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ch112 > nucleic acids > Flashcards

nucleic acids Flashcards

1
Q

nobel prize winners

A

watson ,crick, and wilkins for nucleic acids

fire, mello for rna gene splicing

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2
Q

information storage

A

stored and transmitted from one generation to the next via DNA

genes are the hereditary units of the chromosomes, which are long strands of DNA.

stored in the base-pair sequences of the DNA strands.

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3
Q

nucleosides

A

Each nucleoside is an aldopentose sugar linked to a purine or pyrimidine base.

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4
Q

dna structure

A

chain of 2-deoxy-D-ribose rings linked by 3’ to 5’ phosphodiester linkages

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5
Q

rna structure

A

a chain of D-ribose rings linked by 3’ to 5’ phosphodiester

additional -OH group at the 2’ position of each ribose ring

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6
Q

pyrimidines

A

six membered rings with two nitrogens and two carbonyl oxygens

cytosine and thymine

uracil similar to thymine but missing a methyl group

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7
Q

purines

A

five membered ring fused to a six membered ring

adenine and guanine

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8
Q

glycosidic linkaes

A

C-N bond replaces the N-H bond in the free nucleotide bases

ribose sugars by a C-N bond at the C-1’ position of the ribose ring, in place of the -OH group.

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9
Q

5’ and 3’ nucleotides

A

phosphate is attached to the sugar at the 3’ position then it is a nucleotide-3’-phosphate

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10
Q

oligonucleotides

A

link connects the 3’ position on one nucleotide to the 5’ position on another nucleotide through a phosphodiester linkage

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11
Q

heterocycles

A

nucleotide bases have nitrogen atoms as part of their rings, so are heterocyclic

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12
Q

bronsted lowry bases

A

nitrogen atoms can gain a proton and become charged

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13
Q

acid base equilibria

A

nitrogen atoms tend to form three bonds, leaving a ‘lone pair’ of electrons that can act as a brønsted-lowry base

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14
Q

pka and base strength

A

large pKa value indicates that an equilibrium lies to the left hand side.

indicates strong base

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15
Q

pyrrole

A

weak base, nitrogen lone pair is involved in pi bonding

nitrogen is sp2 trigonal planar with one p orbital containing two electrons - aromatic - more stable

nitrogen lone pair is not available for bonding

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16
Q

nucleophiles

A

pyridine and imidazole have nitrogen lone pairs, so they are nucleophilic and can react with electrophiles, such as methyl iodide

chemical carcinogens are electrophilic and react with the nitrogen lone pairs of the basic nitrogens of the nucleotide bases.

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17
Q

tautomerisation

A

transfer of a hydrogen atom from one place to another, within the same molecule, resulting in a different structure.

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18
Q

lactim and lactam

A

lactam is present in vast excess

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19
Q

amino and imino

A

amino is present in vast excess

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20
Q

hydrogen bonds

A

functional groups with lone pairs of electrons are classified as hydrogen bond acceptors

functional groups with an O-H or N-H bond are classified as hydrogen bond donors.

if hydrogen bond donor and acceptor groups line-up correctly on pairs of molecules then the hydrogen bonding is said to be complementary.

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21
Q

tautomerisation in nucleic acids

A

donors - acceptors

acceptors - donors

leads to incorrect base pairing, and changes DNA sequence which can be carcinogenic

occurs once every 10^4 base pairs copied

human genome is ∼ 3 × 10^9 `base pairs in length, this would lead to ∼ 300 000 errors every time the cell divided

actual in vivo error rate is one in 10^8 base pairs copied, due to the presence of proof reading enzymes

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22
Q

alkoxy groups

A

OR

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23
Q

phosphodiester linkages

A

in phosphate esters it is possible to replace all three hydroxy groups (OH) on the phosphorus with alkoxy groups (OR) of an alcohol

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24
Q

phosphodiester hydrolysis

A

phosphate esters are relatively stable and their hydrolysis requires harsh conditions

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25
Q

phosphodiester hydrolysis in rna

A

rna is much less stable to hydrolysis than DNA, due to the presence of an -OH group at the 2’ position of the ribose ring

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26
Q

sugar base link cleavage

A

sugar-base link (a C-N bond) is unstable to acid hydrolysis, especially in the purines. Protonation at N-7 aids the hydrolysis with the loss of the nucleotide base to give a basic DNA

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27
Q

deprotonation

A

phosphate groups are deprotonated at physiological pH, meaning that polynucleotides are negatively charged (polyanions)

28
Q

earlt theories of DNA

A

Chargaff’s rules - by hydrolysing DNA, separating and analysing the resulting bases it was determined that DNA has an equal number of adenine and thymine bases (A = T) and an equal number of guanine and cytosine bases (G = C).

NMR and X-ray data - correct tautomeric forms of the bases were determined.

X-ray diffraction photographs - information that DNA is helical.

29
Q

B-DNA

A

most common form
conditions for high stability B-DNA are high humidity(>92%), as found in aqueous environment

presence of metal cations (Na+) which interact with the negatively charged phosphate groups

30
Q

watson-crick structure

A

two deep grooves between the sugar-phosphate chains, a relatively narrow minor groove and a relatively wide major groove, unequal sizes because deoxyribose rings are assymetric, and the top edge of each base pair is structurally different from the bottom edge

aromatic bases occupying the central core of the helix, forming complementary base pairs (GC, AT), essentially planar - stack on top of one another, planes are nearly perpendicyular to the helical axis (6% tilt)

a right handed, antiparallel, double helix formed by two sugar-phosphate chains wound about a central helical axis

31
Q

B-DNA dimensions

A

helix diamter is 20 angstroms

base pair has a thickness of 3.4 angstroms

helical pitch is ~34 angstroms

human genome is 1.02m

32
Q

A-DNA

A

A-DNA is also a right handed, antiparallel double helix.

A-DNA is a wider and flatter double helix than B-DNA, with a helix diameter of ~ 26 Å.

The helical pitch is similar to B-DNA at ~ 34 Å, but there are 11.6 base-pairs per full turn of the double helix. This means that the aromatic bases have a closer contact, which favours crystal formation.

33
Q

A-DNA structure

A

The planes of the base-pairs in A-DNA are tilted by ~20o with respect to the helical axis.

The base-pairs are displaced away from the helical axis, leading to a central helical cavity.

The major groove of A-DNA is very deep and the minor groove is very shallow.

34
Q

Z-DNA

A

forms when the concentration of cations (typically Mg 2+) is high

interact with the charged oxygen atoms which are closer than in B-DNA (8 angstroms vs 12 angstroms)

left handed, antiparallel, double helix

sugar phsophate chains zig zag down the outside of the double helix

35
Q

Z-DNA dimensions

A

helix diamter is ~18 angstroms

helical pitch of ~44 angstroms

12 base pairs per full turn

found in local segemnts of B-DNA where the DNA is interacting with proteins (enzymes that repair and modify the bases)

36
Q

denaturation

A

leads to changes in the DNA’s physical properties (eg. viscosity decreases) and spectroscopic properties (UV-vis absorbance increases)

absorbs strongly in the wavelength range 200 - 300 nm, but each nucleotide base has its own absorption profile

aromatic systems of the purine and pyrimidine bases undergo electronic transitions (involving their p electrons) when a photon of the correct wavelength, l, is absorbed

37
Q

hyperchromic shift

A

base pairs become unstacked

free nucleotide bases have a ~40% higher absorbance rate

38
Q

relative absorbance

A

denatured - 82 degrees, absorbance at 250nm is ~0.4

native - 25 degrees, absorbance at 250nm is ~0.3

mid-point of the melting curve is known as the melting temperature (Tm).

39
Q

stabilty of DNA towards denaturation

A

the solvent
ions present
pH
DNA composition (percentage GC vs AT)

GC base-pairs have three hydrogen bonds, compared to just two in AT base-pairs. Thus, more energy is required to separate GC base-pairs.

40
Q

quenching

A

denatured DNA is rapidly cooled

resulting DNA will only be partially paired, as probability of pairing in the correct order is almost zero

41
Q

renaturation

A

denatured DNA is heated to a temperature ~25 oC below its Tm and held at that temperature for long enough, the DNA will eventually ‘renature’

process involves continual melting and re-forming of short base-paired regions (annealing).

enough thermal energy is present to separate weakly bound (incorrect) base-pairs, but there is not enough thermal energy to completely denature the DNA

42
Q

local breathing

A

at moderate temperatures, short sections of DNA can separate (they no longer associated by hydrogen bonding) for a short period of time, before re-associating

43
Q

mutations

A

during DNA local breathing, at the separation site, the base pairs are not hydrogen bonded. The hydrogen bond acceptor groups of the nucleotide bases can now behave as nucleophiles and may react with electrophilic chemicals present

can cause mutation of the DNA and disrupting the base pairing and can cause the incorrect base to be incorporated during replication

44
Q

circular DNA

A

double helical DNA can form a closed loop by covalently bonding the 5’ and 3’ ends of both strands (to each other)

45
Q

superhelical DNA

A

circular DNA can be twisted further, leading to highly strained states (akin to a wound up rubber band). These forms of DNA are said to be supercoiled, supertwisted, or superhelical.

two forms of superhelical DNA that can only be interconverted by breaking and re-forming covalent bonds are said to be topoisomers

enzymes responsible for converting DNA from one topoisomer to another are called topoisomerases.

46
Q

supercoiled DNA in the cell nucleus

A

supercoiled DNA interacts favourably with proteins called histones. the complex formed is called chromatin.

further coiling of the DNA spacers in chromatin produces a compact chromatin found in the cell nucleus

strain energy present in supercoiled DNA is used to drive some biological processes

47
Q

topoisomerase inhibitors

A

molecules that interfere with the function of topoisomerases (topoisomerase inhibitors) are effective antibiotics and cancer chemotherapy agents

48
Q

intra strand base pairing

A

RNA can fold back on itself via intra-strand base pairing to create a variety of folds, bends (hairpin turns), U-turns, loops, bulges and junctions.

49
Q

rna helix formation

A

steric repulsion between the 2’-hydroxy and the C-3’ oxygen and C3’-phoshodiester means that RNA does not form the B-form but can form short lengths of the A-form

50
Q

parental and daughter strands

A

parental DNA double helix must be unwound to expose base pairs that are not hydrogen bonded. this requires another class of enzyme (type IIA topoisomerases - some of which are called DNA gyrase)

point at which double stranded (parental) DNA is unwound is called a ‘replication fork’

51
Q

transcription

A

several turns of the DNA double helix unwind to form a ‘bubble’ that exposes the bases of the two strands

52
Q

nucleotide monomers

A

nucleotide monomers in rna synthesis are nucleotide triphosphates
ATP adenosine triphosphate
CTP cytidine triphosphate
GTP guanosine triphosphate
UTP uridine triphosphate

53
Q

rna chain growth

A

pyrophosphate[P2O7]4- is released as the next nucleotide base is added to the growing rna chain

54
Q

ribosome

A

two thirds rrna and one third protein

evidence that the rRNA of the ribosome catalyses the peptide bond formation rather than the protein part

ribosome binds mRNA, which serves as a template to pass on the genetic information

mRNAs can be regarded as a series of consecutive 3-nucleotide sequences, known as codons. Each codon specifies a particular amino acid

55
Q

trna

A

tRNAs deliver amino acids to the ribosome. Each tRNA carries one amino acid which is covalently linked at the 3’-hydroxy position

single stranded tRNA is folded into a clover leaf secondary structure with 3 loops and at least 4 regions with complementary base pairings

on the middle loop, opposite the 5’ and 3’ ends there is an anticodon sequence of three nucleotides that is complementary to the codon sequence

56
Q
A

ribosome binds mRNA and this facilitates the binding of multiple tRNA molecules, through complementary hydrogen bonding (between codons and anticodons

ribosome catalyses the transfer of an amino acid from one tRNA molecule to another, which increases the length of the growing polypeptide by one amino acid

once tRNA has passed its amino acid to the growing polypeptide, it is ejected

57
Q

rna self splicing

A

self-splicing involves the removal of a central segment (intron) from an rna strand and joining together the resulting end portions (exons) without an external catalyst

a 421-nucleotide intron is removed from a 6.4 kbase precursor to give the mature RNA.

58
Q

human genome project

A

first draft was in 2000

complete sequence was published in 2003

allows us to manipulate and harness the genetic information

59
Q

dna sequencing

A

dna molecules are too large to be sequenced intact, so must be cleaved into fragments

enzymes that cleave the dna at specific base pair sequences are called restriction endonucleases

60
Q

base sequence specific cleavage

A

each of the 200 known endonuclease will cleave DNA at well defined points in the chain

61
Q

solving the puzzle

A

cutting the dna with other enzymes with different selectivity will lead to partial overlap

these overlaps must be identified to be able to determine and complete the dna sequence

sanger method is used in sequencing machines

62
Q

sanger method

A

ecoli dna polymerase I is used to synthesize complementary copies of the single stranded dna fragments being sequenced

only one fragment at a time

each fragment is incubated with:

dna polymerase I

a dna primer (klenow fragment)

four dntp monomers

a small amount of dideoxynucleoside triphosphate(ddNTP)

63
Q

ddNTPs

A

missing an OH group at the 3’ position, meaning that no phosphate group can be attached

can be radiolabelled or labella by attachment of a fluorescent dye

64
Q

automated sequencing

A

requires fluorescent labeling

all of the chain growth reactions are carried out in a single vessel

analysed by gel electrophoresis

terminal base is identified according to its characteristic fluorescence(diff colours for each ddNTP)

large numbers of machines are used >100

65
Q

uv and radiation damage

A

generate hydroxy radicals from water

with dioxygen, peroxy radicals are formed

large concentration of water and dioxygen in biological systems

ch112 (4 decks)

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