Biochemistry - Nucleic Acids Flashcards
Does DNA leave the nucleus?
No. Slide 5
What happens after transcription?
Pre-mRNA is processed through splicing to produce mRNA which leaves through the nucleic pore. Slide 5
What are nucleotides made up from?
Base, sugar, phosphate. Slide 6
What is attached to C1’?
Base. Slide 6
What is attached to C5’?
The phosphate. Slide 6
What is so important about C3’?
It always has an OH group on it in a nucleotide, as this is where the phosphate binds. Slide 6
What bases are purines?
Adenine and guanine. Slide 7
What bases are pyrimidines
Cytosine, thymine and uracil. Slide 7
Which molecules are bigger? Purines or pyrimidines?
Purines - short name, larger molecule. Slide 7
What is a nucleoside?
A base linked to a sugar. Slide 8
What are the nucleoside names of the 5 bases?
Adenosine, cytidine, guanosine, thymidine, uridine. Slide 8
What are the DNA building blocks?
dATP, dCTP, dGTP, dTTP
e.g. deoxy-adenosine-triphosphate. Slide 8
What are the RNA building blocks?
ATP, CTP, GTP, UTP
e.g. uracil-triphosphate. Slide 8
Where is the phosphodiester bond formed to replicate the DNA?
Between the free 3’ OH group and a 5’ triphosphate. Slide 9
Why is it called a phosphodiester bond?
C - O - P - O - C. Slide 11
What happens to the building blocks when they’re to be added to the free 3’ end?
Two phosphates are cleaved off leaving it to become a monophosphate and is added to the 3’ OH group. Slide 9
What happens to the pyrophosphate ion?
It is broken down into 2 phosphate ions releasing energy and driving the reaction. Slide 9
Why is there energy released from the pyrophosphate?
Each molecule is charged, so repel each other. Slide 10
Why do nucleotide analogues work as drugs?
They are incorporated into the growing DNA of the virus and on the 3’C there is no OH group but a different group. This means chain elongation is terminated so it cannot grow anymore. Slide 12
Why do nucleotide analogues not kill humans?
Viruses reverse transcriptase have a higher affinity for the nucleotide analogues used than human DNA polymerase. Slide 12
How many H bonds are between adenosine and thymine?
2 H bonds. Slide 13
How many H bonds are between guanine and cytosine?
3 H bonds. Slide 13
Why does one pyrimidine and one purine pair?
There isn’t enough space for two purines, too large. Slide 13
What does DNA polymerase require to start?
RNA primer. Slide 14
What is special about replication in eukaryotes?
Many origins of replication and is bidirectional. Slide 15
What does the DNA bubble do?
Allows there to be 4 points of DNA replication in that one origin so it’ll be replicated faster. Slide 15
Do all origins of replication start at the same time?
No. Slide 15
Which end are nucleotides added to?
To the free 3’ end. Slide 16
Which is the leading strand and which is the lagging?
Leading = 3' -5' Lagging = 5' -3'. Slide 16
What happens during replication of the lagging strand?
Can only be replicated in 3’ to 5’ fashion so it is replicated in fragments called okazaki fragments and then sealed together. Slide 16
What does exonuclease activity allow DNA polymerase to do?
Acts as proof reading, so if in incorrect nucleotide has been placed, then DNA polymerase removes it and this improves error rate. Slide 34
Since RNA is single stranded, what is its classic form?
Stretches of intramolecular base-pairing in stem-loops, the loop is formed by unpaired nucleotides. Slide 35
What are the 3 classes of RNA?
mRNA, tRNA and rRNA. Slide 35
What are the 2 most stable RNA molecules?
rRNA and tRNA. Slide 35
What is always on the RNA molecule?
CCA terminus where the amino acid will be conjugated. Slide 35
What does an anticodon consist of?
3 nucleotides. Slide 37
What depends on the anticodon sequence?
The specific amino acid attached to the 3’ end. Slide 37
How many types of RNA polymerase does prokaryotes and eukaryotes have?
Prokaryotes = 1 Eukaryotes = 3. Slide 38
What are the three types of RNA polymerase in eukaryotes?
Pol I, Pol II, Pol III. Slide 38
How can the 3 types of RNA polymerase be distinguished from each other?
Their sensitivity to toxins e.g. alpha-amanitin. Slide 38
Are all the types of RNA made from the same polymerase?
No. Slide 38
What are the steps for transcription?
RNA polymerase binding to initiation sites with transcription factors.
DNA chain separates so there’s access to the nucleotide sequence.
Transcription initiation when the first nucleotide is bound and then elongation of the RNA chain.
Termination when the finished RNA is released. Slide 39
What do the transcription factors do?
Allow general synthesis of RNA or are stimulated through external communication on which genes need to be transcribed so they activate certain genes. Slide 39
What does the TATA box do?
It is in the promoter region on the gene and allows RNA polymerase to start transcribing at Nucleotide +1. Slide 40
How many nucleotides is the TATA box away from the transcriptional start?
25, makes the TATA box end to be nucleotide -25. Slide 40
What is the TBP?
TATA box Binding Protein which binds to the TATA box. Slide 41
What does TFIID do?
It is a general transcription factor, required for all Pol II transcribed genes and introduced a kink into the DNA which determines which direction transcription will occur in. Slide 41
What is essential to the initiation of transcription?
Pol II and TFIIF. Slide 42
Keeping TFIID at the promotor what does that allow?
It means a new initiation complex can assemble so enables transcription at low, basal rates. Slide 42
In transcription of RNA what direction does the bubble go in?
One direction along the DNA. Slide 43
What way is the RNA chain synthesized?
5’ to 3’ direction. It is complementary to the template and therefore identical to the coding strand except for U instead of T. Slide 43
How is the transcription of RNA terminated?
Makes a stem-loop and is followed by a stretch of Us, RNA is cleaved and released. Slide 44
What does specific regulation of transcription require?
‘Specific’ transcription factors: DNA binding domain and the transcriptional activation domain. Slide 45
What do enhancers do during regulation of transcription?
Bind to specific DNA sequences in the vicinity of a promotor. Slide 45
Explain coordinated gene expression in terms of regulated transcription?
Stress.
Activates transcription of regulatory protein.
Binding of regulatory protein to stress response element stimulates transcription of genes A, B and C…
Different proteins in stress response are made. Slide 47
What are the noncoding sequences called?
Introns. Slide 50
What happens during the processing the ends of mRNAs?
A GTP is added to the 5’ end of the mRNA and a poly(A) tail is added (AAAAA). Slide 51
What does the processing of the pre-mRNA allow?
A more stable form of mRNA and recognition when outside the nucleus from other carrier molecules. Slide 51
What do the anticodons of tRNA molecules form base pairs with during translation?
The codons on the mRNA. Slide 53
The 64 possible combinations of the four different nucleotides code for how many amino acids?
- Slide 53
In context of the genetic code, what does degenerate mean?
Many amino acids have more than one codon. Slide 54
Why is it important that each codon is unambiguous?
So it only codes for one amino acid or a stop codon and always know what amino acid to bring. Slide 54
What codon always starts translation?
AUG codes for methionine. Slide 54
Why is it important to understand that there are 3 different reading frames in an RNA molecule
As it depends on where translation starts because there can be untranslated codons at the start. Slide 55
What are the 7 components of translation?
Amino acids, tRNAs, Aminoacyl-tRNA synthetases, specific set of protein factors, ATP and GTP, ribosomes and mRNA. Slide 56
What do aminoacyl-tRNA synthetases do?
Bind amino acids to their corresponding tRNA molecules which are highly specific. Slide 57
How do aminacyl-tRNA synthetases work when binding to tRNA?
The enzyme activates the amino acid which catalyses a reaction with ATP to form a high energy AMP-amino acid and a pyrophosphate ion. The amino acid specific tRNA is then reacted with the activated amino acid by the enzyme. The enzyme is so specific that it makes sure it is the correct tRNA bound to the amino acid and then the charged tRNA delivers the appropriate amino acid. Slide 57
What is special about the aminoacyl-tRNA synthetases?
They each have their own specific amino acid. Slide 57
How many rRNA molecules do ribosomes have in eukaryotes?
4 rRNA molecules. Slide 58
How many rRNA molecules do ribosomes have in bacteria?
- Slide 58
What is the size of eukaryotic ribosomes?
60S and 40s. Slide 58
What are the 3 tRNA binding sites?
Exit, peptidyl and aminoacyl. (E, P and A). Slide 59
How is energy for the initiation of translation provided?
Through hydrolysed GTP. Slide 60
How is translation initiated?
Small ribosomal subunits bind to the 5’ end of mRNA and move along until AUG (start codon) is found. The special initiator tRNA carrying the UAC anticodon base pairs carrying methionine. Larger subunits join and the initiator tRNA is located din the P site. Slide 60
How is the chain elongated?
An elongation factor brings the next aminoacyl-tRNA to the A site where GTP is hydrolysed allowing the tRNA to be released from the EF. A second elongation factor regenerates the first factor to pick up another aminoacyl-tRNA. Slide 61
What are the 2 elongation factors called?
EF-1 alpha
EF beta gamma. Side 61
What enzyme catalyses the peptide bond formation between the amino acids at the P and A sites?
Petidyl transferase. Slide 62
What happens when the elongation factor EF-2 moves the ribosome along the mRNA?
The empty tRNA moves to the E site where is exits and the other tRNA with the growing peptide moves to the P site where the A site is left free for the next aminoacyl-tRNA. Slide 62
How is translation terminated?
When the A site of the ribosome encounters a stop codon as no aminoacyl-tRNA can base pair with it. Slide 64
What happens when translation is terminated?
Release factor binds to the stop codon and the finished protein is cleaved off tRNA and all the components dissociate. Slide 64
What are the 5 types of genetic mutations at base pair level?
Point mutation Missense mutation Nonsense mutation Silent mutation Frameshift mutation. Slide 66
What are the 4 types of genetic mutations at chromosomal level?
Deletions
Duplications
Inversions
Translocations. Slide 68
What are the 3 things that happen to a finished protein?
Targeting
Modification
Degradation (unwanted/damaged). Slide 69
What is the difference between bound and free ribosomes?
One type are ‘free’ in the cytosol which make proteins for the nucleus, mitochondria and are translocated POST-TRANSLATIONALLY
The other are on the rough ER to make proteins for the PM, ER, Golgi, secretion and translocated CO-TRANSLATIONALLY. Slide 70
What does co translocationally mean?
They are being moved as they are translated. Slide 70
What are the 4 different post-translational modifications?
Glycosylation - adding carbohydrates to the ER/Golgi.
Disulphide bonds in ER.
Folding of multi-subunit proteins in ER.
Specific proteolytic cleavage in ER, Golgi and secretory vesicles. Slide 72
