Chapter 9 Molecular Structure of DNA and RNA

9.1 - 9.7

Molecular Genetics

the study of DNA structure and function at the molecular level.

Deoxyribonucleic Acid (DNA)

the genetic material. It is a double-stranded structure, with each strand composed of repeating units of deoxyribonucleotides.

Ribonucleic Acid (RNA)

a nucleic acid that is composed of ribonucleotides. In living cells, RNA is synthesized via the transcription of DNA.

Genetic material must meet four criteria to fulfill its role:

Information, Transmission, Replication, and Variation

Information

must provide the instructions to construct an entire organism

Transmission

must be capable of being transmitted from parent to offspring without change

Replication

Must be capable of being copied accuratetly

Variation

Must vary (by mutation) in ways that can account for phenotypic differences within each species.

Frederick Griffith

A scientist that studied the bacteria streptococcus pneumoniae. The bacteria contained two strains: S Strait and R Strain.

S (Smooth) Strain

A strain of the bacteria streptococcus pneumoniae. It had a capsule and virulent.

R (Rough) Strain

A strain of the bacteria streptococcus pneumoniae. It lacked a capsule and nonvirulent.

When Type S Bacteria were injected the live mouse…

It proliferated within in the mouse’s bloodstream and ultimately killed the mouse. The bacteria also lived.

When Type R Bacteria were injected into the live mouse…

The mouse lived. No living bacteria survived.

When Heat-killed Type S Bacteria were injected into the live mouse…

The mouse lived. No living bacteria survived.

When Heat-killed Type S Bacteria AND Living Type R Bacteria were injected into the live mouse…

The mouse died. Living Type S bacteria survived.

Results from Griffith’s experiment…

The Dead Type S bacteria transformed the Type R bacteria into Living Type S Bacteria via transformation. The substance that caused this transformation was unidentified but was termed the “transforming principle”.

Oswald Avery, Colin MacLeod, and Maclyn McCarty

Used Griffith’s observations to identify the unknown transforming principle. They prepared extracts from Dead Type S Bacteria strains that contained DNA, DNase, RNase, and protease. They mixed Live Type R Bacteria and Dead Type S Bacteria containing a certain extract together to see if transformation occur.

Result of Avery, MacLeod, and McCarty’s experiment…

Only DNA, RNase, and protease transformed Dead Type S Bacteria into Live Type S Bacteria. Since RNase breaks down RNA and protease breaks down proteins, it proved RNA and Proteins are not the genetic material. Since DNase (that breaks down DNA) did not transform the bacteria, this ultimately proved that DNA is the genetic material and the transforming principle.

Alfred Hershey and Martha Chase

Scientists that proved that DNA is the genetic material of viruses. Their research centered on the study of a virus known as T2 bacteriophage, a virus that infects bacteria called Escherichia coli. Their experiment consisted of phages containing radioactive isotopes, phosphporus-32 and sulfur-32, to infect bacterial cells. Phosphorus represented DNA because phosphorus atoms are found in DNA but not proteins. Sulfur represented proteins because sulfur atoms are found in proteins but not DNA.

Result of Hershey and Chase experiment…

Most of 32-P had entered bacterial cells, whereas most of 35-S remained outside the cells. These results were consistent with the idea that the genetic material of bacteriophages is DNA, not proteins.

Nucleic Acids

DNA or RNA. A macromolecule that is composed of repeating nucleotide units.

Nucleotides

The building blocks of nucleic acids (DNA and RNA).

One nucleotide has three components:

A pentose sugar, a nitrogenous base, and at least one phosphate group.

Pentose Sugar

Deoxyribose and Ribose.

Purine

a type of nitrogenous base that has a double-ring structure. Examples are adenine and guanine.

Pyrimidines

a type of nitrogenous base that has a single-ring structure. Examples are cytosine, thymine, and uracil.

DNA contains…

deoxyribose, adenine, thymine, guanine, cytosine, one or two phosphate group(s)

RNA contains…

ribose, adenine, uracil, guanine, cytosine, and one or two phosphate group(s)

Adenine and guanine are…

purines

cytosine, thymine, and uracil are…

pyrimidine

The base is always attached to…

the 1-prime carbon atom

the phosphate group is always attached to…

the 5-prime carbon atom

the OH (hydroxyl) group is always attached to…

the 3-prime carbon atom

nucleoside

structure in which a base is attached to a sugar, but no phosphate is attached to the sugar. an example is if ribose is attached to adenine, this nucleoside is called adenosine. if deoxyribose is attached to adenine, this nucleoside is called deoxyadenosine.

nucleotide

the covalent attachment of one or more phosphate molecules to a nucleoside. an example is if a nucleotide contains ribose, adenine, and one phosphate, it is named adenosine monophosphate (AMP).

phosphodiester linkage

in a DNA or RNA strand, a linkage in which a phosphate group connects two sugar molecules via two ester bonds.

backbone

the portion of a DNA or RNA strand that is composed of covalently linked phosphates and sugar molecules. it is negatively charged due to the negative charge on each phosphate group.

a phosphodiester linkage involves.….

1) attachment of a phosphate to the 3-prime carbon in one nucleotide.

2) attachment of THE SAME phosphate to the 5-prime carbon in the next nucleotide.

directionality

In DNA and RNA, refers to the 5′ to 3′ orientation of nucleotides in a strand.

Rosalind Franklin

Used X-ray diffraction to study wet DNA fibers. She made marked advances in X-ray diffraction techniques while working with DNA.

Result of Franklin’s research…

• The pattern was consistent with a helical structure.

• The diameter of the helical structure was too wide to be only single-stranded helix.

• The diffraction pattern indicated that the helix contains about 10 base pairs (bp) per complete turn.

These observations were instrumental in solving the structure of DNA.

Erwin Chargaff

Discovered that the amount of adenine was similar to that of thymine, and the amount of guanine was similar to that of cytosine.

Chargaff’s rule

the observation that in DNA the amounts of A and T are equal, as are the amounts of G and C. A = T, G = C.

James Watson and Francis Crick

Using molecular models. they determined:

1) two strands in DNA molecule. 2) the nitrogenous bases are in the middle, between the two strangs. 3) adenine in one strand is hydrogen bonded to a thymine in the other strand. 4) cytosine in one strand is hydrogen bonded to a guanine in the other strand.

base pair (bp)

the structure in which two nucleotides in opposite strands of DNA hydrogen bond with each other. For example, an A-T base pair is a structure in which an adenine-containing nucleotide in one DNA strand hydrogen bonds with a thymine-containing nucleotide in the complementary strand.

AT/GC Rule

in DNA, the phenomenon in which an adenine base in one strand always hydrogen bonds with a thymine base in the opposite strand, and a guanine always hydrogen bonds with a cytosine. it also gives the notion that purines always bonds with a pyrimidines.

G and C have how many hydrogen bonds?

three hydrogen bonds

A and T have how many hydrogen bonds?

two hydrogen bonds

DNA sequences with high proportions of [blank] tend to form more stable double-stranded structures.

G and C

complementary

describes sequences in two DNA strands that match each other according to the AT/GC rule. For example, if one strand has the sequence 5′ -ATGGCGGATTT-3′ , then the complementary strand must be 3′ -TACCGCCTAAA-5′ ; in DNA, complementary sequences are also antiparallel.

antiparallel

refers to an arrangement in a double helix in which one strand is running in the 5′ to 3′ direction, while the other strand runs in the 3′ to 5′ direction.

base stacking

In DNA, the orientation of base pairs in which the flat sides of the bases are facing each other. Along with hydrogen bonding, it is a structural feature that stabilizes the double helix by excluding water molecules, which are polar. The stability of the helical structure of the DNA backbone depends on the hydrogen bonding between bases in the base pairs and also on (term).

grooves

in DNA, the indentations where the atoms of the bases are in contact with the water in the surrounding cellular fluid. In B DNA, there is a smaller minor groove and a larger major groove.

The DNA helix has two grooves winding around its outer surface:

a narrow minor groove and a wider major groove.

minor groove

a narrow indentation in the DNA double helix in which the bases have access to water.

major groove

a wide indentation in the DNA double helix in which the bases have access to water.

The DNA double helix can form different types of structures:

B DNA and Z DNA.

B DNA

the predominant form of DNA in living cells. It is a right-handed DNA helix with 10 bp per turn. The bases tend to be centrally located, and the hydrogen bonds between base pairs are oriented perpendicular to the central axis.

Z DNA

a left-handed DNA double helix that is found occasionally in living cells. the helical backbone appears to zigzag slightly as it winds itself around the double-helix structure. has 12.0 bp in one 360 degrees turn. The bases are substantially tilted relative to the central axis.

DNA methylation

A regulatory mechanism in which an enzyme covalently attaches a methyl group (-CH3) to a base in DNA. In eukaryotes, the base is cytosine. In prokaryotes, both adenine and cytosine can be methylated.

RNA Structure

• Usually single-stranded
• Nucleotides contain ribose
• The nitrogenous bases are adenine, guanine,
cytosine, and uracil
• Usually much shorter than DNA
• Nucleotides linked by phosphodiester bonds
• Has directionality

Complex RNA Structure

• Under physiological conditions RNA can have double-stranded regions and display complex 3D structure
• These structures are created by base pairing
• Base pairing may occur between nucleotides in the same molecule (intramolecular) or between nucleotides of different strands (intermolecular)
• Structure of biological molecules is intimately related to their function. For example, tRNA^PHE depicts a antiparallel ribbons structure.