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Molecular Biology > Chromosomes and DNA > Flashcards

Chromosomes and DNA Flashcards

1
Q

What is the process from DNA to RNA?

A

Transcription

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2
Q

What is the process from RNA to protein?

A

Translation

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3
Q

What comprises the double helix of DNA?

A

Sugar-phosphate backbone, together with bases: note that a purine always base-pairs with a pyramidine.

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4
Q

Which bases are purines?

A

Adenine and Guanine

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5
Q

Which bases are pyramidines?

A

Cytosine, Thymine and Uracil

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6
Q

Describe the positions of the bases and phosphates in the double helix.

A

The bases are buried on the inside of the DNA structure, and the phosphates are on the outside.

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7
Q

How can chromosomes be distinguished?

A

By size and ‘G-banding’

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8
Q

What is the largest chromosome?

A

1

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9
Q

What is the smallest chromosome?

A

22

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10
Q

What is G-banding?

A

Staining chromosomes using Giemsa which gives them a unique banding pattern.

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11
Q

What is cytogenetics and what is it used for?

A

A branch of genetics that is concerned with how the chromosomes relate to cell behaviour, particularly to their behaviour during mitosis and meiosis.

It is basically aligning the chromosomes (pairing them up) and is used to check for chromosomal abnormalities.

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12
Q

How does a DNA double helix become a tightly-packed chromosome?

A

Via packaging around histone proteins.

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13
Q

What are the regions of a chromosome?

A
  • Telomere - tip of the chromosome
  • Centromere - centre of the chromosome
  • This is important when the chromosomes come to replicate. At the centromere they will become attached to the kinetochore and onto the mitotic spindle at that point.
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14
Q

Describe the form of a histone protein.

A
  • They are extremely positively charged.
  • They are like ‘beads on a string’, but importantly, they have a long tail which protrudes outside their main structure.
  • There are multiple sites within the N terminus of a particular histone which can be varied.
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15
Q

What is the importance of the long tail of the histone protein?

A
  • The tail is important because depending on what is happening within the cell, the packaging of parts of the chromosome might need to vary.
    • The packaging might need to be relaxed so that the DNA can be actively used for things like transcription. So, the packaging must be able to contract and expand.
  • This requires energy which is facilitated by the long tails of the histone proteins which can be modified in a way that is responsive to the conditions within the cell.
  • There are multiple sites within the N terminus of a particular histone which can be varied.
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16
Q

Describe the hydrogen bonding of A-T and G-C.

A
  • A forms 2 hydrogen bonds with T
  • C forms 3 hydrogen bonds with G
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17
Q

Where do the amino-terminals of the histone protrude from?

A

Amino-teminals protrude from the nucleosome

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18
Q

How does the structure of chromatin relate to function?

A

Condensed chromatin prevents the genes located on the DNA from being accessed, therefore prevents gene expression.

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19
Q

What is epigenetics?

A
  • The study of heritable phenotype changes that do not involve alterations in the DNA sequence.
  • E.g. DNA mathylation - methyl group can repress or activate DNA gene expression, but the DNA sequence itself is not altered.
    • When DNA methylation occurs in the gene promoter region, DNA methylation typically acts to repress DNA transcription.
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20
Q

What is acetlyation?

A

Decreases positive charge of the histone which decreases the interaction with the negative phosphate of the DNA. It becomes a relaxed structure and therefore causes increased transcription and thus protein production.

21
Q

What is heterochromatin?

A

Highly packaged DNA. The cell decides that this part of the genome isn’t needed for that particular cellular function. It is transcriptionally inactive.

22
Q

Describe the characteristics of repetitive DNA.

A
  • Over 2/3 of the human genome is DNA repeats.
  • SINE (short interspersed nuclear elements) and LINE (long interspersed nuclear elements) are often derived from retroviruses.
  • Tandem repeats are where a sequence of nucleotides are repeated and the repetitions are directly adjacent to each other.
  • Interspersed repetitive DNA is found in all eukaryotic genomes. They differ from tandem repeat DNA - they are dispersed and non-adjacent repeats.
23
Q

Describe the characteristics of mtDNA.

A
  • Circular
  • 2-10 copies of mtDNA per mitochondria
  • Maternally inherited
  • Implications for mitochondrial disease; higher mutation rate than genomic DNA.
24
Q

What is semi-conservative replication?

A

Each daughter molecule consists of one old strand (template) and one newly synthesised strand.

25
Q

With a replication rate of 2kb/minute, replicating one human chromosome would require approximately 35 days. What is the solution to this?

A

DNA replication initiates at many different sites simultaneously.

26
Q

Which element specifies which ase is to be added next in the 5’→3’ direction?

A

The template strand

27
Q

What is added to the 3’ end of the growing strand?

A
  • Monomers (dNTPs)
    • CTP
    • TTP
    • ATP
    • GTP
28
Q

How are bases linked?

A
  • Bases are linked via the 5’→3’ phosphodiester linkage.
  • 3’ oxygen of the base is linked to a phosphorus which is linked to the 5’ oxygen (hydroxide group) of the next base. This is the linkage.
  • The incoming base brings a phosphate and attacks the free hydroxide group on the 3’ end of the existing chain to give the DNA its specific orientation.
29
Q

Describe the replication fork.

A
  • Asymmetrical
  • Created by helicases, which break the hydrogen bonds holding the 2 DNA strands together.
    • Creates a ‘bubble’.
    • Only one of the strands provides a template in the correct orientation so that the new strand can be synthesised in the 5’→3’ direction.
      • This is the leading strand.
    • The resulting structure has 2 branching ‘prongs’, each one made up of a single strand of DNA.
    • These 2 strands serve as the template for the leading and lagging strands, which will be created as DNA plymerase matches complementary nucleotides to the templates.
30
Q

Which direction is DNA always synthesised in?

A

5’→3’

31
Q

What is the leading strand?

A
  • The strand of the newly formed DNA which is being synthesised in the same direction as the growing replication fork - 5’→3’.
    • Subject to continuous DNA replication.
    • The bases that are inserted are as dictated by the existing parental strand.
32
Q

What is the lagging strand?

A
  • The strand of the new DNA whose direction of synthesis is opposite to the direction of the growing replication fork.
  • This poses a problm as it is not in the correct orientation to allow DNA synthesis in a 5’→3’ direction.
  • It is synthesised in short, separated segments, ~150 bases long.
  • A primase enzyme ‘reads’ the template DNA and initiates synethesis of a short complementary RNA primer.
    • DNA polymerase itself cannot initiate DNA synthesis.
  • DNA polymerase extends the primed segments, forming Okazaki fragments.
  • RNA primers are removed and replaced with DNA.
  • Okazaki fragments are joined by DNA ligase.
  • Antibiotics and chemotheraputic agents target this pathway.
33
Q

What is the function of DNA helicase in DNA replication?

A
  • Also known as ‘helix destabilising enzyme’
  • Helicase separates the 2 strands of DNA at the replication fork behind the topoisomerase.
34
Q

What is the function of DNA polymerase in DNA replication?

A
  • The enzyme that is responsible for catalysing the addition of nucleotide substrates to DNA in the 5’→3’ direction.
    • Also performs proof-reading and error correction.
    • Different types of DNA polymerase, each of which perform different functions in different types of cells.
35
Q

What is the function of DNA clamp in DNA replication?

A

A protein which prevents elongating DNA polymerases from dissociating from the DNA parent strand.

36
Q

What is the function of single-strand binding (sSSB) proteins in DNA replication?

A

Bind to ssDNA and prevent the DNA double helix from re-annealing after DNA helicase unwinds it, thus maintaining the strand separation, and facilitating the synthesis of the nascent strand.

37
Q

What is the function of Topoisomerase in DNA replication?

A

Relaxes the DNA from its super-coiled nature.

38
Q

What is the function of DNA gyrase in DNA replication?

A

Relieves strain of unwinding by DNA helicase

39
Q

What is the function of DNA ligase in DNA replication?

A

Re-anneals the semi-conservative strands and joins Okazaki fragments of the lagging strand.

40
Q

What is the function of primase in DNA replication?

A
  • Provides a starting point of RNA (or DNA) for DNA polymerase to begin synthesis of the new DNA strand.
    • An RNA primer is added to the lagging strand 3’→5’.
41
Q

What is the function of telomerase in DNA replication?

A
  • Lengthens telomeric DNA by adding repetitive nucleotide sequences to the ends of eukaryotic chromosomes.
    • This allows germ cells and stem cells to avoid the Hayflick limit on cell division.
42
Q

Give a summary of DNA synthesis.

A
  • In a replication fork, 2 DNA polymerases collaborate to copy the leading strand template and lagging strand template DNA.
  • After an Okazaki fragment has been synthesised, the clamp that keeps one of the DNA polymerases attached to the lagging strand of DNA dissociates, temporarily releasing the DNA polymerase from the lagging strand template DNA.
  • As the helicase continues to unwind the parental DNA, the primase becomes activated and synthesises a short RNA primer on the growing lagging strand.
    • Single-stranded binding proteins bind to the unwound lagging strand to prevent the bases from re-annealing with themselves.
  • The DNA polymerase binds again and becomes locked in with the clamp.
  • The DNA polymerase uses the RNA primer to synthesise a short copy (~150 base pairs) of the lagging strand template DNA.
  • The polymerase stalls when it reaches the RNA primer of the preceding Okazaki fragment.
  • Entire cycle repeats
43
Q

What is Werner’s syndrome and what does it cause?

A
  • Problem associated with replicating the ends of DNA.
    • Inherited disorder
    • Premature ageing
44
Q

What happens at the end of the DNA?

A
  • As the lagging strand is synthesised, eventually it might not be able to create a full Okazaki fragment because the template for that lagging strand might not be long enough.
    • Some DNA must be ‘uncovered’ before synthesis can start back the way.
  • It is unstable to have a single strand at the end of the DNA.
    • It would make genetic information shorter and shorter over generations.
  • In order to prevent the progressive reduction in DNA length, particularly in stem cells, telomerase brings an RNA template (relatively short) which can then be used to extend the template strand of DNA, which can then be utilised to synthesise a new Okazaki fragment.
  • Once the template strand has been sufficiently extended, the DNA ploymerase can create an Okazaki fragment.
  • Telomerase isn’t expressed as highly in somatic cells.
    • Cancerous somatic cells will start to express telomerase again to prolong its ability to carry out DNA replication.
  • Telomerase adds telomere repeat sequences to the 3’ end of telomeres in the 3’→5’ direction.
45
Q

Describe how errors in DNA replication can be removed during protein synthesis.

A
  • DNA polymerase has a polymerase site and an ‘editing site’.
  • As the newly synthesised DNA is created, before it can exit from the polymerse, it twists round into the editing site.
    • If it is not the right base, it is excised.
    • 3’→5’ exonuclease activity.
46
Q

Describe how mutations can be repared post-relication.

A

DNA mismatch repair (MMR) is a system for recognising and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage.

47
Q

Describe inherited defects in mismatch repair.

A
  • Mut proteins are the major active components of the mismatch repair system.
  • Mutations in the human homologues of the mut proteins affect genomic stability, which can result in microsatellite instability, implicatd in some human cancers.
48
Q

What is the normal mutation rate (after fixing)?

A

~1 error for every 3 genomes replicated

Molecular Biology (5 decks)

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