DNA replication, transcription and translation Flashcards
Competitive/non-competitive and reversible/irreversible inhibition examples
reversible competitive (methanol, dehydrogenase (formic acid, formaldehyde), ethanol)
reversible non-competitive (fructose-6-phosphate, phosphofructokinase, xylitol-5-phosphate)
irreversible competitive (peptidoglycan (bacteria cell wall), transpeptidase which catalyzes peptidoglycan production, penicillin)
irreversible non-competitive (heavy metals like Hg and Pb)
Name the monomer of nucleic acids and draw and annotate its structure
nucleotide (deoxyribonucleotide or ribonucleotide), …, pentose sugar (deoxyribose, ribose), a phosphate group, and one nitrogenous (N) base (adenine (A), guanine (G), cytosine (C) and thymine (T) in DNA or uracil (U) in RNA
The difference in nitrogenous bases’ structures
adenine and guanine are purines (two rings), and cytosine, thymine, and uracil pyrimidines (one ring)
Full names of DNA nucleotides (for each N-base)
deoxyriboadenosine, deoxyriboguanosine, deoxyribocytosine, and deoxyribothymosine
Draw and annotate the dehydration reaction between two nucleotides, and name the bond between them
…, phosphodiester bond (3’ to 5’ linkage) – form a polynucleotide chain
What is the shape of two polynucleotide strands, in what relation are the two strand
coiled around each other in a double helix, they are antiparallel which means that they run alongside each other but in opposite directions (each is oriented in the direction from 5’ to 3’) – the two connected strands need to have complementary N-base pairs (A-T, C-G) – A and T form two H-bonds, and C and G three
Three types of RNA
messenger, transfer and ribosomal
Describe the Hershey-Chase experiment – phage (radioactive S (protein)/P (DNA)) infects bacteria
only phages with radioactive DNA produced radioactive E. coli (which was turned into a phage-producing factory) – reflected as a radioactive pellet (bacteria are denser so they fall as a pellet (instead of supernatant) after being separated from phages in a centrifuge). It was hypothesized that proteins carry genes because they have more capacity for variation 20^n vs 4^n, but DNA can be any length, unlike proteins which adds to the potential diversity of sequences
DNA replication, semiconservative meaning
the process of cloning the DNA to produce two identical copies which happens prior to cell division so that each daughter cell receives one copy of the original DNA – newly synthesized DNA is made of one old and one new polynucleotide chain
Summarize the process of DNA replication
DNA helicase attaches to one site on the parent DNA and unwinds and unzips the two strands. It creates a replication fork (where the DNA is opened) – primers (ribonucleoside triphosphates) get added to both template strands to start the polymerization process – there is only one on the leading and multiple on the lagging strand (creating Okazaki fragments) – then free DNA nucleotides (deoxyribonucleoside triphosphates) bases get linked with their complementary bases on the template strand by the DNA polymerase III (forming phosphodiester bonds) – DNA synthesis may occur bi-directionally from the origin – primers are later removed by DNA polymerase I, and enzyme ligase seals the gaps in the chains – gyrase (topoisomerase) moves in advance of helicase and coils the DNA strand to relieve the pressure made by supercoiling of the DNA (because of helicase’s unwinding) which could cause a block in replication – SSB (single-strand binding) proteins attach to template strands to prevent their spontaneous rejoining
Origin of replication in prokaryotic vs eukaryotic DNA
there is more than one origin of replication on eukaryotic DNA because eukaryotic chromosomes are much larger and more numerous than prokaryotic – speeding up the process
How are deoxyribonucleoside triphosphates different from bound nucleotides
have three phosphate groups: ATP (3) -> ADP (2) -> AMP (1) – as the phosphodiester bond is formed, the two phosphate groups are removed from the free nucleotides, providing E for the bonding
What is the limitation of DNA polymerase III
its specificity; it can only add new nucleotides onto a preexisting chain of nucleotides so it cannot initiate polymerization
What is the central dogma of molecular biology, are there any exceptions to it
the process of gene expression, retroviruses (their RNA gets turned into DNA and then into mRNA) – reverse transcription
Gene
a part of the DNA with a specific base sequence that codes for the a-a sequence of one polypeptide chain
Describe the transcription process
only one (anti-sense) strand is used for transcription, the one complementary to the one carrying genetic info – initiation: RNA polymerase binds to the promotor region (short DNA seq. before the gene), unzips the gene and lets ribonucleoside triphosphates (ATP, GTP, CTP, UTP) pair up with the anti-sense strand free nitrogenous bases – elongation: RNA polymerase forms bonds between ribonucleoside triphosphates (in 5’ to 3’ direction) – termination: RNA polymerase reaches the terminator region (end of the gene) and the polymerization is stopped (mRNA is complete, it gets released from the template strand and travels to the cytoplasm (ribosomes))
Which two processes in gene expression can occur simultaneously?
DNA replication and transcription
Repair mechanisms purpose
maintaining the stability of DNA templates during transcription when the sense strand is more exposed and subjected to the impact of mutagens – they minimize mutations but deteriorate as we age so mutations accumulate and cause diseases
Describe post-transcriptional modification
introns (the non-coding regions of the DNA) get spliced out of the pre mRNA by spliceosome because they should not get translated (only in eukaryotic because prokaryotic only have exons – transcription and translation occur almost simultaneously) – also, poly-A-tail gets added to the 3’ end of pre mRNA because it aids in the translation, it transports mRNA to the cytoplasm and protects it from enzymatic digestion in the cytoplasm
What is mRNA organized in
in codons, that is, groups of three nitrogenous bases that code for one amino acid – some codons signal for the end of translation (stop codons)
Genetic code function
enables cells to convert base sequences into amino acids – it is universal (used by all species) and degenerate which means that more than one codon will code for the same a-a (reduces the effect of base pair substitution mutations)
Ribosome structure
proteins and ribosomal RNA – composed of two subunits, one big and one small which are usually separated but join during translation – there are three tRNA binding sites (E-exit, P-peptidyl, A-acceptor)
tRNA function, structure
transports amino acids towards ribosomes and attaches to specific binding sites on the ribosome – made out of base pairs and has a shape like a clover as a result of attraction forces between complementary bases – in its middle, there is an anticodon which is complementary to the mRNA codon (they later pair up) – the 3’ end is the a-a attachment site where the a-a specific for that tRNA joins to be transported to a ribosome
Describe the translation process
polypeptide synthesis using mRNA as a guide – initiation: mRNA binds to the mRNA binding site on the small subunit, initiator t RNA binds to the start codon, big subunit joins and initiator fits into the P-site, the next t RNA bind onto A-site and a peptide bond is formed between the two a-a – the first a-a detaches (dipeptide carried by the one in P) – elongation: ribosome moves for one codon towards 3’ of m RNA (P->E), new t RNA attaches to A site and the chain grows – termination: when a stop codon attaches to the A-site and the release factor (protein) is added instead of an a-a – it releases the polypeptide chain and ribosome disassembles
