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Biology A-Level -James > Chapter 2.3- Nucleic Acids > Flashcards

Chapter 2.3- Nucleic Acids Flashcards

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1
Q

What is a nucleotide?

A

molecule consisting of a five carbon sugar(pentose sugar), a phosphate group and a nitrogenous base

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2
Q

What carbon atom is the nitrogenous base linked to, and what carbon atom/s is the phosphate group linked to?

A
  • nitrogenous base is linked to carbon C1 (carbon 1)

- phosphate group is linked to either C5 or C3

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3
Q

What is a monomer?

A

molecule that when repeated makes up a polymer. Amino acids are the monomers of proteins. Nucleotides are the monomers of nucleic acids

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4
Q

What are nucleic acids?

A

macromolecules made out of units called nucleotides and come in two naturally occurring varieties; deoxyribonucleic acid(DNA) and ribonucleic acid (RNA)

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5
Q

What is the function of DNA compared to RNA?

A
  • DNA is used to store the genetic information-the instructions an organism needs to grow and develop
  • RNA is used to make proteins from the instructions in DNA
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6
Q

How does the structure of DNA differ from RNA?

A
  • The pentose sugar in a DNA nucleotide is called deoxyribose whereas in RNA the pentose sugar is called ribose
  • DNA is made up of two polynucleotide chains, whereas RNA is made up of a single polynucleotide chain
  • In DNA the four nitrogenous bases are adenine (A), thymine(T), cytosine (C) and guanine (G). In RNA, URACIl replaces thymine as a base
  • DNA is a long molecule, whereas RNA is a shorter molecule
  • There are three forms of RNA; messenger RNA(mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA)
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7
Q

What is a phosphorylated nucleotide?

A

when the nucleotide contains more than one phosphate group

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8
Q

What is the full name of ATP?

A

adenosine triphosphate

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9
Q

What is the structure of ATP?

A
  • contains the base adenine
  • the sugar ribose
  • THREE phosphate groups
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10
Q

What is full name of ADP?

A

adenosine diphosphate

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11
Q

What is the structure of ADP?

A
  • contains the base adenine
  • the sugar ribose
  • TWO phosphate groups
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12
Q

What is the job of ATP and ADP within the body?

A
  • ATP provides the energy for chemical reactions in the cell
  • ATP is synthesised from ADP and inorganic phosphate (Pi) using the energy from a energy-releasing reaction, e.g. the breakdown of glucose in respiration. This is catalysed by the enzyme ATP synthase.
  • The ADP is phosphorylated to form ATP and a phosphate bond is formed
  • Energy is stored in the phosphate bond. When this energy is needed by a cell, ATP is broken back down into ADP and inorganic phosphate (Pi). Energy is released from the phosphate bond and used by the cell. This is catalysed by the enzyme ATP hydrolase
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13
Q

What is the full name of AMP?

A

adenosine monophosphate

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14
Q

Apart from being the monomers of nucleic acids and being responsible in the energy production within the body, what are the two other processes that use nucleotides?

A
  • nucleotides help regulate the metabolic pathways, for example by ATP, ADP and AMP
  • may be components of coenzymes. For example, NAD in respiration, NADP in photosynthesis, FAD in respiration and coenzyme A in respiration
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15
Q

What are pyrimidine and purine bases?

A
  • purine bases contain two carbon-nitrogen rings joined together
  • pyrimidine bases contain only one carbon-nitrogen ring
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16
Q

What nitrogenous bases are pyrimidine and which are purine?

A
  • adenine and guanine are purines

- cytosine and thymine and pyrimidines

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17
Q

What is adenosine made up of?

A
  • ribose sugar and adenine

- it is a nucleoside

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18
Q

What is the bond called that joins together the phosphate group and the 5 carbon sugar?

A
  • phosphodiester bond

- covalent bond formed in a condensation reaction

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19
Q

How do you break the phosphodiester bond in nucleotides?

A

adding water (hydrolysis)

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20
Q

What is a macromolecule?

A

molecule which is made up of a large number of atoms

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21
Q

What is the full name of DNA?

A

deoxyribonucleic acid

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22
Q

What is the structure of DNA?

A
  • consists of two polynucleotide strands, made up of nucleotides
  • the two strands run in opposite directions, so they are described as being anti-parallel
  • Each DNA nucleotide consists of a phosphate group, a five-carbon sugar called deoxyribose, and one of four nitrogenous bases: adenine, guanine, thymine or cytosine
  • very long so can carry a lot of encoded genetic information
  • covalent bond between sugar residue and the phosphate group in a nucleotide is called a phosphodiester bond formed in a condensation reaction
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23
Q

What is a polynucleotide?

A

large molecule containing many nucleotides

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24
Q

What is the bond that forms between the two antiparallel DNA strands joining them together?

A

hydrogen bonds

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25
Q

What nitrogenous bases pair up and form hydrogen bonds together in DNA?

A
  • adenine always pairs with thymine, by means of two hydrogen bonds
  • guanine always pairs with cytosine, by means of three hydrogen bonds
26
Q

Why does a purine always pair with a pyrimidine?

A

to give equal sized ‘rungs’ on the DNA ladder which can then twist, like twisting a rope ladder around an imaginary axis, into the double helix (coil). This gives the molecule more stability

27
Q

What is a double-helix?

A

shape of a DNA molecule, due to coiling of the two sugar-phosphate backbone strands into a right-handed spiral configuration

28
Q

What does the ‘opposite direction’ of the two strands refer to?

A

the direction that the third and fifth carbon molecules on the five-carbon sugar, deoxyribose, are facing

  • the 5’ end of the molecule is where the phosphate group is attached to the fifth carbon atom of the deoxyribose sugar
  • The 3’ end is where the phosphate group is attached to the third carbon atom of the deoxyribose sugar
29
Q

Where in the cell is DNA and RNA found?

A
  • DNA is found only in the nucleus

- RNA is found in both the nucleus and the cytoplasm

30
Q

How is DNA organised within eukaryotic cells?

A
  • each DNA molecule is tightly wound around histone proteins into chromosomes. Each chromosome is one molecule of DNA
  • mitochondria and chloroplasts contain a loop of DNA, without the histone proteins
31
Q

How is DNA organised within prokaryotic cells?

A
  • DNA is in a loop and is within the cytoplasm, not enclosed in a nucleus
  • not wound around histone proteins, and described as being naked DNA.
32
Q

What are the steps in extracting and purifying DNA by precipitation?

A
  • gather the thing that you want to extract DNA from
  • put it in a test tube and add salt and ethanol (so the DNA precipitates out of solution)
  • the DNA will then start to form clumps within the solution in the test tube
  • put the solution into a centrifuge which spins the solution around. This creates a force which forces all the DNA to the bottom of the tube and what you are left with is a tube full of liquid and a pellet (DNA) at the bottom of the tube.
33
Q

What are the ways in which the structure of the DNA molecule enables it to carry out its function?

A
  • two strands make it stable
  • bases are located within the sugar-phosphate backbone and so they are protected and the integrity of the code is maintained
  • the molecules are long so that they can store a lot of genetic information
  • hydrogen bonds between the bases can be broken which enables the molecule to unzip for transcription and replication
34
Q

What is meant by the genome of the cell?

A

all the DNA within a cell, which contains all the information required to make and maintain the organism that cells forms part of

35
Q

What stage in the cell cycle does DNA replicate?

A

interphase

36
Q

What is meant by the term semi-conservative replication?

A

how DNA replicates, resulting in two new molecules, each of which contains one old strand and one new strand. One old strand is concerned in each new molecule

37
Q

What is the role of the enzyme gyrase in DNA replication?

A

catalyses the unwinding of the DNA a bit at a time

38
Q

What is the role of DNA helicase?

A

unzips the DNA by breaking the hydrogen bonds between the nucleotide bases. Results in two single strands of DNA with exposed nucleotide bases

39
Q

After the DNA is unzipped, what happens next in DNA replication?

A

free phosphorylated nucleotides which are present in the nucleoplasm within the molecules, are bonded to the exposed bases by hydrogen bonds, following complimentary base-pairing rules

40
Q

What is the role of the DNA polymerase enzyme?

A

catalyses the addition of the new nucleotide bases, in the 5’ to 3’ direction, to the single strands of DNA; it uses each single strand of unzipped DNA as a template

41
Q

What is meant by the lagging (discontinuous) strand and the (continuous) leading strand?

A
  • the leading strand is synthesised continiously as the DNA polymerase catalyses the addition of nucleotide bases in the 5’ to 3’ direction
  • the lagging strand is synthesised in fragments as this DNA strand runs in the opposite direction (3’ to 5’ direction).
42
Q

What is the role of ligase enzymes?

A

joins the fragments of the lagging strand

43
Q

What provides the energy for the formation of phosphodiester bonds between the sugar residue of one nucleotide and the phosphate group of the next nucleotide?

A

hydrolysis of the activated nucleotides, which releases the extra phosphate group

44
Q

What is the chance that the wrong nucleotide is inserted during DNA replication?

A

1 in 10^8 base pairs

45
Q

Where do the free nucleotide bases in the nucleoplasm come from?

A
  • 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.
46
Q

What is meant by a gene?

A

a length of DNA that codes for a polypeptide or for a length of RNA that is involved in regulating gene expression

47
Q

What does the sequence of DNA base triplets within each gene code for?

A

-amino acid (primary structure of a protein)

48
Q

What is a protein?

A

a large polypeptide of 100 or more amino acids. However, the terms are often used synonymously, and insulin may be described as a small protein

49
Q

What is a polypeptide?

A

a polymer made of many amino acid units joined together by peptide bonds.

50
Q

Why is it important that the primary structure of a protein is correct?

A
  • primary structure determines the tertiary structure and shape of the protein which Is important because:
  • the shape of the active site of enzymes must be complimentary to the shape of the substrate molecule
  • part of an antibody molecule must have a shape complimentary to that of the antigens on the surface of an invading pathogen
  • receptor on a cell membrane must have a shape complementary to the shape of the cell-signalling molecule, such as a hormone or a drug, that it must detect
  • ion-channel protein must have hydrophilic amino acids lining the inside of the channel, and lipophilic amino acids on the outside portion that will be next to the lipid bilayer of the plasma membrane
51
Q

How is the genetic code universal?

A

in almost all living organisms the same triplet of DNA bases codes for the same amino acid

52
Q

Why is the genetic code described as being degenerate?

A

for all amino acids, except methionine and tryptophan, there is more than one base triplet which can code for the same amino acid

53
Q

Why is the genetic code described as being non-overlapping?

A
  • genetic code is read starting from a fixed point in groups of three bases.
  • if a base is added or deleted then it causes a frame shift, as every base triplet after that, and every amino acid, is changed
54
Q

What is the process of transcription?

A

the process of making messenger RNA from a DNA template

55
Q

What are the steps in transcription of a gene?

A
  1. gene unwinds and unzips(hydrogen bonds break)
  2. RNA polymerase catalyses temporary bonding between RNA nucleotides and DNA bases. The DNA strand is called the template strand
  3. A length of RNA that is complimentary to the template strand of the gene is produced. It is called the coding strand
  4. the mRNA then passes out of the nucleus, through the nuclear envelope, and attaches to a ribosome.
56
Q

Where are ribosomes made and how are they made?

A
  • Ribosomes (rRNA) are made in the nucleolus, in two smaller subunits ad pass separately out of the nucleus, through pores in the nuclear envelope, and then come together to form the ribosome. Mg^2+ help to bind the two subunits together.
57
Q

What is translation?

A

formation of a protein, at ribosomes, by assembling amino acids into a particular sequence according to the coded instructions carried from DNA to the ribosome by mRNA.

58
Q

Where in the cell does translation take place?

A
  • at ribosomes which can be found freely in the cell and code for proteins that are used within the cell
  • or at ribosomes which are found on the RER, where amino acids are made which are used outside the cell
59
Q

Where is transfer RNA (tRNA) made and what is its structure?

A
  • made in the nucleolus and pass out of the nucleus into the cytoplasm
  • single stranded polynucleotides, which can twist into a hairpin shape.
  • at one end is a trio of nucleotide bases that recognises and attaches to a specific amino acid
  • at the loop of the hairpin is another triplet of bases, called an anticodon, that is complimentary to a specific codon (triplet) of bases on the mRNA.
60
Q

What are the steps in translation?

A
  1. tRNA molecules bring the amino acids and find their place when the anticodon binds by temporary hydrogen bonds to the complimentary codon on the mRNA molecule on.
  2. As the ribosomes moves along the length of mRNA, it reads the code, and when two amino acids are adjacent to each other a peptide bond forms between them.
  3. After the polypeptide has been assembled, the mRNA breaks down. Its component molecules can be recycled into new lengths of mRNA, with different codon sequences
61
Q

What does a chaperone protein do?

A

newly synthesised polypeptide is helped to fold correctly into its 3D shape or tertiary structure

Biology A-Level -James (18 decks)

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