Nucleic acids: structure and function Flashcards
1
Q
each nucleotide contains 3 components
A
- a nitrogenous heterocyclic base
- purine or pyrimidine
- A pentose sugar
- ribose (RNA) or deoxyribose (DNA)
- A phosphoric acid group in ester linkage to the 5’ carbon of the pentose
2
Q
describe the structure of purines and pyrimidines
A
- Purines are heterocyclic compounds consisting of a pyrimidine fused to a 5 member imidazole ring
- Pyrimidines are heterocyclic compounds containing N atoms at position 1 and 3 of a 6 member ring
3
Q
describe nucleosides
A
Nucleosides consist of a nitrogenous base and a ribose or deoxyribose sugar
4
Q
describe nucleotides
A
- Nucleotides consists of nitrogenous base, a ribose of deoxyribose sugar and a phosphate group
5
Q
explain when nucleosides 5’-triphosphates are acidic and negative and the functions
A
- Nucleosides 5’-triphosphates are acidic at neutral pH and possess 4 negative charges
- Function
- Precursors of the nucleotides for RNA and DNA
- ATP - universal chemical energy
- GTP - protein synthesis
- UTP - biosynthesis
- CTP - phospholipid biosynthesis
- Formation of coenzymes
6
Q
explain what DNA/RNA polyermase does
A
- DNA/RNA polymerase catalyze the formation of a phosphodiester bond between the 3’ OH group of the deoxyribose/ribose on the last nucleotide and the 5’ phosphate of the dNTP/NTP precursor
7
Q
describe the function of DNA ligase
A
- DNA ligase is responsible for sealing nicks in DNA during replication and repair and creates phosphodiester bonds
- Creates phosphodiester bond between 3’OH and monophosphate
8
Q
describe the melting temperature (Tm) of DNA and what influences it
A
- Tm is the temp. at which 50% of the DNA becomes single stranded
- Tm increases with G-C content
- Tm is influenced positively by ionic strength
9
Q
describe annealing and the rate
A
- Single strands of complementary DNA Acan reanneal with each other by H-bond formation
- The rate of annealing is dependent on the size and complexity of the DNA strands
10
Q
describe the secondary structures of DNA
A
- B-DNA
- Basis of Watson-Crick model
- Right hand helix
- Can contain considerable variations of structure depending on the nucleotides present. Important in influencing DNA-protein binding
- Z-DNA
- Left hand helix
- Seen in sequences containing alternating pyrimidine and purines
- Maybe involved in gene regulation
- A-DNA
- Right hand helix
- Dehydrated state
- No biological significance
11
Q
describe the different types of structures (primary, secondary…)
A
- Primary structure
- The sequence of nucleotides (bases) along the polynucleotide chain
- Secondary structure
- The 3D structure e.g. double helix of DNA
- Tertiary structure
- Includes supercoiling of the secondary structure
- Quaternary structure
- the interaction of nucleic acids with proteins
12
Q
describe the different types of RNA and their functions and percentage
A
- mRNA
- Linear single stranded molecule
- carries codon information for translation
- 2% of total RNA
- tRNA
- folded stem loop structures formed by intramolecular H-bonding
- carries amino acid to ribosome
- 16% of total RNA
- rRNA
- linear single stranded, folded molecule
- complexes with protein to form ribosome
- 82% of total RNA
13
Q
describe the role of rRNA
A
- overall structure of ribosome
- catalytic activtiy (forming covalent peptide bonds)
14
Q
describe snRNA
A
- snRNA are small nuclear ribonucleic acid
- Involved in generation of mature mRNA transcripts
- Central components of the splicing apparatus
- Involved in regulation of:
- transcription factors
- RNA pol II activity
- telomere maintenance
15
Q
describe miRNA
A
- microRNA
- Silencing of gene expression
- 1000 human genes that encode miRNAs (3% of genome)
Process
- primary miRNA transcript
- undergoes nuclear processing
- pre miRNA
- undergoes cytoplasmic processing
- mature miRNA
- miRNA + RNA-induced silencing complex (RISC)
- 2 functions
- translation of target DNA is repressed
- target mRNAs are degraded
- 2 functions
16
Q
describe what azidothymidine (AZT)/zidovudine/didanosine does
A
- It is utilized by the viral reverse transcriptase
- Upon incorporation into the ds DNA chain termination occurs due to lack of 3’OH
- Specificity for infected cells lies in the fact that these drugs have a 100-300 fold greater affinity for incorporation by reverse transcriptase than eukaryotic DNA polymerase
- Zidovudine can:
- prolong life in HIV infected individuals
- reduce mother to baby transmission by more than 20%
17
Q
describe what tenofovir does
A
- Tenofovir diphosphate competes with its natural nucleotide counterpart, deoxyadenosine 5’-triphosphate, for incorporation into newly forming HIV DNA
- Once successfully incorporated, termination of the elongating DNA chain ensues and DNA synthesis is interrupted
18
Q
explain what cytosine arabinoside (araC) is and does
A
- It is a cytosine nucleoside analogue
- AraC has a 3’ OH group to act as an acceptor for further chain elongation. However the OH gap at position 2 prevents polymerase adding the next dNTP due to stereo restraints, which leads to chain termination
- This is important in the therapy of leukemia, in particular acute myeloid leukemia and lymphoma
- Instead of altering the base (like in nucleotide base analogues) AraC alters the sugar
19
Q
describe the function of acyclovir
A
- Viral thymidine kinase = much more effective in catalyzing 1st phosphorylation event thatn hose thymidine kinase
- Only infected cells possess the viral kinase, therefore, acyclovir is only activated in infected cells
- Causes chain termination due to lack of 3’OH 30x more potent against viral DNA polymerase than host
- Acyclovir has high specificity for herpes simplex and varicella zoster
20
Q
describe the process of cytidine analogues
A
- Once incorporated into DNA and RNA they cause hypomethylation as a methyl group cannot be added to the N at position 5. Additionally, these drugs are known to bind and inhibit DNA methyltransferase enzymes
- In eukaryotes, methylation of cytosine is an important mechanism of transcriptional regulation
- Decitabine
- used in DNA
- 5-azacytidine
- used in RNA
21
Q
what is an example of DNA hypomethylating agents in cancer
A
- Hypomethylation of CDKN2B correlates with response to decitabine
- Used in myelodysplastic syndrome and acute myeloid leukemia
