Topic 1 - Nucleic Acids Flashcards
Get yo' genes Come get yo' genes
What is the genome?
All of our DNA content - including ‘junk’
What does the human genome consist of?
- 22 autosomes
- 2 sex chromosomes
- Small amount of DNA present in mitochondria
How many chromosomes do (most) human cells contain?
46
How do cardiomyocytes in newborn mice differ from adult mice?
Newborn = 2n
Adult = 4n
Newborn mice can repair heart damage, adults can’t
Do women have 46 functional chromosomes in each 2n cell?
No - they inactivate one copy of the X chromosome, and push it to the edge of the nucleus creating the Barr body.
What is the Barr body?
A small, densely staining structure in the cell nuclei of females, consisting of a condensed, inactive X chromosome.
What is synteny?
Where long DNA sequences (genes) are present in the same order across species.
Why do humans have 46 chromosomes while chimps have 48?
Human chromosome 2 is a fusion of chimp chromosomes 12 and 13.
What is translocation?
Chromosome breakage and reforming. It may cause disease in pts.
What can translocations cause?
Parent germ cells -> inherited developmental abnormalities
Cancer -> Philadelphia chromosome causes chronic myelogenous leukemia
What can genes be transcribed into?
- Structural RNAs (rRNA or tRNA)
- Regulatory RNAs (microRNAs and Xist)
What is Xist?
X inactivation specific transcript (RNA that switches off a copy of X in XX cells).
What are introns?
Noncoding sections of DNA that are spliced out during transcription.
What are exons?
Coding sections of DNA that are transcribed into mRNA.
What is at the ends of mRNA?
a 5’ UTR and a 3’ UTR end - untranslated regions
If the protein coding content of genes doesn’t vastly differ between species, why are some much more complex?
Some genomes are much more compact than others
What is a retrovirus?
RNA viruses that insert a copy of their own genome into the genomic DNA of cells that they infect
Why is human DNA not extremely compact?
The ancient remains of retroviral DNA remain scattered through our DNA
What are pseudogenes?
Stretches of DNA that have sequence in common with functional human genes but which are non-functional.
What are the two ways pseudogenes are generated?
- Gene duplication
- Reverse transcription
What is a promoter?
A region of DNA that leads to initiation of transcription of a particular gene. Promoters are located near the transcription start sites of genes, upstream on the DNA
What is a VNTR?
Variable Number Tandem Repeats - created by the occasional slippage of polymerase in transcription.
What causes Huntington’s disease?
Expansion of a long CAG repeat in the Huntington protein gene.
What are SNPs?
Single Nucleotide Polymorphisms
What is a polymorphism?
A difference present in 1% or more of the population
What is polygenic disease?
A genetic disorder that is caused by the combined action of more than one gene.
How are SNPs analysed?
Genome Wide Association Studies
Where is mRNA translated?
Cytosol
What happens to mRNA molecules once they enter the cytosol?
They become covered in ribosomes to make a ‘polysome’.
The proteins synthesized on the polysome are deposited in the cytosol.
What is cytosol?
The thick liquid/gel surrounding the organelles.
What is cytoplasm?
The cytosol and the organelles but not the nucleus
What are the ER and Golgi body responsible for?
Packaging and secretion of proteins that are due to be released from cells:
- Blood proteins
- Plasma membrane proteins
What do lysosomes do?
They are full of degradative enzymes and degrade certain molecules imported into the cell, as well as old and damaged cellular components.
What are mitochondria?
The sites of energy generation in the cell by burning fuels to make ATP.
How do proteins travel from the nucleus to the ribosomes?
Through nuclear pores. They have targeting sequences.
What does polymerase 1 do?
Transcribes ribosomal RNA
What does polymerase 3 do?
Transcribes tRNA
What does polymerase 2 do?
Transcribes mRNA, microRNA and non-coding RNAs.
How is transcription started?
- At the promoter elements - including the TATA box.
- Transcription factors bind.
- RNA polymerase 2 binds.
- Some transcription factors disassociate and transcription begins.
What is the TATA box?
Short run of T and A bases that vary slightly from gene to gene. A promoter element.
It may be that Ts and As are used as they form the lowest energy base-pairs (easiest to unwind).
What are CpG islands?
Stretches of DNA where there are multiple points at which C is followed by G.
These occur upstream of many genes and appear to have promoter activity.
How is X-inactivation done?
Methylation of the CpG island
How is transcription terminated in eukaryotes?
Transcription continues past the point where a polyadenylation sequence is present.
The mRNA is then cut near the poly A sequence and a polyA tail is added. (3’)
The other end (5’) has a capping nucleotide added.
How is transcription ended in prokaryotes?
Same with the 5’ capping nucleotide but they do not have a polyA tail at 3’
What is splicing?
Removal of intronic sequences from the pre-mRNA
What removes introns from pre-mRNA?
Spiceosome - at specific sites at start and end of each intron
What happens in translation?
- RNA polymerase II makes transcripts from the antisense (template) strand of DNA
- Some regulatory sequences are close while some may be a long way away and enclose other genes
- These transcripts are capped, spliced, polyadenylated and exit the nucleus
- The mature mRNA molecules are translated
Give three examples of the functions of enzymes present in the cytosol:
- Convert glucose to pyruvate (glycolysis)
- Oxidation in mitochondria (CO2 to H2O)
- Anaerobic conversion of lactate to cytosol
How are membrane bound ribosomes formed?
They start off as cytosolic ribosomes but they attach to an mRNA that happens to encode a secretory protein.
What is a signal sequence?
The stretch of 20 hydrophobic amino acids on an mRNA translated by cytosolic ribosomes. A signal recognition particle binds to this and causes the ribosome to dock on the ER. After the newly synthesized protein is fed through a channel into the ER the signal sequence is cut off.
What keeps the transmembrane proteins in the membrane?
A stretch of approx. 20 consecutive hydrophobic amino acids called the transmembrane domain - this stretch leaves the channel and embeds in the membrane.
What are multi-pass/polytopic proteins?
Transmembrane proteins that pass through the membrane multiple times.
Eg. Beta-adrenergic receptor passes the bilayer 7 times.
Which signal can send proteins to lysosomes?
Addition of a phosphate group to mannose, a sugar added in the ER.
How is insulin made?
1. Preproinsulin: Signal sequence cleaved off in the ER 2. Proinsulin Disulphide bonds form in the ER 3. Insulin The connecting C-peptide loop is cut away in secretory granules by proteases.
How do we know the biological role of DNA?
- Griffith (1928)
- Avery (1944)
- Hershey and Chase (1952)
What was Griffiths experiment in 1928?
- Streptococcus pneumoniae
- Two strains, one grew ‘rough’ colonies and is harmless, the other grew ‘smooth’ colonies and was deadly
- Heat killed smooth strain didn’t kill mice
- HOWEVER, when rough train and heat killed smooth strain were mixed the mice died
- Something in the heat killed smooth strain could transform the rough strain to be deadly
What was Avery’s experiment in 1944?
- Showed that DNA was the transforming element in Griffith 1928
- Out of purified DNA, RNA, protein, carbohydrate and lipid only DNA from heat killed virulent strain could induce virulence to non-virulent strain
What was Hershey and Chase’s experiment in 1952?
- Confirmed the role of DNA as the genetic material
- The protein and DNA components of bacteriophages were labelled with different radioactive molecules (protein - sulfur and DNA - phosphorus)
- After infection of cell, blending and centrifugation no phosphorus was detected in supernatant, while sulfur was.
Which experiments helped us find the structure of DNA?
-Erwin Chargaff (1952)
-Watson and Crick (1953)
Honorable mention Rosalind Franklin
What did Erwin Chargaff find out about DNA in 1952?
The % of adenine was always very similar to the % of thymine and the % of guanine was similar to % cytosine
What did Watson and Crick discover in 1953?
The structure of DNA
What is the structure of DNA?
- Antiparallel strands form double helix
- Sugar phosphate backbone
- Base pairs join complementary strands together by hydrogen bonding
- A and T, C and G
What are the building blocks of DNA?
Nucleotides
What is the structure of nucleotides?
-Deoxyribose sugar, phosphate group and base
What is the structure of DNA’s phosphate backbone?
-A sugar phosphate polymer
-Adjacent deoxyribose sugars are linked by phosphodiester bonds
=5’ and 3’ give the strands directionality
How is DNA packed on a larger scale?
- DNA is tightly coiled with the help of proteins to fit it’s length into the nucleus
- DNA plus (histone) proteins is known as chromatin
- Active genes are more loosely coiled than silent ones
What does semiconservative replication mean?
Each new double stranded molecule contains an original (template) strand and a newly synthesized complementary strand.
Which experiment proved that DNA replication is semiconservative?
Meselson Stahl
Where does DNA synthesis initiate?
Origin of replication, utilizing a dynamic structure called the replication fork
What happens at the start of DNA replication at the replication fork?
- helicases unwind the double stranded DNA and allow replication to occur
- single strand binding proteins stabilise the denatured DNA
- DNA primase synthesises a short RNA primer to allow replication to commence
- DNA polymerase carries out the elongation of the new strand of DNA
What building blocks does DNA synthesis require?
Four deoxy nucleoside tri-phosphates: Adenine Guanine Thymine Cytosine
Which direction does DNA synthesis occur in?
5’ to 3’
What is the role of DNA polymerase?
To catalyse the formation of a new phosphodiester bond - addition of a new nucleotide to the growing strand requires a free 3’-OH initially provided by the RNA primer
Which DNA polymerase carries out DNA replication in prokaryotes?
DNA polymerase III
How is DNA synthesised on the lagging strand?
In short strands, each one primed with a new RNA primer.
DNA polymerase I replaces the RNA primers with DNA and DNA ligase seals the gaps between fragments
How are errors in DNA replication reduced during?
- DNA polymerases have a 3’ to 5’ editing function to remove incorrectly inserted bases. Reduces error frequency to around 1 x 10^7
- Other enzymes check for mismatched bases. Reduces error rate to around 1 x 10^9
How are mutations caused?
- May arise spontaneously due to error in replication
- Induced by DNA damage
- Radiation/Chemicals
What are mutagens?
Chemicals that can damage DNA leading to mutations. Most carcinogens are mutagens
What is an example of a mutagen?
Ethyl Methane Sulphonate (EMS)
What does Ethyl Methane Sulphonate do to DNA?
Alkylates the DNA to form O6-ethylguanine adduct
This adduct mispairs with thymine during replication producing a CG->AT mutation
What are the types of gene mutation?
- Base substitution
- Deletion of bases
- Insertion of bases
- Rearrangement of bases
When can a mutation be inherited?
When it occurs in a germ cell
How is DNA damage repaired?
- Base extinction repair proteins cut out damaged bases - they are specific to specific types of damage
- Nucleotide excision repair proteins are less specific and cut out sections of damaged DNA strand
- DNA polymerase I replaces the DNA by copying the intact strand, DNA ligase seals the gap
What causes the Huntington gene mutation?
DNA slippage - causing abnormal number of glutamine residues
What is an example of a base excision repair enzyme?
Uracil N-glycosylase:
Recognises uracil in DNA and cuts it out
What leads to Uracil sometimes being found in DNA?
Spontaneous deamination of cytosine - occurs slowly in solution and changes sequence of DNA strand
How is yeast used to make artificial insulin?
- A protease recognition site was engineered in to release insulin from the fusion protein
- Shortened and mutated C peptide was made
- Since the ‘real’ C peptide doesn’t work in yeast
- Cleavage of the artificial C peptide
What is ‘pharming’?
Producing pharmaceutical products from farm animals
What is polycistronic?
A type of messenger RNA that can encode more than one polypeptide separately within the same RNA molecule
What are trans-acting factors/elements?
Trans-regulatory elements are genes which may modify/regulate the expression of distant genes. Trans-regulatory elements are DNA sequences that encode transcription factors.
What is polyadenylation?
Polyadenylation is the addition of a poly(A) tail to a messenger RNA. In eukaryotes, polyadenylation is part of the process that produces mature messenger RNA (mRNA) for translation.
What happens to eukaryotic mRNA to produce mature mRNA?
It is:
- Spliced
- Polyadenylated
- Has a 5’ cap added
What is the poly(A) tail?
The poly(A) tail consists of multiple adenosine monophosphates; it is a stretch of RNA that has only adenine bases.
What is the function of mRNA capping?
5’ capping is essential for mRNA stability, enhancing mRNA processing, mRNA export and translation. After successful capping, an additional phosphorylation event initiates the recruitment of machinery necessary for RNA splicing, a process by which introns are removed to produce a mature mRNA.
Is all mammalian mRNA spliced and polydenylated?
Almost all eukaryotic mRNAs are polyadenylated, with the exception of animal replication-dependent histone mRNAs.
What are wobble-base pairs?
A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules.
What are the four main wobble base pairs?
Guanine-uracil (G-U), hypoxanthine-uracil (I-U), hypoxanthine-adenine (I-A), and hypoxanthine-cytosine (I-C).
Which codon codes for the first amino acid in a eukaryotic polypeptide chain, and which amino acid is it?
AUG - methionine
What is the modified version of methionine that bacteria add into the first position of protein chains?
N-formylmethionine
What is the relevance of fMet in the immune system’s response to bacterial infection?
In the human body, fMet is recognized by the immune system as foreign material, or as an alarm signal released by damaged cells, and stimulates the body to fight against potential infection.
What are the 3 tRNA binding sites on a ribosome?
P - peptidyl
A - aminoacyl
E - exit
How is synthesis of the polypeptide chain terminated?
The termination of protein synthesis occurs when a stop translation codon (UAA, UAG, UGA) is in the A site of the ribosome. A releasing factor enters the A site and disconnects the peptide from the P site.
