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D1 Flashcards

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1
Q

What is DNA replication?

A

The production of new DNA strands using existing strands. Involves seperating strands and then using the single strand as a template for a new DNA strand

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2
Q

What is meant by “semi-conservative” in reference to DNA replication?

A

It refers to the fact that at the end of each round of DNA replication, each double helix contains one “old” strand of DNA, and one new strand from replication

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3
Q
A
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4
Q

What are the two processes requiring DNA replication

A
  1. Growth and repair of tissue- DNA replication before mitosis
  2. Reproduction- DNA replication before meiosis produces sex cells
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5
Q

How does complimentary base pairing facilitate DNA replication?

A

Specific base pairing rules mean that each original strand can serve as a template for its complimentary strand. This allows semi-conservative replication to occur.

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6
Q

How did the Messelsohn- Stahl experiment show that DNA replication is semi-conservative?

A

They used nitrogen isotopes to track original DNA through generations to show that replication is semi-conservative. Original was marked with N15 and new marked with N14. Demonstrated that N15 always remained but decreased over time, therefore is semi-conservative

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7
Q

Explain the role of helicase in DNA replication

A

Helicase is a ring-shaped enzyme that pulls one strand of DNA through its ring to break the hydrogen bonds between base pairs. This seperates the original DNA strands.

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8
Q

Explain the role of DNA polymerase III in prokaryotic DNA replication

A

DNA polymerase is a group of enzymes that work off the primers to attach new DNA base using free nucleotides in the nucleus, and pairing it with the template strand using base pairing rules to build 5’ to 3’ strands on the leading and lagging strands. This then hydrogen bonds between complimentary bases to build the new strand which is also proofread to check for mistakes and mutations.

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9
Q

What is the conservative theory of DNA replication? (disproven)

A

Original strand stays together, so in each generation there will be one full original double helix

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10
Q

What is the dispersive theory of DNA replication? (disproven)

A

Original DNA is spread randomly throughout the subsequent generations.

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11
Q

What is a replication fork?

A

The place where DNA is currently being seperated into 2 single strands. It is where helicase is. There is 2 replication forks heading in each direction of the origin (where it started being split)

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12
Q

What is a primer?

A

RNA primer is placed to indicate where DNA polymerase III must begin the new strand of DNA. In the leading strand, only one primer is placed, but in the lagging strand, multiple primers must be placed.

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13
Q

What is the leading strand in DNA replication?

A

The leading strand is the original DNA strand that runs 3’ to 5’, so that the new strand can easily be built 5’ to 3’, as new bases can only be added to the 3’ end of the new strand. It can be built continuously, therefore is faster.

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14
Q

What is the lagging strand in DNA replication?

A

The lagging strand is the original strand that runs 5’ to 3’. As new bases can only be added to the 3’ end of the new strand, the lagging strand must be built backwards in fragments which are combined later. This means it is slower, and thus lags behind.

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15
Q

What are Okazaki fragments?

A

Okazaki fragments are short, copied fragments resulting from building lagging strand backwards and in sections. These are glued together later to create a complete strand.

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16
Q

What is DNA proofreading?

A

DNA proofreading ensures correct placement of complimentary bases and reduces mutations. In prokaryotes, this is done by DNA polymerase III which cuts out mistaken base pairs, through exonuclease activity.

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17
Q

What is the difference between the 5’ and 3’ end of a nucleotide?

A

3’ refers to the 3rd carbon of the pentose sugar on the DNA nucleotide, while 5’ refers to the 5th carbon, where the P group is attached.

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18
Q

What are the limitations of DNA polymerases when building new strands of DNA?

A
  1. It cannot initiate a brand new strand of DNA- can only add to an existing nucleotide, thus needs primers to build new strand
  2. It can only add a new nucleotide to the 3’ end of existing nucleotides, thus can only build 5’ to 3’.
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19
Q

How does the directionality of DNA polymerase lead to a leading and lagging strand in replication?

A

DNA polymerase III can only add bases to the 3’ end, so it cannot use the first primer on the 5’ to 3’ strand, thus a second primer must be placed, and the fragment can be built from the second primer to the first primer.

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20
Q

What is the role of DNA primase in prokaryote DNA replication?

A

DNA primase builds and places the correct complimentary RNA primer along the original DNA strand to initiate replication. For leading strands, only one primer is required, but in lagging strands, multiple primers are needed.

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21
Q

What is the role of DNA polymerase I in prokaryotic DNA replication?

A

DNA polymerase I removes RNA primers in the lagging strand, acting as an exonuclease and then adding new DNA nucleotides, acting as a polymerase.

Note: it cannot seal the gaps between the Okazaki fragments and the primers.

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22
Q

What is the role of DNA ligase in prokaryote DNA replication?

A

DNA ligase repeats the lagging strand by creating phosphodiester bonds between Okazaki fragments so they appear as a continuous DNA strand.

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23
Q

Explain the steps of DNA replication

A
  1. Helicase seperates the strands of DNA by breaking hydrogen bonds
  2. Gyrase prevents supercoiling of the helix ahead of helicase
  3. Single Stranded Binding Proteins (SSB’s) hold newly seperated strands apart
  4. DNA primase builds and places complimentary RNA primers at the origin, and along the lagging strand
  5. DNA polymerase III adds complimentary DNA bases to a free 3’ end of a nucleotide to build leading strand and Okazaki fragments, and proofreads new strand
  6. DNA polymerase I removes RNA primers (exonuclease) and replaces with DNA primers (polymerase)
  7. DNA ligase creates phosphodiester bonds between Okazarki fragments
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24
Q

What is a thermocycler?

A

A thermocycler is a small machine that runs multiple PCR samples simeltaneously by using quick heating and cooling metal wells to PCR can rapidly generate DNA.

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25
What are primers in PCR?
Primers in PCR are made of DNA and are used to identify the section of DNA to be copied and start the new strands for polymerase to act on.
26
What is Taq polymerase?
Taq polymerase is the polymerase used in PCR. It is adapted to hot environments so it functions optimally at 72 degrees, the temp in the final stage of PCR.
27
What is Gel Electrophoresis?
Gel electrophoresis allows negative DNA fragments to move through agarose gel to a positive electrode, which is stopped before all reach the end. Smaller fragments move faster than bigger ones so the fragments are scattered by size.
28
What is DNA profiling?
DNA profiling is the process of creating a unique DNA banding pattern using restriction enzymes to cut DNA, then gel electrophoresis seperates the fragments by size. It can be used in forensics, paternity testing and genetic screening
28
What are short tandem repeats?
STR's are short 2-7 base pair fragments that are repeated, but the number of repeats varies widely between individuals.
29
What is the purpose of PCR?
To take small amounts of DNA and create many copies often of a specific fragment. PCR allows a small amount of DNA to generate and produce visible strands on gen after electrophoresis
30
Explain the steps of PCR, including what happens and the temperatures.
1. Denaturation to seperate the double stranded DNA into 2 strands by heating to 95 degrees to break H bonds b/w bases 2. Annealing- drop temperature to 54 degrees and lots of primers are added to bind to the target sequences to show taq polymerase where to start copying 3. Extension- heated to 72 degrees which is taq polymerase's optimum temperature. Taq polymerase adds complimentary free nucleotides next to the primer to build new complimentary strands
31
How does electrophoresis seperate fragments by size?
DNA has a negative charge, so it is attracted to the positive electrode. It is placed in agarose gel, which is porous so the DNA can move through. Smaller fragments move fast, larger fragments move slower. Thus they become seperated by size
32
How is PCR used to test for Coronavirus?
Viral DNA is turned into DNA by reverse transcriptase, primers used to copy fragments only in the virus. Markers bind to viral DNA if present, once PCR makes enough fragments
33
How is PCR and electrophoresis used for paternity testing?
DNA samples from mother, child and potential fathers are taken. PCR replicates short tandem repeats which are then used in gel electrophoresis. The child should have the same number of repeats as the mum or dad. Bands the child has but the mother doesn't have must come from the father.
34
What is gene expression?
Gene expression is the using of the instructions in a gene. Synonymous with protein synthesis.
35
What is a gene?
Agene is a segment of DNA that codes for one protein
36
What is transcription?
Transcription is step 1 in protein synthesis. Involves synthesysing a strand of mRNA from the template DNA for a gene. mRNA can leave nucleus via pores to go to the ribosome.
37
What is a template strand?
A template strand is the strand of DNA that is used to build the mRNA strand. Also called the anti-sense strand.
38
What is the sense/ coding strand?
It is the strand that is not used to build the mRNA strand. Will be the same as mRNA but with T instead of U
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What is messenger RNA?
mRNA is a type of RNA that is a copy of the template DNA strands. mRNA carries the instructions from the nucleus to the ribosomes for protein synthesis.
43
What is transcriptome?
Transcriptome are the actual DNA bases that will be transcribed to make proteins.
44
What is a promoter?
A promoter is the section of DNA (approximately 1-100bp long) before the gene that shows RNA polymerase and transcription factors where to bind to begin transcription
44
What are transcription factors?
Transcription factors are proteins that bind to the promoter to either promote and start transcription, or bind to the promoter to prevent transcription. Lots of promoters have both to regulate transcription. Most genes require transcription factors for RNA polymerase to bind to start transcription
45
What is the most common promoter and why?
TATA box- sequence of thymines and adenines that are easy to break, thus often used as a promoter
46
What are the functions of RNA polymerase in transcription?
* Unwind the helix into two strands * Move along the template strand and positions complimentary RNA nucleotides * Creates phosphodiester bonds between RNA nucleotides * Detach the RNA from the DNA so it can reform into a helix
47
What direction does transcription occur in and why?
RNA polymerase can only add nucleotides to the 3' end of a nucleotide so it creates a 5' to 3' strand (basically leading strand only). The template strand must be orientated to be read 3' to 5' in order to build a 5' to 3' strand.
48
What is the difference between the sense and antisense strand?
Antisense strand- used to build mRNA, so has the complimentary base pairs to the mRNA, not the same bases Sense strand- has the same bases as the mRNA (except T/U) but is not used as a template
49
What are the complimentary base pairing rules in transcription?
DNA Guanine= RNA Cytosine DNA Cytosine= RNA Guanine DNA Thymine= RNA Adenine DNA Adenine= **RNA Uracil**
50
What is the difference between a cell's genome and a cell's transcriptome?
Genome refers to every single base of DNA (including promoters, telomeres and introns) Transcriptome is only the coding DNA bases for mRNA, therefore is smaller than the genome
51
What are exons?
Exons are coding sections of DNA in a gene that are maintained in the mature mRNA and directly used as codons that code for amino acids to make proteins. Will leave the nucleus and fo to the ribosome
52
What are introns?
Introns are sections of DNA in the coding region of the gene that do not carry sequences for amino acids. Introns are spliced out of the mRNA before it leaves the nucleus.
53
What are spliceosomes?
Spliceosomes are a protein and RNA complex that splices introns. 4x snRNP's (short RNA strands wrapped around proteins) join together with other proteins to form spliceosome. Spliceosomes bind to the end of each exon and cut the intron between them.
54
What is alternate splicing?
Alternate splicing is an explaination as to why we have introns. After introns are removed, exons can be rearranged so one gene can be used to make slightly different but similar proteins.
55
What are the types of non-coding DNA sequences?
**S**: Satellite DNA **T**: Telomeres **I**: Introns **N**: Non coding RNA genes **G**: Gene regulatory sequences
56
What is the role of satellite DNA?
Satellite DNA contains short tandem repeats
57
What is the role of telomeres?
Telomeres protect against chromosome degeneration
58
What is the role of non-coding RNA genes?
Code for RNA not turned into proteins e.g genes for tRNA
59
What are examples of gene regulatory sequences?
* Promoters * Enhancers * Silencers
60
What is the role of the 5 prime cap modification? | Only in eukaryotes
Five prime caps are special G- nucleotide that is a triphosphate (2x phosphates broken off later for energy). Provides protection/ stability to the mRNA in the cytoplasm
61
What is the role of the Poly A tail? | eukaryotes only
Poly A tails are 100-200 Adenine nucleotides added to the 3' end of the mRNA to protect it. If enzymes break off nucleotides of the mRNA, it will be the non-coding A's instead of important nucleotides
62
Why does the mRNA need protections before entering the cytoplasm?
mRNA needs protection against the nuclease enzymes in the cytoplasm that intentionally degrade mRNA no longer translated into proteins. Nuclease enzymes act on the 3' end. Can be used to regulate gene expression as high protein yield genes have longer poly A tails to allow translation before they are broken down.
63
Why is post-transcription modification not possible in prokaryotes
Post transcription modification must occur before mRNA leaves the nucleus for translation. Porkaryotes have no nucleus, so translation can begin before transcription is complete- translation begins when mRNA runs into a ribosome
64
How does alternative splicing effect the troponin T gene in the heart muscle?
Triponin is a protein used for contraction in the heart muscles. From one gene, four forms of triponin can be made by alternate splicing to include or exclude exons 4 and 5. 2 forms are made in foetal development, 1 for healthy adults, and 1 for diseased adults.
65
What is translation?
The process that makes polypeptides at ribosomes. Involves "reading" mRNA codes and joining together amino acids by peptide bonds
66
What is transfer RNA?
tRNA delivers the correct amino acid to the polypeptide chain. tRNA has anticodons that are complimentary to the mRNA that codes for amino acid.
67
What is ribosomal RNA?
rRNA are strands of RNA that wrap around proteins to make ribosomal subunits. rRNA is structural only- its function is to form ribosomes
68
What is a codon?
A 3 base group of mRNA, as 3 mRNA bases code for one amino acid. Codons are on mRNA and determine which amino acid will be added.
69
What is an anti-codon?
The anti-codon is a group of 3 bases at the bottom of the tRNA that tell the tRNA where to deliver the amino acid so it lands on the correct mRNA codon
70
What is the genetic code?
Every mRNA codon always codes for the same amino acid all the time in every organism. These universal rules are the genetic code
71
What role does complimentary base pairing play in translation?
There are complimentary base pairs between mRNA codons and the tRNA anti-codons. This ensures the amino acid is delivered to the correct codon. G-C, A-U
72
Explain the structure of a tRNA molecule
tRNA has double stranded regions that form a hairpin (lower case t) shape with single stranded loops at each point. At the bottom of the molecule there is a 3 base anti-codon. At the top is the attachment point for amino acid.
73
What does it mean to say that the genetic code is degenerate?
Degenerate means that more than one codon codes for a specific amino acid. There are 64 codons and only 20 amino acids. This is why silent mutations exist- codon can change but not amino acid
74
What does it mean to say that the genetic code is universal?
The same codons code for the same amino acid in every organism
75
What is the A site of the ribosome?
Arrival site- tRNA arrives with the amino acid. As soon as they land a peptide bond forms using energy and catalyst (ribosomal RNA is an enzyme)
76
What is the E site of the ribosome?
Exit site- the tRNA leaves the ribosome to be reused after the amino acid chain has been transferred to the next amino acid
76
What is the P site of the ribosome?
Peptidyl site- where the amino acid bonds to the chain and the tRNA holds the chain of amino acids
77
What are the main steps of translation?
1. tRNA carrying an amino acid arrives at the A site- correct site ensured by anti-codon 2. The amino acid forms a peptide bond to connect and move it to the growing chain from the tRNA 3. The tRNA is moved to the P site as the ribosome moves down 4. Once another tRNA arrives at A site, and a new peptide bond forms, the chain will shift to the new tRNA 5. At the same time, the original tRNA is shifted by ribosome movement to the E site where it leaves the ribosome 6. The tRNA will have a new amino acid connected and start again
78
What is the initiator tRNA?
An initiator tRNA molecule is a tRNA molecule with a UAC anticodon and a methionine anticodon. This is the first tRNA to arrive at the ribosome and triggers translation at the AUG start codon
79
What is the ternary complex?
The ternary complex is the initiator tRNA with the amino acid bound to the small subunit of the ribosome. This binds to the 5' end of the mRNA and scans for the start codon
80
What is a proteome?
A proteome is the full set of proteins that are made within an organism. Due to alternate splicing and modifications, there are lots more proteins than genes
81
What are proteases?
Proteases are any enzyme that breaks down bonds to digest/ break down proteins. They are often small and intentional for digestion
82
What is ubiquitin?
Ubiquitin is a small chain of proteins that identifies proteins to be degraded if they are damaged. It is recognised by the proteasome subunits that come together and digest the protein into dipeptides
83
What are proteasomes?
Proteasomes are large, cylinder shaped protein digesting complex. At the top and bottom, it has ubiquitin to identify proteins to be broken down. The core has catalytic proteins that break down polypeptides using energy from ATP.
84
What are the steps involved in intiating translation?
* Aminoacyl and RNA synthetase attaches methionine to tRNA with UAC anti-codon * Initiator tRNA binds to make ternary complex * Ternary complex moves along mRNA from 5' end to find start codon * Large ribosomal subunit joins small subunit with UAG at P site * Next tRNA with amino acid arrives
85
What are some of the modifications that can be made to a polypeptide following translation?
* Removal of methionine * Chemical changes to R group side chains * Folding for tertiary structure * Removal of parts of the polypeptides * Combining polypeptides for quaternary structure
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IB Biology (12 decks)

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