Nucleotides and Nucleic acids

DNA

A nucleic acid used to store genetic information

What is the difference between pyrimidines and purines

Purines contains 2 carbon rings (one imidazole) whereas pyrimidines only have 1.

What are the pyrimidines

Cytosine, Thymine and Uracil

What are the purines

Adenine and Guanine

Phosphate group

Inorganic, acidic, negative

Nitrogenous base

A complex organic molecule containing 1 or 2 carbon rings in its structure as well as nitrogen

Pentose sugar

Contains 5 carbon atoms

Structure of DNA

• Made of 2 antiparallel polynucleotide strands

• Monomers bonded by covalent phosphodiester bonds

• Enzyme DNA polymerase catalyses reaction and is complementary to 3’ end only

• Bases bonded by hydrogen bonds

• Double helix coil

• Macromolecule and is very long to store lots of information

• Purines and Pyrimidines always pair

• The 5’ end is where phosphate is attached to the 5th Carbon and 3’ end on the 3rd carbon

How do nucleotides link?

Nucleotides link via phosphodiester bonds between the phosphate group of 1 and deoxyribose sugar by another to form a strong deoxyribose sugar - phosphate group backbone.

Sugar-phosphate backbone and double helix structure

Provides strength and stability

Protects bases and hydrogen bonding between base

Long molecule

Can store a lot of information

Helix structure

Compact

Base sequence

Codes for amino acids and therefore proteins

Double stranded

Allows semi-conservative replication, as each strand can act as a template

Complementary base pairing, A-T and C-G

Allows accurate replication

Hydrogen bonds between bases are weak

Allows unzipping and separating of strands for replication

Many hydrogen bonds in the whole molecule

Strong and stable molecule

RNA structure

• contains nucleotides that have a ribose sugar

• Uracil instead of thymine

• Single polynucleotide chain

Phosphodiester bonds

• A condensation reactions forms phosphodiester bonds between nucleotides

• This creates a sugar-phosphate backbone

• Polynucleotides can be broken down into nucleotides again by breaking the bonds - hydrolysis reaction

Process of DNA replication

• The double helix unwinds

• DNA helicase breaks the hydrogen bonds between the bases and DNA unzips

• Two strands act as templates

• In nucleus there are free floating DNA nucleotides. Free nucleotide align next to complementary bases and hydrogen bonds form

• DNA polymerase forms phosphodiester bonds (condensation reaction) between the nucleotides to create new polymer chain

Lagging and Leading Strands

• DNA polymerase can only add bases in one direction

• One of new strands (leading) is made continuously

• Other strand (lagging) runs in opposite direction so isn’t continuous

• DNA can only make sequences in 5’-3’ direction

Conservative model

An entirely new molecule is synthesised from a DNA template

Semi-conservative model

Each new molecule consists of one newly synthesised strand and one template strand

Dispersive model

New molecules are made of segments of new and old DNA

Proving that DNA is semi-conservative

• Meselson and Stahl

• Uses radioactive isotopes of nitrogen

• DNA molecules were produced using the heavier 15N (heavy blue) and the induced to replicate in the presence of the lighter 14N (light yellow)

• DNA samples were then separated via centrifugation to determine the composition of DNA in the replicated molecules

• Results support semi-conservative model

mRNA characteristics

• single stranded polynucleotide chain

• copy of a single gene on the DNA

• contains uracil

Degenerate

Different codons can code for the same amino acids

Structure of tRNA

• one polynucleotide chain

• regions where its double stranded and regions where its single stranded - clover leaf

• amino acid attachment site

• regions of 3 bases called anticodon

• anticodon is specific to amino acid carried by tRNA

rRNA

Makes up the 2 subunits in a ribosome

rRNA in the ribosome help catalyse the formation of peptide bonds between amino acids during translation

Transcription

1. DNA is copied in the nucleus

2. DNA double helix is unwound by DNA helicase, hydrogen bonds breaking inbetween base pairs

3. DNA opens at transcription start site

4. Anti-sense strand acts as the template

5. Free RNA nucleotides form hydrogen bonds with complementary DNA nucleotides.

6. RNA polymerase forms phosphodiester bonds to make the backbone of the mRNA molecule

7. Stops when RNA polymerase reaches a termination signal sequence

8. mRNA detaches and leaves via nuclear pores in membrane.

9. Travels to ribosomes

Translation

1. mRNA attaches to small subunit in ribosome

2. Ribosome attaches at 3’ end of mRNA at start codon, AUG

3. tRNA molecule with the complementary anticodon to the AUG codon aligns opposite the mRNA

4. Ribosome moves along mRNA molecule to enable another complementary tRNA to attach to the next codon on the mRNA, delivering the correct amino acid

5. 2 amino acids that have been delivered by the tRNA are then joined via peptide bonds which is catalysed by peptidyl transferase

6. Continues to occur until ribosome reaches stop codon, ribosome detaches and translation ends

7. Polypeptide chain is created and enters golgi body

Characteristics of genetic code

Triplet nature

Degenerate

Nonoverlapping

Universality

Duplication/Insertion

Base is inserted twice

Each triplet is altered, so large impact as 3D protein will be completely different

Deletion

A base is missed out

Each triplet is altered, so large impact as 3D protein will be completely different

Substitution

A base is replaced by a different one

One triplet is altered, one codon on mRNA will be different resulting in max impact of one different amino acid. May by chance still code for same amino acid, so no impact on 3D shape.

Inversion

A sequence of bases on a triplet code is reversed

One triplet is altered, one codon on mRNA will be different resulting in max impact of one different amino acid. May by chance still code for same amino acid, so no impact on 3D shape.

Properties of ATP

Small - moves easily, in and out of cells

Soluble - most active processes happen in aq environments

Intermediate amounts of energy released - enough for cellular reactions, but not so much that it is all wasted as heat

Easily regenerated - renewable energy source

How ATP is used in cells

• Biosynthesis

• Contraction

• Chemical activation

• Importing metabolites

• Active transport

• Cytoplasmic transport

Structure of ATP

3 phosphate groups, adenine and ribose

Why do cells need energy

Synthesis of large molecules such as proteins

Transport - pumping molecules or ions across cell membranes by active transport

Movement - protein fibres in muscle cells that cause muscle contraction