Nucleic Acids and DNA Structure

denaturation of DNA

the helix can split to form two ss DNA molecules

Genome

the total genetic information contained in a cell, an organism, or a virus

type II topoisomerases

make transient double-strand breaks in DNA

formation of nucleic acids

1. DNA and RNA are polymers of nucleotides joined by phosphodiester linkages. 2. This creates a backbone consisting of alternating sugar and phosphate groups. 3. The identity and order of the bases distinguish one polynucleotide from another (primary structure). 4. A polynucleotide has one free phosphate group at the 5' end and one free OH group at the 3' end. 5. In DNA, the sequence of the bases carries the genetic information of the organism

formation of DNA double helix

1. A purine base on one strand always hydrogen bonds with a pyrimidine base on the other strand. 2. Thus, there are complementary base pairs that always hydrogen bond together in a particular manner. 3. Adenine pairs with thymine with 2 hydrogen bonds to form an A—T base pair. 4. Cytosine pairs with guanine using 3 hydrogen bonds to form a C—G base pair.

2 different monosaccharides used to make nucleotides

1. Aldopentose D-ribose is used to make ribonucleic acid (RNA) 2. Aldopentose D-2-deoxyribose is used to make deoxyribonucleic acid (DNA)

Restriction endonucleases

1. identify specific palindromic DNA sequences and cleave them 2. Used in bacteria as defense mechanism against viral infection

DNA condensation heiarchy

1. DNA combines with histones to form nucleosomes 2. Nucleosomes zig and zag to form fiber 3. Fibers loop out from central scaffold 4. Loops also rotate to form radial structure - chromosome

Chromatin

1. DNA complexed with histones and other proteins; typically dispersed throughout the nucleus during interphase 2. one half protein by mass 3. A majority of the protein is histones 4. Histones are positively charged and bind readily to the negative phosphate groups on DNA 5. Histones are highly conserved implying they are critical for cell function and intolerant to change

How are base pairs uniform?

1. Each base pair has approximately the same width, which accounts for the near- perfect symmetry of the DNA molecule, regardless of base composition. 2. A-T and G-C base pairs are interchangeable. 3. In contrast, any other combination of bases would significantly distort the double helix (too wide or too narrow)

DNA loops that make up chromosomes

1. Fibers will wind around a central scaffold forming DNA loops that project from the center. 2. These loops also wind around the central scaffold radially stacking

Pseudogenes

1. Gene families often include pseudogenes 2. Until recently pseudogenes were thought to be nonexpressed genes with no biological function; however, it is more likely that the role of pseudogenes in the human genome is not understood

protein-DNA interactions

1. Interactions can be specific or non-specific 2. Histone binding is non-specific (any DNA can bind) 3. Other proteins needs a particular sequence or conformation to bind (specific) 4. Interactions help regulate overall structure of DNA, as well as its expression 5. DNA expression is regulated by repressors (prevent DNA from being expressed) and transcription factors (promote gene expression)

Alu sequences

1. So named because of the AluI restriction site found in the sequences 2. There are more than 1 million copies of these 300 bp sequences in the human genome

intron sequences

1. Some intron sequences are highly repetitive 2. The presence of introns (intervening sequences) increases the size of the eukaryotic genome 3. Some eukaryotic genes do not have introns (most histone genes do not)

The DNA double helix

1. The DNA model was initially proposed by Watson and Crick in 1953 based on research from Rosalind Franklin. 2. DNA consists of two polynucleotide strands that wind into a right-handed double helix. 3. The two strands run in opposite directions; one runs from the 5' end to the 3' end and the other runs from the 3' end to the 5' end. (Antiparallel) 4. The sugar-phosphate groups lie on the outside of the helix and the bases lie on the inside.

How is DNA denatured?

1. The UV absorbance of double and ss DNA at various wavelengths have similar curves, but denatured DNA has more absorbance (Hyperchromic effect). 2. Upon heating DNA, the amount of absorbance can be seen to increase within a small range of temperatures; denaturation of one part of the DNA structure destabilizes the rest. 3. The amount of heat needed to denature a DNA molecule is dependent upon the solvent, the ions in solution, the pH and number of GC base pairs (stacking energy not extra H-bond)

B form DNA

1. The bases occupy the core of the helix while the sugar-phosphate backbones wind around the outside, forming the major and minor grooves. Only the edges of the base pairs are exposed to solvent. 2. There are 10 base pairs (bp) per turn (a helical twist of 36o per bp) and, since the aromatic bases have van der Waals thicknesses of 3.4 Å and are partially stacked on each other, the helix has a pitch (rise per turn) of 34 Å. 3. The two antiparallel polynucleotide strands wind in a right- handed manner around a common axis to produce an 20Å- diameter double helix.

Multiple variants of a gene

1. Variants of the same gene may be expressed in different tissues or at different stages of development 2. Some variants are produced via alternate splicing, but many will have a completely separate gene

Chromosome

1. a compact strand of DNA that is encoded with genes; composed of chromatin (eukaryotic); formed during nuclear division 2. Consist of both DNA and protein; chromatin 3. Have telomeres on the end (red below) 4. Centromere holds replicated chromatids together

nucleotide

1. a monosaccharide, an N-containing base (Nitrogenous Base) and a phosphate group 2. formed by adding a phosphate group to the 5′-OH (Hydroxyl group on the 5th Carbon) of a nucleoside

RNA

1. a single stranded, and smaller than DNA. 2. Is only many thousands of nucleotides long. 3. Several types of RNA molecules including Ribosomal RNA (rRNA), Messenger RNA (mRNA) and Transfer RNA (tRNA). 4. As it is single stranded it has a tendency to fold in on itself to form stem-loop or hairpin loop structures (right)

packaging of eukaryotic DNA

1. confined to the nucleus and wrapped around protein assemblies called histones 2. chromatin must be further condensed during cell division 3. Chromatin during interphase can exist in two major forms: -Euchromatin - transcriptionally active -Heterochromatin - much thicker, transcriptionally inactive

How is DNA renatured?

1. cooling will reanneal it. 2. Not straightforward as annealing can cause intra or intermolecular aggregation 3. If the molecule is rapidly cooled partial hybridization may occur 4. If cooled slowly or left slightly below the melting point the molecules will eventually completely hybridize

topoisomerase

1. group of enzymes that control the supercoiling of DNA 2. alter the topological state (linking number) of circular DNA but not its covalent structure.

supercoiling of DNA, L

1. the linking number, is the number of times that one DNA strand winds around the other 2. This integer quantity is most easily counted when the molecule is made to lie flat on a plane. 3. Found by adding twist to writhing number.

DNA

1. the sequence of the bases carries the genetic information of the organism. 2. Molecules contain several million nucleotides 3. Is contained in the chromosomes of the nucleus, each chromosome having a different type of DNA 4. Humans have 46 chromosomes (23 pairs), each made up of many genes.

supercoiling of DNA, T

1. the twist, is the number of complete revolutions that one polynucleotide strand makes around the duplex axis. 2. By convention, T is positive for right- handed duplex turns so that, for B-DNA, the twist is normally the number of base pairs divided by 10 (the observed number of base pairs per turn of the B-DNA double helix in aqueous solution).

supercoiling of DNA, W

1. the writhing number, is the number of turns that the duplex axis makes around the superhelix axis. 2. It is a measure of the DNA's superhelicity. 3. When a circular DNA is constrained to lie in a plane, W 0.

Duplication of functional genes

If a cell requires large amounts of a gene product, such as the ribosome or tRNA, many copies of the gene may be found

satellite DNA

Multiple tandem repeats of short sequences like (GCGGGAC)n can be visualized via density gradients

Gene

a chromosomal segment that encodes for a single polypeptide chain or RNA molecule or plays a regulatory function

nucleoside

a nucleotide without the Phosphate Group, therefore: A nucleoside is formed by joining a carbon of the monosaccharide with a N atom of the base

renaturation of DNA

bringing two ss nucleic acids (DNA or RNA) together based on complementary base pair sequences; reannealing; to for a DNA:DNA or DNA:RNA hybrid.

type I topoisomerase

creates transient single-strand breaks in DNA