DNA & Genomics Flashcards
(42 cards)
Sugar-phosphate backbone shows directionality. What is meant by the 5’ end and 3’ end of the chain?
5’: free phosphate group attached to C5 of deoxyribose
3’: free hydroxyl group attached to C3 of deoxyribise
Compare the structure of DNA and RNA.
- Location
- Amount
- Macro features
- DS vs SS
- Chemical stability
- Size
- directionality (S)
- Sugar phosphate backbone (S) - Variation/forms
- Nt
- basic unit
- sugar residue (S/D)
- nitrogenous bases
- ratio of bases
- bond (S/D)
What are the advantages of DNA being double stranded?
- DNA mlcs more stable in structure as collective H bonds between base pairs strengthen double-helical structure
- One strand can act as a template for DNA repair of the other strand
- DNA can be replicated accurately via semi-conservative replication (each strand serves as a template for synthesis of a new complementary strand)
What is the importance of Chargaff’s rule/1:1 ratio in the structure of DNA?
⇒ indicate cbp, where A pairs w T, G pairs w C
⇒ H bonds between complementary bases stabilize struc of DNA
⇒ pairing between purine & pyrimidine→ constant width of 2.0nm between 2 sugar-phosphate backbone
What is the role of DNA?
Store info, pass it from one generation to the next
What makes DNA a suitable store of information?
- Can be accurately replicated: daughter cells have identical copies of DNA as parent cell
- Weak H bonds between 2 strands→ can separate & act as templates for new strand synthesis
- Complementary base pairing: A=T, G≡C - Stable molecule→ passed on to next gen wout loss of coded info
- Collectively, numerous H bonds hold 2 DNA strands tgt
- adj nucleotides in each strand joined by strong covalent phosphodiester bond - Backup of the code
- DNA is ds
- One strand can serve as template for the repair of the other, when mutations occur on either one - Coded info readily utilised/accessed
- Weak H bonds between 2 strands→ template strand can separate from non-template strand allowing transcription to take place
- Complementary base pairing: faithful transfer of info from DNA to RNA during transcription, which will subsequently be translated to protein
Describe the role of mRNA in protein synthesis.
- synthesized from transcription, by cbp w DNA serving as a template, where A=U, T=A, G w C
- Acts as a messenger and carrier of genetic code, to carry transcripts of info from gene in nucleus to ribosomes in cytoplasm/RER, where translation takes place, via nuclear pores
- template for translation
- each codon in the coding region specifies an aa in a polypeptide chain→ seq of codons on mRNA code for aa seq in a single polypeptide
- During translation:
> codons in mRNA cbp with anticodons of a specific tRNA carrying a specific aa
> mRNA has recognition sites that allow it to bind to the small ribosomal subunit
> mRNA has start/stop codons - gene expression can be regulated (varying the rate of mRNA synthesis/rate of breakdown)
Describe the role of tRNA in protein synthesis.
Brings in specific aa (to the growing polypeptide at ribosome) in a seq corresponding to seq of codons in mRNA.
It can facilitate translation because:
- 3’ end w CCA stem→ ability of tRNA w specific anticodon to bind to specific single aa during aa activation
- ability of its specific anticodon to base-pair to a specific mRNA codon during translation (A bp w U; G bp w C, by forming H bonds)→ ensures seq of nt on mRNA translated into a specific seq of aa in polypeptide chain.
tRNA is then released after aa joins polypeptide, and reused, attaching to another specific aa
Describe the role of rRNA in protein synthesis.
- associates w ribosomal proteins→ ribosomes
- small subunit: cbp between rRNA in mRNA binding site and mRNA, where A base pairs w U, G base pairs w C→ small subunit binds to mRNA
- large subunit
- enables binding of aminoacyl-tRNAs to Peptidyl site (P site) & Aminoacyl site (A site) via cbp
- part of it acts as peptidyl transferase, catalysing formation of peptide bond between 2 aa
What is the function of ribosomes?
Synthesise polypeptide under direction of mRNA by:
- hold tRNA and mRNA closely, allow interaction between codon of mRNA & anticodon of tRNA
- positions new aa for addition to growing polypeptide
- peptidyl transferase catalyses formation of peptide bonds between 2 aa
What’s the difference between ribosomes in prokaryotes and eukaryotes?
- eu: 80S (small (40S) + large (60S))
- pro: 70S (small (30S) + large (50S))
Define gene.
a specific seq of nucleotides in a DNA molecule, which codes for a specific seq of aa in one polypeptide chain. It’s located in a fixed position (locus) on chromosome/DNA mlc, and specifies a particular biological function (phenotype).
Template strand/antisense strand = non-coding seq, mRNA complementary to it. True/False?
True
Outline the features of the genetic code (+ definition)
Describes the manner in which a particular nucleotide sequence is translated into its corresponding amino acid sequence
- Triplet code, where each seq of 3 consecutive nt/codon codes for 1 aa
- If 1 nt coded for 1 aa→ only be 4 aa; If 2 nt code for 1 aa→ only be 16 (42) aa; If 3 nt code for 1 aa→ only be 64 (43) aa, > enough to code for all 20aa - Universal: same triplet of nt codes for same aa in all organisms (basis of genetic engineering)
- Degenerate: For some aa out of the 20, an aa may be coded for by >1 codon
- Non-overlapping: Codons read as successive groups of 3 nucleotides
- Continuous: no nucleotides ‘skipped’ between codons; code read as continuous seq of nt bases
- Includes ‘start’ & ‘stop’ seq
- Start codon: AUG→ signals initiation site for translation of mRNA into seq of aa. It codes for methionine
- Stop codon: UAA/UAG/UGA→ don’t code for any aa; stop signals for termination of polypeptide chain synthesis during translation
What is conservative DNA replication?
2 parental strands separate, act as templates for synthesis of new strands→ reassociate→ restored original double helix + daughter DNA molecule consisting of 2 newly synthesised strands
What is dispersive DNA replication?
parental DNA fragmented and dispersed→ daughter molecules w mixture of old & newly synthesised parts
Describe semi-conservative DNA replication.
parental DNA molecule separates into 2 single strands through breakage of H bonds, each act as template for synthesis of complementary daughter/new strand through cbp→ 2 new DNA molecule, each a hybrid of 1 parental strand & 1 newly synthesised strand
What is the advantage of having multiple Ori?
DNA polymerase can add dNTPs at a certain max rate (fixed). Multiple Ori in a single DNA molecule→ many DNA pol can work simultaneously→ speed up copying of very long DNA mlcs
Describe DNA replication: START
- replication starts at Ori
- Helicase breaks H bonds between complementary base pairs of 2 strands→ unzips DNA double helix & separates the 2 parental DNA strands
- single-stranded binding proteins bind to and stabilise separated ssDNA, keeping them apart so that they remain ss and can serve as templates for synthesis of complementary DNA strand
- Topoisomerase relieves overwinding strain ahead of replication forks by breaking, swivelling & rejoining DNA strands
Describe DNA synthesis: synthesis of new strands
- Primase catalyses synthesis of RNA primer on each parental DNA strand→ provides free 3’ OH needed for DNA polymerase to initiate DNA synthesis
- Cbp occurs between template strand and free incoming dNTPs, where A forms 2 H bonds w T and G forms 3 H bonds w C
- DNA polymerase catalyses the formation of phosphodiester bonds, linking DNA nucleotides & synthesizing the new strand in the 5’ to 3’ direction
- Anti-parallel parental strands→ 2 new strands synthesised in opposite directions
> Leading strand synthesised continuously towards replication fork
> Lagging strand synthesised discontinuously away from replication fork, forming Okazaki fragments - DNA polymerase (part of it) “proof-reads” previous region as it moves along the parental strand→ ensures proper base pairing between bases. If incorrect DNA nt added, it’s removed by DNA polymerase and replaced w correct one→ ensures fidelity of DNA seq
- Different DNA pol removes RNA primer and replaces it w DNA nucleotides
- DNA ligase catalyse formation of phosphodiester bond between nt of adjacent DNA fragments, sealing nicks in DNA
Compare DNA replication in eukaryotes and prokaryotes.
- When
- Where
- No. of Ori
- Ends at
- Rate
Describe transcription
Process: Initiation
- RNA polymerase attach to promoter of gene w aid of transcription factors (protein)→ transcription initiation complex
- RNA polymerase unzips DNA double helix (and separates the 2 strands of DNA) by breaking H bonds between complementary base pairs.
- 3’ to 5’ strand/1 strand used as template strand to synthesise complementary mRNA strand
Process: Elongation
- Free ribonucleotides will bind by cbp to nt on DNA template strand: A=U, T=A, G≡C
- RNA polymerase catalyses formation of phosphodiester bonds between free ribonucleotides→ sugar phosphate backbone
- New mRNA strand synthesised in 5’ to 3’ direction
- Region of DNA that has been transcribed reanneals, forming double helix
Process: Termination
RNA polymerase dissociate from template DNA strand after it transcribes the termination seq
ss pre-mRNA molecules released
Describe post-transcriptional modification: capping
add 5’ methylguanosine cap→ methylated guanosine nucleotide added to 5’ end of pre-mRNA as soon as ~25 nucleotides produced (protects from degradation by ribonucleases, export of mature mRNA, recognition of mRNA)
Describe post-transcriptional modification: splicing
- introns excised, exons joined
- done by spliceosome with high accuracy
