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IB Biology > Nucleic Acids - 7.1 DNA Structure, Replication, Transcription and Translation (SL/HL) > Flashcards

Nucleic Acids - 7.1 DNA Structure, Replication, Transcription and Translation (SL/HL) Flashcards

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1
Q

Scientists behind the experiment that proved DNA was the carrier of genetic information rather than proteins (1952)

A
  1. Alfred Hershey
  2. Martha Chase
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2
Q

Hershey and Chase’s experiment:

A

phosphate and proteins are in a virus that are then attached to a bacteria

1) Made phosphate (in DNA) radioactive (ie. like putting a flag on it)
DNA goes into bacteria - and tracked with its “flag”
&
Made the proteins in sulphur radioactive (ie. like putting a flag on it)
Sulfur won’t go into bacteria = if important, will be seen on outside = protein does not go in

2) remove virus from bacteria (via shaking)

3) Bacteria is tested for radioactive DNA => only phosphate DNA was radioactive => conclude: DNA is responsible for passing into along = genetic material => protein does not enter (the bacteria from virus) = not responsible for genetic material

https://ib.bioninja.com.au/higher-level/topic-7-nucleic-acids/71-dna-structure-and-replic/hershey-and-chase.html

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3
Q

“DNA is found in almost all cells, and carries the genetic code that controls many aspects of cellular structure and function. EXPLAIN HOW DNA MOLECULE CARRIES GENETIC INFO.

A

DNA molecules carry genetic info in the 4 bases (A,T,G,C) which can then be re-arranged into any order to code for anything - differences for the individual thing occurs in a liner sequence and nucleotides in DNA. The pattern of arrangement codes for different proteins and thus characteristics

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4
Q

DNA in Prokaryotes

A

So small it can only be seen under an electron microscope (DNA in circular)

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5
Q

DNA in Eukaryotes + understanding

A

(DNA is wound around proteins = HISTONES - grouped into bead-like structures of eight molecules with other histones on the outside of the DNA) = this grouping - NUCLESOME

Between the beads, DNA continues as an open string

Understanding:
Nuclesomes help to supercoil the DNA

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6
Q

DNA and cell division

A

The chromosomes have to be wound up so they do not het tangled as they move into diff. cells - the beaded coils from tight chromatin coils = CHROMATIN FIBERS

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7
Q

LOOPED DOMAINS

A

The chromatin fibers form loops = looped domains = attached to a non-histone protein scaffold = the looped domains coil and fold - forming the characteristic chromosome in a cell

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8
Q

DNA FUCTIONS

A

Understanding - some regions of SNA do not code for proteins but have other important functions

A strand of DNA contains coding refions (exons) and non-coding regions - only about 10% of the human genome (total SNA complement of a cell) are exons (ie. genes that code from proteins). The rest consist of:

Satellite DNAm
telomeres,
introns,
non-coding RNA genes,
gene regulatory sequences

== STING

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9
Q

exons =

A

DNA containing coding regions

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10
Q

genome

A

Total DNA complement of a cell (can be exons)

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11
Q

STING - S

A

Satellite DNA -

tandemly repeating sequences of DNA that make up a structural part of heterochromatin and centromeres

Repeated sequences of 2-4 base pais (showing a variaation in the # of repeats) = short tandem repeats (STRs)

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12
Q

How are STRs (Short tandem repeats) used

A

they are used in forensic DNA profileing as they are highly bariable

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13
Q

STING - T

A

Telomeres -

Regions of repetitive DAN at the end of a chromosome that protext chromosomes from being damaged during DNA replication

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14
Q

STING -I

A

Introns -

non-coding regions within genes that are removed before the formation of mRNA

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15
Q

STING - N

A

Non-coding RNA genes -

codes for RNA that is not translated into protein but result in the formation of other molecules such as tRNA

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16
Q

STING - G

A

Geme regulatory sequences -

Sequences that are involved in transcription, including; promoters, enhancers and silencers

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17
Q

exons in protein synthesis

A

During protein synthesis the INTRONS are edited out so that only coding regions (exons) are used

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18
Q

Understandings (DNA structure and replication):

A
  1. DNA structure suggested a mechanism for DNA replication
  2. DNA polymerases can only add nucleotides to the 3’ end of a primer
  3. DNA replication is continuous on the leading strand and discontinuous on the lagging strand
  4. DNA replication is carried out by a complex system of enzymes
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19
Q

DNA polymerase enzyme and 5’-3’

A

DNA polymerase enzyme can only add nucleotide in the 5’ to 3’ direction (ie DNA polymerases can only add nucleotides to the 3’ end of a primer)

So one strand is build continuously as it unzips (LEADING STRAND) and the other is built in small reverse sections (LAGGING STRAND)

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20
Q

Leading strand

A

can be synthesised as a continuous strand by Polymerase 3 enzyme

On the leading strand, DNA polymerase is moving towards the replication fork and so can copy continuously

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21
Q

Lagging strand

A

they must be constructed using “pre-fabricated” sections = Okasaki fragments:

  • RNA polymerase (PRIMASE) makes RNA primers which attach to Okasaki fragments (primers are then removed).
  • DNA polymerase 3 extends the primer by joining Okasaki fragments
  • DNA polymerase 1 exzyme extends small sections of the DNA strand and has an important role in repair if there are errors in the base paring
  • fragments are later joined together using DNA LIGASE
  • two new strands of DNA coil up into a helix - forming a chromatid
  • DNA replication is semi-conservative as each of the new chromatids contains a strand of the original DNA

On the lagging strand, DNA polymerase is moving away from the replication fork, meaning copying is discontinuous

As DNA polymerase is moving away from helicase, it must constantly return to copy newly separated stretches of DNA
This means the lagging strand is copied as a series of short fragments (Okazaki fragments), each preceded by a primer
The primers are replaced with DNA bases and the fragments joined together by a combination of DNA pol I and DNA ligase

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22
Q

Okasaki fragments

A

“pre-fabricated” sections - the short lengths of DNA that are produced by the discontinuous replication of the lagging strand

DNA polymerase cannot initiate replication, it can only add new nucleotides to an existing strand

For DNA replication to occur, an RNA primer must first be synthesised to provide an attachment point for DNA polymerase

DNA polymerase adds nucleotides to the 3’ end of a primer, extending the new chain in a 5’ → 3’ direction

Free nucleotides exist as deoxynucleoside triphosphates (dNTPs) – they have 3 phosphate groups
DNA polymerase cleaves the two additional phosphates and uses the energy released to form a phosphodiester bond with the 3’ end of a nucleotide chain

23
Q

chromatid

A

one of the two identical halves of a chromosome that has been replicated in preparation for cell division. The two “sister” chromatids are joined at a constricted region of the chromosome called the centromere (in mitosis and meiosis)

24
Q

semi-conservative

A

genetic replication of a portion of DNA that is the same (ie contains a strand of the original DNA)

25
Q

Eukaryotes role in DNA replication

A

DNA replication is initiated at many points along the chromosome in eukaryotes

26
Q

Role of nucleotides containing deoxyribonucleic acid to stop DNA replication in the preparation of samples for base sequencing

A

Dideoxynucleotides (ddNTPs) dont have the 3’-hydroxyl group used for bonding to phosphate groups

If they are present during DNA sequencing the nucleotide chain cannot elongate so replication is stopped.

(the length of a prepared DNA sequence will depend on the position where the ddNTP is incorporated)

27
Q

Meselson and Stahl’s Experiment (showing semi-conservative replication of DNA)

A

1 - Meselson and Stahl grew cells for many generations in a medium containing only heavy nitrogen (15N) so that all the nitrogen in the cells DNA was 15N

2 - When centrifuged it created a band low in the test tube

3 - They transferred the cells to medium containing only light nitrogen (14N)

4 - After one generation the hybrid band was at a higher position

5 - after second generation two bands - one for the hybrid and one for the light nitrogen were both formed

(THIS SHOWS = the semi-conservative nature of DNA replication)

28
Q

(quick) summary of DNA coding for proteins

A
  1. information for control and development of an organism is contained in DNA
  2. DNA carries this info in the form of GENES
  3. Genes code for POLYPEPTIDES
  4. Polypeptides make up PROTEINS

proteins = a range of structural and regulatory functions

29
Q

Protein’s roles in organisms

A
  1. structural
  2. regulatory
  3. contractile
  4. immunological
  5. transport
  6. catalytic
30
Q

Protein’s roles in organisms = structural

A

They are responsible for forming the structural components (eg collagen, keratin)

31
Q

Protein’s roles in organisms = regulatory

A

regulating cellular functions - hormones (eg. insulin)

32
Q

Protein’s roles in organisms = contractile

A

forming contractile elements in muscles (eg. muosin, actin)

33
Q

Protein’s roles in organisms = Immunological

A

Functioning to combat invading microbes (antibodies, antitoxins)

34
Q

Protein’s roles in organisms = transport

A

Acting as carrier molecules (eg. carrying oxygen to the haemoglobin)

35
Q

Protein’s roles in organisms = catalytic

A

Catalysing all the biochemical reactions in the body

36
Q

Proteins in polypeptide chains

A
  1. Proteins are POLYMERS (ie large molecules made up of repeating units)
  2. Units (or monomers) are amino acids (that are linked together)
  3. when amino acids are joined - a polypeptide is formed

= a protein is a functional unit made up of more than one polypeptide chains

37
Q

“DNA code is universal”

A

ie genes from one organism can be put into the genome of another (due to their similarity)

  • eg. production of human insulin in bacteria
37
Q

“DNA code is universal”

A

ie genes from one organism can be put into the genome of another (due to their similarity)

  • eg. production of human insulin in bacteria
38
Q

Role of amino acids in polypeptides - information

A

A polypeptide is coded for by a gene - the sequence of bases determines the sequence of the amino acids - three bases (triplet) codes for one amino acid (the number of amino acids is very variable can be between 50 - 10,000 = over 2 million polypeptide sequences have been discovered

39
Q

From the scattering pattern produced by a DNA molecule, certain inferences could be made about its structure - bioninja

+ Photo 51 – Evidence for the Structure of DNA via X-Ray Diffraction

A

Composition: DNA is a double stranded molecule
Orientation: Nitrogenous bases are closely packed together on the inside and phosphates form an outer backbone
Shape: The DNA molecule twists at regular intervals (every 34 Angstrom) to form a helix (two strands = double helix)

Adenine and thymine paired via two hydrogen bonds, whereas guanine and cytosine paired via three hydrogen bonds

+ Photo 51 – Evidence for the Structure of DNA via X-Ray Diffraction

40
Q

onsequently, DNA structure suggests two mechanisms for DNA replication:

A

Replication occurs via complementary base pairing (adenine pairs with thymine, guanine pairs with cytosine)

Replication is bi-directional (proceeds in opposite directions on the two strands) due to the antiparallel nature of the strands

41
Q

DNA replication (HL) - bioninja

A

DNA replication is a semi-conservative process that is carried out by a complex system of enzymes

  1. Helicase
  2. DNA Gyrase
  3. Single Stranded Binding (SSB) Proteins
  4. DNA Primase
  5. DNA Polymerase III
  6. DNA Polymerase I
  7. DNA Ligase
42
Q

DNA replication - Helicase

A

Helicase unwinds and separates the double-stranded DNA by breaking the hydrogen bonds between base pairs
This occurs at specific regions (origins of replication), creating a replication fork of two strands running in antiparallel directions

43
Q

DNA replication - DNA Gyrase

A

DNA gyrase reduces the torsional strain created by the unwinding of DNA by helicase
It does this by relaxing positive supercoils (via negative supercoiling) that would otherwise form during the unwinding of DNA

44
Q

DNA replication - Single Stranded Binding (SSB) Proteins

A

SSB proteins bind to the DNA strands after they have been separated and prevent the strands from re-annealing
These proteins also help to prevent the single stranded DNA from being digested by nucleases
SSB proteins will be dislodged from the strand when a new complementary strand is synthesised by DNA polymerase III

45
Q

DNA replication - DNA Primase

A

DNA primase generates a short RNA primer (~10–15 nucleotides) on each of the template strands
The RNA primer provides an initiation point for DNA polymerase III, which can extend a nucleotide chain but not start one

46
Q

DNA replication - DNA Polymerase III

A

Free nucleotides align opposite their complementary base partners (A = T ; G = C)
DNA pol III attaches to the 3’-end of the primer and covalently joins the free nucleotides together in a 5’ → 3’ direction
As DNA strands are antiparallel, DNA pol III moves in opposite directions on the two strands
On the leading strand, DNA pol III is moving towards the replication fork and can synthesise continuously
On the lagging strand, DNA pol III is moving away from the replication fork and synthesises in pieces (Okazaki fragments)

47
Q

DNA replication - DNA Polymerase I

A

As the lagging strand is synthesised in a series of short fragments, it has multiple RNA primers along its length
DNA pol I removes the RNA primers from the lagging strand and replaces them with DNA nucleotides

48
Q

DNA replication - DNA Ligase

A

DNA ligase joins the Okazaki fragments together to form a continuous strand
It does this by covalently joining the sugar-phosphate backbones together with a phosphodiester bond

49
Q

Dideoxynucleotides

A

DNA sequencing refers to the process by which the base order of a nucleotide sequence is elucidated
= The most widely used method for DNA sequencing involves the use of chain-terminating dideoxynucleotides

Dideoxynucleotides

Dideoxynucleotides (ddNTPs) lack the 3’-hydroxyl group necessary for forming a phosphodiester bond
Consequently, ddNTPs prevent further elongation of a nucleotide chain and effectively terminate replication
The resulting length of a DNA sequence will reflect the specific nucleotide position at which the ddNTP was incorporated
For example, if a ddGTP terminates a sequence after 8 nucleotides, then the 8th nucleotide in the sequence is a cytosine

50
Q

Sequencing

A

DNA sequencing refers to the process by which the base order of a nucleotide sequence is elucidated
= The most widely used method for DNA sequencing involves the use of chain-terminating dideoxynucleotides

Sequencing

Dideoxynucleotides can be used to determine DNA sequence using the Sanger method

Four PCR mixes are set up, each containing stocks of normal nucleotides plus one dideoxynucleotide (ddA, ddT, ddC or ddG)
As a typical PCR will generate over 1 billion DNA molecules, each PCR mix should generate all the possible terminating fragments for that particular base
When the fragments are separated using gel electrophoresis, the base sequence can be determined by ordering fragments according to length
If a distinct radioactive or fluorescently labelled primer is included in each mix, the fragments can be detected by automated sequencing machines
If the Sanger method is conducted on the coding strand (non-template strand), the resulting sequence elucidated will be identical to the template strand

51
Q

Nucleosomes

A

In eukaryotic organisms, the DNA is packaged with histone proteins to create a compacted structure called a nucleosome

Nucleosomes help to supercoil the DNA, resulting in a greatly compacted structure that allows for more efficient storage
Supercoiling helps to protect the DNA from damage and also allows chromosomes to be mobile during mitosis and meiosis

A nucleosome consists of a molecule of DNA wrapped around a core of eight histone proteins (an octamer)

The negatively charged DNA associates with positively charged amino acids on the surface of the histone proteins
The histone proteins have N-terminal tails which extrude outwards from the nucleosome
During chromosomal condensation, tails from adjacent histone octamers link up and draw the nucleosomes closer together

52
Q

Organisation of Eukaryotic DNA

A

The DNA is complexed with eight histone proteins (an octamer) to form a complex called a nucleosome
Nucleosomes are linked by an additional histone protein (H1 histone) to form a string of chromatosomes
These then coil to form a solenoid structure (~6 chromatosomes per turn) which is condensed to form a 30 nm fibre
These fibres then form loops, which are compressed and folded around a protein scaffold to form chromatin
Chromatin will then supercoil during cell division to form chromosomes that are visible (when stained) under microscope

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