The central dogma of molecular biology. Bacteriophages attached to the surface of a bacterium. Page 84.

The central dogma of molecular biology.

Bacteriophages attached to the surface of a bacterium.

Pag

e 84

FIGURE 17.10 The Hershey-Chase Experiment

The Hershey-Chase experiment.

1952 Alfred Hershey and Martha Chase

Diagram of T2 bacteriophage injecting its DNA into an E. coli cell.

FIGURE 17.9 Fred Griffith’s Experiment

WHAT IS DNA?

Scientists have studied how organisms organize and process genetic information, revealing the following principles:

1. DNA directs the function of living cells and is transmitted to offspring

DNA is composed of two polydeoxynucleotide strands forming a double helix

Figure 17.2 Two Models of DNA Structure

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

A gene is a DNA sequence that contains the base sequence information to code for a gene product, protein, or RNAThe complete DNA base sequence of an organism is its genomeDNA synthesis, referred to as replication, involves complementary base pairing between the parental and newly synthesized strand

Figure 17.2 Two Models of DNA Structure

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

2. The synthesis of RNA begins the process of decoding genetic information

RNA synthesis is called transcription and involves complementary base pairing of ribonucleotides to DNA basesEach new RNA is a transcriptThe total RNA transcripts for an organism comprise its transcriptome

Figure 17.3a An Overview of Genetic Information Flow

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

3. Several RNA molecules participate directly in the synthesis of protein, or translation

Messenger RNA (mRNA) specifies the primary protein sequenceTransfer RNA (tRNA) delivers the specific amino acidRibosomal RNA (rRNA) molecules are components of ribosomes

Figure 17.3b An Overview of Genetic Information Flow

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

The proteome is the entire set of proteins synthesized

4. Gene expression is the process by which cells control the timing of gene product synthesis in response to environmental or developmental cues

Metabolome refers to the sum total of low molecular weight metabolites produced by the cell

Figure 17.3b An Overview of Genetic Information Flow

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

The Central dogma schematically summarizes the previous information

Includes replication, transcription, and translationThe central dogma is generally how the flow of information works in all organisms, except some viruses have RNA genomes and use reverse transcriptase to make DNA (e.g., HIV)

Section 17.1: DNA

DNA RNA Protein

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

DNA consists of two polydeoxynucleotide strands that wind around each other to form a right-handed double helix

Each DNA nucleotide monomer is composed of a nitrogenous base, a deoxyribose sugar, and phosphate

Figure 17.4 One strand of DNA

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Nucleotides are linked by 3′,5′-phosphodiester bonds

These join the 3′-hydroxyl of one nucleotide to the 5′-phosphate of another

Figure 17.4 DNA Strand Structure

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

5’

3’

5’

3’

FIGURE 17.11 X-Ray Diffraction Study of DNA by Rosalind Franklin and R. Gosling

Two strands of DNA are oriented in opposite orientations –they are antiparallel.

The antiparallel nature of the two strands allows hydrogen bonds to form between the nitrogenous bases

Two types of base pair (bp) in DNA: (1) adenine (purine) pairs with thymine (pyrimidine) and (2) the purine guanine pairs with the pyrimidine cytosine

Figure 17.5 DNA Structure

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

3’

5’

5’

3’

Oxygen is missing in 2’deoxyribose

Page 40

Page 40

The dimensions of crystalline B-DNA have been precisely measured:

1. One turn of the double helix spans 3.32 nm and consists of 10.3 base pairs

Figure 17.6 DNA Structure: GC Base Pair Dimensions

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

2. Diameter of the double helix is 2.37 nm, only suitable for base pairing a purine with a pyrimidine3. The distance between adjacent base pairs is 0.29-0.30 nm

Figure 17.6 DNA Structure: AT Base Pair Dimensions

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

DNA is a relatively stable molecule with several noncovalent interactions adding to its stability

1. Hydrophobic interactions—internal base clustering2. Hydrogen bonds—formation of preferred bonds: three between CG base pairs and two between AT base pairs3. Base stacking—bases are nearly planar and stacked, allowing for weak van der Waals forces between the rings4. Hydration—water interacts with the structure of DNA to stabilize structure5. Electrostatic interactions—destabilization by negatively charged phosphates of sugar-phosphate backbone are minimized by the shielding effect of water on Mg2+

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Tautomerism of nucleobases• Prototropic tautomers are structural isomers that

differ in the location of protons• Keto-enol tautomerism is common in ketones• Lactam-lactim tautomerism occurs in some

heterocycles• Both tautomers exist in solution but the lactam

forms are predominant at neutral pH

FIGURE 17.7 A Tautomeric Shift Causes a Transition Mutation

DNA Structure: The Nature of MutationDNA Structure: The Nature of MutationDNA is eminently suited for information storage but not staticDespite its stability, it is vulnerable to certain disruptive forces that can cause mutations

Most negative or neutral rare positive mutations can enhance the adaptation of the organism

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Mutation types—The most common are small single base changes, also called point mutations

This results in transition or transversion mutationsTransition mutations, caused by deamination, lead to purine for purine or pyrimidine for pyrimidine substitutionsTransversion mutations, caused by alkylating agents or ionizing radiation, occur when a purine is substituted for a pyrimidine or vice versa

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Point mutations that occur in a population with any frequency are referred to as single nucleotide polymorphisms (SNPs)

Point mutations that occur within the coding portion of a gene can be classified according to their impact on structure and/or function:

Silent mutations have no discernable effectMissense mutations have an observable effectNonsense mutations changes a codon for an amino acid to that of a premature stop codon

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Inversions result when deleted DNA is reinserted into its original position in the opposite orientationTranslocation is when a DNA fragment inserts else where in the genomeDuplication is the creation of duplicate genes or parts of genes.

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Tautomeric shifts are spontaneous changes to nucleotide base structure

Amino to imino groups and keto to enol groupsIf tautomers form during replication, base mispairings can occur

The imino form of adenine does not pair with thymine; it pairs with cytosine

Several spontaneous hydrolytic reactions can cause DNA damage

Depurination or deamination is also possible, which could cause a mutation in the next round of replication

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Figure 17.7 A Tautomeric Shift Causes a Transition Mutation

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Ionizing radiation (e.g., UV and X-rays) can alter DNA structureRadiation-induced damage via free radical mechanisms can cause strand breaks, DNA-protein cross linking, ring openings, and base modificationsThe most common UV-induced products are thymine-thymine dimers

Figure 17.8 Thymine Dimer Structure

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Xenobiotics can damage DNA; classes include:Base analogues have structures so similar to bases they can be incorporated into DNA Alkylating agents cause alkylation, which is the electrophilic attack on molecules with unpaired electrons

Often add carbon-containing alkyl groupsOften base pair incorrectly, leading to transition or transversion mutations

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Nonalkylating agents—a variety of other chemicals can modify DNA structure

For example, nitrous acid and sodium nitrite can deaminate bases

Intercalating agents are planar polycyclic aromatic molecules that can distort DNA by inserting themselves between the stacked bases

Causes base pair deletion or insertionThe intercalating agent ethidium bromide is a fluorescent tag molecule used as a nucleic acid stain

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

DNA Structure: The Genetic MaterialDNA Structure: The Genetic MaterialIn the early decades of the twentieth century, life scientists believed that of the two chromosome components (DNA and protein) that protein was most likely responsible for transmission of inherited traits

The work of several scientists would lead to another conclusion

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

In 1928, Fred Griffith performed a remarkable set of experiments involving pneumococcal strains: smooth (S) and rough (R)

Identified the concept of transformation, though few accepted his discoveryFigure 17.9 Fred

Griffith’s Experiment

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

In 1944, Oswald Avery and colleagues reported the identification of Griffith’s transforming principle as DNA

Everyone was still not convincedIt was not until 1952, when Hershey and Chase demonstrated the different functions of protein and DNA with their T2 bacteriophage experiment, that DNA was accepted as the genetic material

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

The Hershey-Chase experiment confirmed DNA as the transforming principle

Figure 17.10 The Hershey-Chase Experiment

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Determining the structure of DNA became an obvious priority

Investigators including Linus Pauling, Maurice Wilkins, Rosalind Franklin, James Watson, and Francis Crick all worked toward this goal

Watson and Crick won the race for the double helix and published their findings in the journal Nature in 1953

They were awarded the Nobel Prize in chemistry in 1962

Section 17.1: DNA

Figure 17.1 The First Complete Structural Model of DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

Information used to construct the model of DNA:

1. Chemical and physical dimensions of deoxyribose, nitrogenous bases, and phosphate2. 1:1 Ratios of adenine to thymine and cytosine to guanine (Chargaff’s rules)3. X-ray diffraction studies of Rosalind Franklin

Figure 17.11 X-Ray Diffraction Study of DNA by Rosalind Franklin and R. Gosling

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

4. Wilkins and Stokes diameter and pitch estimates from X-ray diffraction5. Linus Pauling’s recent demonstration that proteins could exist in a helical conformation

Figure 17.12 X-Ray Diffraction Study of DNA by Rosalind Franklin and R. Gosling

Section 17.1: DNA

From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press