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2024 SEM 1 CYTOGENETICS > dna structure and replication > Flashcards

dna structure and replication Flashcards

1
Q

it is the different building blocks combine in sequences which enables to carry information

A

nucleic acids

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2
Q

what are the 2 classes of nucleic acids

A

DNA and RNA

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3
Q

it is the single building block of DNA

A

nucleotide

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4
Q

nucleotide consist of

A

1 deoxyribose sugar (5 carbon sugar)
1 phosphate group (phosphorus atom bonded to 4 oxygen atoms)
1 nitrogenous base
- purines: adenine and guanine
- pyrimidines: cytosine and thymine

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5
Q

it forms the “rails” of the DNA helix, providing structure

A

sugar-phosphate backbone

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6
Q

purines vs pyrimidine

A

purines: 2 ring structure
pyrimidine: 1 ring structure

their pairing (1 big and 1 small) ensures that the DNA helix maintains a consistent width throughout

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7
Q

phosphodiester bond vs hydrogen bond

A

phosphodiester bond:
Link the sugar of one nucleotide to the phosphate group of the next in the DNA backbone.

hydrogen bond:
Hold the complementary nitrogenous bases (A-T, G-C) together between the two DNA strands.

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8
Q

why must dna be replicated

A

To ensure that genetic information is passed to daughter cells during cell division, maintaining the continuity of genetic information across generations.

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8
Q

dna sequences are measured in

A

measured in numbers of base pairs
- kilobase (kb): thousands
- mega base (mb): millions

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8
Q

it is the information-containing parts of DNA because they form sequences

A

nitrogenous bases

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9
Q

it is a chain that forms when nucleotides link together that held together phosphodiester bons

A

polynucleotide chains

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10
Q

what are phosphodiester bonds

A

they are formed between deoxyribose sugars and the phosphate groups

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11
Q

it is a continuous link that are formed between deoxyribose sugars and the phosphate groups

A

sugar-phosphate backbone

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12
Q

it is when in a DNA molecule, the two polynucleotide chains run in opposite directions

A

antiparallelism

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13
Q

briefly explain antiparallelism

A

One chain runs from the 5′ end (5 prime) to the 3′ end (3 prime)
while the other runs from the 3′ end to the 5′ end
= head-to-toe alignment.

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14
Q

5’ -
3’ -

*structure of sugar-phosphate backbone structure

A

5’ - have phosphate group attached to 5th C
3’ - end w hydroxyl grp attached to 3rd C

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15
Q

explain how the sugar-phosphate backbone is formed

A

These carbons are numbered from 1 to 5, starting from the carbon next to the nitrogenous base and moving
clockwise

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16
Q

nucleotides and pairing

A

adenine pairs w thymine
guanine pairs w cytosine

A & T - 2 hydrogen bonds
G & C - 3 hydrogen bonds

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17
Q

true or false:
a single strand of DNA will form a helix

A

flase - will not

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18
Q

purine-pyrimidine couples are called

A

complementary base pairs

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19
Q

why is the hydrogen bonds are weak individually but strong collectively

A

the bonds are between base pairs
that maintains the stability of the DNA structure

they are strong collectively butt weak enough to allow the strands to separate when needed

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20
Q

this is formed when the DNA strands twist and when they are antiparallel

A

double helix structure

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21
Q

true or false:
DNA molecules are extremely long

A

true

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22
Q

how long is the the DNA of the smallest human chromosome, if stretched out

A

14 millimeters (thousandths of meter)

*but it is packed into a chromosomes that during cell division, its only 2 micrometers (millionths of a meter)

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23
Q

how is the DNA in chromosomes is highly compacted

A

by shrinking its length by a factor of 7000 to fit inside the cell nucleus

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24
Q

what are the role of proteins in DNA folding

A

○ Scaffold Proteins
Provide a framework for organizing DNA strands

○ Histones
DNA wraps around these proteins to form structures called nucleosomes.
Each nucleosome consists of 8 histone proteins and 147 DNA base pairs.

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25
Q

each nucleosome consists of

A

8 histone proteins
147 DNA bases

aka “DNA bead”

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26
Q

what is the structure of the nucleosomes

A

the 5th histones anchors nucleosomes to short linker regions of DNA, which tightens the nucleosomes into 30 nm fibers.

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27
Q

true or false:
at any given time, only small sections of the DNA double helix are exposed.

A

true
*most of the DNA is wrapped up

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28
Q

what do the chromatin consists of

A

aka “colored material”
■ 30% histone proteins
■ 30% scaffold protein and other other DNA-binding proteins
■ 30% DNA
■ 10% RNA

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29
Q

what happens when a chromatin is loose

A

(not condensed into chromosomes)
it forms loops at abt 10000 places in the genome

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30
Q

it bring together parts of the DNA sequence within the same long molecule to form the overall “loop-ome” structure

A

CTCF
CCCTC-binding

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31
Q

briefly explain the sites of chromatin attachment to the nuclear membrane

A

they are not random and the
placement may control which genes a cell is using to make proteins

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32
Q

closed chromatin vs open chromatin

A

closed chromatin:
heterochromatin
more densely packed

open chromatin:
euchromatin
less compact structure

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33
Q

this help form and maintain the chromatin loops

A

CTCF anchor protein

loop domain
- large loops of DNA formed by chromatin

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34
Q

it is a genetically rare disease that resembles rapid aging in children

A

progeria

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35
Q

this bring together regions of the genome that work together

A

chromatin loops

*a way for the cell to organize its genetic material, bringing tgt parts tht need to work tgt and influence which genes r active (gene regulation)

36
Q

what happens if there is an alteration in a chromatin loops

A

it may contribute to disease like cancer

37
Q

briefly explain the positioning of loops within the nucleus

A

linked to which genes are active in a particular cell.

38
Q

why do the DNA must be copied or replicated

A

so that the genetic information it contains can be passed on to future cell generations while also guiding the production of proteins

39
Q

who uncovered the double helix structure of DNA in 1953

A

James Watson and Francis Crick
*the mechanism for DNA replication became clear

40
Q

briefly explain the DNA replication process

A

2 strands of the double helix unwind and separate
each strand serve as a template to attract complementary bases from free nucleotides available in the cell
= 2 identical DNA double helices

41
Q

briefly explain semiconservative replication

A

semi - half
conservative - to keep

each new DNA molecule keeps half of the original DNA
(1 old strand and 1 new strand = genetic info is accurately copied and passed on)

42
Q

who provided proof for semiconservative replication.

A

Researchers Matthew Meselson and Franklin Stahl

Their experiment showed that after replication, DNA molecules had a mix of heavy and light strands, confirming the semiconservative model.

43
Q

where do the replication occurs

A

it occurs during the S phase of the cell cycle

44
Q

in order, what are the enzyme used in DNA replication

A

helicase - unwinds parental double helix

binding proteins - stabilize separate strands

primase - adds short primer to template strand

DNA polymerase - bind nucleotides to form new strands

ligase - joins okazaki fragments and seals other nicks in sugar-phosphate backbone

*okazaki fragments that are up to 150 nucleotides long

45
Q

in the step of DNA replication,
what happens in unwinding and separation of DNA

A

helicase enzyme breaks the hydrogen bonds between base pairs = double helix to unwind and separate into 2 single strands

= formed replication fork, where the DNA is opened for replication.

46
Q

in the step of DNA replication,
what happens in stabilizing strands

A

binding proteins attach to the single DNA strands, keeping them apart to prevent re-annealing of the hydrogen bonds

47
Q

in the step of DNA replication,
what happens in formation of RNA primer

A

primase enzymes synthesize RNA primer (short RNA sequences)

this is cos the main enzyme that replicates DNA, DNAPolymerase cannot initiate replication on its own - it can only add nucleotides to an existing strand

48
Q

in the step of DNA replication,
what happens in extension of the DNA strand

A

DNA polymerase:
1) adds DNA nucleotides complementary to the
bases on the parental DNA strand
= form hydrogen bonds with their complementary bases
2) links the sugar-phosphate backbone of the new strand = strong chain.

49
Q

in the step of DNA replication,
what happens in leading and lagging strand synthesis

A

leading strand:
antiparallelism of the DNA strands
causes one strand to be synthesized continuously in the 5′ to 3′ direction

lagging strand:
synthesized discontinuously in short fragments called Okazaki fragments since it runs in the opposite direction
DNA polymerase adds nucleotides in pieces, moving from the replication fork outward

50
Q

in the step of DNA replication,
what happens in sealing the DNA strands

A

ligase enzyme joins the Okazaki fragments by sealing the sugar-phosphate backbone = DNA strand is continuous

51
Q

in the step of DNA replication,
what happens in proofreading and rewinding

A

DNA polymerase has a proofreading function - ensure that incorrect bases are removed and replaced with the correct ones
annealing helicase helps rewind the
DNA that remains unwound during replication.

52
Q

a powerful biotechnology tool used to amplify a specific DNA sequence outside of cells

A

Polymerase Chain Reaction
* it can produce millions to billions of copies of a specific DNA sequence in a short period

53
Q

Polymerase Chain Reaction is a vital technique for replicating DNA and has a wide range of applications such as

A

forensic analysis
genetic research
ecological studies

54
Q

what are the steps of PCR

A

denaturation (heat separation):
DNA containing the target sequence is heated to a high temperature (around 95°C) - break H bonds

annealing (primer building):
temp is lowered, typically to 50-65%, allow primers to bind to complementary sequences at each end of the target DNA

extension (DNA synthesis):
heat-tolerant DNA polymerase (Taq polymerase)

adds nucleotides to the primers, extending them and synthesizing new DNA strands complementary to the original single-stranded templates.

55
Q

a known target sequence of DNA that is to be amplified

A

target DNA sequence

56
Q

two synthetic single-stranded DNA primers that are complementary to the opposite ends of the target sequence

A

primers

57
Q

abundant copies of the four nucleotide bases (A, T, G, C) required to build the new DNA strands

A

DNA nucleotides

58
Q

a heat-resistant enzyme from the bacterium Thermus aquaticus, which can survive the high temperatures necessary for DNA denaturation during PCR

A

Taq Polymerase

59
Q

how does PCR works

A

3 temperature-dependent steps
denaturation > annealing > extension = amplification to occur exponentially

after each cycle, no. of copies of the target DNA doubles
for instance, after 30 cycles, PCR can generate more than a billion copies of the specific DNA sequences

60
Q

it is a sanger sequencing

A

called chain termination
today’s version PCR

  • altered bases w fluorescent tags
61
Q

Why would a DNA structure in which each base type could form hydrogen bonds with any of the other three base types not produce a molecule that is easily replicated

A

If bases could pair randomly, the complementary base-pairing rule would break down, making it impossible for the DNA to form consistent pairs, and this would prevent accurate copying during replication

62
Q

What part of the DNA molecule encodes information

A

The nitrogenous bases (adenine, thymine, cytosine, and guanine) encode genetic information by forming specific sequences

63
Q

Explain how DNA is a directional molecule in a chemical sense

A

DNA has directionality because its two strands run antiparallel. One strand runs from the 5′ carbon to the 3′ carbon, while the other runs from 3′ to 5′. DNA polymerase adds nucleotides in the 5′ to 3′ direction

64
Q

How can very long DNA molecules fit into a cell’s nucleus?

A

DNA molecules are compacted through several levels of coiling and looping, including wrapping around histone proteins to form nucleosomes, which then coil further into chromatin.

65
Q

Explain how loop formation enables gene-gene interactions.

A

Proteins called CTCF bring together different regions of the DNA molecule that contain related genes, allowing them to interact and regulate gene expression​.

66
Q

How are very long strands of DNA replicated without becoming twisted into a huge tangle?

A

DNA helicase unwinds the strands
an enzyme called annealing helicase helps rewind any sections that remain unwound
Okazaki fragments prevents tangling

67
Q

List the steps in DNA replication.

A

DNA unwinds and separates.
RNA primer is added by primase.
DNA polymerase adds nucleotides to form the new strand.
RNA primers are replaced, and DNA ligase seals gaps in the sugar-phosphate backbone

68
Q

an enzyme that adds new bases to replicating DNA and corrects mismatched base pairs

A

DNAPolymerase

69
Q

a locally opened portion of a replicating DNA double helix

A

replication fork

70
Q

what are the two jobs that the genetic material carry out

A

duplicate itself
control the development of the rest of the cell

  • Francis Crick and James Watson discovered
71
Q

who described DNA when he isolated nuclei from white blood cells in pus on soiled bandages

A

Friedrich Miescher, swiss physician and biochemist

  • he discovered in the nuclei an unusual acidic substances containing nitrogen and phosphorus

nuclein -> later called nucleic acid. named by Miescher in 1871

72
Q

who was the first to link inherited disease and protein

A

Archibald Garrod, english physician

73
Q

who took the first step in identifying DNA as the genetic material

A

Frederick Griffith, english microbiologist

he worked with two types of Streptococcus pneumoniae bacteria

Type R (Rough): These bacteria had a rough surface and were easily recognized and destroyed by the mouse’s immune system, so they didn’t cause disease.
Type S (Smooth): These had a smooth surface due to a protective capsule that hid them from the mouse’s immune system, causing severe infections.

Griffith found that when he mixed harmless type R bacteria with heat-killed type S bacteria (which alone didn’t cause illness), the mixture somehow made the mice sick and die. He called this change transformation, as the type R bacteria had seemingly turned into the deadly type S. He couldn’t identify what part of the dead S bacteria caused this change before his untimely death during World War II.

74
Q

why did the mouse immune system cant recognize the type S bacteria

A

as it was enclosed in a polysaccharides capsule (a type of carbohydrate)

however, when the bacteria were heated, it killed them

75
Q

who continued Frederick Griffith’s work and what did they discover/ their findings

A

Oswald Avery
Colin MacLeod
Maclyn McCarty

to find out exactly what part of the dead type S bacteria was responsible for transforming the harmless type R bacteria into the deadly form by:

treating the bacteria with
- protease, tht dismantles protein (no change)
- deoxyribonuclease DNase, an enzyme that dismantles dna (have change = disrupt the transformation)

76
Q

who infected Escherichia coli bacteria with a virus that consisted largely of a protein head or coat surrounding DNA.

A

Alfred Hershey and Martha Chase

virus infect bacterial cells by injecting their DNA = produce more virus while protein cots remain outside the bacterial cells

77
Q

what were the experiments and results of Alfred Hershey and Martha Chase

A

Experiment:
They grew one group of viruses in a medium with radioactive sulfur, which made the protein shells of the viruses radioactive.
They grew another group of viruses in a medium with radioactive phosphorus, which made the DNA inside the viruses radioactive.
Blender test: They mixed these labeled viruses with bacteria and used a blender to shake off the virus shells from the outside of the bacteria. Then, they spun the mixture in a centrifuge to separate the bacteria from the lighter virus shells.

Results:
Sulfur-labeled viruses:
The radioactivity was found only in the fluid with the protein shells, not in the bacteria. This showed that the proteins stayed outside the bacteria.

Phosphorus-labeled viruses:
The radioactivity was found in the bacteria at the bottom of the tube, showing that the DNA had entered the bacteria.

Conclusion: Only the DNA entered the bacteria and directed them to produce more viruses. This experiment confirmed that DNA is the genetic material, not protein.

78
Q

who identified the 5-C sugar ribose and deoxyribose and when did he discovered it

A

Phoebus Levene, russian american biochemist

1909 - ribose
1929- deoxyribose

79
Q

what are the major chemical distinction between RNA and DNA that Levene revealed

A

RNA:
serve as a carrier of the info in a dna molecule
DNA: instructs the cell to manufacture a particular protein

80
Q

true or false:
all the three parts of a nucleic acid that are present in equal proportions

A

true

81
Q

who showed that DNA in several species contains equak amounts of these bases adenine (A) and thymine (T) and equal amounts of the bases Guanine (G) and cytosine (C)

A

Erwin Chargaff

82
Q

it is a technique where DNA is bombarded with X rays

A

x-ray diffraction
used by English physicist Maurice Wilkins and English chemist Rosalind Franklin

83
Q

who provided the pivotal clue that there were two forms of DNA

A

Rosalind Franklin
- She distinguished a dry, crystalline “A” form from the wetter type seen in cells, the “B” form.
- It took her 100 hours to obtain the now famous photo 51 of the B form in May 1952.

84
Q

the famed biochemist who suggested a triple helix structire for dna

A

Linus Pauling
- this was proven incorrect

85
Q

how did Watson and Crick found the answer of the double helix of the dna

A

using cardboard cutouts of the DNA components

  • April 25, 1953: Published their findings in an issue of Nature magazine where they built a more detailed and traditional ball-and-stick metal model.
  • received the Nobel Prize
86
Q

a section of dna molecule whose order of bases specifies the sequences of aa in a protein

A

gene

87
Q

it is considered diverse because proteins have diverse functions

A

inherited traits

88
Q

how fast the human dna replicates

A

at a rate of about 50 bases per second

89
Q

what are the steps in PCR and the required temp

A
  1. denaturation, 95 degree Celsius
    heated to separate strands
  2. annealing, 55 degree Celsius
    primers bind to target dna sequences
  3. extension, 72 degree Celsius
    dna polymerase, exends (make it long)

2024 SEM 1 CYTOGENETICS (11 decks)

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