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Biochemistry - Foundation Module > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

Functions of Nucleic acids:

A
  • Function primarily as informational molecules
  • For the storage and retrieval of information regarding the primary sequence of polypeptides.
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2
Q

Two types of Nucleic Acids:

A

(1) Deoxyribonucleic acid (DNA)
(2) Ribonucleic acid (RNA)

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3
Q

Each nucleotide contains: [3]

A
  1. A 5-carbon pentose sugar
  2. A nitrogenous base
  3. One or more phosphate groups.
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4
Q

Pentose sugars:
What is it?
What is it for DNA and RNA?

A

it is a 5 carbon sugar.

The sugar in DNA is deoxyribose.
The sugar in RNA is ribose

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5
Q

Pentose sugars:
What is it?
What is it for DNA and RNA?

A

it is a 5-carbon sugar.

The sugar in DNA is deoxyribose.
The sugar in RNA is ribose

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6
Q

Phosphate groups:

Function?
charge given to Nucleic Acid?

A

links the sugar on one nucleotide onto the phosphate of the next nucleotide to make a polynucleotide.
Gives a negative charge to the nucleic acid.

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7
Q

Four bases of DNA?

A

Thymine
Adenine
Cytosine
Guanine

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8
Q

Four bases of RNA?

A

Uracil
Adenine
Cytosine
Guanine

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9
Q

Two types of bases in DNA and RNA?

A
  1. Purine bases (two ring-shaped molecules joined
    together)
  2. Pyrimidine bases (a single ring)
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10
Q

What are the Purine bases?

In both DNA and RNA? (True/False)

A

Adenine (A) and Guanine (G)
True - Present in both DNA/ RNA

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11
Q

What are Pyrimidine bases?

What is in DNA? What is in RNA?

A

*Cytosine –C
*Uracil – U
*Thymine – T

DNA - C and T
RNA - C and U

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12
Q

Composition of a Nucleoside?

In RNA/ DNA?

A

Purine or pyrimidine base covalently attached to a sugar molecule

RNA – Ribonucleoside
DNA – Deoxyribonucleoside

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13
Q

What is a Nucleotide?

In RNA/ DNA?

A

Nucleoside (B+S) is covalently joined to a phosphate group.

RNA – Ribonucleotide
DNA – Deoxyribonucleotide

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14
Q

What is a polynucleotide?

A

Made up of many different nucleotides covalently joining with one another by 3’-5’ phosphodiester bonds.

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15
Q

Why do polynucleotides have “polarity”?

A

Because each chain has a 5’phosphate end 3’hydroxyl end.

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16
Q

What are the characteristic features of DNA double Helix? [2]

A

Two DNA strands are **wound around each other **to form the double helix (Two strands are twisted together around a common axis - right handed)

Run in opposite directions – **Anti-parallel **(one running from 5’ to 3’ and the other from 3’ to 5’)

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17
Q
  1. Chargaff’s rule?
  2. Why is this rule like this?
A
  1. COMPLEMENTARY BASE PAIRING
  • Adenine and Thymine always join together
  • Cytosine and Guanine always join together
  1. This is because there is exactly enough room for one purine and one pyrimidine base between the two polynucleotide strands of DNA.
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18
Q

Where can we find DNA in a cell?

A

DNA is present in the nucleus and mitochondria (mitochondrial DNA).

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19
Q
  1. Three types of DNA structures?
  2. What is the most common one?
  3. When can we get the two uncommon ones?
A
    • B type
    • A type
    • Z type
  2. B type is the most common naturally occurring form
  3. Under certain in vitro conditions, A-DNA and Z-DNA double helices can form
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20
Q

What is the B type DNA structure? [3 key points]

A
  • right-handed helix
  • 10 base pairs per turn.
  • The intertwined strands make two grooves of different widths, referred to as the major groove and the minor groove.
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21
Q

Significance of the Major Groove and the Minor Groove?

A

May facilitate binding with specific regulatory proteins..

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22
Q

What can you say about the content of GC in DNA? [5 key points]

A

A=T
G=C
but AT≠GC

Generally GC~50%, but extremely variable
Distribution of GC is not uniform in genomes

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23
Q

CONSEQUENCES OF GC CONTENT?

A
  • GC slightly denser: Higher GC DNA moves further in a gradient
  • more stable DNA.
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24
Q

Forces that help to form the DNA double helix?
[5 forces] [!! Important to list in order of significance !!]

A
  1. Rigid phosphate backbone
  2. Base stacking interactions between bases (Van der Waals interactions)
  3. Hydrophobic interactions (highly negative phosphate backbone vs. non-polar bases facing interior)
  4. Hydrogen bonding (not the most energetically significant component)
  5. Ionic interactions - salt stabilizes the duplex form of DNA shielding of the phosphate backbone

(Remember Because Helps Hold Information)

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25
Q

Denaturation of DNA - What is the “Melting temperature of DNA”?

A

The Temperature at which 1⁄2 the DNA sample is denatured is called the melting temperature (Tm)

26
Q

Describe the Denaturation & Renaturation of DNA?

  1. How can we separate DNA strands?
  2. How can we renature DNA?
  3. What can we say about the re-association of DNA?
A
  1. The two strands of the double helix separate reversibly at high temperatures,
  2. If the temperature is lowered, the strands renature (reanneal),
  3. The rate of re-association is inversely proportional to the complexity of the DNA.
27
Q

What are the key characteristics determining the application of “denaturation of DNA”?

A

Critical importance in any technique that relies on complementary base pairing

28
Q

4 examples of denaturation of DNA?

A
  1. PCR
  2. Southern blots
  3. Northern blots
  4. DNA-DNA hybridization
29
Q

Differentiate between Southern and Northern blots.

A

SB - separates DNA
NB - Separates RNA

30
Q

What are the factors affecting the “melting temperature of DNA”? [5 main factors]

A
  1. G-C content of the sample
  2. Presence of intercalating agents (anything that disrupts H-bonds or base stacking)
  3. Salt concentration
  4. pH
  5. Length
  6. Denaturants
31
Q

What is Chromatin?

A

Chromatin is the chromosomal material in the nuclei of eukaryotic cells.

32
Q

4 main components of Chromatin?

A
  1. dsDNA
  2. Histones; most abundant chromatin proteins
  3. Non-histone proteins ( most are acidic)
  4. RNA (small quantity)
33
Q

Histones?

  1. What are they?
  2. What is their main function?
A
  1. A set of small basic proteins
  2. They bind with DNA and stabilize DNA structure.
    Also, participate in gene regulation
34
Q

What are the features of Histone proteins that allow them to perform their function? [2 points]

A
  1. Basic amino acids (positively charged) abundant in
    histone proteins are Histidine, lysine, and Arginine.
  2. Form ionic bonds with negatively charged
    phosphate groups.
35
Q

What are the 4 levels of genome Packing?

A

Level I - the B form of the double helix
Level II - The nucleosome (beads-on-a-string structure) Level III – Chromatin fiber
Level IV - Radial loop domain

36
Q

Describe the Level 2 DNA Packing - the Nucleosome.
[5 key points]

A
  1. A complex of DNA and histone proteins
  2. Eight core histone proteins aggregate to form the histone core (octamer complex) of the nucleosome.
  3. Nucleosome - DNA wrapped two times around the octamer core/octamer complex.
  4. The DNA fragment is negatively supercoiled in the left-handed direction.
  5. Nucleosomes are linked together by “linker ‘ DNA.
37
Q

Describe Level 3 of DNA Packing - Chromatin Fibre.
[2 key features]

A
  • It involves the coiling of nucleosomes into
    chromatin fiber.
  • This level of condensation involves the interaction of another histone protein.
38
Q

Describe Level 4 of DNA Packing - Radial Loop Domain.
[2 key features]

A
  • Involves a new structure called the chromosome scaffold.
  • Scaffold - made up of several protein components including lamins and topoisomerases.
  • 30 nm chromatin fiber is anchored to the chromosome scaffold and is organized into Radial Loop Domains.
39
Q

Biomedical Importance of DNA [7 key reasons]

A
  1. Storage of genetic information
  2. Understand the Molecular Basis of Disease
  3. Disease diagnosis
  4. Molecular targets of therapy
  5. Genetic Engineering
  6. Pharmacogenomics
  7. Medico-legal/ DNA Fingerprinting
40
Q

RNA structure: levels of organization?

A

3 levels of organization:

Primary, Secondary, Tertiary

41
Q

Bonds in the different levels of RNA?

A

Primary:
- Covalent bonds

Secondary/Tertiary Non-covalent bonds
- H-bonds (base-pairing)
- Base stacking

42
Q

Classes of RNA? [4 points]

A
  • Messenger RNA (mRNA)
  • Transfer RNA (tRNA)
  • Ribosomal RNA (rRNA)
  • Small RNA
43
Q

Features of mRNA? [5 features]

A
  1. Single-stranded.
  2. Serves as a template for protein synthesis.
  3. Synthesized in the nucleus and passes to the cytoplasm.
  4. Higher molecular weight compared to other types of RNA.
  5. Short half-life.
44
Q

Features of tRNA?

A
  1. Smallest RNA.
  2. Contains intra-strand/intra-chain base pairing.
  3. serves as an “adaptor” molecule that carries its specific amino acid
  4. At least 20 tRNA molecules in every cell, at least one corresponding to each of the 20 amino acids.
  5. Involved in the translation process.
  6. contain a high percentage of unusual bases (eg. dihydrouracil)
45
Q

Features of rRNA?

A
  1. Contributes to the structure and function of ribosomes.
  2. Necessary for ribosomal assembly and binding of mRNA to ribosomes.
  3. Performs peptidyl transferase activity (ribozymes)
46
Q

RNA functions? [4 points]

A
  • Storage/transfer of genetic information
  • Structural
  • Catalytic
  • Regulatory
47
Q

storage/ transfer function of RNA?

A
  1. Genomes [in viruses]
  2. mRNA
48
Q

the structural function of RNA?

A

rRNA, which is the major structural component of ribosomes.

49
Q

The catalytic activity of RNA?

A

*rRNA haspeptidyltransferaseactivity

  • Also, many small RNAs are enzymes. “ribozymes”

(Enzymatic activity responsible for peptide bond formation between amino acids in growing peptide chain)

50
Q

Regulatory Function of RNA?

A
  • miRNA forms imperfect RNA-RNA duplexes (multiple mRNA targets)
  • siRNA usually forms perfect RNA-RNA hybrids (specific mRNA targets)
  • both inhibit gene expression (gene-silencing effects)
    *Potential therapeutic agents for cancers and infections.
51
Q

Biomedical importance of RNA?

A

*Storage of genetic information in pathogens
* understand the pathophysiology and the genetic basis of diseases
- E.g. gene *RNA therapeutics; anti-cancer therapy
expression studies
*Prevention of disease; mRNA vaccines (Pfizer/Moderna)
*For the diagnosis of diseases; reverse- transcriptase(RT)-PCR, Northern blotting

52
Q

What is the Genome?

A
  • total genetic information carried by a cell/organism.
53
Q

What is a Gene?

A
  • A unit of heredity.
  • It is a region of DNA that is responsible for a
    particular characteristic.
  • Only about 10% human DNA contain genes.
  • Every gene in humans/animals has a specific sequence.
54
Q

What is a Gene Sequence?

A

The order of the nucleotide arrangement. Ex: ACCGTATC

55
Q

Three types of Genetic Variants?

A
  1. Nuclear sequence-level variants
  2. Nuclear structural variants (1 kb and larger in size)
  3. Mitochondrial variants
56
Q

Examples of “Nuclear sequence-level variants” in Genetic Variants.

A
  • Single nucleotide variants
  • Small insertions
  • Small deletions
57
Q

Examples of “Nuclear structural variants” in Genetic Variants.

A
  • large insertions,
  • Large deletions
  • copy-number variants
  • Inversions
  • Translocations
58
Q

Types of epigenetic modifications?

A

*DNA methylation
*Histone modifications
- Methylation
- Acetylation
- Phosphorylation
*RNA-mediated modifications (e.g. gene silencing effects of miRNAs and siRNAs)

58
Q

Types of epigenetic modifications?

A

*DNA methylation
*Histone modifications
- Methylation
- Acetylation
- Phosphorylation
*RNA-mediated modifications (e.g. gene silencing effects of miRNAs and siRNAs)

59
Q

What are Epigenetic Modifications?

A
  • Does not involve alteration of DNA coding sequence
  • Reversible
  • Inherited/ transgenerational (maybe lost over several generations)
  • Involves:
    – Enzymes: DNA Methyltransferase
    – Small RNAs; microRNA/ siRNA
  • Important in Tumorigenesis/Carconogenesis/Neurodegenerative diseases/ ASD/ Autoimmune diseases.

Biochemistry - Foundation Module (8 decks)

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