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Biology > Nucleotides, Nucleic acids and enzymes > Flashcards

Nucleotides, Nucleic acids and enzymes Flashcards

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1
Q

What is a nucleotide made from

A
  • Pentose sugar (5 carbon atoms)
  • Nitrogenous base (nitrogen containing)
  • Phosphate group
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2
Q

What elements are found in nucleotides

A

C,H, O, N, P

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3
Q

Why are nucleotides important

A

They are monomers that make up DNA and RNA and therefore a form of nucleic acid. DNA stores genetic information and RNA is used to make proteins

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4
Q

What is the sugar in DNA called

A

Deoxyribose

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5
Q

What is the pentose sugar in a DNA nucleotide called

A

Deoxyribose

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6
Q

What does each DNA nucleotide have

A

Same sugar and a phosphate group but the base can vary

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7
Q

What type of bases are adenine and guanine

A

Purine

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8
Q

What type of bases are cytosine and thymine

A

Pyrimidine

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9
Q

What does a purine contain

A

Two carbon-nitrogen rings joined together

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10
Q

What does a pyrimidine contain

A

One carbon-nitrogen ring so is smaller than a purine base

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11
Q

What does a molecule of DNA contain

A

Two polynucleotide chains made up of lots of nucleotides joined together

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12
Q

What is the sugar in RNA called

A

Ribose

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13
Q

What does RNA contain

A

A phosphate group and one of four bases

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14
Q

What is an RNA molecule made up form

A

A single polynucleotide chain

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15
Q

What does it mean to phosphorylate a nucleotide

A

Adding one or more phosphate groups to it

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15
Q

What is ADP and what does it contain

A

Adenosine diphosphate and contains adenine, the sugar ribose and two phosphate groups

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16
Q

What is ATP and what does it contain

A

Adenosine triphosphate and contains adenine, the sugar ribose and three phosphate group

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17
Q

How is ATP synthesized

A

From ADP and inorganic phosphate (P) using energy from an energy-releasing reaction. ADP is phosphorylated to form ATP and a phosphate bond is formed

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18
Q

Where is energy stored and released

A

Stored in the phosphate bond and is released when ATP is broken back down into ADP and inorganic phosphate.

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19
Q

What do nucleotides join together to form and how

A

Polynucleotides are joined between the phosphate group of one nucleotide and the sugar of another through a condensation reaction

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20
Q

What does nucleotides joining together form

A

Two ester bonds and a phosphate known as a phosphodiester bond

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21
Q

What is the sugars and phosphate known as

A

Sugar-phosphate backbone

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22
Q

How can polynucleotides be broken down

A

Hydrolysis

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23
Q

How many hydrogen bonds form between adenine and thymine

A

2

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24
Q

How many hydrogen bonds form between cytosine and guanine

A

3

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25
Q

What twists to form a double helix DNA

A

Two antiparallel polynucleotide strands

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26
Q

How do you purify DNA

A

Precipitation reaction
1) Break up cells in the sample using a blender
2) Make a solution of detergent, sodium chloride (salt) and distilled water
3) Add cells to beaker in a water bath at 60 degrees for 15 minutes
4) Put the beaker in an ice bath to cool the mixture down and filter into a clean boiling tube
5) Add protease enzymes to break down proteins
6) Dribble some cold ethanol down the side of tube to form a layer on top
7) DNA will form as a white precipitate

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27
Q

Stages of DNA replication

A

1) DNA helicase breaks the hydrogen bonds between the two nucleotide DNA strands. The helix unzips and forms two single strands

2) Each original single strand acts as a template for a new strand. Free-floating DNA nucleotides join to the exposed bases on each original template strand by complementary base pairing

3) The nucleotides of the new strand are joined together by the enzyme DNA polymerase forming the sugar-phosphate backbone. Hydrogen bonds form between the bases on the original and new strand forming a double-helix

4) Each new DNA molecule contains one strand from the original DNA molecule and one new strand

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28
Q

What is semi-conservative replication

A

When half of the strands in each new DNA molecule are from the original piece of DNA

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29
Q

Why does DNA need to be replicated accurately

A

To make sure genetic information is conserved each time the cell is replicated

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30
Q

What does a mutation mean

A

A random spontaneous change in DNA base sequence as an abnormal protein is produced that may function better or not at all compared to the original one

31
Q

What is a gene

A

A sequence of DNA nucleotides that codes for a polypeptide forming the primary structure of a protein

32
Q

What is RNA

A

A single polyculeotide strand containing uracil as a base

33
Q

What is mRNA

A
  • Made in the nucleus
  • Three adjacent bases are a codon
  • Carries the genetic code from the DNA in the nucleus to the cytoplasm, where it is used to make a protein in translation
34
Q

What is tRNA

A
  • Found in the cytoplasm
  • Has an amino acid binding sit at one end and a sequence of three bases at the other called an anticodon
  • It carries the amino acids that are used to make proteins to the ribosomes during translation
35
Q

What is rRNA

A
  • Forms the two subunits in a ribosome
  • The ribosome moves along the mRNA strand during protein synthesis. The rRNA in the ribosome helps to catalyze the formation of peptide bonds between amino acids
36
Q

What is genetic code

A

The sequence of base triplets in DNA or mRNA which codes for specific amino acids

37
Q

Features of genetic code

A

Non-overlapping = each base triplet is read in sequence separate from the triplet before

Degenerate = there are more possible combinations of triplets than there are amino acids (20 but 64 possible triplets) meaning amino acids are coded for by more than one base triplet

Universal = the same base triplets will code for the same amino acid across all organisms

38
Q

What happens during transcription

A

1) This starts when RNA polymerase attaches to the DNA double helix at the start of a gene

2) The hydrogen bonds break separating the strands and the DNA uncoils

3) One of the strands is then used as a template to make an mRNA copy

4) The RNA polymerase lines up free RNA nucleotides along the template strand. Complementary base pairing means that the mRNA strand ends up being a complementary copy of the DNA template strand apart from T is replaced by U

5) Once the RNA nucleotides have paired with their specific bases they are joined together forming an mRNA molecule

6) The RNA polymerase moves along the DNA separating the strands and assembling the mRNA strand

7) The hydrogen bonds between the uncoiled strands of DNA re-form once the RNA polymerase has passed by and the strands coil back into a double-helix

8) When RNA polymerase reaches a stop codon it stops making mRNA and detaches from the DNA

9) The mRNA moves out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm

39
Q

What happens during translation

A

1) The mRNA attaches itself to a ribosome and tRNA molecules carry amino acids to the ribosome

2) A tRNA molecule, with an anticodon that’s complementary to the start codon on the mRNA, attaches itself to the mRNA by complementary base pairing

3) A second tRNA molecule attaches itself to the next codon on the mRNA in the same way

4) rRNA in the ribosome catalyzes the formation of a peptide bond between the two amino acids attached to the rRNA molecules. This joins the amino acids together. The first tRNA molecule moves away leaving its amino acid behind.

5) A third tRNA molecule binds to the next codon on the mRNA. Its amino acid binds to the first two and the second tRNA molecule moves away

6) This process continues producing a chain of linked amino acids until there’s a stop codon on the mRNA molecule

7) The polypeptide chain moves away from the ribosome and translation is complete

40
Q

What are enzymes

A

Biological catalysts that speed up reactions as the metabolic reactions are sped up. Their action can affect structure in an organism as well as functions

41
Q

Two type of enzyme action

A

Intracellular or extracellular

42
Q

Intracellular examples

A

Hydrogen peroxide is the toxic by-product of reaction that can kill cells

Catalase is an enzyme that works inside cells to catalase the breakdown of hydrogen peroxide to harmless oxygen and water

43
Q

Extracellular enzyme examples

A

Amylase and trypsin work both out of cells in the human digestive system

Amylase is found in saliva and catalyzes the hydrolysis of starch into maltose

Trypsin catalyzes the hydrolysis of peptide bonds turning big polypeptides into smaller ones and is produced in the pancreas secreted into the small intestine

44
Q

What type of proteins are enzymes

A

Globular

45
Q

What type of protein structure is an enzyme

A

Tertiary

46
Q

What do enzymes do to the activation energy

A

It reduces it allowing reactions to occur at lower temperatures speeding up the rate of reaction

47
Q

Why does the enzyme activation energy change

A

1) If two substrate molecules need to be joined attaching to the enzyme holds them close together reducing any repulsion between molecules

2) If the enzyme is catalyzing a breakdown reaction, fitting into the active site puts strain on bonds in the substrate meaning the molecule breaks up more easily

48
Q

Two Theory’s of enzyme fit

A

1) Lock and Key =They substrate fits perfectly to create an ESC and then when substrate leaves the enzyme is unchanged

2) Induced fit = Substrate does not have to be correct fit as the active site will change shape

49
Q

Impact of temperature on enzyme activity

A

The rise in temp means more vibrations between enzyme molecules until it reaches an optimum temp. Then the active site will change and no longer fit leading to the enzyme to denature

50
Q

What is Q10

A

The value to show how much the rate of reaction changes when temperature is raised by 10 degrees celcius

51
Q

Equation for calculating Q10

A

R2 (rate at higher temperature) /
R1 (rate at lower temperature)

52
Q

What does a value of 2 mean for Q10

A

The rate doubles when the temp is changed by 10 degrees

53
Q

How does pH affect enzyme activity

A

There is an optimum value most are at 7 except pepsin is 2 as is found in the stomach.

Above and below the optimum pH, H+ and OH- ions found in acids acids and alkalis can mess up the ionic bonds and hydrogen bonds holding the enzymes tertiary structure in place. Making the active site change shape so the enzyme is denatured

54
Q

How does enzyme concentration affect the rate of reaction

A

The more enzyme molecules there are in a solution, the more likely a substrate molecule is to collide with one and form an ESC. Therefore increasing Concentration increases ROR

However the amount of substrate is a limiting factor as there comes a point when there’s more than enough enzymes for substrate and has no further effect

55
Q

How does substrate concentration affect ROR

A

The higher the substrate concentration, the faster the reaction as more active sites will be used. This is only true until a ‘saturation’ point as there are only so may substrate molecule that the enzymes have and then all the active sites are full.

Substrate concentration decreases with time during a reaction so if all other variable remain the same, the ROR will decrease over time time making the initial ROR the highest

56
Q

How to measure the Rate of an enzyme controlled reaction using hydrogen peroxide solution

A

Catalase catalyzes the breakdown of hydrogen peroxide into oxygen and water as it is fed through a delivery tube to an upside down measuring cylinder. The amount of oxygen is then measured or the time for it to stop bubbling

57
Q

How to measure the Rate of an enzyme controlled reaction using starch solution and amylase enzyme

A

You can measure the disappearance of the substrate rather than appearance of the product as the mixture sampled is put in a drop of iodine in potassium iodide and timed till when the iodine solution no longer turns blue-black as the start has then been broken down

58
Q

How to investigate the effect of temperature on catalase activity

A

1) Set up boiling tubes containing the same volume and concentration of hydrogen peroxide, add equal volumes of a buffer solution to each tube

2) Set up the apparatus to measure the volume of oxygen produced form each boiling tube

3) Put each boiling tube in a water bath set to a a different temp e.g 10-40. And set up another tube of catalase

4) Use a pipette to add the same volume and concentration of catalase to each boiling tube

5) Record how much oxygen is produced in the first 60 seconds

6) Repeat the experiment at each temperature three times and calculate the mean

59
Q

What are cofactors

A

Substances that enzymes need to work, another non-protein substance

60
Q

What are inhibitors

A

Inhibit enzymes action such as poisons

61
Q

How do inorganic cofactors work

A

They help by helping the enzyme and substrate bind together, but do not directly participate in the reaction so are not used up or changed

62
Q

How do organic cofactors work

A

They are known as coenzymes and participate in the reaction and are changed by it

63
Q

What is a cofactor tightly bound to an enzyme

A

A prosthetic group

64
Q

What are non-competitive inhibitors

A

Molecules that bind to all the enzyme away from its active site known as the allosteric site. Causing the active site to change shape so the substrate will no longer be able to fit.

64
Q

What are competitive inhibitors

A

Have similar shat to that of the substrate molecules and compete with the substrate molecules to bind to the active site blocking it so that the substrates cannot fit.

How much it is inhibited is dependent on the relative concentrations of the inhibitor and substrate.

65
Q

What are irreversible inhibitors

A

Have strong covalent bonds where the inhibitor can’t be removed easily and the inhibition is irreversible

66
Q

What are reversible inhibitors

A

Have weaker hydrogen bonds or weak ionic bonds so the inhibitor can be removed and the inhibition is reversible

67
Q

Examples of drugs and metabolic poisons being enzyme inhibitors

A

1) Antiviral drugs such as HIV (reverse transcriptase inhibitors) inhibit the enzyme reverse transcriptase which catalyzes the replication of viral DNA preventing the virus replicating

2) Antibiotics such as penicillin inhibits the enzyme transpeptidase which catalyzes the formation of proteins in bacterial cell walls weakening the cell wall and preventing the bacterium from regulating so the cell bursts an the bacterium is killed.

3) Cyanide is an irreversible inhibitor of cytochrome C oxidase that catalyzes respiration reactions

4) Malonate inhibits succinate dehydrogenase

5) Arsenic inhibits the action of pyruvate dehydrogenase and enzyme that catalyzes respiration reactions

68
Q

What is a metabolic pathway

A

A series of connected metabolic reactions. The product of the first reaction takes part in the second and so on

69
Q

What is product inhibition

A

When enzymes are inhibited by the product of the reaction they catalyse

70
Q

What is end-product inhibition

A

When the final product in a metabolic pathway inhibits an enzyme that acts earlier on in the pathway

71
Q

Why is end-product inhibition useful

A

It regulates the pathway and controls the amount of end-product that gets made

72
Q

What are inactive precursors

A

Used in metabolic pathways to prevent damage to cells such as proteases are synthesized like this to stop protein damage

73
Q

What happens when the precursor molecule is removed

A

The enzyme is no longer inhibits and becomes active

Biology (20 decks)

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