Unit 1 DNA and the Genome

antiparallel

The two strands of a DNA molecule run in opposite directions and are said to be antiparallel to each other. One strand has deoxyribose (3′) at one end of the molecule, but its complementary strand has a phosphate group (5′) at the same end of the molecule.

DNA

Deoxyribose nucleic acid. A double-stranded molecule made up from chemical units called nucleotides. DNA holds the genetic code in living organisms.

phosphate group

Makes up part of a DNA nucleotide Found at the 5' end of a DNA strand.

Nucelotide

repeating sub units of a DNA molecule

Adenine, Thymine, Guanine, Cytosine

4 bases of DNA

Deoxyribose Sugar

Makes up part of a DNA nucleotide. Found at the 3' end of a DNA strand.

sugar-phosphate backbone

Strong bonds form between the deoxyribose sugar of one nucleotide and the phosphate of the next nucleotide. These strong bonds form a sugar-phosphate backbone.

Plasmids

Circular loops of genetic material (DNA) found in prokaryotic organisms and yeast.

Prokaryotes

Do not contain a membrane bound nucleus. Include bacteria and archaea.

Eukaryotes

contain a membrane bound nucleus. Include fungi, animal and plant cells.

Circular chromosomes

Found in prokaryotes.
Found in the mitochondria and chloroplasts of eukaryotes.

linear chromosomes

Organisation of DNA in the nucleus of eukaryotes, . Tightly coiled around proteins.

Histones

Protein around which linear chromosomes are coiled.

Yeast

Special eukaryotic cells, with linear chromosomes in their nuclei and circular chromosomes in their mitochondria, but also having plasmids in their cytoplasm.

DNA polymerase

Enzyme that adds complementary DNA nucleotides to the 3′ end of a primer/newly forming DNA strand.

Ligase

The enzyme which joins the DNA fragments on the lagging strand.

Requirements for DNA replication

Template DNA strand, primers, nucleotides, enzymes

template strand of DNA

The original strand to be replicated

Primers

Small pieces of single-stranded DNA. Required to start DNA replication. Bind to the 3' end of the template DNA, allowing DNA polymerase to add DNA nucleotides.

Polymerase Chain Reaction (PCR)

A technique used to amplify DNA

Denaturation

First stage of PCR.
The DNA is heated at approx. 92-98 °C for a few seconds.
This causes the DNA to denature, hydrogen bonds break and the strands to separate.

Annealing

Second stage of PCR.
The DNA is cooled to approx. 50-65 °C for a few seconds.
This allows short primers to bind (anneal) to the 3' end of the separated DNA strands.

Extension

Third stage of PCR.
The DNA is heated again to 70-80 °C for a few minutes.
This allows heat-tolerant DNA polymerase (taq polymerase) to add nucleotides to the 3' end and extend the DNA strands.

Requirements for PCR

Template DNA strand, free nucleotides, primers, Heat tolerant DNA polymerase

Heat-tolerant DNA polymerase

Does not denature at high temperatures.Adds nucleotides to the 3' end.

Practical applications of PCR

Solve crimes, settle paternity suits, help diagnose genetic disorders.

Peptide Bonds

Bonds between amino acids

Polypeptide

long chain of amino acids that makes proteins

Hydrogen bonds

Holds together the 3D shape of a protein.

RNA

ribonucleic acid. Single stranded molecule. Nucleotides contains a phosphate, ribose sugar and one of 4 bases.

RNA bases

Adenine, Uracil, Cytosine, Guanine (A-U, C-G)

Messenger RNA (mRNA)

carries a complementary copy of the genetic code from the nucleus to the ribosome

tRNA (transfer RNA)

type of RNA molecule that transfers specific amino acids to ribosomes during protein synthesis. Has an amino acid attachment site and an anticodon

Ribosomal RNA (rRNA)

type of RNA that combines with proteins to form ribosomes

Transcription

The synthesis of mRNA from DNA

RNA polymerase

Enzyme that moves along the DNA strand and unwinds it. Adds free RNA nucleotides in a 3' to 5' direction.

Introns

non-coding regions of DNA

Exons

Coding regions of DNA

RNA splicing

Process by which the introns are removed from RNA transcripts and the remaining exons are spliced together.

Mature transcript of mRNA

Produced after RNA splicing, contains only exons (coding regions of DNA)

alternative RNA splicing

Producing different mature mRNA transcripts, depending on which introns and removed and which exons are retained and spliced together.

Translation

Process by which mRNA is used to produce a protein

Anticodon

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

mRNA codon

3 base pair on an mRNA molecule that codes for a specific amino acid

Cellular Differentiation

process by which a cell expresses certain genes to produce proteins characteristic for that type of cell.

Stem cells are

Unspecialised cells in animals that can divide and differentiate

Embryonic stem cells can differentiate in to

ANY TYPE OF CELL

Pluripotent means

All the genes can be switched on

Tissue stem cells can differentiate in to

A NARROW RANGE OF CELL TYPES.

Multipotent means

They can only differentiate in to cells of their tissue

Therapeutic use of stem cells

Repair of damaged/diseased organs. Eg skin grafts

Research use of stem cells

Used as model celLs to study how diseases develop

Meristems

Unspecialised cells in plants

Genome

All the hereditary material within an organism

Fates of on coding regions of genome

Regulate transcription or transcribed but not translated

Mutation

Random change to an organisms DNA

Substitution

One base replaced by another in the DNA

Missense

One amino acid is changed for another

Nonsense

A premature stop codon is produced

Splice site mutation

Some introns being retained/exons not included in the mature transcript.

Deletion

One base is removed from the DNA

Insertion

One base is added in to the DNA

Frame shift mutation

All codons and all amino acids after the mutation are changed

Deletion (chromosome)

Section of a chromosome is removed

Inversion

Section of a chromosome is reversed

Translocation

Section of a chromosome is added to another chromosome, not its homologous partner

Duplication

Section of a chromosome is added from its homologous partner

Importance of duplication mutations

allows potential beneficial mutations to occur in a duplicated gene.
The original gene can still be expressed to produce its protein

Vertical gene transfer

genes transferred from parent to offspring

horizontal gene transfer

Genes transferred between individuals in the same generation

Natural selection is faster in

Prokaryotes

Natural selection is

Non random increase of frequency in DNA sequences that increase survival and non random reduction in frequency of DNA sequences that decrease survival

Stabilising selection

Average phenotype is selected for and extremes of phenotype range are selected against

Directional selection

One extreme of the phenotype range is selected for

Disruptive selection

Two or more phenotypes are selected for

Species

Group of organism capable of interbreeding to produce fertile offspring

Allopatric speciation

the process of speciation that occurs with geographic isolation

Sympatric speciation

The process of speciation that occurs with behavioural or ecological isolation

Isolation Barriers are important because

They prevent gene flow between sub populations

Bioinformatics

Use of computers and statistics to compare sequence data

Phylogenetics

the study of evolutionary relationships among species

Required to produce a phylogenetic tree

Sequence data, fossil evidence

Molecular clocks assume

A constant mutation rate and show differences in DNA sequences or amino acid sequences

3 domains of life

bacteria, archaea, eukaryotes

Pharmacogenetics

Use of genome to select most effective dosage and type of medicines for individuals