GCD 3022 chapter 9- Molecular structure of DNA and RNA

Molecular Genetics

the subfield of biology that studies the molecular structure and function of genes

Information, Transmission, Replication, Variation

The genetic material must meet four criteria

Information

DNA must provide the blueprint for determining the inherited traits of an organism

Transmission

during replicationmthe genetic material must be passed from parent to offspring

Replication

DNA must be copied

variation

within any species, a significant amount of phenotypic differences occur

Griffiths experiment

S. pneumoniae was able to transfer its DNA to non lethal streptococcus strand which demonstrated Variation, transmission, replication, and information

transformation

process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria

DNase

breaks down DNA

RNase

degrades RNA

protease

enzyme that digests protein

bacteriophage

A virus that infects bacteria

nucleic acids

DNA and RNA

- acidic molecules that release hydrogen ions in solution and have a negative charge at neutral PH

Nucleotides

Basic units of DNA molecule, composed of a sugar, a phosphate, and one of 4 DNA bases

strand

nucleotides that are covalently linked to one another

double helix

two strands of dna interact with each other through hydrogen bonds to form this structure

Deoxyribose

A five-carbon sugar that is a component of DNA nucleotides

Ribose

A five-carbon sugar present in RNA

Adenine

The base that pairs with Thymine in DNA, and Uracil in RNA

purine

Guanine

The base that pairs with Cytosine in DNA

purine

Cytosine

The base that pairs with Guanine with DNA

pyrimidine

thymine

A component of nucleic acid that carries hereditary information in DNA in cells. Chemically, it is a pyrimidine base.

uracil

a nitrogen-containing base found in RNA (but not in DNA) and derived from pyrimidine

clockwise

which direction are deoxyribose and ribose numbered where the fifth carbon is outside the ring

1'

which carbon is the nucleotide connected to

5'

which carbon are phosphate groups attached to

3'

which carbon has an OH group attached to it which is important in linking nucleotides to form covalent linkages.

Nucleoside

base + sugar

guanosine

guanine + ribose

cytidine

cytosine + ribose

uridine

nucleoside of uracil

adenosine

a nucleoside; a combination of ribose

deoxyadenosine

Adenine + deoxyribose

deoxyguanosine

Guanine + Deoxyribose

deoxythymidine

thymine + deoxyribose

deoxycytidine

cytosine + deoxyribose

ester bond

how are sugar groups attached to a phosphate group

phosphodiester linkage

a phosphate group connects two sugar molecules via two ester bonds

backbone

the phosphates and sugar molecules of a strand

directionality

all sugar molecules have the same orientation in a strand in the direction of 5' to 3'

ball and stick model

a molecular model that proved the alpha helix secondary structure of proteins which was a step in discovering the shape of dna

X-ray diffraction

when a purified substance such as dna is subjected to x-rays it produces a well defined diffraction pattern if the molecular structure has a repeating pattern

- helped discover the double helix shape of DNA

- determine 10 bp per rotation

AT GC rule

the number of A nucleotides = the number of T and G=C

2

how many hydrogen bonds are within A-T linkage

3

how many hydrogen bonds are between G-C

Chargaff's Rule

A=T and C=G

- helped determine the shape of DNA by helpind watson and Crick build a ball and stick model of DNA

Base pairs

stabilizes a double helix through hydrogen bonding

there are 10 of these in one 360 degree turn of a double helix

antiparallel

The opposite arrangement of the sugar-phosphate backbones in a DNA double helix.

Base Stacking

Stabilizing hydrophobic interactions between bases in the same strand of DNA.

- structural feature stabilizes the double helix by excluding water molecules which are polar.

- DNA molecules are oriented so that the flat sides of the bases are facing each other

Grooves

indentations where the atoms of the bases are in contact with the surrounding cellular fluid

minor groove

A smaller groove that spirals around the DNA double helix.

major groove

the larger of the two grooves in the DNA double helix

B DNA

Right-handed helical structure of DNA that exists when water is abundant; the secondary structure described by Watson and Crick and probably the most common DNA structure in cells.

Z DNA

Secondary structure of DNA characterized by 12 bases per turn, a left-handed helix, and a sugar-phosphate backbone that zigzags back and forth.

- plays a role in transcription (certain proteins recognize it)

-affects level of compaction

Methylation

a biochemical process that influences behavior by suppressing gene activity and expression

- occurs when cytosine group attaches to a methyl group

anticodon

group of three bases on a tRNA molecule that are complementary to an mRNA codon

acceptor site

binds incoming aminoacyl-tRNA

RNA world

period on earth in which RNA molecules but not DNA or proteins were replication and is carried out by three key functions

1- information storage in its nucleotide base sequence

2- self replication by functioning as a ribozyme and using RNA as a template to make complementary RNA molecules

3- Catalytic activity

glycocidic bond

bond between monosaccharides

- this is how base pairs are connected

three

how many atoms does it take to make a hydrogen bond

greater catalytic potential

why did proteins replace RNA

Glycocydic bond

bond between a base and a DNA or RNA sugar