Nucleotides and Nucleic acids Flashcards

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1
Q

What is a nucleotide ?

A
  • DNA and RNA are nucleic acids: polymers that are made up of many repeating units (monomers) called nucleotides
  • Each nucleotide is formed from:
  • A pentose sugar (a sugar with 5 carbon atoms)
  • A nitrogen-containing organic base
  • A phosphate group
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2
Q

DNA nucleotide

A
  • DNA nucleotides - to store genetic information
  • The components of a DNA nucleotide are:
  • A deoxyribose sugar with hydrogen at the 2’ position
  • A phosphate group
  • One of four nitrogenous bases - adenine (A), cytosine(C), guanine(G) or thymine(T)
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3
Q

RNA nucleotide

A
  • The components of an RNA nucleotide are:
  • A ribose sugar with a hydroxyl (OH) group at the 2’ position
  • A phosphate group
  • One of four nitrogenous bases - adenine (A), cytosine(C), guanine(G) or uracil (U)
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4
Q

Why is RNA more susceptible to hydrolysis ?

A
  • The presence of the 2’ hydroxyl group makes RNA more susceptible to hydrolysis
  • This is why DNA is the storage molecule and RNA is the transport molecule with a shorter molecular lifespan
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5
Q

What are purines and pyridymines ?

A

Purines & pyrimidines
The nitrogenous base molecules that are found in the nucleotides of DNA (A, T, C, G) and RNA (A, U, C, G) occur in two structural forms: purines and pyrimidines
The bases adenine and guanine are purines – they have a double ring structure
The bases cytosine, thymine and uracil are pyrimidines – they have a single ring structure

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6
Q

What are the differences between DNA and RNA ?

A

-DNA has the bases of A,C,TG whereas RNA has A,C,U,G
- RNA has a ribose , DNA has a deoxyribose sugar

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7
Q

What is a phosphodiester bond ?

A
  • DNA and RNA are polymers (polynucleotides), meaning that they are made up of many nucleotides joined together in long chains
  • Separate nucleotides are joined together via condensation reactions
  • These condensation reactions occur between the phosphate group of one nucleotide and the pentose sugar of the next nucleotide
  • A condensation reaction between two nucleotides forms a phosphodiester bond
  • It is called a phosphodiester bond because it consists of a phosphate group and two ester bonds
  • The chain of alternating phosphate groups and pentose sugars produced as a result of many phosphodiester bonds is known as the sugar-phosphate backbone (of the DNA or RNA molecule)
  • As the synthesis of polynucleotides requires the formation of phosphodiester bonds, the same is true for the reverse process: the breakdown of polynucleotides requires the breakage of phosphodiester bonds
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8
Q

What is ATP?

A
  • Adenosine triphosphate (ATP) is the energy-carrying molecule that provides the energy to drive many processes inside living cells
  • ATP is another type of nucleic acid and hence it is structurally very similar to the nucleotides that make up DNA and RNA
    It is a phosphorylated nucleotide
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9
Q

DNA structure

A
  • DNA molecules are made up of two polynucleotide strands lying side by side, running in opposite directions – the strands are said to be antiparallel
  • Each DNA polynucleotide strand is made up of alternating deoxyribose sugars and phosphate groups bonded together to form the sugar-phosphate backbone. These bonds are covalent bonds known as phosphodiester bonds
    The phosphodiester bonds link the 5-carbon of one deoxyribose sugar molecule to the phosphate group from the same nucleotide, which is itself linked by another phosphodiester bond to the 3-carbon of the deoxyribose sugar molecule of the next nucleotide in the strand
  • Each DNA polynucleotide strand is said to have a 3’ end and a 5’ end (these numbers relate to which carbon on the pentose sugar could be bonded with another nucleotide)
    As the strands run in opposite directions (they are antiparallel), one is known as the 5’ to 3’ strand and the other is known as the 3’ to 5’ strand
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10
Q

Explain the hydrogen bonds

A

-The two antiparallel DNA polynucleotide strands that make up the DNA molecule are held together by hydrogen bonds between the nitrogenous bases
-These hydrogen bonds always occur between the same pairs of bases:
-The purine adenine (A) always pairs with the pyrimidine thymine (T) – two hydrogen bonds are formed between these bases
-The purine guanine (G) always pairs with the pyrimidine cytosine (C) – three hydrogen bonds are formed between these bases
-This is process is known as complementary base pairing and the pairs are known as complementary base pairs

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11
Q

What is the DNA structure ?

A

Double helix

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12
Q

What type of replication takes place (DNA)?

A

Semi - conservative replication

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13
Q

What is meant by the term ‘ semi- conservative replication’ ?

A
  • The process is called this because in each new DNA molecule produced, one of the polynucleotide DNA strands (half of the new DNA molecule) is from the original DNA molecule being copied
  • The other polynucleotide DNA strand (the other half of the new DNA molecule) has to be newly created by the cell
  • Therefore, the new DNA molecule has conserved half of the original DNA and then used this to create a new strand
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14
Q

What is the importance of retaining one original DNA strand ?

A
  • Retaining one original DNA strand ensures there is genetic continuity (i.e. genetic information is conserved) between generations of cells
  • In other words, it ensures that the new cells produced during cell division inherit all their genes from their parent cells
  • This is important because cells in our body are replaced regularly and therefore we need the new cells to be able to do the same role as the old ones
  • Replication of DNA and cell division also occurs during growth
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15
Q

What stage of the cell cycle does DNA replication take place ?

A

DNA replication occurs during the S phase of the cell cycle (which occurs during interphase, when a cell is not dividing)

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16
Q

What happens in DNA replication ?

A

-The enzyme DNA helicase unwinds the DNA double helix by breaking the hydrogen bonds between the base pairs on the two antiparallel polynucleotide DNA strands to form two single polynucleotide DNA strands. —The enzyme DNA gyrase unwinds the DNA
- The double helix structure unzips and unwinds
- There are free DNA nucleotides in the nucleus.
- The bases of the free floating nucleotides complimentary base pair with nucleotides on DNA template​ A-T,C-G (The Adenine - Thymine base pair is held together by 2 hydrogen bonds while the Guanine - Cytosine base pair is held together by 3 hydrogen bonds. )
- The new nucleotides are then joined together by the enzyme DNA polymerase which catalyses condensation reactions to form a new strand
- The original strand and the new strand join together through hydrogen bonding between base pairs to form the new DNA molecule
- This method of replicating DNA is known as semi-conservative replication because half of the original DNA molecule is kept (conserved) in each of the two new DNA molecules

17
Q

What is DNA polymerase ?

A

-The enzyme DNA polymerase synthesises new DNA strands from the two template strands
-It does this by catalysing condensation reactions between the deoxyribose sugar and phosphate groups of adjacent nucleotides within the new strands, creating the sugar-phosphate backbone of the new DNA strands
-DNA polymerase cleaves (breaks off) the two extra phosphates and uses the energy released to create the phosphodiester bonds (between adjacent nucleotides)

18
Q

What is a mutation ?

A
  • Although the process is astonishingly accurate considering it is happening constantly in cells and at a considerable speed, occasional mistakes occur in the form of:
  • Bases being inserted into the complementary strand in the wrong order
  • An extra base being inserted by accident
  • A base being left out by accident
  • These mistakes in the process of semi-conservative replication of DNA result in the occurrence of random, spontaneous mutations (i.e. errors in the genetic code)
19
Q

What is a gene ?

A
  • A gene is a sequence of nucleotides that forms part of a DNA molecule (one DNA molecule contains many genes)
20
Q

Do genes determine protein structure?

A
  • The genes in DNA molecules, therefore, control protein structure (and as a result, protein function) as they determine the exact sequence in which the amino acids join together when proteins are synthesised in a cell
21
Q

What is a triplet code ?

A

-The sequence of DNA nucleotide bases found within a gene is determined by a triplet (three-letter) code.
-Each sequence of three bases (i.e. each triplet of bases) in a gene codes for one amino acid
- These triplets codes for different amino acids – there are 20 different amino acids that cells use to make up different proteins.
For example:
-CAG codes for the amino acid valine
-TTC codes for the amino acid lysine
- Some of these triplets of bases code for start (TAC – methionine) and stop signals
- These start and stop signals tell the cell where individual genes start and stop
- As a result, the cell reads the DNA correctly and produces the correct sequences of amino acids (and therefore the correct protein molecules) that it requires to function properly

22
Q

What are the three important things about the genetic code ?

A
  • non-overlapping
  • degenerate
  • universal
23
Q

What is meant by non-overlapping ?

A

-Each base is only read once in which codon it is part of (don’t overlap)

24
Q

What is meant by degenerate ?

A

-Multiple codons can code for the same amino acids
-The degenerate nature of the genetic code can limit the effect of mutations

25
Q

What is meant by universal ?

A

-meaning that almost every organism uses the same code (there are a few rare and minor exceptions)
-The same triplet codes code for the same amino acids in all living things (meaning that genetic information is transferable between species)
-The universal nature of the genetic code is why genetic engineering (the transfer of genes from one species to another) is possible

26
Q

What is a codon?

A

-Once mRNA has been formed and left the nucleus it moves to the ribosomes where it can as a template for protein synthesis
-Each triplet within the mRNA code is described as a codon

27
Q

What is an anti-codon?

A

-The tRNA molecules that transfer amino acids possess anticodons which are complementary to the codons on mRNA

28
Q

What are the two stages of protein synthesis?

A

-Transcription – DNA is transcribed and an mRNA molecule is produced
-Translation – mRNA (messenger RNA) is translated and an amino acid sequence is produced

29
Q

What is transcription ?

A
  • This stage of protein synthesis occurs in the nucleus of the cell.
  • Part of a DNA molecule unwinds (the hydrogen bonds between the complementary base pairs break) , using DNA helicase.
  • The exposed gene can then be transcribed (the gene from which a particular polypeptide will be produced)
    -A complimentary copy of the code from the gene is made by building a single-stranded nucleic acid molecule known as mRNA (messenger RNA)
  • Free RNA nucleotides pair up (via hydrogen bonds) with their complementary (now exposed) bases on one strand (the template strand) of the ‘unzipped’ DNA molecule A-U (this is RNA)
  • The sugar-phosphate groups of these RNA nucleotides are then bonded together (by phosphodiester bonds) by the enzyme RNA polymerase to form the sugar-phosphate backbone of the mRNA molecule
  • When the gene has been transcribed (when the mRNA molecule is complete), the hydrogen bonds between the mRNA and DNA strands break and the double-stranded DNA molecule re-forms
  • The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope this is because DNA is too big
30
Q

Explain the direction of the strand

A

RNA polymerase moves along the template strand in the 3’ to 5’ direction
This means that the mRNA molecule grows in the 5’ to 3’ direction

31
Q

What is the difference between the the DNA coding strand and the DNA template strand?

A
  • The coding strand of DNA is the strand that codes for the gene of interest. — The template strand is complementary to this and can be transcribed to produce a piece of RNA with an identical nucleotide sequence to the coding strand (except T’s will be U’s in RNA).
32
Q

What is translation ?

A
  • Translation occurs in the cytoplasm of the cell
  • After leaving the nucleus via a nuclear pore, the mRNA molecule attaches to a ribosome
  • In the cytoplasm, there are free molecules of tRNA (transfer RNA)
  • 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 about 20 different tRNA molecules, each with a specific anticodon and specific amino acid binding site
  • The tRNA molecules bind with their specific amino acids (also in the cytoplasm) and bring them to the mRNA molecule on the ribosome
  • The triplet of bases (anticodon) on each tRNA molecule pairs with a complementary triplet (codon) on the mRNA molecule
  • Two tRNA molecules fit onto the ribosome at any one time, bringing the amino acid they are each carrying side by side
  • A peptide bond is then formed (via a condensation reaction) between the two amino acids
  • This process continues until a ‘stop’ codon on the mRNA molecule is reached – this acts as a signal for translation to stop and at this point the amino acid chain coded for by the mRNA molecule is complete
  • The amino acid chain then forms the final polypeptide