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Topic 7 IB Biology HL

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Describe Hershey and Chase's experiment
- Viruses (T2 phages) were radioactively labelled with 32 S (Protein) and 32 P (DNA)
- These were mixed with E.Coli bacteria, left to infect
- Then virus and bacteria were seperated by centrifugation
- It was found that the majority of radioactivity was in the pellet rather than the supernatant in 32 P as compared to 32 S
- Therefore it was concluded that DNA was the genetic material
Name Enzymes involved in DNA replication (in order w/ functions)
- DNA Gyrase
relieves strain by relaxing the supercoiling
- DNA Helicase
works to uncoil/unwind the double-stranded DNA (-OH bonds broken)
- SSB
Holds the 2 DNA strand apart
- DNA Polymerase III
attaches free nucleotides in 5'-3' direction
- DNA Primase
attaches RNA primer to lagging strand where DNA Polymerase III can attach and attach free nucleotides
- DNA Polymerase III
- DNA Polymerase I
replaces RNA primers on lagging strand with DNA nucleotides
- DNA Ligase
joins the okazaki fragments together on the lagging strand
Describe Okazaki Fragments
short, newly synthesised DNA fragments that are formed on the lagging strand, preceded by a RNA primer
Leading vs Lagging strand
Leading
- replication occurrs towards the replication fork
- continuous

Lagging
- replication occurs away from the replication forl
- discontinuous
- formation of Okazaki fragments
Describe Dideoxynucleotides
- lack the -OH group on the 3rd Carbon atom unlike deoxynucleotides
- prevent elongation of nucleotide and terminate replication as phosphodiester bond cant be made
Examples of Non-Coding DNA
- Introns
non-coding DNA within eukaryotes

- telomeres
regions of repetitive DNA located at each end of a chromatid and function to prevent chromosomal deterioration

- Gene Regulation sequences
sequences involved in process of transcription e.g. promoters, engancers, repressors

- Satellite DNA
tandemly repeating sequences of DNA e.g. short tandem repeats
Nucleosome
structure arisen due to DNA in eukaryotes being associated with an octamer of Histone proteins
Structure of nucleosome
- A core of 8 (octamer) Histone proteins
- Nucleosomes held together/linked by H1 Histone proteins
- Histone proteins have N-terminal tails extruding outwards which link up and draw nucleosomes together during chromosomal condensation
Promoter function of a gene
- responsible for initiation of transcription
- site where RNA polymerase binds
-
Antisense vs Sense Strand
- Antisense strand os the one that acts a s a template during transcription
- transcribed into RNA
Define Transcription
process by which a DNA sequence is copied to a complementary RNA sequence by RNA polymerase
Describe Transcription process
- RNA polymerase binds to promoter and causes unwinding of double strand
- elongation occurs as RNA polymerase adds nucleoside triphosphates in a 5'-3' direction
- once termination sequence reached, RNA strand and enzyme detach
What occurs before eukaryotic mRNA can be translated?
Splicing
non-coding sequences of DNA called introns are removed
this increases no. of diff. proteins an organism can produce
Name another post-transcriptional modification
Polyadenylation
Polyadenylation describes the addition of a long chain of adenine nucleotides (a poly-A tail) to the 3'-end of the transcript

improves the stability of the RNA transcript and facilitates its export from the nucleus
Discuss Transcription factors
- refer to proteins that bind to specific regions of DNA to either enhance or prevent the expression of a gene
- activators bind to enhancers increasing rate of transcription
- repressors bind to silencers decreasing rate of transcription
Promoter proximal elements
-close to the promoter. Proteins need to bind here to initiate transcription
Describe the structure of a ribosome
- 2 sub units, one large and one small
- 3 binding sites for tRNA (A,P,E)
- binding site for mRNA on surface of ribosome
Describe structure of tRNA
- base sequence CCA at 3' end where amino acid is attached
- triplet of bases called the anticodon (opposite end to base CCA sequence)
Role of tRNA activating enzymes?
- activation of a tRNA molecule includes the attachment of a amino acid to the 3' end (base sequence) by a tRNA activating enzyme

- energy from ATP is needed for the attachment of an amino acid

- once the ATP and amino acid are attached at the active side, the amino acid is activated by a bond forming between the enzyme and AMP

- The activated amino acid is then covalently attached to the tRNA molecule

- Energy from this bond will be later used to add the amino acid to the growing chain of polypeptides during translation
Stages of translation (names only)
Initiation
Elongation
Termination
Describ Translation
INITIATION
- involves assembly of components involved
- mRNA molecule binds to mRNA binding site of small ribosome
- initiator tRNA binds to start codon AUG
- large unit binds to small unit
- initiator tRNA is at P site
- next codon signals another tRNA to bind, at the A site
- peptide bond formed b/w amino acids in A and P sites

ELONGATION
- elongation occurs through a series of repeated steps
- The ribosome moves three bases accross the mRNA, moving the tRNA in the P site to the E site (freeing it) and allowing the tRNA with the appropriate anticodon to the next codon to bind to the vacant A site

TERMINATION
- the process continues until stop codon (at 3' end) is reached and then the free polypeptide chain is released
- at the stop codon, no complimentary tRNA carries an anticodon so a special protein (release factor) fill A site and causes bonds to break
- Polypeptide chain released and ribosome dissociates back into 2 units
Free Ribosomes vs Bound Ribosomes
Free Ribosomes
synthesise proteins for use primarily within the cell

Bound Ribosomes
synthesise proteins for use outside of the cell (fro secretion) or in lysozomes
How is transcription and translation coupled together in prokaryotes?
Due to a lack of the nuclear membrane
Primary Structure
the SEQUENCE and NUMBER of amino acids in the polypeptide
Secondary Structure
refers to the formation of ALPHA HELICES and BETA PLEATED sheets stabilized by H-Bonding
Tertiary Structure
overall 3D shape of a protein arising from interactions between the -R groups of aminoacids

e.g.
- hydrophobic interactions
- hydrogend bonds between polar sections
- disulphide bridges
Quaternary Structure
- exists in proteins with more than one polypeptide chain
- linking together of polypeptides to form a protein
- also refers to addition of non-polypeptide components e.g. heme in haemoglobin