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cell bio > DNA Replication > Flashcards

DNA Replication Flashcards

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1
Q

semi-conservative rep stages

A

Initiation
Unwinding
Elongation
Termination

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2
Q

SCR Initiation

A

The origin for DNA replication in E. coli is known as oriC, this genetic locus contains the binding site for the initiator protein DnaA, single stranded binding protein (Ssb) holds the DNA bubble open allowing DnaB protein to bind. DnaB is a helicase which uses ATP to melt double stranded DNA

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3
Q

SCR Unwinding

A

After DNA helicase travels along the template strand and opens it for copying, supercoiling is prevented by DNA gyrase (type II topoisomerase). DNA gyrase lessens supercoiling (relaxes tension) which builds up during DNA unwinding, preventing DNA breakage.

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4
Q

SCR Elongation

A

leading and lagging strand primers are elongated by the DNA polymerase III holoenzyme, the subunit is a dimer, the leading and lagging strands are synthesized simultaneously. The leading strand is made as a continuous piece (5’-3’ direction), whilst the lagging strand is made in fragments (okazaki) in a 3’-5’ direction. The looping of the lagging strands makes the process possible, DNA polymerase I fills in the gaps once the primers are removed, DNA ligase makes the final phosphodiester bond between the fragments

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5
Q

transcription Initiation

A

RNA polymerase binds to double stranded DNA and initiates transcription
at regions called promoters, where DNA unwinds (hydrogen bonds are broken)
the enzyme aids RNA synthesis
RNA polymerase and its cofactor are known as
the transcription complex.
No primers are required.

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5
Q

SCR Termination

A

the 2 replication forks meet 180 degrees opposite oriC, these forks are arrested by binding the tus gene product at termination sites around this region.
Topoisomerase IV unlinks the interlinked product which can now be separated into the 2 daughter cells.

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6
Q

transcription Elongation

A

RNA polymerase locally unwinds the DNA strand as it adds on ribonucleotides to the growing 3’end of the RNA strand.
Thymine is exchanged for uracil in a RNA molecule.

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7
Q

oriC

A

site of initiation of bacterial chromosomal replication

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8
Q

DNA ligase

A

enzyme that forms phosphodiester bonds

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8
Q

DNA helicase

A

enzyme that unzips DNA for replication, separates the double strands

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9
Q

DNA gyrase

A

type of topoisomerase II which reduces the supercoiling of DNA, under winds the DNA molecule (negative supercoiling)

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10
Q

transcription Termination

A

dissociation of the transcription complex which occurs at the terminator site (specific DNA sequence)
terminator sites usually have hairpin or stem loop structures which ceases transcription
process may be rho-
dependent or rho-independent
RNA transcript undergoes modification such as 3’ polyadenylation, 5’ capping, RNA splicing to prevent molecular degradation, then it enters the cytoplasm via the nuclear pores

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11
Q

products of transcription

A

mRNA
microRNA
transfer RNA
small nuclear RNA
ribozymes

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12
Q

Messenger RNA (mRNA)

A

product of DNA which encodes a protein
the main template for protein synthesis via the process of translation

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13
Q

Retroviruses

A

RNA viruses which utilise RNA-dependent DNA polymerase to replicate the RNA genome through a DNA intermediate (reverse transcription)

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14
Q

DNA Replication function

A

make DNA copy for a daughter cell
synthesise an identical DNA copy

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15
Q

DNA polymerase III

A

enzyme utilized in prokaryotic DNA replication for the leading and lagging strands

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16
Q

Leading strand

A

the strand of DNA that is replicated continuously

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17
Q

Lagging strand

A

strand of DNA that is replicated in fragments (Okazaki) due to the orientation of the DNA molecule

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18
Q

Okazaki fragment

A

fragments of DNA molecules produced discontinuously and later linked by DNA ligase. Complementary to the lagging DNA strand

19
Q

Primase

A

synthesizes the primer that aids DNA replication

20
Q

DNA polymerase I

A

enzyme utilized to remove the RNA primers and replacing it with nucleotides which allows the connection of Okazaki fragments
Also have a DNA repair function

21
Q

Single strand binding proteins

A

allows the unwound DNA strand to remain open for DNA replication

22
Q

Folic acid deficiency

A

folic acid is made from folate (vitamin B9). Its deficiency leads to anaemia. Folic
acid is utilised in the synthesis of DNA

23
Q

DNA Transcription

A

using double stranded DNA template strands to make
single stranded RNA. RNA synthesis occurs in a 5’-3’ direction and its sequence are
complementary to the DNA template strand/ antisense strand

24
Q

DNA Transcription Initiation

A

RNA polymerase binds to double stranded DNA and initiates transcription
at regions called promoters, where DNA unwinds (hydrogen bonds are broken), the enzyme aids RNA synthesis RNA polymerase and its cofactor are known as
the transcription complex.
No primers are required.

25
Q

DNA Transcription Elongation

A

RNA polymerase locally unwinds the DNA strand as it adds on ribonucleotides to the growing 3’end of the RNA strand.
Thymine is exchanged for uracil in a RNA molecule.

26
Q

DNA Transcription Termination

A

begins with the dissociation of the transcription complex which occurs at the terminator site (specific DNA sequence). These terminator sites usually have hairpin or stem loop structures which ceases transcription. This process may be rho-dependent or rho-independent. The RNA transcript undergoes modification such as 3’ polyadenylation, 5’ capping, RNA splicing to prevent molecular degradation, then it enters the cytoplasm via the nuclear pores

27
Q

DNA rep products

A

DNA molecules
Daughter strands bonded to original strands
stay within nucleus

28
Q

Gene transcription products

A

RNA molecules
mRNA and non-coding RNA
mRNA exported to the cytoplasm

29
Q

DNA Rep enzymes

A

DNA helicase
DNA polymerase
DNA ligase

30
Q

Gene transcription enzymes

A

DNA helicase
RNA polymerase

31
Q

DNA rep happens when

A

S phase

32
Q

Gene transcription happens when

A

G1 and G2 phases

33
Q

RNA polymerase

A

enzyme of transcription that is used to transcribe DNA into RNA

34
Q

Promoters

A

DNA sequences that determine where transcription of a gene begins

35
Q

RNA splicing

A

removal of introns and connection of exons; introns are noncoding regions of the genes

36
Q

Ribonucleotides

A

nucleotides found in RNA molecules, the pentose sugar is ribose, in RNA thymine is
usually replaced with uracil

37
Q

region codon is translated

A

between the initiation and the termination

38
Q

3 main stages of protein synthesis

A

Initiation
Elongation
Termination

39
Q

Translation Initiation

A

main aim of this step is to assemble a ribosome molecule onto the start/initiation codon (AUG) of an mRNA molecule. The components of this first stage are the large and small ribosomal units, mRNA, tRNA, initiation factors and GTP. The initiation factors bind to ribosome, together they recognize ribosome binding site (RBS) on the mRNA molecule, initiator tRNA binds to the P site by base pairing with its anticodon to the codon on the mRNA. There are 2 sites for tRNA binding sites on the ribosome (Aminoacyl and peptidyl sites). AUG encodes methionine.

40
Q

Translation Elongation

A

stage begins when the 50S subunit of the ribosome binds forming the 70S complex
amino-acyl-tRNA delivery
peptide bond formation
translocation
subsequently after amino-acyl-tRNA delivery, A and P sites are filled and peptidyl transferase activity of the 50S subunit forms the peptide bond between the 2 amino acids. Discharged tRNA moves on to the exit site and is ejected when the next aminoacyl-tRNA. Eukaryotic mRNA translation usually involves a 80S ribosome and occurs in the cytosol

41
Q

Translation Termination

A

Cycle is repeated until one of the three termination codons (UAA, UAG, and UGA) is encountered. Release factors aid the release of the polypeptide chain. If a base is damaged or no encountered stop codon, a ribosome may stall on an mRNA. The newly made polypeptide chain usually undergoes further processing in the Golgi apparatus after which it may be stored or released.

42
Q

Prokaryotes and Eukaryotes Translation Differences

A

1.Transcription and translation are simultaneous processes
Transcription and translation are discontinuous processes
2. Utilises 30S and 50S subunit (70S) Utilises 40S and 60S subunit (80S)
3. Occurs in the cytoplasm Occurs in the cytosol
4. mRNA produced by transcription of operons
mRNA produced by transcription of single genes
5. Faster process
Slower process
6. Cap independent initiation Cap dependent initiation, 5’cap recruits the ribosomes.
7. Its mRNA does not contain a 5’cap and 3’ tail
Its mRNA does not contain a 5’cap and 3’ tail
8. 3 initiation factors (IF1, IF2, IF3)
9 initiation factors (1,2,3,4A, 4B,4C,4D, 5 &6)
9. Single release factor eRF1
2 release factors (RF1 & RF2)
10. No definite phase of occurrence
Occurs in G1 and G2 phase

43
Q

Aminoacyl sites

A

binding site for charged tRNA molecules during protein synthesis. First site that tRNA binds to on the ribosome

44
Q

Peptidyl sites

A

2nd binding site for tRNA on the ribosome, site at which the tRNA holding the growing polypeptide chain binds unto

45
Q

Exit sites

A

site where tRNA binds onto after donating their amino acid molecule to the growing polypeptide chain

46
Q

Mutations

A

Mutations are alterations in the genetic material of a cell in a living organism.
Mutation can occur in genes or chromosomes; genetic mutations are changes in the nucleotides that make up the gene (point mutation).
Chromosomal mutations can result from certain regions being translocated, deleted, duplicated, inserted and inverted; chromosomal mutation may arise from a virus, irradiation, and chemical assaults (mutagen).

cell bio (11 decks)

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