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Foundations > Nucleic acids > Flashcards

Nucleic acids Flashcards

1
Q

What are nucleotides

A

Biological molecules that participate in nearly all biochemical processes

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2
Q

What is the structure of a nucleotide

A

phosphate esters of pentose sugars were a nitrogenous base is linked to the C1 of the sugar residue
-Phosphate group is linked to either the C5 or C3 Of sugar residue by covalent bonds formed by condensation reactions

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3
Q

What do nucleotides form the monomers of

A

DNA and RNA

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4
Q

What is ATP

A

An energy rich end product of most energy releasing biochemical pathways used to drive most energy requiring metabolic processes in cells

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5
Q

What do nucleotides help regulate

A

Many metabolic pathways for example ATP ADP and AMP

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6
Q

What is DNA

A

the hereditary material that carries coded instructions used in development and functioning of all named living organisms

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7
Q

What is DNA made up of

A

nucleotides

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8
Q

What is the structure of DNA and how is it suited to its function

A

double stranded
each strand acts as a template
H bonds easily break/form between bases
complimentary base pairs
Purines always pair with pyrimidines - equal rungs
Hydrogen bonding between comp base pairs

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9
Q

How many hydrogen bonds does each base form

A

A-T=2
C-G=3

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10
Q

What are the purines and pyrimidines

A

Purine : adenine or guanine (two rings)
Pyramidine: thymine or cytosine (one ring)

-Purines always pairs with pyramidines giving equal sized rungs on DNA ladder these can twist into double helix giving molecule stability

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11
Q

What is the difference between Deoxyribose and ribose

A

Deoxyribose contains an H instead of an OH

Condensation reaction gives off 2H2O

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12
Q

What is the formation of DNA

A

2 strands running in an antiparrallel 5’ 3’ direction twisted into a double helix

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13
Q

Describe the five prime end and the three prime end

A

-Direction of the two DNA molecules strands
- 5’ phosphate attached to fifth carbon - terminal phosphate group
-3’ phosphate attached to third carbon- teminal hydroxyl group - O2 facing downwards

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14
Q

How is DNA organised in eukaryotic cells

A

-majority of DNA content is in nucleus
-each molecule of DNA is tightly wound around histone proteins to form linear chromsomes
-One molecule of DNA = one chromosome

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15
Q

How is DNA organised in chloroplasts/ mitochondria/prokaryotes

A

Naked DNA not contained in a nucleus
Not wound around histone proteins

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16
Q

How do you extracted and purify DNA by precipitation

A

-Wear eye protection
- extract from source such as strawberry which has lots of chromosomes
-Extraction process is simple and involves simply macerating tissue adding strong detergent (washing up liquid) and then adding ethanol
-DNA precipitates out of solution
-DNA can be further purified by removal of unwanted salts and can then be concentrated

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17
Q

How does a DNA molecule replicate

A

-semi conservative
-double helix unwinds
-hydrogen bonds break
-each strand acts a template
free nucleotides align with exposed bases
-comp base pairs
hydrogen bonds reform
-sugar phosphate reforms/adjacent nucleotides join
-DNA polymerase catalyses formation of phosphodiester bonds
-each new molecule one old/one new

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18
Q

What is semi-conservative replication

A

DNA is composed of one old strand and one new strand

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19
Q

Describe semi conservative replication (in detail)

A

DNA starts as a double helix, DNA gyrase - untwists
-DNA helicase unzips - breaks hydrogen bonds and nucleotides left exposed
-single stranded binding proteins attach to prevent reanneling (binding back together)
-free nucleotides in nucleoplasm fly in and attach via complimentary base pairs, hydrogen bonds from
-DNA polymerase binds to the leading strand and forms covalent phosphodiester bonds at the start of the replication fork
-moves in a 5’ 3’ direction
-lagging strand synthesised discontinuously
-DNA ligase closes the gaps in the backbone (joins fragments made on lagging strand)
- each new strand consists of one old strand and one new

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20
Q

What happens if the sequence of nucleotides change

A

-there is a different combination of amino acids
-different tertiary structure
-cant perform specific function

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21
Q

What supplies the energy for phosphodiester bonds

A

hydrolysis of activated nucleotides in the nucleoplasm

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22
Q

How to prokaryotes/mitochondria/chloroplasts replicate

A

-bubble sprouts
-unwinds/unzips
-complimentary bases join to exposed nucleotides
-eventually whole loop is copied

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23
Q

What is the complimentary base pairs

A

purines always pair with pyrimidines so rungs on the ladder are always the same length

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24
Q

What is the meslston and Stahl experiement

A

proof of semi - conservative replication
1st - heavy as old DNA
2nd - 1X heavy 1x light
3rd- 1x hevay 2x light

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25
Q

What is a mutation

A

point mutation
mistakes in base sequences such as base deletion/insertion/substituted

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26
Q

How is a mutation avoided

A

enzymes proofread and delete out any incorrect nucleotides
different version - alleles

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27
Q

How is energy supplied for phosphodiester bonds

A

Hydrolysis of activated nucleotides to release extra phosphate groups supplies energy to make phosphodiester bonds between sugar residue of one nucleotide and phosphate group of the next

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28
Q

What are some examples of harmful mutations

A

sticky mucous leads to cystic fibrosis
sickle cell anemia - distorts shape of RBC

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29
Q

What is the lagging strand synthesized in

A

Okazaki fragments

30
Q

How many DNA Bases code for a single amino acid

A

3

31
Q

How many different combinations of amino acids are there

A

4(3) - 64 combinations

32
Q

What happens to the remaining combinations of amino acids

A
  • several codons can code for one amino acid
  • some used for start/stop/termination
    -mutation results in a change in amino acid and a new one can easily be inserted
33
Q

What is the definition of a gene

A

a gene is a section of DNA that codes for the production of a polypeptide

34
Q

Describe the process of transcription briefly

A

-DNA/ gene copied and transcribed into mRNA
- free activated (RNA) nucleotides
-line up by complimentary base pairing
-Catalysed by RNA polymerase

35
Q

Describe briefly process of translation

A
  • Mrna moves to ribosomes
    -tRNA binds to mRNA
  • anticodons bind to codons
  • complimentary amino acid attaches to tRNA
    -formation of peptide bond between amino acid
36
Q

What is the importance of complimentary base pairing

A
  • DNA can be replicated without error / same sequence of amino acids produced
    -reduces occurrence of mutation
  • allows formation of hydrogen bonds
37
Q

Describe the structural relationship between deoxyribose and the other components of the
DNA molecule.

A

-part of a nucleotide
- bonded to base and phosphate
- phosphate joined to C5/C3 base at C1
-part of backbone of DNA
-links to next phosphate on adjacent nucleotide
-nucleotide is a monomer of DNA

38
Q

How is information coded on genes is used to synthesis a polypeptide

A

synthesis
-DNA, copied into /, mRNA or described ;
-transcription / transcribed ;
-one strand copied ;
-complementary base-pairing ;
-triplet code / code read in threes / codon is 3 bases ;
-base sequence determines amino acid sequence ;
-translation ;
-ribosomes ;
-role of tRNA described

39
Q

How do polypeptides control the physical development of an organism

A

-haemoglobin e.g
-enzyme reactions/metabolism
-hormones
-receptors
-turning genes on/off

40
Q

What does mRNA consist of

A

-contains ribose
-contains uracil

41
Q

processes of transcription (detail)

A

1)The hydrogen bonds between the complementary bases break and the DNA uncoils
thus separating the two strands
2) Nucleotide bases are left exposed
2) One of the DNA strands is used as a template by RNA polymerase to make the
mRNA molecule. the DNA template is called the antisense strand
3) Free nucleotides line up by complementary base pairing and adjacent nucleotides
are joined by phosphodiester bonds made by RNA polymerase thus forming a single
stranded molecule of mRNA
4)mRNA then moves out of the nucleus through a pore and attaches to a ribosome in
the cytoplasm which is the site of next stage of protein synthesis called translation

42
Q

What are ribosomes made up of

A
  • 2 subunits one large and one small
    -protein and rRNA
43
Q

What are the features of the genetic code

A
  • universal - same in all organisms

-degenerate - multiple codes for one amino acid
-non-overlapping -each codon only read once

44
Q

process of translation (detail)

A
  • small subunit of rRNA binds to mRNA then large
    -hydrogen bonds temporarily form between the mRNA and ribosme
    -tRNA binds to amino acids in cytoplasm and carries the aa to the mRNA at one end of its molecule whilst it carries the anticodon which is complimentary to the mRNA codon at the other
    -tRNA attaches itself to mRNA by complementary base pairing (U-A, C-G) – two molecules
    attach to mRNA at a time
    -Codon and anti-codon temporary bonded by hydrogen bonds
  • The amino acids attached to two tRNA molecules join by a peptide bond via a condensation reaction and then
    tRNA molecules detach themselves from the amino acids, leaving them behind
    -ribosome moves along mRNA;
    ATP needed
45
Q

Structure of tRNA

A

These tRNA molecules have a triplet of unpaired bases at one end (known as the anticodon) and a region where a specific amino acid can attach at the other
There are at least 20 different tRNA molecules, each with a specific anticodon and specific amino acid binding site

46
Q

What contains carbon on the nucleotide molecule

A

all except the phosphate group

47
Q

How many purines and pyramidines are on the DNA molecule

A

50% purines
50% pyrimidines

48
Q

How many strands of polynucleotides are in tRNA

A

1 strand

49
Q

What happens after complimentary base pairing

A

(involves) DNA polymerase sugar-phosphate backbone (re)forms / condensation reaction between phosphate and sugar
DNA winds into double helix

50
Q

Similarites in DNA rep and transcription

A

 DNA unwinds and unzips
Helicase enzymes
Template DNA      
Complementary base pairing
Hydrogen bonds broken and formed
Free, activated nucleotides
Polymerase enzymes
-Both occur in the nucleus

51
Q

What is the primary structure

A

The sequence of amino acids

52
Q

Start codon

A

AUG

53
Q

Differences between transcription and DNA rep

A

Transcription:
-Only part of the DNA molecule involved
-RNA polymerase
-Produces one molecule of mRNA
-Occurs in G1 of interphase
-Only one strand is used as the template strand
-

54
Q

Differences between transcription and DNA rep

A

Transcription:
-Only part of the DNA molecule involved
-RNA polymerase
-Produces one molecule of mRNA
-Occurs in G1 of interphase
-Only one strand is used as the template strand
- A,U,C,G
-Ribose

DNA replication
-Involves whole molecule
-DNA polymerase
-Produces two molecules of DNA
-S phase
-Both DNA strands are templates
-A,T,C,G
-Deoxyribose

55
Q

What is meant by the ‘Amino acid code is degenerate’

A

The amino acid code being degenerate and how is the DNA molecule degenerate: Some amino acids have more than one triplet code, for example valine has four codons

56
Q

How is the genetic code degenerate

A

There are 64 possible combinations of bases (4 bases in groups of 3, so 43 ) but only 20 amino acids (plus stop codons); as there are more than 21 triplets, some amino acids are coded by more than one triplet

57
Q

How is the genetic code being degenerate advantageous to living organisms

A

Degeneracy reduces the effects of (point) mutations; so reduces changes to amino acid sequence of proteins (and therefore changes to tertiary structure

58
Q

Macromoleule / Polynucleotide

A

A large organic molecule
Larg molecule containing many nucleotides

59
Q

How does the structure of the DNA molecule enable it to perform its function

A

Two strands make it stable
-the bases are located inside the sugar–phosphate backbones, and so they are protected and the integrity of the code is maintained
-molecules are long, so they can store a lot of genetic information
-the hydrogen bonds between the bases can break, enabling the molecule to unzip for transcription and replication.

60
Q

Gyrase/Helicase/ DNA polymerase

A

Gyrase - unwinds the DNA molecule
Helicase – Unzips the DNA molecule / Catalyses the breaking of hydrogen bonds between the complimentary pairs in the DNA molecule
DNA polymerase – Catalyses the formation of phosphodiester bonds / Catalyses the addition of new nucleotides to both old strands

61
Q

If the melhson and Stahl experiment got repeated a 4th time what would the results produce

A

One-eighth hybrid and seven-eighths light

62
Q

If the replication of the DNA was dispersive what would the results have produced

A

All would have been hybrid, but the band would be slightly higher in the tube, as more nucleotides of each new molecule would contain 14N.

63
Q

Where do the free nucleotides from the nucleoplasm come from

A

6) From food. As all food is derived from living organisms, it will contain DNA. We have enzymes called nucleases to digest DNA to nucleotides, and nucleotidase enzymes to break down nucleotides to bases, sugars and phosphates.

64
Q

When is the DNA most likely to mutate

A

During interphase when the DNA replicates, before the cell enters mitosis or meiosis

65
Q

What stains are used to show the distribution of DNA/RNA in a cell

A

DNA - methyl green
RNA - pyronin

66
Q

Experiment to show the distribution of RNA/DNA in a cell

A

1) Using a sharp knife cut a fixed root in longitudinal sections about 3mm long
2) Place under a microscope slide and cover with methyl green-pyronin stain for 30 mins
3) Use a pipette to remove the stain and add distilled water to the root tips
4) Change the water several times to wash the root tip sections
5) Add a drop of distilled water and then add a cover-slip
6) Observe cells under low power then high power
7) Should see DNA stained blue-green in the nuclei of the cells and RNA stained red in the cytoplasm

67
Q

During which physiological process is the ATP needed for protein synthesis made in cells

A

Respiration

68
Q

List all the organelles used within a cell that is carrying out protein synthesis and for each briefly describe its process

A

Ribosomes – act as catalysts, allowing (two) amino acids to align so that a peptide bond forms between them Nucleus/nucleolus – where mRNA is made (tRNAs and ribosomes are also made there) Endoplasmic reticulum – newly made proteins pass into the cisternae and go to the
Golgi apparatus to be modified/finished Mitochondria – make ATP.

69
Q

How are ribosomes catalysts

A

They are unchanged at the end of the reaction. They allow (two) amino acids to come close together, so that a peptide bond can form between them. This makes protein synthesis much quicker than by random association

70
Q

RNA polymerase vs DNA polymerase

A

RNA polymerase
-makes (mRNA; tRNA ; rRNA)
-transcription
-one short section of DNA used

DNA polymerase:
-DNA replication
-Semi conservative
-Before nuclear division

Foundations (5 decks)

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