DNA, RNA AND GENETICS

who discovered DNA

Friedrich miescher

how did miescher discover DNA

• he collected bandages from a nearby clinic and washed off the pus

• experimented and isolated a new molecule- nuclein- from the cell nucleus

• determined that nuclein was made up of H, O, N and P and there was a unique ratio of P:N

• also isolated nuclein from other cells and later used salmon sperm as a source

Avery’s experiment

• neutralised bacteria is harmless to animals

• extracts from pathogenic bacteria are harmful- becomes infectious (transformed)

• extracts from pathogenic bacteria treated with proteinases- are still infectious (transformed)

• extracts from pathogenic bacteria treated with nucleases-are not infectious

• thus DNA is the genetic material

what is the flow of genetic information

DNA to RNA to protein

how many ways can drugs target DNA

indirectly by targeting the processing enzymes

directly by interacting with the structure

purine bases

adenine

guanine

attaches to the sugar residue through N9

pyrimidine bases

cytosine

thymine

attaches to the sugar residue through N1

what is the sugar molecule that attaches

beta-D-2’-deoxyribose sugar

it connects to form a polymer through a phosphate diester bond at the 3 and 5 positions

adenine

guanine

thymine

cytosine

general nucleotides structure

phosphate

sugar: ribose- X = OH (RNA) 2’-deoxyribose: X-H (DNA)
nucleobase

RNA equivalent of thymine

uracil

nomenclature of a nucleotide with one phosphate- example adenine

deoxygadenosine 5’-monophosphate (dAMP)

nomenclature of a nucleotide with two phosphate- example adenine

deoxygadenosine 5’-diphosphate (dADP)

nomenclature of a nucleotide with three phosphate- example adenine

deoxygadenosine 5’-triphosphate (dATP)

DNA is double stranded

it forms a helical structure- sugar phosphate backbone lies on the outside and the bases on the inside

formed through hydrogen bonding

base pairs are stacked with van de Waals interactions between them

chains are complimentary

how many rings are in pyrimidine

1 carbon ring

how many rings does purine have

2 carbon rings

base pairs

A and T

C and G

is the helix right or left handed

right handed

DNA is stabilised by stacking

• the base pairs are flat

• pi-pi interactions

• stabilising energy from the vertical pi-pi stacking interaction between sets of pairs in the stack

  • they are more hydrophobic than sugar phosphate backbone

• sugar phosphate backbone is negatively charged

DNA structure is polyanionic

• pKa of a phosphodiester is about 1, which gives DNA water solubility

• DNA will carry counter ions inside the cells (Na⁺, K⁺, Mg²⁺)

• hydrophobic effect

  • when hydrophobic groups come together

  • better than van Der Waals forces

  • water surrounds DNA

  • spine of hydration in the grooves

hydrogen bond donors

NH and OH

hydrogen bond acceptor

O,N and F

difference between thymine and uracil

thymine has a CH₃ group so it can have a hydrophobic interaction and differentiate between AT & TA base pair

nucleosome

8 histone proteins around which DNA wraps 1.65 times

chromatin

a coiled string of nucleosomes

DNA tertiary structure

DNA is packed into the cell through interaction with histones to form nucleosomes

Using the DNA

• double helix coils into a 3D shape- supercoiling

• double helix has to unravel during replication

• unravelling leads to strain

• relieved by enzyme-catalysed cutting and repair of DNA chain

• crossing an intact strand through the broken strand

• topoisomerase

the action of topoisomerase II

• the enzyme pulls the chains apart to create a gap

• the residues form covalent bonds to DNA

• the intact strand of DNA is passed through the gap

• the gap is sealed

do DNA strands run parallel or antiparallel

antiparallel to each other

where do proteins bind

in the major groove

RNA vs DNA

1. sugar: deoxyribose (DNA) vs ribose (RNA)

2. nucleobase: thymine (DNA) vs uracil (RNA)

3. secondary structure: double (DNA) vs single strand (RNA)

4. size: DNA » RNA (75 to a few thousand nucleotides)

is RNA more or less stable than DNA

less stable

you don’t want RNA to stick around

RNA structure

• RNA double helices are in the A-form (they have a wide, shallow minor groove and a deep, narrow major groove)

• can form hairpins, loops and bulges

types of RNA

• mRNA

• tRNA

• rRNA

• snRNA

• snoRNA

• miRNA

• siRNA

• lncRNA

messenger RNA (mRNA)

encodes proteins

75-3000 nucleotides in length

25% of total RNA

relays the code for a protein from DNA to the protein production site

transfer RNA (tRNA)

acts as adaptor between mRNA and amino acids

75-90 nucleotides in length

16% of total RNA

the adapter unit linking the triplet code on mRNA to specific amino acids

ribosomal RNA (rRNA)

forms the ribosome function

100-3100 nucleotides in length

82% of total RNA

present in ribosomes

small nuclear RNA (snRNA)

functions in various nuclear processes

small nucleolar RNA (snoRNA)

facilitates chemical modification of RNAs

micro RNA (miRNA)

regulates gene expression

small interfering RNA (siRNA)

silences gene expression

long non-coding RNA (lncRNA)

regulates gene expression

what is structurally different between RNA and DNA

RNA has a 2’-OH group

3 types of DNA replication

semi-conservative

conservative

dispersive

DNA replication

before a cell can divide it must duplicate all its DNA

the enzyme DNA polymerase catalyses the addition of a nucleotide to the 3’-OH group of the polynucleotide chain

base pairing happens first

DNA synthesis

• new DNA is made by enzymes called DNA polymerase

• it requires a template and primer

• synthesise DNA only in the 5’ to 3’ direction

• DNA polymerase proof-reads as it moves along

Replication fork

leading strand

one strand that is continuously replicated

the lagging strand

is replicated in small sections (Okazaki fragments which are later joined together)

DNA transcription and translation

Transcription

the copying of a segment of DNA which codes for a specific protein

RNA polymerase

• RNA polymerase attaches to the template DNA strand

• catalyses production of complementary RNA

• polymerases are large enzymes composed of approximately 12 subunits and when active on DNA, they are also typically complexed with other factors

Process of transcription

• transcription initiation is when the RNA polymerase binds to the DNA upstream (5’) of the gene at a specialised sequence called a promoter

• then the DNA double helix unwinds and RNA polymerase reads the template strand- strand elongation

  • adding nucleotides to the 3’ end of the growing chain

• transcription continues until a terminator sequence

• RNA polymerase reads the template strand

• mRNA is therefore a complement of the template strand so it’s the same as the coding strand

mRNA transcripts

• modification to the mRNA can occur where a middle section (intron) is removed

• end regions (exons) are then spliced together

translation

• the process of protein synthesis after transcription of DNA to RNA

• mRNA is decoded in a ribosome outside the nucleus to produce a specific amino acid chain

• the ribosome facilitates decoding

  • inducing the binding of complementary tRNA anticodons to the mRNA codons

  • the tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is ‘read’ by the ribosome

anticodon

contains 3 bases that are specific for the attached amino acid base pairs to the complementary triplet codon on mRNA

codon

sequence of 3 DNA or RNA nucleotides that correspond to a specific amino acid or stop signal

stop codons

UAA

UAG

UGA

start codon

AUG

3 phases of translation

1. initiation

2. elongation

3. termination

Initiation

• the ribosome assembles around the target mRNA

• the first tRNA is attached at the start codon

elongation

• the last tRNA transfers the amino acid it carries to the large ribosomal subunit which binds it to the previous one (transpeptidation)

• the ribosome then moves to the next mRNA codon to continue the process creating an amino acid chain

termination

• when a stop codon is reached, the ribosome releases the polypeptide

• the ribosomal complex moves onto the next mRNA to be translated

translocation process

• as the ribosome travels along the mRNA it reveals the triplet code

• the growing chain is transferred to the new tRNA which enters at the aminoacyl ‘a’ site

• the empty/ used tRNA leaves the peptidyl ‘p’ site

• the ribosome can then move along the mRNA towards the next codon

• a new tRNA can come and join up, but only if it has the correct anticodon for the codon on the mRNA

• the empty/used tRNA leaves and the ribosome moves along and the new incoming tRNA can join

Genome

the entire genetic material present in the cell of an organism

genetic code

the rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences of codons) into proteins

genetics

branch of biology concerned with the study of genes, genetic variation and heredity in organisms

genetic inheritance

the transfer of traits from parents to offspring

first studied by Mendel

Mendel’s experiment

he crossed plants through cross-pollination by transferring the pollen the flower from one flower to another

he studied 7 traits of pea plants:

1. seed shape

2. seed colour

3. flower colour

4. flower position

5. pod shape

6. pod colour

7. stem length

dominant trait

a trait is expressed even if only one version is present

can have a homozygous genotype (2 dominant) or heterozygous genotype (1 dominant and 1 recessive)

recessive trait

trait is only expressed if both versions are present

only appear in homozygous genotypes

law of segregation

mendel concluded that each trait is controlled by discrete factors:

• for every trait, there exist 2 such factors

• these discrete factors get separated during gamete formation and so that every gamete gets only one of the 2 discrete factors

• they join together as the gametes fuse to form a zygote

homologous chromosome

the pairs are identical in structure and composition

there are 22 pairs

non-homologous chromosomes

they have different compositions and structures

sex chromosomes are non-homologous

gene

a segment of DNA that codes for the synthesis of one particular protein

allele

the portion of a chromosome that carries a particular gene

you get one maternal one and one paternal one

genotype

the entire genetic makeup or all the alleles present in an individual

phenotype

the traits observed in an individual

epigenetic

any heritable changes in gene expression not caused by DNA sequence

mutation

change in the nucleotide sequence of the genome of an organism

how can mutations result

• errors during DNA replication, mitosis or meiosis

• damage to DNA or the repair pathway

• insertion or deletion of segments of DNA due to mobile genetic elements

point mutations

substitution

insertion

deletion

substitution

one base is incorrectly added during replication and replaces the pair in the corresponding position on the complementary strand

insertion

one or more extra nucleotides are inserted into replicating DNA

deletion

one or more nucleotides is skipped during replication or otherwise excised

chromosomal mutations

inversion

deletion

duplication

translocation

inversion

one region of a chromosome is flipped and reinserted

translocation

a region from one chromosome is aberrantly attached to another chromosome

gene amplification

the number of tandem copies of a locus is increased

expanding trinucleotide repeat

the normal number of repeated trinucleotide sequences is expanded

causes of mutations

UV radiation

X-rays

cigarette smoke

HPV

polymorphism

variability between individuals

genetic disorder

a health condition caused by abnormalities in the genome

can be caused by a mutation in a single gene (monogenic) or multiple genes (polygenic) or by a chromosomal abnormality

autosomal dominant

inheritance of a mutation from 1 parent only is sufficient for the person to be affected

autosomal dominant disorder

produced by a single mutated allele even though the other allele is normal

autosomal recessive

mutated alleles have to be inherited from both parents in order for a person to be affected