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biology > topic 7 - Nucleic Acid (HL) > Flashcards

topic 7 - Nucleic Acid (HL) Flashcards

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1
Q

How did Hershey and Chase provide evidence that DNA is the genetic material of the cell and not protein?

A

Known that viruses insert their genetic material into cells

radioactive viruses grown –> allowed to infect a bacterium (E. colu)

  • Viruses grown in 35S had radioactive proteins (no DNA) but did NOT transfer this radioactivity to bacterium (remained in supernatant)
  • Viruses grown in 32P had radioactive DNA (no protein) and DID transfer this radioactivity to infected bacterium (found in pellet)

virus & bacteria separated via centrifugation. Showed the above results

This demonstrated that DNA, not protein, was the genetic material because DNA was transferred to the bacteria

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2
Q

Who used X-ray diffraction to elucidate DNA structure?

A

Franklin and Wilkins

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3
Q

What is X-ray Diffraction?

A
  • X-rays will diffract when targeted at crystallised DNA molecules
  • The scattering pattern created can be used to determine structure
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4
Q

From the scattering patter created by X-Ray Diffraction, what are the properties that can be deduced?

A
  • Composition: DNA is a double-stranded molecule
  • Orientation: The bases face inwards and the phosphates face out
  • Shape: DNA forms a double helix (10 bases per twist)
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5
Q

True or False?

In eukaryotes, DNA associates with eight histone proteins to form a nucleosome

A

TRUE

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6
Q

How does nucleosomes help to supercoil DNA?

A
  • Makes DNA compact (better storage)
  • Prevents DNA damage (less exposed)
  • Assists in cell division (more mobility)
  • Involved in transcriptional regulation
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7
Q

What are the regions of DNA that do not code for protein?

A

Think: STING

  • Satellite DNA (tandem repeats)
  • Telomeres (chromosome ends)
  • Introns (non-coding sequences)
  • Non-coding RNA genes
  • Gene regulatory sequences
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8
Q

What are used in DNA profiling?

A

Tandem repeats

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9
Q

Describe how DNA –> Chromosome

A

DNA is bound with histone proteins to form nucleosomes that are then linked together to form strings of chromatosomes
These coil to form solenoids, which condense into 30 nm fibres, before being compressed and folded into chromatin
Chromatin will then supercoil during cell division to form chromosomes that are visible (when stained) under microscope

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10
Q

What is the role of helicase in DNA replication?

A
  • Helicase separates the DNA strands to form a replication fork (breaks the hydrogen bonds between complementary base pairs)
  • Single stranded binding proteins prevent strands re-annealing
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11
Q

What is the role of DNA Gyrase in DNA replication?

A
  • DNA gyrase reduces the torsional strain created by helicase
  • It prevents the DNA from supercoiling as it is being unwound
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12
Q

What is the role of DNA primase in DNA replication?

A

• DNA primase generates a short RNA primer on each strand
• PrimersprovideaninitiationpointforDNApolymeraseIII
(DNA pol III can only add nucleotides to 3’-end of a primer)

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13
Q

What is the role of DNA Polymerase III in DNA replication?

A
  • Free nucleotides (dNTPs) line up opposite complementary bases
  • DNA polymerase III covalently joins free nucleotides together
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14
Q

What is the role of Okazaki Fragments in DNA replication?

A
  • DNA strands are antiparallel, so replication occurs bidirectionally (replication always occurs in a 5’ → 3’ direction on each strand)
  • Synthesisiscontinuousontheleadingstrand(towardsfork) and is discontinuous on the lagging strand (away from fork)
  • Discontinuous segments are called Okazaki fragments
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15
Q

What is the role of DNA Polymerase I in DNA replication?

A

• DNA pol I removes RNA primers and replaces them with DNA

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16
Q

What is the role of DNA ligase in DNA replication?

A

• DNA ligase covalently joins the Okazaki fragments together

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17
Q

Briefly describe the DNA replication process

A
  1. origins in DNA (eukaryotes have multiple, prokaryotes only have ONE)
  2. helicase unwinds DNA
    2a. single-stranded binding (SSB) proteins keep DNA separated
    2b. topiosomerase prevents supercoiling
  3. Primase makes RNA primers
  4. DNA polymerase III builds the new strand in ONLY 5’ –> 3’ direction; proof reading ability prevents mistakes
  5. DNA polymerase I removes primer
  6. ligase seals Okazaki fragments on lagging strand tgth
  7. new strand
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18
Q

What is DNA sequencing?

A

Sequencing is a technique by which the nucleotide base order of a DNA sequence is elucidated (typically via Sanger method)

Use of nucleotides containing dideoxyribonucleic acid to stop DNA replication in preparation of samples for base sequencing (use of chain-terminating dideoxynucleotides)

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19
Q

Briefly describe the mechanism of DNA sequencing. What is the Sanger method?

A

Dideoxynucleotides (ddNTPs) lack the 3’-hydroxyl group needed to form covalent bonds (they terminate replication)

SANGER METHOD:
Four PCR mixtures are prepared – each with stocks of normal bases and one dideoxynucleotide (ddA, ddT, ddG, ddC)

Whenever the dideoxynucleotide is randomly incorporated, the DNA sequence is terminated at that base position

Because a complete PCR cycle generates millions of sequences, every base position is likely to have been terminated

These sequences are separated by gel electrophoresis to determine base sequence
(according to ascending sequence length)

Automated machines can determine the sequence quickly if fluorescent labeling of the dideoxynucleotides has occurred

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20
Q

True or False?

A gene is a sequence of DNA which is transcribed into RNA • Most genes encode proteins, but some do not (e.g. tRNA)

A

True

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21
Q

What are the 3 main sections of a gene sequence?

A
  • Promoter (transcription initiation site)
  • Coding sequence (the region transcribed)
  • Terminator (transcription termination site)
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22
Q

True or False
As DNA is double stranded, only one strand is transcribed
• The antisense strand is not transcribed into RNA
• The sense strand is transcribed into RNA

A

FALSE

As DNA is double stranded, only one strand is transcribed
• The antisense strand is transcribed into RNA
• The sense strand is not transcribed into RNA

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23
Q

True of False?

Gene expression is regulated by proteins (transcription factors) that bind to specific sequences associated with a promoter

A

True

24
Q

True or False?

Transcription Factors:
Activators bind enhancer sites (⬇︎︎ rate of transcription)

A

False

• Activators bind enhancer sites (⬆︎︎ rate of transcription)

25
Q

True of False?

Transcription Factors
• Repressors bind silencer sites (⬇︎︎ rate of transcription)

A

TRUE

26
Q

Gene expression is regulated by proteins that bind to specific base sequences in DNA.

What are regulatory proteins? What is their purpose?

A

The presence of regulatory proteins may be tissue-specific or may be influenced by chemical signals (e.g. hormones)

proteins bind to DNA sequences outside of the promoter and interact with the transcription factors

27
Q

Type of Regulatory Proteins:

What are activator proteins?

A

bind to enhancer sites and increase the rate of transcription (by mediating complex formation)

Result: high levels of transcription

28
Q

Type of Regulatory proteins:

What are repressor proteins?

A

bind to silencer sequences and decrease the rate of transcription (by preventing complex formation)

Result: low levels of transcription

29
Q

What are Basal transcription factors?

A

gene transcribed at moderate levels

Result: normal levels of transcription

30
Q

How do nucleosomes help regulate transcription in eukaryotes?

A

Histones proteins have protruding tails that determine

how tightly the DNA is packaged within nucleosome

31
Q

How does modifications to the protruding tails of histone proteins alter DNA packaging?

A

Acetylation makes DNA less tightly packed

Methylation makes DNA more tightly packed

32
Q

Cells package DNA differently according to genetic needs. How are active genes packaged?

A

Active genes remain unpackaged as euchromatin

33
Q

Cells package DNA differently according to genetic needs. How are inactive genes packaged?

A

Inactive genes are tightly packed as heterochromatin

34
Q

What is DNA methylation? How does this affect transcription?

A

DNA can also be directly methylated to change expression patterns of genes over time in response to external stimuli
• Increased methylation = decreased transcription

35
Q

True or False.

DNA methylation patterns influenced by heritability but is not genetically pre-determined (identical twins may have different DNA methylation patterns)

A

True

DNA methylation patterns differ b/w clones (twins) and change over time

36
Q

Eukaryotic cells modify RNA after transcription has occurred. Modifications must occur to produce mature mRNA. Thus, non-coding regions within genes are removed. What is this process called?

A

Splicing

37
Q

What are introns?

A

Introns are non-coding regions in genes

THINK: intruding

38
Q

What are exons?

A

• Exons are the coding regions of genes

THINK: expressing

39
Q

What is alternative splicing?

A

Exons can be selectively removed to form different proteins from the same gene

40
Q

What is an examples of non-coding DNA? What is its functions?

A

Example: promoter

The non-coding sequence responsible for the initiation of transcription
The core promoter is typically located immediately upstream of the gene’s coding sequence
The promoter functions as a binding site for RNA polymerase (the enzyme responsible for transcription)
The binding of RNA polymerase to the promoter is mediated and controlled by an array of transcription factors in eukaryotes
These transcription factors bind to either proximal control elements (near the promoter) or distal control elements (at a distance)

41
Q

what is capping in transcription?

A

Capping involves the addition of a methyl group to the 5’-end of the transcribed RNA
The methylated cap provides protection against degradation by exonucleases
It also allows the transcript to be recognised by the cell’s translational machinery (e.g. nuclear export proteins and ribosome)

42
Q

What is polyadenylation in transcription?

A

Polyadenylation describes the addition of a long chain of adenine nucleotides (a poly-A tail) to the 3’-end of the transcript
The poly-A tail improves the stability of the RNA transcript and facilitates its export from the nucleus

43
Q

The environment of a cell and of an organism has an impact on gene expression

True of False?

A

True

Chemical signals within the cell can trigger changes in levels of regulatory proteins or transcription factors in response to stimuli
This allows gene expression to change in response to alterations in intracellular and extracellular conditions

Also organisms responding to environmental changes:
Hydrangeas change colour depending on the pH of the soil (acidic soil = blue flower ; alkaline soil = pink flower)

44
Q

True of False?

Ribosomes are the site of polypeptide synthesis. They are composed of ribosomal RNA and protein

A

TRUE

Polypeptide synthesis IS translation

45
Q

What are the 2 subunits that ribosomes consist of?

A
  • Small subunit contains an mRNA binding site

* Large subunit contains three tRNA binding sites (E, P, A

46
Q

Fill in the Blank.

Multiple ribosomes can translate a single mRNA sequence simultaneously (these are collectively called a __________)

A

Multiple ribosomes can translate a single mRNA sequence simultaneously (these are collectively called a POLYSOME)

47
Q

What is transfer RNA (i.e. tRNA)?

A

Transfer RNA (tRNA) carries amino acids to the ribosome • Amino acids are attached by tRNA-activating enzymes

48
Q

What are the two steps that tRNA-activating enzymes function.

A
  • The enzyme joins ATP to an amino acid (‘charging’)

* ‘Charged’ amino acid is linked to tRNA (AMP is released)

49
Q

Fill in the Blank

The purpose of ‘charging’ the amino acid is to __________________

A

The purpose of ‘charging’ the amino acid is to

ANS: create a high energy bond that can be be used during translation

50
Q

The purpose of ‘charging’ the amino acid is to create a high energy bond that can be be used during translation. What does ribosomes use this energy for?

A

Ribosomes use this energy to synthesise peptide bonds

51
Q

Fill in the Blank

Each tRNA-activating enzyme is specific to a particular amino acid, but may bind multiple tRNA. Due to __________

A

Degeneracy

52
Q

True or False

In prokaryotes, the absence of a nuclear membrane allows translation to occur immediately after transcription.

A

True

53
Q

In eukaryotes, translation will occur at one of two locations. What are these two locations? Describe each one

A

• Free ribosomes (cytosolic) synthesise intracellular proteins
• Bound ribosomes (rER) synthesise proteins destined for
secretion from the cell or for use in lysosomes

54
Q

True or False.

Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane

A

TRUE

55
Q

What is a polysome?

A

a group of two or more ribosomes translating an mRNA sequence simultaneously

appear as beads on a string (each ‘bead’ represents a ribosome ; the ‘string’ is the mRNA strand)

56
Q

What is the function of free ribosomes?

A

Free ribosomes synthesise proteins for use primarily within the cell

57
Q

What is the function of bound ribosomes?

A

Bound ribosomes synthesise proteins primarily for secretion or for use in lysosomes

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