PH1123 - DNA and that Flashcards
what are the pyramiding bases ?
The pyrimidine bases are cytosine (C), thymidine (T) and Uracil (U)
monocyclic pyrimidines
What are the Purine bases ?
The purine bases are adenine (A) and guanine (G).
What base is different in DNA and RNA ?
Thymidine in found only in DNA while uracil is found only in RNA.
what are the two sugars in DNA and RNA ?
The sugars in DNA and RNA are pentoses.
They are D-ribose in RNA
and
2-deoxy-D-ribose in DNA.
- In all cases, the sugar is present in a five-membered acetal ring form.
Whats the difference between Beta and alpha glucose ?
Alpha OH group goes downwards
Beta OH group goes upwards (same side as OH group on carbon 5 )
Describe the structure of DNA
DNA is made up of long unbranched chain of oligonucleotides( a polymer of nucleotides), which are linked via a phosphate group that joins the sugar unit with the nucleobase.
- The ester linkage between nucleotides is often a phosphodiester bond.
- The phosphodiester bond links a 5’- of one nucleotide to the 3’-of the next nucleotide.
- Thus, nucleic acids have two ends; 5’- and 3’-ends.
- In some organisms, some bacteria and viruses, the 5’- and 3’-ends of DNA are linked to give circular DNA!
- The base sequence of DNA is written from the 5’- to the 3’-end.
e. g: 5’-ATCCGATG-3’
The nucleobases in DNA have the ability to form hydrogen bonds with between themselves. * This property is essential to the double-helix arrangement of the DNA, translation and transcription via RNA. * The poly nucleotide chain of DNA coils into a helix, which gets bonded to another helical strand by hydrogen bonds between the appropriate base pairs. * In DNA, the base pairs are A-T and C-G. * A-T are bonded by two hydrogen bonds while C-G are bonded by three hydrogen bonds.
The DNA double helix has to poly nucleotide chains twisting on a common axis.
- The bases are directed inwards to allow hydrogen bonding (base pairing).
- The sugar units and the phosphodiester bonds will of the main chains form the outside part of the double helix.
- The planes of the base pairs are perpendicular to the helix axis.
- The helix makes a complete turn every 10 bases.
- The two chains are complementary in sequence. If you know the identity of one chain you can work out the second chain.
- The chains are antiparallel. which means one strand is 5’ to 3’ and the other strand is 3’ to 5’
How many hydrogen bonds form between adenine and thymine and how many between guanine and cytosine
Guanine and cytosine = 3
adenine and thymine = 2
what are the three enzymatically mediated steps in DNA replication ?
initiation, elongation and termination
Explain the process of DNA replication
DNA helices breaks the hydrogen bonds between bases unwinding the DNA double strand.
Each of these unwound strands acts as a template for the synthesis of a new DNA strand
Describe the glycosidic bond between a nucleobase and a sugar unit.
The nucleobase is always linked to the sugar unit through an N-glycosidic bond on carbon 1
The linkage between them is always Beta (the orientation is always going up)
The orientation is always Beta in DNA and RNA
Whats the difference between a nucleotide and a nucleoside ?
Nucleotide = base, sugar and phosphate(s) Nucleoside = base sugar
Describe the nature of the phosphate group in nucleotides
The PHOSPHATE GROUP in the nucleotide is attached via a phospho ester linkage
The phosphate group could be attached to the 5’ hydroxide group or the 3’ hydroxide group
What would the first, second and third phosphates be called in a nucleotide
phosphate 1 (bound to nucleoside) = alpha phosphate 2 = beta phosphate 3 = gamma
What are grooves in DNA
the glycoside bond between sugars and bases of a particular base pair are not directly opposite each other which causes gabs between base pairs
the groove with big gaps is the major groove and the groove with small gaps is the minor groove
the grooves are mainly occupied by water but certain anti cancer agents exploit it and bind to the minor grooves of the DNA stopping the functioning of the DNA.
What do Okazaki fragments do ?
I
Why is DNA replication semiconservative ?
Because each of the new DNA molecules made have one of the strands from the previous DNA molecule.
Why is DNA replication semiconservative ?
Because each of the new DNA molecules made have one of the strands from the previous DNA molecule.
What are 3 main ways in which RNA differs to DNA ?
RNA differs structurally from DNA in 3 important ways.
- The sugar in RNA is ribose while in DNA its deoxyribose.
- Thymine is replaced by uracil in RNA.
- RNA is usually single stranded. DNA stores genetic information and RNA participate in the processes by which this information is used. Three major forms of RNA are found in prokaryotic cells; mRNA, tRNA and rRNA.
What are the precursors for the synthesis of new DNA strands and what happens to them ?
The precursors are Nucleoside triphosphates
The triphosphates are susceptible to nucleophilic attack from hydroxyl groups and therefore the hydroxyl groups on a DNA nucleotide bind to the alpha phosphate group breaking the triphosphate structure and causing diphosphate to leave.
What is a gene ?
a gene is a DNA segment that contains the information necessary for the synthesis of one protein
How does a codon contribute to the production of an amino acid ?
Every amino acid in a protein is specified by a sequence of 3 nucleotides called a codon.
What is the process of transcription ?
Dna helicase unwinds the DNA strand by breaking the hydrogen bonds.
The RNA nucleotides match with the corresponding base pairs
RNA polymerase catalyses the reaction
Takes place in the nucleus
What is the process of translation
mRNA leaves the nucleus and moves to the cytoplasm and a ribosome
tRNA is specific to a specific amino acid
The codon of the mRNA has to match with the anticodon of the tRNA
how is termination achieved?
- achieved by blocking the replication fork
what does DNA ligase do in DNA replication? (2)
- joins nucleotide bases
- continuous amino sequence
what is a gene?
- a DNA segment that contains the information necessary for the synthesis of one protein
what is a codon?
- a three-nucleotide sequence that codes for an amino acid
where does synthesis of mRNA occur?
Nucleus
what is the acylation of tRNA? (2)
- negative COO- binds to Pi which produces aminoacyl-AMP + 2Po
- requires ATP
what does the ribosome do in translation? (2)
- reads the mRNA and produces a chain of amino acids
- mRNA is read from the 5’ to 3’ end
how are the codon and anticodon bonded?
Hydrogen bonding
why are there lots of side effect for drugs that affect DNA?
- healthy cells are damages/affected
what is involved in the design of antiviral drugs? (3)
- viral DNA binding inhibitors
- target virus and cell membrane binding
- inhibit reverse transcriptase
what happens in reverse transcription? (9)
- primer tRNA binds to a complementary primer binding site (PBS)
- DNA sequence is synthesized from 5’ to 3’
- the viral R and Ur regions (LTRs) at the 5’ end are removed by RNase H
- the newly synthesised DNA segment makes a jump to the 3’ end of the viral RNA and binds to the R region by base pairing
- a long DNA sequence complimentary to viral RNA is synthesised
- the viral U3 and R regions are removed by RNase H leaving the PP regions
- a complementary DNA sequence (5’ to 3’) is synthesised
- the tRNA primer is removed and a second jump of the cDNA to the 3’ end takes place
- this is followed by the synthesis of a complemetary DNA sequence
What is gemcitabine used to treat?
Used to treat various cancers such as pancreatic, breast cancer and lung cancer.
What does gemcitabine triphosphate do?
Causes apoptosis through inhibition of DNA elongation.
what does gemcitabine diphosphate do?
Inhibits ribonucleotide reductase an enzyme that converts ribonucleotides into deoxyribonucleotides and DNA synthesis will be inhibited.
