Molecular Biology Flashcards
What are the monomers of nucleic acids?
Nucleotide/nucleoside
What makes up a nucleotide?
Sugar (ribose), base and phosphates
What makes up a nucleoside?
Sugar (ribose) and base. No phosphate. It helps to specify the number of phosphates.
Ribose vs Deoxyribose
Ribose has two OH on 2’ and 3’ of the ribose sugar. Deoxyribose has only one OH on the ribose sugar
Which direction does synthesis occur in nucleic acids?
5’ to 3’
What is phosphodiester linkage?
Links two nucleotides together.
What are the three pyrimidines?
Cytosine, uracil and Thymine (one ring)
What are the two purines?
Adenine and Guanine (two rings)
What holds base pairings together?
Hydrogen bonds. 3 for C and G. 2 for A and T
What has a single circular DNA genome?
Prokaryotes
What are restriction enzymes?
They chop up DNA that is not methylated.
How do prokaryotes protect their DNA in the cytoplasm from restriction enzymes?
They methylate their DNA
What does supercoiling do for DNA of prokaryotes?
It protects their DNA.
What runs supercoiling for bacteria?
DNA gyrase
What has several linear chromosomes?
Eukaryotes
What are histones
Used to wrap DNA twice around the histone to form nucleosomes
What are a collection of coiled nucleosomes called?
Chromatin
How do eukaryotes protect their DNA?
They put it in a nucleus and don’t let it hang around in the cytoplasm like prokaryotes do
What is a centromere?
1) location where sister chromatids attach
2) location where spindle fibers attach
What are short arms in terms of chromosomes?
Short side of a chromosome
What are long arms in terms of chromosomes?
Long side of a chromosome
What are telomeres?
They are short nucleotide repeats found at the ends of linear chromosome and they stabilize the ends of chromosomes by capping them.
What is the central dogma of molecular biology?
DNA to RNA to Proteins
What are codons?
Three nucleotides that make up one amino acid
Codon AGA corresponds to arginine
What is the start codon?
AUG
What is the stop codon
UAA, UGA, UAG
you are annoying
you go away
you are gone
What is the codon of tryptophan?
UGG. It is specified by just one codon like methionine.
What are the four sources of mutation?
Polymerase errors, endogenous damage, exogenous damage and trasposons
What is the effect on DNA due to polymerase errors?
1) Point mutations
2) Small repeats
3) Insertions/deletions (small, frameshift)
What are point mutations?
Single base pair change
What are the three types of point mutations?
1) Missense: change amino acid
2) Nonsense: stop codon (shorter protein)
3) Silent: no effect, only third codon changed leading to the same amino acid
What are frameshift mutations?
Caused by insertions and deletions. It changes the reading frame leading to big bad mutations.
What are endogenous damage?
Damage caused within the cell. Due to reactive oxygen species or physical damage
What effects does reactive oxygen species have on DNA?
It can lead to oxidized DNA (base) which causes the bases to no longer be able to base pair to each other
What effects does cross-linked bases have on DNA?
Bases are physically linked together instead of hydrogen bond which makes it hard to unlink DNA.
What are effects of endogenous damage?
1) Oxidized DNA
2) Cross-linked bases
3) Physical damage
4) Polymerase errors
What are exogenous damage?
Damage from outside the cell. Due to radiation or other chemicals.
What effects do UV radiations have on DNA?
Pyrimidine dimers
What effects do X-rays have on DNA?
Double stranded breaks and translocations
What effects do chemicals have on DNA?
Physical damage or intercalation (insertion of a molecule) which leads to polymerase errors
What are transposons also known as?
Jumping genes
What effects do transposons have on DNA?
large insertions/deletions, inversions and duplications
What do transposons consist of?
Transposase flanked by inverted repeats
Transposase: cut and paste activity
Inverted repeats
What are the type of transposons?
1) IS element
2) Complex transposon - gene included within the inverted repeats
3) Composite transposon - has two transposons flanking a central region of DNA
What happens if a transposon is inserted into an intergenic region?
No problems occur
What happens if a transposon is inserted into a coding region?
Mutation occurs
Can inversion occur in a DNA?
Yes. If you have two transposons facing the opposite direction, then inversion can occur
What source of mutation does not trigger DNA repair mechanisms?
Transposons
What ways can polymerase errors be repaired?
Mismatch repair pathway (after replication) or Nucleotide excision repair (before replication)
How do you differentiate between a parent strand and a daughter strand?
Parent strand is methylated but daughter strand has yet to be methylated
What ways can endogenous damage be repaired?
1) Nucleotide excision repair (before replication)
2) Homologous/ non-homologous end joining
What does homologous end joining do (best one instead of non-homologous end joining)?
Repairs double-stranded DNA breaks and it occurs after replication. Sister chromatid used as a template
What does non-homologous end joining do?
Repairs double-stranded DNA brakes but has no sister chromatid to use as a template.
What causes translocations?
Recombination between non-homologous chromosomes or faulty DNA repair.
What ways can exogenous damage be repaired?
1) Direct reversal by white light for dimers
2) Homologous/non-homologous end joining
3) Nucleotide excision repair
What does direct reversal do?
White light directly reverses the dimer caused by UV light.
What cuts DNA and relaxes supercoiling?
Topisomerase
What is an RNA primer?
A sequence that is put down by primase and is the origin of DNA polymerase
What links okazaki fragments?
DNA ligase
What is DNA polymerase III (main replicating enzyme in prokaryotes)?
1) High processivity
2) It has a 5’ to 3’ polymerase activity and a 3’ to 5’ exonuclease activity (only cuts at the end of DNA strand). It has no known function in DNA repair.
What is DNA polymerase I?
1) Low processivity
2) Slow 5’ to 3’ polymerase activity and 3’ to 5’ exonuclease activity. It can also have 5’ to 3’ exonuclease activity to remove primer.
3) It functions to some extent as DNA excision repair
What are DNA polymerase IV and V?
They are error prone and are involved in DNA repair.
Prokaryote vs eukaryote replication
Prokaryotic replication occurs from one origin while eukaryotic replication occurs at multiple origins
What happens to the ends of chromosomes in eukaryotes during replication?
The ends become shorter and shorter because the RNA primers removed at the end lead to a single strand sticking which degrades. (Aging process)
What are characteristics of telomerase?
1) Built in RNA primer
2) Reverse transcriptase activity
What is the catalytic part of functional ribosome?
rRNA
What is the sequence of codons that determines amino acid sequence of protein?
mRNA
What carries amino acids to ribosome?
tRNA
What is the initial unprocessed transcript of mRNA found in eukaryotes?
hnRNA (heterogeneous nuclear RNA)
What two types of RNA help regulate gene expression?
miRNA (micro RNA) and siRNA (small interfering RNA)
Replication vs transcription
Transcription has a stop site but replication does not
Transcription does not require a primer but replication does (RNA primer)
Transcription does not go through editing unlike replication
What is the template strand known as in transcription?
Anti-sense strand
What is the coding strand known as in transcription?
Coding strand
How does a cell regulate transcription?
1) Promoter - strong vs weak promoter
2) DNA binding proteins - repressors and enhancers
What is the best way to regulate transcription?
DNA binding proteins
Where can repressors bind in prokaryotes to halt transcription?
Operator
Transcription and translation- Prokaryotes vs Eukaryotes
Transcription and translation occurs in the same place in prokaryotes unlike eukaryotes.
Eukaryotes also process their mRNA (5’ G-cap, 3’ poly-A tail and splicing (removing introns)) unlike prokaryotes.
Prokaryotes are polycistronic - they can synthesis several proteins from the same mRNA. Eukaryotes are monocistronic
Prokaryotes only have 1 RNA polymerase while eukaryotes have 3 RNA polymerases.
What polymerase transcribes rRNA in eukaryotes?
RNA polymerase I
What polymerase transcribes mRNA in eukaryotes?
RNA polymerase II
What polymerase transcribes tRNA in eukaryotes?
RNA polymerase III
What is wobble pairing
Third anticodon is flexible
What are the five bases of tRNA
Adenine, Cytosine, Thymine, Guanine and Inosine.
What can adenine on tRNA be converted to?
Inosine
What is the difference in writing between a loaded tRNA and unloaded tRNA
loaded = met - tRNA(met)
Unloaded = tRNA(met) (potential of carrying a met)
For methionine
What is the tRNA with an amino acid attached to it called?
Amino-acyl tRNA
What attaches an amino acid to a tRNA?
Amino-acyl tRNA synthetase
What is the cost of ATP per load of amino acid
2 ATP
What is the number of tRNA in a cell?
Atleast 20 and at most 61.
What are the ribosomal subunits in prokaryotes?
50S and 30S
total of 70S (the small and large subunits don’t add up)
What are the ribosomal subunits in eukaryotes?
60S and 40S
total of 80S (the small and large subunits don’t add up)
What forms the peptide bond between amino acids in the P and A site?
The energy released from the 2 ATP used to attach the amino acid to the tRNA by tRNA amino-acyl synthetase
What is translocation in ribosome?
Movement of amino acid from A site to P site or P site to E site.
What happens when stop codon is in A site?
No tRNA recognizes the stop codon but instead a release factor binds to it and breaks the bond between the final tRNA and the amino acid to release a completed protein.
What is an enzyme zymogen?
It is an inactive form of that enzyme which can then have a certain part cleaved off to be active
