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2024 SEM 1 BIOCHEMISTRY (LEC) > nucleic acids > Flashcards

nucleic acids Flashcards

1
Q

levels of structure in nucleic acids

A
  • Primary structure
    Order of bases in the polynucleotide sequence
    Specifies the genetic code
  • Secondary structure
    Three-dimensional conformation of the polynucleotide backbone
  • Tertiary structure
    Supercoiling of the molecule
  • Quaternary structure
    Interaction with other classes of macromolecules, such as proteins
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2
Q

what are the structure in nucleic acids and proteins

A

a nucleic acid:
5’ to 3’

a protein:
N terminal to C terminal

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3
Q

monomer of nucleic acid

A

nucleotides

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4
Q

structure of nucleic acids

A

nitrogenous base
phosphate group
pentose sugar

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5
Q

Nitrogen-containing aromatic compounds that make up the coding portion of nucleic acids

A

nucleic acid bases

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6
Q

5 membered ring, polysaccharides

A

pentose sugar

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7
Q

ribose vs deoxyribose

A

Ribose
* Present in RNA
* Contains -OH group at carbon

Deoxyribose
* Present in DNA
* Lacks -OH group at carbon 2

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8
Q

Purine or pyrimidine base bonded to a sugar (ribose or deoxyribose)

A

nucleoside
*lacks phosphate group

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9
Q

Formed when phosphoric acid is esterified with an —OH of the monosaccharide, most commonly either the 3′ —OH or the 5′ —OH

A

nucleotide
*base + sugar + phosphate

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10
Q

what reaction is a nucleoside formation and how is it formed

A

condensation reaction
The base is attached to C1′ position of the sugar (β- configuration, pataas)

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11
Q

Formed by the addition of a phosphate group to a nucleoside

A

nucleotide
*water is released when phosphate is attached to C5’

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12
Q

it is the bond between ribose/ deoxyribose and each base

A

b-glycosidic bond

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13
Q

DNA vs RNA

A
  • Deoxyribonucleic acid (DNA)
    – Found within the cell nucleus
    – Stores and transfers genetic information
    – Passed from existing cells to new cells during cell division
  • Ribonucleic Acid (RNA)
    – Occurs in all parts of a cell
    – Primary function is the synthesis of proteins
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14
Q

3′ —OH of one 2-deoxy-D-ribose is
joined to the 5′ —OH of the next 2-deoxy-D- ribose by a

A

phosphodiester bond

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15
Q

it consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphate

A

biopolymer

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16
Q

what is the overall charge of the nucleotide

A

The nitrogenous base can contribute a +1 charge if it is protonated, and the phosphate groups typically contribute a -2 charge. Therefore, when you consider these charges together, the overall charge of a nucleotide is usually negative (approximately -1), especially when accounting for one phosphate group. If there are multiple phosphate groups (as in ATP, for example), the overall charge would be even more negative. So, in summary, the nucleotide’s typical charge is negative due to the phosphate groups outweighing any potential positive contribution from the nitrogenous base.

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17
Q

a nucleotide chain has directionality

A

5’ end: free phosphate group
3’ end: free hydroxyl group

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18
Q

Sequence of bases along the pentose-phosphodiester backbone of a DNA molecule

A

primary structure of DNA

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19
Q

Ordered arrangement of nucleic acid strands

A

secondary structure of DNA

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20
Q

Three-dimensional arrangement of all atoms of a nucleic acid

A

tertiary structure of DNA
*referred to as supercoiling

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21
Q

Two polynucleotide chains wrapped around each other

A

DNA double helix

proposed by James Watson and Francis Crick in 1953
based on X-ray crystallography

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22
Q

how are the base pairs are held together

A

by hydrogen bonds
- which keeps the 2 strands of DNA aligned
- stabilize the double helix

23
Q

The two strands run in opposite directions

A

antiparallel
one from 3’ to 5’ and the other from 5’ to 3’

24
Q

how does one know if the bases are the most stable or preferred pairs

A

through x-ray cystography

25
Q

briefly explain the different types of DNA configurations

A

index card

26
Q

how does bases interact w each other

A

bases are hydrophobic
hence via hydrophobic bonding

27
Q

true or false:
In standard B-DNA, each base is rotated 32° with respect to the preceding one

A

true -
* Perfect for maximal base pairing but not optimal for maximum overlap of bases
* Bases that are exposed to the minor groove must come in contact with water

[This allows for good base pairing but isn’t perfect for base stacking.
Some bases are exposed to water in the DNA’s minor groove.]

28
Q

why do many bases adopt a propeller twist

A

Base-pairing distances are less optimal
base stacking is more optimal
- water is eliminated from minor-
groove contacts with bases

[Bases often twist like propeller blades to improve their positioning.]

29
Q

why do bases slide sideways

A

allow them to interact better w the bases abv and below them
*the twist and slide depend on which bases are present

30
Q

prokaryotic DNA

A

circular and forms supercoils

31
Q

Extra twists (over and above those of the double helix) in closed circular DNA

A

DNA supercoils

32
Q

Type of double-stranded DNA in which the 5′ and 3′ ends of each strand are joined by phosphodiester bonds

A

circular DNA

33
Q

briefly explain the negative and positive supercoiling in simple terms

A
  • Negative supercoils: Circular
    DNA with fewer than normal number of turns of the helix
  • Positive supercoils: Circular DNA with more than normal number of turns of the helix
34
Q

Enzymes that relax supercoiling in closed circular DNA

A

Topoisomerases

35
Q

Complex of DNA and protein found in eukaryotic nuclei

A

chromatin
- resembles beads on a string

36
Q

Basic proteins found complexed to eukaryotic DNA

A

histones
(H1, H2A, H2B, H3, and H4)
*rich in lys and arg

37
Q

Globular structure in which DNA is wrapped around an aggregate of histone molecules

A

nucleosome

38
Q

the how to break the hydrogen bonds of DNA and to disrupt the stacking interactions

A

denaturation
energy must be added - heating

heat denaturation is called melting
bases absorbs light in the 260nm wavelength region

39
Q

true or false:
the separated strands cannot reconnect

A

false - that renaturation, when cooled slowly, the separated DNA strands can reconnect

40
Q

hyperchromicity

A

DNA strands separate, they absorb more light

41
Q

why does G-C pairs has a higher melting temperature

A

because G-C pairs have three hydrogen bonds, while A-T pairs have only two.

42
Q

Consists of long, unbranched chains of nucleotides joined by phosphodiester bonds between the 3′ —OH of one pentose and the 5′ —OH of the next

A

RNA
* pentose unit is b-D-ribose (It is B-deoxy-D-ribose in DNA)

43
Q

Single-stranded polynucleotide chain between 73 and 94 nucleotide residues long

A

Transfer RNA, tRNA
- short-single stranded RNA
- has a specific aa attached at one end
- carries aa to ribosomes for protein building

44
Q

Ribonucleic acid found in ribosomes, the site of protein synthesis

A

Ribosomal RNA, rRNA
- 60-65% weight of the ribosomes
-35-40% weight of the protein portion
- protein synthesis

45
Q

how many subunits are there in a ribosomes

A

2 subunits
- 1 larger than the other

46
Q

Initially formed as a larger precursor molecule

A

heterogeneous nuclear RNA (hnRNA)

47
Q

Ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteins

A

Messenger RNA, mRNA
- small amt and short lived in cells
- tells ribosomes what proteins to make, directly copied from DNA

48
Q

Found in nucleus of eukaryotic cells and recently discovered

A

Small nuclear RNA (snRNA)
- helps process other RNA s, especially mRNA
- works w protein t form snRNPs

49
Q

snRNA complexes with protein and forms

A

small nuclear ribonucleoprotein particles (snRNPs)

50
Q

what is the difference between
tRNA:
rRNA:
mRNA:
snRNA:
(found in)

A

tRNA: Amino acid carrier (cytoplasm)
rRNA: Part of protein-making machinery (ribosomes- cytoplasm and ER)
mRNA: Genetic message carrier (cytoplasm)
snRNA: RNA processing helper (nucleus)

51
Q

which RNA is the most short lived

A

mRNA

52
Q

list the RNA in order from shortest to long

A

snRNA: Shortest
tRNA: Short
mRNA: Varies, can be long
rRNA: Long

53
Q

list the abundance of the RNA from most to low abundance

A

rRNA: Most abundant
tRNA: Fairly abundant
mRNA: Least abundant
snRNA: Low abundance

2024 SEM 1 BIOCHEMISTRY (LEC) (19 decks)

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