Notes 

Chapter 11 Nucleic Acid structure, DNA replication, and chromosome structure

DNA  has 4 roles (copy p. 215-216)

1)      Information    3) Transmission

2)      Replication      4) variation

*In 1183, August Weisman and Karl Nageli thought a chemical in living cells was responsible for transmission of traits from parents to offspring. 

*Read Griffith’s experiment on P. 216

*and Feature investigation

Chromosomes: The cellular structures that contain the genetic material

Transformation: Process by which a substance from dead type S bacteria is transforming the type R bacteria into type S bacteria.

DNAase – enzyme that digest DNA

RNAase – enzyme that digest RNA

Protease – enzyme that digest proteins

1952 Heshey and Chase studied the T2Bacteriophage. (fig. 11.4 p. 220

A bacteriophage (or a phage): A virus that infects bacteria cells.(Fig. 11.3 p. 219)

Four parts head (capsid), sheath, tail fibers, and base plate.

*DNA found in the head

*Phage coat made of protein.

* Must inject genetic material into the cytoplasm of a host cell.

Nucleic acids: DNA and RNA

Supernate – the lighter liquid in a centrifuge.

DNA was discovered in 1869 by Friedrich Miescher.

Structural Features of DNA

(1)Nucleotides: The building blocks of DNA

*Nucleotides contain a phosphate, a sugar and a Base (p.221)

(2)Strand: A structure of DNA (or RNA) formed by the covalent linkage of nucleotides in a linear manner.

(3)Double helix: The form that takes the two strands of DNA that have hydrogen-bonded with each other.

(4)Chromosomes: In living cells, the association of DNA associated with an array of different proteins.

(5)Genome: Complete complement of an organism’s genetic material.

Nucleotides contain a phosphate, a sugar and a base.

Purine and Pyrimidine: The two categories into which the five bases are subdivided.

Adenine (A)

Guanine (G)

Purine base (double-ring structure)

Thymine (T)

Cytosine (C)

Uracil (U)

Pyrimidine base (single-ring structure)

*The carbons in the sugar are numbered 11,21,31,41, and 51.  The base is attatched at the 11 carbon and the phosphate group is attatched at the 51 carbon.

Phosphodiester linkage: The linkage of DNA and RNA strands(A covalent bond between phosphorus and oxygen)

*The phosphorous is in the phosphate group of one base and the oxygen is in the sugar molecule of the other nucleotide.

Backbone: The phosphates and sugar molecules form the backbone of DNA or RNA strands.

*The phosphate group is connected to the 51 carbon of one nuecleotide and the 31 carbon of another nucleotide.

Directionality: A strand has a directionality based on the orientation of sugar molecules within that strand.              (Fig. 11.8 p. 222)

*51 carbon has a phosphate group

*31 carbon has an OH group (hygroxyl)

DNA sequence is usually 51 – ACG-31

Base pairs: The structure of DNA is stabilized by hydrogen bonding between the bases in opposite strands to from base pairs.

Table 11.1 p. 223

James Watson and Francis Crick dsinged a 3-D model of DNA based on Rosalind Franklin’s x-ray diffraction and Erwin Chargraff’s base composition.

*x-ray diffraction showed helical structure with eniform diameter. (2nm)

*Base composition showed A and T were about equal and G and C were about equal.

AT/GC rule(chargraff’s rule): DNA contains equal amount of A and T, and equal amount of G and C.

Complementary: Due to the AT/GC rule, the base sequences of two DNA strands are complementary to each other.

Antiparallel: The arrangement in DNA where one strand runs in the 5’ to 3’ direction while the other strand is oriented in the 3’ to 5’ direction.

Grooves: The indentations where the atoms of the base make contact with the surrounding water.

Major groove/Minor groove: These two grooves spiral around the double helix.

Major grooves are sites where proteins bind to a particular sequence of bases and affect the expression of a gene.

11.3 An overview of DNA Replication

DNA replication: The process in which DNA id copied.

*The original DNA strand serves as a template for the synthesis of new DNA strands

Daughter strands: The two newly made strands.

Parental strands: The original strands.

Models of DNA replication

A)Semiconservative mechanism: The double-stranded DNA is half conserved following the replication process such that the new double-stranded DNA contains one parental strand and one daughter strand.

B)Conservative mechanism: Both parental strands of DNA remain together following DNA replication.

*Meselson and Stahl used density measurements to investigate the three proposed mechanisms of DNA replication in the 195’s.

C)Dispersive mechanism: Segments of parental DNA and newly made DNA are interspersed in both strands following the replication process.

Template strands:  During the replication process the two complementary strands of DNA separate and serve as template strands (also called parental strands) for the synthesis of new daughter strands of DNA.

11.4 Molecular Mechansism of DNA Replication.

Origin of replication: A site within a chromosome that serves as a starting point for DNA replication.

Replication fork: The area where two DNA strands have separated and new strands are being synthesized.

Bidirectional replication: The process in which DNA replication proceeds outward from the origin in opposite directions.

DNA helicase: The enzyme that separates the two strands of DNA at each fork and moves outward from the origin.

*The helicase moves from the 5 to the 3 direction of one DNA Strand.

*ATP is used in this process.

DNA topoisomerase: The action of DNA helicase generates additional coiling just ahead of the replication fork that is alleviated by another enzyme called DNA topoisomerase.

An enzyme that uncoils the DNA just ahead of the replication fork so the DNA helicase can move along the strand.

p. 228 Fig 11.6

Single – strand binding proteins = These proteins coat the single strands of template DNA and prevent them from reforming a double helix.

*This allows room for complimentary base pairs to bind.

DNA polymerase: This enzyme is responsible for covalently linking nucleotides together to form DNA strands.

*Identified by Arthur Kornberg in the 1950’s.

Deoxynucleoside triphosphates: Free nucleotides with three phosphates groups.  That bind via a hydrogen bond to template strand according to the AT/GC rule.

*DNA polymerase breaks a bond between the first and second phosphate and then attaches the resulting nucleotide with one phosphate group to the 3 end.

*This exergonic provides energy to connect adjacent nucleotides.

*Bacteria Syntheses DNA at a rate of 500 nucleotides/second, white eukaryotes made DNA at a rate of 50/sec.

DNA primase: This enzyme is required if the template strand is bare.

Primer: A short segment of RNA, 10 to 12 nucleotides in length.

*These strands start prime DNA replication

*DNA can only synthesize in a 5 to 3 direction.

Leading strand: The strand that is made in the same direction that the fork is moving.

Lagging strand: The strand that is made as a series of small fragments that are subsequently connected to each other to form a continuous strand.

*p. 230 Figure 11.19*

Okazaki fragments: Short segments of DNA synthesized in the lagging strand during DNA replication.

*Named after Reiji and Tuneko Okazaki who discovered them in the 1960’s.

DNA ligase: This enzyme catalyzes the formation of a covalent bond between these two DNA fragments to complete the replication process in the lagging strand. (Enzyme that connects the two Okazaki fragments)

DNA Reclication is very accurate

*Only 1 in 100 million nucleotides is a mistake made.*

Proofreading: Event in which a DNA polymerase identifies a mismatched nucleotide and removes it from the daughter strand.

Telomere: Region at the ends of eukaryotic chromosomes.

Telomerase – Enzyme that attatches many copies of the organisms repeat sequence at the end of the DNA Strand to prevent shortening.

Senescent: Cells that have doubled many times and have reached a point where they have lost the capacity to divide any further.

*All mammals appear to have a predetermined life span.  Finite number of doubling.

*As a cell ges, the telomeres shorten. (cause or effect)

*In 90% of all cancers, telomeres have been present in ghigh levels.

*11.5 Molecular Structure of Eukaryotes chromosomes.

Chromatin: The DNA-protein complex that makes up eukaryotic chromosomes.

Histones: Proteins that DNA wrap around.

Nucleosome: A repeating structural unit of eukaryotic chromatin, in which DNA is wrapped around histones.

*Shortens DNA sevenfold.

Linker DNA – The DNA the spans from one nucleosome to another nucleosome (20 -100bp)

30-nm fiber: A more compact structure that is 30 nm in diameter into which nucleosome units are organized.

p. 235 Figure 11.24

Nuclear matrix: A filamentous network of proteins that is found inside the nucleus and lines the inner nuclear membrane. The nuclear matrix serves to organize the chromosomes.

Nuclear lamina: A collection of filamentous proteins that lines the inner nuclear membrane; part of the nuclear matrix.

Radial loop domains: Often 25,000 to 200,000 base pairs in size; they are anchored to the nuclear matrix.

Heterochromatin: The highly compacted regions of chromosomes.

Euchromatin: The less condensed regions of chromosomes.

*Prior to cell division, chromosomes become more compacted or condensed.  This aids in the alignment of chromosomes during metaphase. (Chap. 15)