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biology > DNA and genomics > Flashcards

DNA and genomics Flashcards

1
Q

What are the monomers of nucleic acid?

A

Nucleotides

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2
Q

What are the two types of nucleotides and what do they form when joined together respectively?

A

Deoxyribonucleotides -> deoxyribonucleic acid (DNA)

Ribonucleotides -> ribonucleic acid (RNA)

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3
Q

What are the structures of nucleotide?

A
  1. Pentose sugar
    - Ribose and Deoxyribose
    - H atom found at 2’ carbon atom in deoxyribose while OH atom found in ribose
  2. Phosphate group
    - makes DNA negatively charged
  3. Nitrogenous base
    - purines (2 fused ring) : Adenine and Guanine (AG)
    - pyrimidines (1-ringed structure) : Cytosine, Uracil and Thymine (CUT)
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4
Q

What is located at the 3’ carbon atom of both DNA and RNA?

A

OH group

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5
Q

Is DNA or RNA more chemically reactive?

A

RNA. Presence of extra OH group makes the RNA more polar and reactive.

  • so DNA is more stable -> storage of genetic info
  • RNA is temporary molecule meant to be broken down
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6
Q

How is the nucleotide formed?

A

The 3 components are linked up to form a nucleotide via condensation reaction.

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7
Q

What and how is the bond formed when a phosphate group join the pentose sugar?

A

Phosphoester bond (O-P=O) is formed when phosphate joined the sugar molecule at the 5’ carbon atom via condensation rxn

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8
Q

What and how is the bond formed btw pentose sugar and base?

A

Glycosidic bond (R-C-O-R) is formed when nitrogenous base is joined to 1’ carbon atom via condensation rxn

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9
Q

How is a polynucleotide formed?

A

A condensation rxn btw the 5’ phosphate group of one nucleotide and the 3’ hydroxyl group of another to form a phosphodiester bond (O=POOO) and this process is repeated to form a polynucleotide.

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10
Q

What is a sugar-phosphate backbone?

A

It is made up of alternating sugar and phosphate group with the bases projecting from the backbone.

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11
Q

What is the structure of DNA?
(7 points but only 2 are here)

A
  1. DNA molecule consists of 2 polynucleotide strands twisted around each other to form a double helix
  2. The 2 strands are antiparallel
  3. One complete turn of the DNA double helix comprises 10 base pairs and spans a distance of 3.4nm. Sugar-phosphate backbone face outside while nitrogenous base faces centre
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12
Q

How are bases joined together btw opposite strands in DNA?

A

Hydrogen bonding.

Purine always pair with pyrimidine.
A pairs with T to form 2 H bonds while C pairs with G to form 3 H bonds via complementary base pairing.

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13
Q

What is the ratio of pairings btw bases like?

A

Ratio of A : T is 1 and the ratio of C : G is also 1.

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14
Q

What is the width between the 2 strands of polynucleotides?

A

Constant width (2nm) btw the sugar phosphate backbone of DNA molecule which equals to the width of a purine and pyrimidine.

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15
Q

What is the bond formed between stacked nitrogenous bases?

A

Hydrophobic interactions

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16
Q

What is the bond formed btw nucleotides?

A

Phosphodiester bond

17
Q

How can H bonds, phosphodiester bond and hydrophobic interactions help the molecule?

A

They help to stabilize the structure of the double helix.

18
Q

Which mechanism allows DNA replication?

A

Semi-conservative mechanism

19
Q

How does the semi-conservative replication occur?

A

Through this mechanism, both strands of a DNA molecule separate and act as templates for the synthesis of new daughter strands

Hydrogen bond formed between bases of parental strand and newly-synthesized daughter strand to form a daughter DNA molecule.

20
Q

Briefly state the steps for semi conservative DNA replication.

A
  1. Before the replication, free nucleotides are synthesized in the cytoplasm and transported into the nucleoplasm via nuclear pores into the nuclear envelope.
  2. Initiation of DNA replication
  3. Synthesis of new DNA strands.
21
Q

What are the roles of proteins and enzymes involved in the initiation of DNA replication?

(5 proteins involved)

A
  1. Helicase - binds to origin of replication, causing DNA to unwind and unzip
  2. Topoisomerase - prevent supercoils by making transient double-stranded breaks in the DNA molecule and reseals it
  3. Single-stranded binding protein (SSBP) - prevent reannealing (reformation of H bonds) and degradation of ssDNA
  4. DNA polymerase III - unable to synthesize polynucleotide by its own and can only add deoxyribonucleotides to the free 3’OH end of the growing DNA strand
  5. Primase - synthesize RNA primer
22
Q

what is a gene mutation?

A

permanent change in the nucleotide sequence of a gene (found in a DNA)

23
Q

what is the link between nucleotide, nucleic acid, mRNA, amino acids, proteins… etc ?

A

nucleotides -> nucleic acids (e.g DNA) -> mRNA -> amino acids (in a polypeptide) -> protein

gene is a specific segment of DNA that determines amino acids sequence in polypeptide which determine the function and stucture of protein.

24
Q

what is the difference between polynucleotide and nucleic acid?

A
25
Q

How does alteration of a nucleotide sequence affects an organism

link to a.a -> protein…

A

change in sequence of nucleotides in a gene -> change in codon sequence in mRNA -> change the sequence of amino acids in a polypeptide -> (if change in physical and chemical properties of amino acid’s R group) -> change in 3D conformation of the protein and function (types of bonds)-> change in phenotype of an organism

26
Q

what is point mutation?

A

change in only one base

27
Q

1 codon is made up of _ bases

A

3

28
Q

What are the types of mutations in DNA

A
  1. Base substitution
  2. Base deletion
  3. Base insertion
29
Q

What are the effects of mutation in DNA?

4 types

A
  1. silent mutation
    - Due to** degeneracy of the genetic code** -> …changed codon codes for the same amino acid -> no change in amino acid sequence coding for protein -> no obervable change in phenotype
  2. missense mutation
    - Change in nucleotide sequence -> codon that codes for diff a.a -> phenotype altered
  3. nonsense mutation
    - change in nucleotide sequence change codon that codes for a.a into a stop codon -> translation will be terminated prematurely -> polypeptide formed truncated -> non-functional protein
    - * may result in frame-shift
  4. frameshift mutation
    - change in the reading frame of the mRNA template during translation -> ribosomes begin to read incorrect triplets from the point of deletion or insertion -> non-functional protein formed
30
Q

Why is sickle-cell anaemia formed?

A
  • haemaglobin S (HbS) is produced due to single-base substitution where thymine is replaced by adenine in the gene coding for B-globin chain
  • in the mRNA produced, one of the codon changed from GAA (coding for a.a glutamate) to GUA (coding for a.a valine)
31
Q

what codes for what?

A

codon codes for amino acids

31
Q

how does glutamate differ from valine?

A

glutamate is hydrophilic while valine is hydrophobic

32
Q

What causes the HbS to form fibres?

A

At low O2 concentration, the hydrophobic portions of the HbS molecules stick together, causing the HbS moleucles to polymerise into fibres. This causes the red blood cell to change from circular biconcave chape to sickle-shape.

33
Q

What causes the sickle-shaped?

A

RBC forms the sickle-shape due to the fibres formed inside the cell

33
Q

What is the problem of sickle-cell RBC?

3 big ones

A
  • obstruct blood capillaries -> deprives multiple organs fo O2 -> cause damage
  • more rigid and fragile thatn normal RBC -> shorter life span -> haemolyse readily resulting in anaemia
  • accumulate in spleen for destruction -> enlargement of the spleen
34
Q

wha is nuclease?

A

enzyme that break down nucleic acid

35
Q
A

biology (20 decks)

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