is?

RNA that initiates DNA synthesis.

E. Coli Replication: Helicases

Enzymes that use energy from ATP to unwind DNA

Single-strand-binding proteins (SSBs) don’t coat strands to keep them apart

False

SSBs are found in prokaryotes and eukaryotes

False, only found in prokaryotes but eukaryotes have a nuclear SSB protein, called Replication protein A (RPA)

Unwinding DNA causes torsional ___ and supercoiling

strain

E. Coli Replication: DNA gyrase

an enzyme that relives strain

SSBs ____ lagging strand template DNA as single

maintain

E. Coli Replication: Replisome Step One

A DNA polymerase III enzyme is active on each strand. Primase synthesizes new primers for the lagging strand

E. Coli Replication: Replisome Step Two

The “loop” in the lagging-strand template allows replication to occur 5’ to 3’ on both strands, with the complex moving to the left

E. Coli Replication: Replisome Step Three

When the polymerase III on the lagging strand hits the previously synthesized fragment, it releases the beta clamp and the template strand. DNA polymerase I attaches to remove the primer.

E. Coli Replication: Replisome Step Four

The clamp loader attaches the beta clamp and transfers this to polymerase III, creating a new loop in the lagging-strand template. DNA ligase joins the fragments after DNA polymerase I removes the primers

E. Coli Replication: Replisome Step Five

After the beta clamp is loaded, the DNA polymerase III on the lagging strand adds bases to the next Okazaki fragment

Eukaryotic Replication uses?

Mulitple Origins

Eukaryotic Replication: Linear Chromoseomes

Must deal with replication of ends

Eukaryotic Replication: Main polymerase is complex of DNA pol epsilon and DNA pol delta

True

Eukaryotic Replication: Telomerse

Specialized structures are found at the ends of eukaryotic chromosomes that protect ends from nucleases and maintain chromosome integrity. (Composed of short repeated DNA sequences)

Eukaryotic Replication: Replicating the End of Linear DNA

The leading strand can be replicated to the end, but unable to replicate last section of the lagging strand

Eukaryotic Replication: The Chromosomes after each round of cell division

Get gradual shorter

Eukaryotic Replication: There is a way to replace primer with DNA

False

Eukaryotic Replication: Telomerase

an enzyme that allows for replication of lagging strang ends, synthesizing the last segment of DNA

Eukaryotic Replication: Telomerase contains

RNA template (matches repeating sequence)

Eukaryotic Replication: Telomerase connections between senescence (cell again) and telomere length

Expressed in embryos and childhood, not expressed in adults (except in stem cells), and cancer cells generally show activation of telomerase

Cells don’t contain multiple DNA Repair Mechanisms

False

Some mistakes remain and maintain genetic variation

True

Mutagens (radiation and chemical)

Increase number of mutations above background level

Two general categories of DNA Repair Mechanisms are called?

Specific and non-specific repair

Specific Repair

targets a single type of DNA damage and repairs only that damage