DNA, RNA and Protein

base and 5 carbon sugar

nucleoside and phosphate group

Adenine and guanine are the two nucleotides that are purines.

cytosine, thymine, uracil are the nucleotide bases that are pyrimidines

They are bonds that form between 3’ OH group and 5’ triphosphate and they link nucleotides.

1)Anti-parallel double helix - One strand 5’ to 3’, other strand 3’ to 5’ 2) Sugar-phosphate backbone 3) Base pairs in the inside, held together with H bonds

1. RNA primer (short strand of RNA) required to start DNA replication
2. Helix unwound by helicase
3. Replication fork with leading and lagging strand
4. Leading synthesized in 5’→ 3’ direction - catalyzed by DNA polymerase
5. Lagging is synthesized in Okazaki fragments which are then joined by DNA ligase

After one round of replication, every new DNA double helix would be a hybrid that consisted of one strand of old DNA bound to one strand of newly synthesized DNA.

Eukaryotic genomes have many origins of replication. It starts simultaneously at several points in the genome which means that:-

1. It is bidirectional
2. It ensures that replication can be finished in a reasonable time.

Nucleotides can only be added to free 3' ends.

1. Leading strand- always has a free 3' end and it keeps extending until it meets another fork within the replication framework.
2. Lagging strand consists of short fragments called the Okazaki fragments. Short RNA primer degrades and Okazaki fragments are joined together.

When the primase attaches to the bottom strand, it creates the RNA primers for strand replication. Then the DNA polymerase attaches to the RNA primer to build the new strands.

DNA helices unwinds the DNA strands by breaking the bonds for the strands to extend.

1. rRNA- combines with proteins to form ribosomes
2. tRNA- carries amino acids to be incorporated into protein
3. mRNA- carries genetic information for protein synthesis

They are single stranded and contain local stretches of intramolecular base pairing because of proximity of bases H bases are formed.

1. DNA information is transcribed into mRNA to make protein.
2. mRNA goes into ribosome made of rRNA and proteins
3. tRNA brings amino acids and allows ribosomes to synthesise a new protein.

It is a bridge between mRNA and the monomers and brings the monomers to mRNA for translation from one polymer to another.

tRNA molecules have a distinct three dimensional structure and when it is flattened into two dimensions, it resembles a cloverleaf structure.

Prokaryotic cells have one type of RNA polymerase. Eukaryotic cells have three types of RNA polymerase:-

1. Pol I
2. Pol II
3. Pol III

It can be distinguished by their sensitivity to toxins like alpha amanitin and Pol II synthesised all mRNA.

1. RNA polymerase binding
2. DNA chain separation
3. Transcription initiation
4. Elongation
5. Termination

1. Detection initiation sites (promoters) on DNA
2. Requires transcription factors- TFIID - first general transcription factor to bind to the promotor, binds to TATA box through TBP (TATA box binding protein). General transcription factor required for all Pol II transcribed genes

1. Selection of first nucleotide of growing RNA.
2. It requires additional general transcription factors.
3. Pol II and TFIIF extend transcript on their own. TFIID remains at promoter, a new initiation complex can assemble.

1. A transcription bubble moves in one direction along the DNA
2. DNA is unwound in front of the polymerase and rewound behind it.
3. RNA chain is synthesised in a 5' to 3' direction. It is transcribed in 5'-3' direction and polymerase thus moves in a 3'-5' direction.
4. The new RNA sequence is complementary to the template strand.
5. It is identical to the coding strand.

1. Newly synthesised RNA makes a stem loop structure.
2. A specific enzyme cleave the new RNA.
3. The RNA gets released and the polymerase dissociates.

It requires specific transcription factors

1. DNA binding proteins
2. DNA binding domain
3. Transcriptional activation domain This regulates transcription positively or negatively.

1. Splice out introns (exons = coding, intron = non-coding)
2. Add poly-adenosine tail- marks the end of coding mRNA
3. Add 5’ cap

Features of the genetic code

1. Degenerate- many amino acids have more than one codon
2. Unambiguous- each codon codes for only one amino acids or a Stop codon.
3. Near universal

1. Initiation - formation of initiation complex, energy provided by GTP
2. Elongation - anticodons of tRNA form base pairs with codons on mRNA, aminoacyl-tRNA synthetases catalyse the covalent attachment of amino acids to their corresponding tRNA molecules
3. Peptide bond formation and translocation- peptidyl transferase catalyzes peptide bond formation between amino acids in P and A sites, EF-2 moves ribosome along mRNA
4. Termination - A site encounters stop codon, termination protein binds to the codon and the ribosome dissociates, leads to a change in peptidyl transferase activity which results in the release of the protein from the last tRNA to which it was attached

A codon is a sequence of three nucleotides in messenger RNA that determines the position of amino acids when a cell starts making proteins. An anticodon is a sequence of three nucleotides in transfer RNA that binds to a corresponding codon and designates a specific amino acid.

1. Targeting- moving a protein to its final cellular destination- many possible locations within a cell depending on the presence of specific amino acid sequences within the translated protein.
2. Modification- addition of further functional chemical groups
3. Degradation- unwanted or damaged proteins have to be removed.

1. Free ribosomes in the cytosol make proteins destined for the cytosol, nucleus. mitochondria and they are translocated post translationally.
2. Bound ribosomes on the rough endoplasmic reticulum make proteins destined for the plasma membrane, ER, Golgi apparatus, secretion and they are translocated co translationally.

3 tRNA binding sires - P, E, A - P (peptidyl site) → A (acceptor site) → E (exit site)

1. Glycolsylation- Addition an processing of carbohydrates in the ER and the Golgi
2. Formation of disulphide bonds in the ER
3. Folding and assembly of multi subunit proteins in the ER.
4. Specific proteolytic cleavage (cleavage of polypeptide allowing it to fold into different shapes) in the ER, Golgi and secretory vesicles.

1. Point mutation
2. Missense mutation
3. Nonsense mutation
4. Silent mutation
5. Framework mutation

change in single base in DNA

results in change of amino acid sequence

creates new termination codon

no change of amino acid sequence and no observable difference in phenotype

addition or deletion of 1 or 2 bases which changes the reading frame of translation