DNA STRUCTURE

NUCLEIC ACIDS Nucleic acids are polymers Nucleic acids are polymers Monomer---nucleotides Monomer---nucleotides Nitrogenous bases Nitrogenous bases Purines Purines Pyrimidines Pyrimidines Sugar Sugar Ribose Ribose Deoxyribose Deoxyribose Phosphates Phosphates +nucleoside=nucleotide +nucleoside=nucleotide } Nucleosides

DNA Functions 1. Storage of genetic information 2. Self-duplication & inheritance. 3. Expression of the genetic message. DNA’s major function is to code for proteins. Information is encoded in the order of the nitrogenous bases.

The Sugars

The Bases PURINES PYRIMIDINES

Bases of DNA (and RNA) RNA only DNA only Purines: Pyrimidines:

Nucleotides

Chemical Structure of DNA and RNA Figure 4.1 RNA DNA Nucleotide Nucleoside 1’ 2’ 4’ The C is named 1’-5’

make up 13-34% of the dry weight in bacteria deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) O CC CC Base H H or OH HH H H CH 2 OP OH O HO Nucleotide: a building block Sugar: RNA – ribose (OH) DNA – deoxyribose (H) Bases: adenine (A), cytosine (C), guanine (G), thymine (T) RNA uses uracil (U) instead of thymine Nucleoside: base + sugar certain nucleotides serve as a storage of energy and reducing power e.g.ATP -> ADP -> AMP hydrolysis (energy is released) Nucleic Acids

DNA Stabilization– Complementary Base Pairing

DNA Stabilization-Base Stacking

DNA Stabilization--H-bonding between DNA base pair stacks

Advantages to Double Helix Stability---protects bases from attack by H 2 O soluble compounds and H 2 O itself. Stability---protects bases from attack by H 2 O soluble compounds and H 2 O itself. Provides easy mechanism for replication Provides easy mechanism for replication

14 Types of DNA Structures Three forms of DNA Three forms of DNA A form: right handed helix A form: right handed helix B form: the most likely biological conformation, right handed helix B form: the most likely biological conformation, right handed helix Z form: form a left handed helix; Z form: form a left handed helix; Need details ??

FORMS OF DNA

DNA supercoiling refers to the over- or under-winding of a DNA strand. DNA supercoiling refers to the over- or under-winding of a DNA strand. Supercoiling is important in a number of biological processes, such as compacting DNA. Additionally, certain enzymes such as topoisomerases are able to change DNA topology to facilitate functions such as DNA replication or transcription. Supercoiling is important in a number of biological processes, such as compacting DNA. Additionally, certain enzymes such as topoisomerases are able to change DNA topology to facilitate functions such as DNA replication or transcription. Mathematical expressions are used to describe supercoiling by comparing different coiled states to relaxed B-form DNA. Mathematical expressions are used to describe supercoiling by comparing different coiled states to relaxed B-form DNA. As a general rule, the DNA most organisms is negatively supercoiled ?? As a general rule, the DNA most organisms is negatively supercoiled ??

G-C Content A=T, G=C, but AT ≠GC A=T, G=C, but AT ≠GC Generally GC~50%, but extremely variable Generally GC~50%, but extremely variable EX. EX. Slime mold~22% Slime mold~22% Mycobacterium~73% Mycobacterium~73% Distribution of GC is not uniform in genomes Distribution of GC is not uniform in genomes

CONSEQUENCES OF GC CONTENT GC slightly denser GC slightly denser  Higher GC DNA moves further in a gradient  Higher GC DNA moves further in a gradient Higher GC of base pairs=more stable DNA, i.e. the strands don’t separate as easily. Higher GC of base pairs=more stable DNA, i.e. the strands don’t separate as easily.

19 Chemical Properties of DNA Factors that affect DNA structure Factors that affect DNA structure Temperature: denaturation (can be reversible) Temperature: denaturation (can be reversible) pH: high pH can denature DNA pH: high pH can denature DNA Salt concentration: lowering salt concentration can denature DNA Salt concentration: lowering salt concentration can denature DNA Chemicals: sodium hydroxide, formamide can also denature DNA Chemicals: sodium hydroxide, formamide can also denature DNA

DNA is Dynamic Like proteins, DNA has 3 º structure Like proteins, DNA has 3 º structure Why so many deviations from normal conformation? Why so many deviations from normal conformation? Effects on transcription (gene expression) Effects on transcription (gene expression) Enhances responsiveness Enhances responsiveness May also serve in packaging May also serve in packaging

Denaturation of DNA The T at which ½ the DNA sample is denatured is called the melting temperature (T m )

Importance of T m Critical importance in any technique that relies relies on complementary base pairing Critical importance in any technique that relies relies on complementary base pairing Designing PCR primers Designing PCR primers Southern blots Southern blots Northern blots Northern blots hybridization techniques hybridization techniques

Factors Affecting T m G-C content of sample G-C content of sample Presence of intercalating agents (anything that disrupts H-bonds or base stacking) Presence of intercalating agents (anything that disrupts H-bonds or base stacking) Salt concentration Salt concentration pH pH

Renaturation Some parameters can be induced to renature (anneal) under proper conditions. Factors to consider: Some parameters can be induced to renature (anneal) under proper conditions. Factors to consider: Temperature Temperature Salt concentration Salt concentration DNA concentration DNA concentration Time Time

Hydrolysis by Enzymes Nuclease—catalyzes hydrolysis of phosphodiester backbone Nuclease—catalyzes hydrolysis of phosphodiester backbone Exonucleases?? Exonucleases?? Endonucleases?? Endonucleases?? Ribozymes?? Ribozymes??

Restriction Enzymes??

Chromosomes in eukaryotes and prokaryotes are different PROKARYOTESEUKARYOTES single chromosome plus plasmids many chromosomes circular chromosome linear chromosomes made only of DNA made of chromatin, a nucleoprotein (DNA coiled around histone proteins) found in cytoplasm found in a nucleus copies its chromosome and divides immediately afterwards copies chromosomes, then the cell grows, then goes through mitosis to organise chromosomes in two equal groups