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MPW biology > 2.1.3 Nucleotides and nucleic acids > Flashcards

2.1.3 Nucleotides and nucleic acids Flashcards

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1
Q

what is included in a nucleotide?

A
  1. A pentose sugar
  2. One phospahte group
  3. A nitrogenous base
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2
Q

Draw a necleotide

A
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3
Q

what are the two types of nitrogenous base

A

Purines and Pyramidines

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4
Q

What bases are purines?

A

Adenine and Guanine

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5
Q

what baseses are pyramidines?

A

In DNA: cytosine or thymine
In RNA: cytosine or uracil

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6
Q

what is a purine

A

Purine bases are larger in size, with a structure consisting of two rings fused together

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7
Q

what is a pyramidine?

A

Pyrimidine bases are smaller in size, with a single ring structure.

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8
Q

what forms between the bases in DNA?

A

Hydrogen bonds

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9
Q

what do you call the bonding between bases? and why?

A

complementary bonding, because of the specific number of hydrogen bonds formed

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10
Q

how to rememember what bases are purines

A

Angels and Gods are pure

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11
Q

how to rememember what bases are pyramdines

A

you just do lmao

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12
Q

What does A bond with?

A

DNA : T
RNA: U

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13
Q

what does T bond with

A

A

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14
Q

What does G bond with

A

C

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15
Q

What does C bond with?

A

G

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16
Q

how any hydrogen bonds between A and T or A and U

A

2 hydrogen bonds

(U sounds like two)

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17
Q

how any hydrogen bonds between C and G

A

3 hydorgen bonds

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18
Q

what is ATP?

A

the energy currency molecule of living cells

modified nucleotide

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19
Q

How does ATP release energy?

A

The ATP molecule is hydrolysed, such that one of the phosphate groups is released (requiring a molecule of water and an enzyme called ATPase); the hydrolysis of ATP releases energy

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20
Q

write the equation for the production and hyrolysis of ATP

A

ADP + Pi (inorganic phosphate) ATP + H2O

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21
Q

ADP, what does it include, and draw it.

A

ribose, ADENINE and two phosphate groups.

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22
Q

ATP, what does it include, and draw it.

A

ribose, ADENINE and three phosphate groups.
look in notes for drawing

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23
Q

what is a polynucleotide and how do they form?

A

Many individual nucleotides joined together, formed via condensation reactions

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24
Q

what bond is present in a polynucleotide

A

phosphodiester bonds.

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25
Q

what are polynucleotide also refered as?

A

nucleic acids

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26
Q

what enzyme is used when catalysing the formation of DNA?

A

DNA polymerase

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27
Q

what enzyme is used when catalysing the formation of RNA?

A

RNA polymerase

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28
Q

What reaction breaks down polynucletide and what enzymes are used?

A

hydrolysis reactions, which use molecules of water to break the phosphodiester bonds between the nucleotide monomers.

DNAse or RNAse enzyme.

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29
Q

label this

A

look in notes

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30
Q

what is the strucutre of DNA?

A

Double helix (Spiral arrangement), with 10 base pairs per double helix.

Sugar-phosphate backbone - structural and protective role

Anti-parallel, with 5’ and 3’ on one end and 3’ and 5’ on the other end

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31
Q

where is the genetic code carried?

A

the genetic code itself is carried by the sequence of bases which (as complementary pairs) occupy the core of the helix.

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32
Q

what are the 8 steps of DNA purification by precipitation

A
  1. Keep temperature low throughout to reduce (nuclease) enzyme activity so that the DNA is not broken down;
  2. If applicable (i.e. for plant tissues), cell walls are mechanically broken by grinding with pestle and mortar or the use of a blender;
  3. Detergent is added to disrupt the structure and hence increase the permeability of the
    plasma membrane and nuclear envelope, releasing the DNA;
  4. RNAse enzyme is added to hydrolyse and thus remove any RNA that is associated with the DNA;
  5. Protease hydrolyses the histone proteins that the (eukaryotic) DNA is wound around;
  6. Salt is added to help the BREAK HYDROGEN BONDS BETWEEN WATER AND DNA and therefore precipitate readily;
  7. Ethanol is added to precipitate the DNA, i.e. cause it to come out of solution;
  8. Finally, the precipitated DNA is ‘spooled’ onto (i.e. twisted around) a glass rod in order to lift it out of the solution.
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33
Q

where in the cell cycle does DNA replication occur?

A

interphase

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34
Q

what is the overall premise of semi conservative replication?

A

Two product DNA molecules that are generated will contain one old (i.e. conserved or original) strand and one newly synthesised strand (which is complementary to the old strand).

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35
Q

3 steps of semi convservative replication

A
  1. An enzyme called DNA helicase attaches to the DNA and unwinds the helix of the DNA molecule, whilst also breaking the hydrogen bonds between the complementary base pairs (‘unzipping’ the DNA). The helicase starts from one end of the chromosome and works its way all the way along to the other end. The region in which the strands are presently being separated is called the replication fork; behind the replication fork, the DNA is now in the form of two separate single strands;
  2. Both original strands now simultaneously act as templates, onto which new,
    complementary DNA strands are synthesised from free DNA nucleotides. First, the free DNA nucleotides attach to the template strand via hydrogen bonding between
    complementary pairs of bases. For example, a free DNA nucleotide containing base G will bind to a nucleotide on the template strand containing base C. The number of hydrogen (H) bonds between a C‐G base pair is three; A‐T pairs form two H bonds.
  3. The enzyme DNA polymerase now joins the correctly base‐paired nucleotides together, forming a new, continuous polynucleotide strand. This strand is complementary to the original strand that was used as a template (and identical in base sequence to the strand present previously). The new bonds formed by DNA polymerase are called phosphodiester bonds; these are between the phosphate group of one nucleotide and the deoxyribose sugar of the next nucleotide. The phosphodiester bonds
    form via condensation reactions (i.e. a new bond is formed and a molecule of water is produced). DNA polymerase ensures that the correctly base paired nucleotides are all joined together to form the new strand, with a continuous sugar‐phosphate backbone.
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36
Q

What are prime endings

A

A further detail to be aware of is that DNA polymerase can only add nucleotides to a free 3’ end of a strand, hence the synthesis of a new DNA strand has to be 5’ to 3’ on both template strands.

However, since the two template strands are antiparallel to one another, this results in a leading strand (that is made continuously) and a lagging strand (made discontinuously as a series of short Okazaki fragments which have to be joined later by DNA ligase enzyme).

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37
Q

what is a mutation?

A

gene mutation is a random change to the DNA base sequence of a gene

38
Q

how do we describe mutations?

A

random and spontanous

39
Q

what is a mutagen?

A

Factors which increase the chance of mutation, e.g ionizing radiation

40
Q

what is a substitution mutation?

A

one (or more) bases are exchanged for bases of a different type

41
Q

what can occur due a substitution mutation?

A

1) No consequences, due to the degeneracy of the gentetic code, where multiplet triplet code for the same amino acid, there may be no change in terms of the protein strucutre, this is a SILENT mutation
2) Slight mutation, where the triplet is changed and now codes for a different amino acid, the primary strcutre of the protein will change, therefre resulting in different folding in the secondary and tertiary strucutre. The protein will still function, however will not be as functional

42
Q

what is a deletion mutation?

A

one (or more) bases are removed from the gene (without being replaced).
This leads to a shorter gene (fewer triplets) and so the encoded polypeptide will have fewer amino acids.

43
Q

what can occur due to a deletion mutation?

A

If the number of bases deleted is not a multiple of three (e.g. if 1, 2,
4 or 5 bases are deleted), then a phenomenon called frameshift occurs as a
consequence of the deletion mutation

44
Q

what is a Insertion/addition mutation?

A 
one (or more) bases are inserted into the gene. This results in a 
longer gene (more triplets) and so the encoded polypeptide will have more amino acids.
45
Q

what can occur due to a Insertion/addition mutation?

A

If the number of bases inserted is not a multiple of three (e.g. if 1, 2, 4 or 5 bases are inserted), then frameshift occurs as a consequence of the insertion mutation

46
Q

what is a point mutation?

A

this is when only a single base is substituted, deleted or inserted.

47
Q

what is a frameshift

A

this occurs when a number of bases is deleted from or inserted into a
gene, that is not a multiple of three (e.g. 1, 2, 4, 5, 7, 8, 10, 11 bases etc); the
consequence is that the way the triplets are grouped is altered (shifted) from the mutation position onwards. We say that the ‘reading frame’ of the gene has been altered.
All triplets beyond that point will become different, hence the sequence of triplets now codes for a different amino acid sequence. The gene will now code for a protein with a very different primary structure and hence a very different 3D shape (tertiary structure). This usually means that protein encoded by the gene is non‐functional, having a negative effect on the organism.

48
Q

what is the definition of the genetic code?

A

The genetic code is the way in which a DNA base/nucleotide sequence specifies (codes for) a specific amino acid sequence. Each triplet (group of three bases) encodes one specific amino acid, hence the sequence of triplets in a gene determines the amino acid sequence (primary structure) of the encoded polypeptide.

49
Q

how do we describe the genetic code?

A

The genetic code is a non‐overlapping, degenerate triplet code, which is (almost) universal across all known living organisms

50
Q

is the genetic code universal?

A

yes

51
Q

what is the triplet code?

A

A sequence of three nitogenous bases, called a codon. Each codon codes for an amino acid.

52
Q

what is the group of three consecutive bases which codes for one amino acid is called in DNA?

A

A triplet/codon

53
Q

what is the group of three consecutive bases which codes for one amino acid is called in RNA?

A

A codon

54
Q

What does non-overlapping code mean?

A

Each base is only a member of one triplet/codon;

55
Q

what is the significance of the code not overlapping?

A

no restriction as to which triplet can follow any previous triplet; this in turn means any amino acid sequence can be encoded.

56
Q

what would occur if the triplets overlapped?

A

If the code overlapped, each base could be part of up to three triplets, hugely restrict which triplet can follow a specific previous triplet

57
Q

how many triplet combinations are there, and how many amino acids are there? What does this mean?

A

64 triplets (4x4x4), 20 amino acids, this means that several different triplets which all code for the same type of amino acid

58
Q

what does degenerate mean?

A

several different triplets which all code for the same type of amino acid

59
Q

what is a consequence of degeneracy?

A

sometimes a mutation (a change to the DNA base sequence) can occur and yet have no consequence in terms of the encoded amino acid sequence, also known as silent mutations.

60
Q

what does univerasal gene code mean?

A

a particular triplet always encodes the same type of amino acid in any living organism.

61
Q

why is the universal code significant? There are 3 points

A
  1. It is strong evidence that life has only arisen once on Earth and that all organisms alive today have evolved from a common ancestor (a small, simple early life form).
  2. It suggests that deviations in the genetic code (e.g. arising through mutation) were always detrimental to the survival chances of the affected organisms. Hence only organisms with the ‘correct’ version of the code ever survived and reproduced; this has led to the genetic code being highly conserved across all kingdoms of living organisms. (Natural Selection)
  3. It means that genetic engineering is possible, i.e. a gene can be deliberately transferred from one species to another and its base sequence will still encode the same amino acid
    sequence.
62
Q

How does a gene determine the sequence of amino acids in a polypeptide

A

A gene is a sequence of DNA nucleotides which codes for a polypeptide. Specifically, each triplet of three nucleotides codes for one specific amino acid, hence the sequence of triplets determines the sequence in which amino acids are joined together to build the
polypeptide, also known as the primary structure of the protein.

63
Q

what is a gene?

A

a section of DNA which contains the complete sequence of bases (triplets) to code for a specific protein

64
Q

when and where is mRNA produced?

A

during transcription in the nucleus

65
Q

what is the function of mRNA?

A

An mRNA molecule is a copy of one specific gene, the mRNA is small enough to be able to leave the nucleus.
The mRNA molecule therefore carries the instructions for protein synthesis out of the nucleus to a ribosome in the cytoplasm

66
Q

Is DNA the same as mRNA codon or tRNA anticode?

A

tRNA anticode

67
Q

what is the function of rRNA?

A

It forms part of the structure of a ribosome. Ribosomes are made of both rRNA and protein.

68
Q

what is the function of tRNA?

A 
Transfer RNA (tRNA) molecules are responsible for bringing the correct amino acids to the ribosome during the TRANSLATION stage of protein synthesis.
There are many different tRNAs each different type of tRNA has a different anticodon, i.e. a specific sequence of three bases (found at one end of the tRNA molecule). Each tRNA can attach to a specific type of amino acid,
which it carries to the ribosome to be incorporated into the new polypeptide chain.
69
Q

draw a tRNA molecule

A

look notes

70
Q

what shape is a tRNA molecule?

A

clover leaf

71
Q

what in on a tRNA molecule?

A

anticodons of 3 bases, to bind to complementary condon on mRNA in the ribosome

72
Q

Is tRNA double or single stranded?

A

Single stranded, formed by intermolecular complemetary base pairing

73
Q

there are x amount of tRNA molecules, why not 64?

A

61 tRNA molecules, not 64 becuase 3 of the mRNA codons are stop codons which dont code for any amino acids.

74
Q

what is a stop codon

A

a triplet base pair which doesnt code for any amino acids

75
Q

what is the definition for protein synthesis?

A

Protein synthesis is the general term for the cellular processes which lead to the production of a particular polypeptide/protein. There are two key stagesinvolved in protein synthesis, called transcription and translation.

76
Q

Basic description of Transcription

A

Transcription is the first stage in protein synthesis; it takes place in the nucleus. During transcription, an mRNA copy of a specific gene is produced.
This mRNA molecule contains a base sequence which codes for production of a specific polypeptide.
The mRNA leaves the nucleus, in order to attach to a ribosome in the cytoplasm so that translation can take place (i.e. the synthesis of the polypeptide encoded by the mRNA).

77
Q

Basic description of translation

A

Translation is the second stage of protein synthesis. It takes place in the cytoplasm, carried out by ribosomes. In a eukaryotic cell, the ‘free’ ribosomes in the cytoplasm synthesise proteins which will remain in that cell; the ribosomes attached to the RER make proteins which are
destined to be incorporated into the cell surface membrane or which will later be secreted from the cell by exocytosis.
In translation, a ribosome attaches to a molecule of mRNA, which contains the sequence of codons that specifies the amino acid sequence of the protein which will be synthesised. The ribosome moves along the mRNA, ‘reading’ the codons; molecules of tRNA bring specific amino acids to the ribosome, to be joined together via peptide bonds to become the primary structure of the protein.

78
Q

order of protein synthesis

A

DNA replication, transcription, translation

79
Q

6 steps of Transcription

A
  1. The enzyme DNA helicase unwinds the double helix of the DNA and breaks the hydrogen bonds between the complementary base pairs. This just occurs for the length of one gene (i.e. not the entire chromosome). The DNA is now single‐stranded, for the length of that gene only.
  2. One of the two DNA strands (only) now acts as a template for the production of an mRNA copy of the gene; this is called the template strand (also known as the antisense or non‐coding strand). The other DNA strand (known as the sense or coding strand) plays no part in transcription.
  3. Free RNA nucleotides line up on the template strand, their bases forming complementary base pairs with the bases on the DNA template strand, via hydrogen bonding. An RNA nucleotide containing the base C will pair with a G base on the DNA template strand, a G will pair with C, an A will pair with T and an RNA nucleotide containing U (uracil) will pair with an A on the DNA template strand.
  4. The enzyme RNA polymerase catalyses the formation of phosphodiester bonds (in condensation reactions) in order to join each RNA nucleotide to the preceding one. The
    RNA polymerase enzyme will only join RNA nucleotides together that are already correctly base‐paired with the bases on the DNA template strand. Hence a continuous RNA polynucleotide, with a sugar‐phosphate backbone, is synthesised; this is the mRNA molecule. The mRNA is a single‐stranded copy of the gene.
  5. Once the mRNA molecule is complete (i.e. the entire length of the gene has been copied), it detaches from the DNA template strand.
  6. The mRNA molecule now leaves the nucleus via a nuclear pore and moves into the cytoplasm. A ribosome will attach to the mRNA in order to commence the second stage of protein synthesis, translation. Meanwhile in the nucleus, the gene itself may be transcribed again, to produce more copies of this mRNA; if no more mRNA copies of the gene are required, the hydrogen bonds between the complementary base pairs and the double helix of the gene’s DNA will be restored.
80
Q

15 steps of translation

A
  1. A molecule of mRNA has been produced via transcription and has left the nucleus via a
    nuclear pore. This mRNA carries a sequence of codons which codes for the amino acid
    sequence of the specific protein which will now be synthesised by translation. (Each mRNA
    codon of three bases codes for one specific amino acid.) This mRNA moves into the cytoplasm;
    a ribosome attaches to the mRNA, at the start codon (which is always AUG).
  2. There are two binding sites for tRNA molecules within the ribosome, because two mRNA
    codons (i.e. six bases) are held within the ribosome at one time.
  3. The first tRNA arrives; it is carrying a specific amino acid and has an anticodon of three
    bases which are complementary to the first codon of the mRNA. The anticodon of the tRNA
    binds to the complementary mRNA codon, via hydrogen bonding between complementary
    bases pairs.
  4. The second tRNA arrives, occupying the second binding site within the ribosome; it is
    carrying a specific amino acid. The anticodon of this tRNA binds to the second codon of the
    mRNA, via hydrogen bonding between complementary pairs of bases.
  5. Now that two tRNA molecules are sitting side by side within the ribosome, the amino acids
    they are carrying are brought into close proximity. An enzyme called peptidyl transferase
    catalyses the formation of a peptide bond between the two amino acids, via a condensation
    reaction (which also releases a molecule of water). The peptidyl transferase enzyme is part of
    the ribosome.
  6. As the peptide bond is forming, the first amino acid is released from the first tRNA. The
    second tRNA is still carrying its amino acid, but this is now joined to the first amino acid as a
    dipeptide.
  7. The ribosome moves along the mRNA by a distance of one codon. This causes the first tRNA
    to be released back into the cytoplasm. (It will be reused, i.e. another amino acid of the same
    specific type will be attached to it.)
  8. The third codon of the mRNA has now been brought into the ribosome. A tRNA, carrying a
    specific amino acid, will arrive and its anticodon will bind to the mRNA codon, via hydrogen
    bonds between complementary bases.
  9. A peptide bond forms between the amino acid carried by this (third) tRNA and the amino
    acid which is still attached to the second tRNA, forming a tripeptide. The reaction is catalysed
    by peptidyl transferase.
  10. The ribosome moves along the mRNA by a distance of one codon, causing the release of
    the second tRNA (which has released its amino acid); the fourth mRNA codon is now brought
    within the ribosome.
  11. The process repeats, with further amino acids being added to the chain, forming a
    polypeptide. Each mRNA codon codes for one specific type of amino acid, hence the order of
    mRNA codons has determined the order in which amino acids have been joined in the
    polypeptide chain, i.e. the primary structure of the protein).
  12. Eventually, the ribosome reaches a stop codon in the mRNA. This codon does not code for
    any amino acid, hence it marks the end of the translation of the encoded polypeptide. The
    ribosome now detaches from the mRNA and the polypeptide chain, now complete, is also
    released.
  13. The secondary structures of the protein begin to fold even before the complete polypeptide
    has been synthesised: some parts of the chain coil into α‐helix, whilst other parts fold back on
    themselves to form β‐pleated sheet. These secondary structures are held in place by hydrogen
    bonding between δ+ hydrogen atoms (from N‐H groups) and δ‐ oxygen atoms (from C=O
    groups) that are found in different parts of the backbone of the same polypeptide chain.
  14. Tertiary structure may also start to form before the synthesis of the polypeptide chain is
    complete. Tertiary structure is the further folding of the polypeptide chain (which has already
    formed regions secondary structure) into its final 3D shape. The types of amino acid R groups
    present determine which types of bonding form; this in turn determines the tertiary structure
    (3D shape) that forms. The relevant types of bond between R groups include disulphide
    bridges, hydrogen bonding, ionic bonding and hydrophobic interactions.
  15. Many proteins are not complete and functional until they have gone further (posttranslational)
    modifications or processing. These modifications typically occur in the Golgi
    apparatus; newly synthesised proteins are transported to the Golgi in vesicles. The types of
    modification that can occur include: attachment of a prosthetic group (e.g. a haem group),
    association of more than one polypeptide chain to form a protein with quaternary structure
    and attachment of carbohydrate to a protein to form glycoprotein. Specific amino acids may
    also be removed from a protein to produce its final, functional form.
81
Q

where does trascription occur

A

In the nucleus

82
Q

where does translation occur

A

ribsoomes in the cytoplasm or RER

83
Q

Where are free nucleotides used only?

A

transcription

84
Q

which RNA moleucles used in transcription?

A

mRNA only

85
Q

which RNA moleucles used in transcription?

A

mRNA, tRNA, and rRNA

86
Q

What is vital before translation can occur?

A

Before translation can begin, a process called activation of amino acids must occur (also referred to as charging of the tRNA molecules). This is an enzyme‐catalysed reaction in which each tRNA (which has a specific anticodon) is attached to its corresponding amino acid. The reaction takes place in the cytoplasm and requires ATP. It is crucial that each tRNA is carrying the appropriate type of amino acid; the role of the tRNA molecules in translation is to bring the correct amino acids to the ribosome, to be joined
together in the sequence encoded by the mRNA codon sequence.

87
Q

why do a purine go with a pyramidine?

A

to maintain a constant diameter in DNA

88
Q

How long is one helix?

A

10 bases

89
Q

what pentose sugar is dna?

A

deoxyrbose

90
Q

what pentiose sugar is RNA and ATP?

A

rIBOSE

MPW biology (26 decks)

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