Genes, Proteins and Meiosis Flashcards
Describe the structure of DNA.
- Double stranded DNA backbone is made of phosphates and deoxyribose sugars.
- Each phosphate carries a negative charge, so DNA is very highly negatively charged.
- Each phosphate forms a phosphodiester bond and hydrogen bonds forms between complementary nitrogenous bases.
- Double strands intertwine to form an antiparallel double helix, as one strand runs 5’ to 3’, and the other runs 3’ to 5’, giving strands a polarity and a direction.
- Guanine and adenine are the purines. Thymine and cytosine are the pyrimidines.
- Guanine and cytosine are complementary and form 3 hydrogen bonds. Adenine and thymine are complementary and form 2 hydrogen bonds.
- Flat edges of the bases are hydrophobic. The sides of the bases and the sugar-phosphate backbone are hydrophilic. This causes the bases to stack together and form a double helix.
Describe the major and minor grooves.
Major and minor groves form by the relative distances between the 2 backbones. A larger distance results in a major groove, and a smaller distance results in a minor groove. Grooves are important because proteins and enzymes need to make bonds (mostly hydrogen bonds) with DNA at the grooves. This is most easily done at the major grooves, as they are more open. Amino acids of the sides of the alpha helixes of the proteins can bind to the DNA. Upon binding, proteins can bend the strand and change its conformation, often by neutralising the DNA complex’s charge.
Name the 4 types of histones and what they come together to form.
Histones are types of DNA binding proteins. There are 4 types: H2A, H2B, H3 and H4. The four come together in a positively charged octameric complex. Negatively charged DNA wraps round the histone octamer twice. The 2 turns of DNA and octamer is a nucleosome, the building blocks of chromosomes.
Describe DNA replication in prokaryotes and eukaryotes.
In bacteria, DNA replication at a unique replication origin and proceeds simultaneously in opposite directions (bidirectionally). In eukaryotes, replication begins at multiple origins, as DNA is so much larger, and proceeds bidirectionally with primers.
Describe the process of DNA replication.
- Initiator proteins bind to the origin and recruit DNA helicase.
- Helicase breaks hydrogen bonds between complementary base pairs and unwinds the double helix to form a single stranded DNA template strand.
- This allows primase to make short RNA primers for DNA polymerase.
- DNA polymerase makes DNA in the 5’ to 3’ direction and adds deoxynucleotide triphosphates, dNTPs, to the 3’ end.
- Energy comes from breaking high energy phosphate bonds in dNTPs, so it is energetically favourable for dNTPs to be added.
- DNA polymerase takes over from primase and elongates the RNA primer, forming an RNA-DNA hybrid.
- As the DNA unwinds, the process repeats and Okazaki fragments are formed.
- Previous Okazaki fragment and old RNA primer on the leading strand.
- New RNA primer is synthesised by primase.
- DNA polymerase with 5’ to 3’ exonuclease activity adds new primer to new Okazaki fragment.
- DNA polymerase finishes DNA fragment and old RNA primer is erased and replaced by DNA.
- The two fragments are joined by DNA ligase.
What is the function of telomerase?
The last primer is close to the end of the strand and primase has no room to synthesise the end of the strand.
- Telomerase is a DNA polymerase that uses a short RNA molecule as a template, and not the DNA.
- It makes repeats on the lagging strand.
- Telomeric repeats are added to the end and prevents telomeres getting shorter and shorter in each replication cycle.
What are the 4 types of DNA repair?
- Mismatch repair – enzymes cut out incorrect base and resynthesise the DNA that has been cut out.
- Direct repair – DNA gets damaged by UV light or chemicals and is directly repaired.
- Excision repair – damaged base can be directly removed by enzymes and re-synthesise the gap.
- Nonhomologous end-joining – if both strands are damaged, the cell has no template. Randomly joining 2 ends of DNA, which is dangerous and may cause lasting mutations, but it is the only way cells can fix this.
Which RNA polymerases make which RNA molecules?
- RNA polymerase I makes rRNA (ribosomal)
- RNA polymerase II makes mRNA
- RNA polymerase III makes tRNA
What must happen before translation can occur?
- Introns are removed by spliceosomes in splicing in the nucleus.
- A 5’ cap is added to mRNA so that it can be recognised by the ribosome.
- Polyadenyl is added to the 3’ end to prevent mRNA from being chewed up the endonucleases.
What are the roles of transcription factors?
- Transcription factors are needed to allow RNA polymerase to bind to the promotor region.
- Transcription factors can activate or suppress the binding to the promotor region, so can allow or prevent RNA polymerase binding.
- Transcription factors can bind to promotor regions or enhancer regions, which can be anywhere in the sequence.
Define epigenetic regulations.
Modifications that amend the gene expression without changing the DNA base sequence.
What is DNA methylation?
DNA methylation creates modifications in the promotor regions of genes and is associated with gene silencing.
What are histone modifications?
Histone modifications can be methylation, acetylation (associated with gene expression), phosphorylation, etc. This changes packaging and how accessible the gene is for transcription.
What are aminoacyl-tRNA synthetase?
At the 3’ end of tRNA, there is a specific amino acid. Aminoacyl-tRNA synthetases are very specifically shaped enzymes that join the correct specific tRNA and amino acids together.
Name and describe the 3 active sites of the ribosome.
- A site – aminoacyl-tRNA synthetase joins
- P site – peptidyl transferase joins. This is where a peptide bond forms.
- E site – empty tRNA
