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nucleic acids Flashcards

1
Q

what are nucleic acids

A

nucleic acids are the most important molecules of which the best known are ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)

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2
Q

what is deoxyribonucleic acid (DNA)

A

DNA carries genetic information

The double helix structure of deoxyribonucleic acid makes it immediately recognisable

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3
Q

what is the monomer sub unit that makes up DNA

A

Despite its complex structure, DNA is made up of nucleotides that have just three basic compounds

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4
Q

what is the structure of a nucleotide

A

Individual nucleotides are made up of three component:

  1. a pentose sugar ( so called as it has five carbon atoms - glucose is a hexose sugar as it has six carbons)
  2. a phosphate
  3. a nitrogen - containing organic base.
    These are: cytosine C, thymine T, uracil U, adenine A and guanine G
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5
Q

how is the pentose sugar, phosphate group and organic base joined together

A

the pentose sugar and phosphate group and organic base are joined as a result of condensation reactions, to form a single nucleotide (mononucleotide)

Two mononucleotides may, in turn be joined as a result of a condensation reaction between the deoxyribose sugar of one mononucleotide and the phosphate group of another

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6
Q

what is the bond that is formed between two mononucleotides called

A

bond formed is called a phosphodiester bond

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7
Q

what is the new structure called when two mononucleotides bond together

A

dinucleotides

The continued linking of mononucleotides in this way forms a long chain known as a polynucleotide

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8
Q

what is the difference between DNA and proteins

A
  1. DNA is a sequence of bases
  2. proteins are a sequence of amino acids
  3. nucleotides join to form a polynucleotide
  4. amino acids join to form a polypeptide
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9
Q

what is ribonucleic acid/ what is its structure

A

ribonucleic acid is a polymer made up of nucleotides. It is a single, relatively short, polynucleotic chain in which the pentose sugar is always ribose and the organic bases are adenine A, guanine G, cytose C and uracil U

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10
Q

what is the function of ribonucleic acid (RNA)

A
  1. one type of RNA transfers genetic information from DNA to the ribosomes.

The ribosomes themselves are made up of proteins and another type of RNA

  1. another type of RNA is involved in protein synthesis
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11
Q

who worked out the structure of DNA

A

In 1953, James Watson and Francis Crick worked out the structure of DNA, following pioneering work by Rosalind Franklin on the X- ray diffraction patterns of DNA

this opened the door for many of the major developments in biology over the half - century

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12
Q

what is the structure of DNA

A
  • in DNA the pentose sugar is deoxyribose
  • the organic bases are adenine A, thymine T, guanine G, and cytosine C
  • it is made up of two strands of nucleotides ( polynucleotides)
    These strands are extremely long and they are joined together by hydrogen bonds between certain bases

In its simplified form, DNA can be thought of as a ladder which the phosphate and deoxyribose molecules alternate to form the “uprights” and the organic base pairs bond together to form the “rungs”

The uprights run in the opposite direction ( are anti -parallel)

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13
Q

what are the base pairings

A

bases on the two strands of DNA attract too each other by hydrogen bonds

The base pairings is specific:
- Adenine A always pairs with T thymine

-Guanine G always pairs with cytosine C

therefore that the quantities of adenine and thymine in DNA are always the same and so are the quantities of guanine and cytosine.
The ratio of A and : G and C varies from species to species

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14
Q

what is the double helix structure of a DNA

A

imagine the ladder like structure of the two polynucleic chains being twisted

The uprights of the phosphate and deoxyribose wind around one another to form a double helix.
The uprights form the structural backbone of the DNA molecule

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15
Q

what is the structure of DNA and how does it relate to its function

A

DNA is the hereditary material responsible for passing genetic info from cell to cell and generation to generation

  • It is a very stable structure which normally passes from generation to generation without significant change - most mutations are repaired, so persistent mutations are rare
  • its two strands are joined only with hydrogen bonds which allows them to separate during DNA replication and protein synthesis
  • It is an extremely large molecule and therefore carries an immense amount of genetic info
  • by having the base pairs within the helical cylinder of the deoxyribose - phosphate backbone, the genetic info is to some extent protected from being corrupted by outside chemical physical forces
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16
Q

what does the function of the DNA molecule depend on

A

the function of DNA molecule depends on the sequence of base pairs that it possess.

The sequence is important to everything it does

The base pairing leads to DNA being able to replicate and to transfer information as mRNA

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17
Q

how does the molecule DNA remain stable

A

DNA is a stable molecule because:

  • the phosphodiester backbone protects the more chemically reactive organic bases inside the double helix
  • hydrogen bonds link the organic base pairs forming bridges (rungs) between the phosphodiester uprights. As there are three hydrogen bonds between cytosine and guanine , the higher the proportion of C-G pairings, the more stable the DNA molecules
  • there are other interactive forces between the base pairs that hold the molecule together ( = base stacking)
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18
Q

what makes DNA molecules differ from one and other

A

-in every molecule of DNA, the phosphate group the deoxyribose and the four bases are always the same

what differs between one molecule and another are the proportions, and more importantly the sequence, of each of the four bases

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19
Q

how do other cells replicate

A

except for zygotes that are formed by cellular fusion, all of the cells that make up multicellular organisms are derived from existing cells by the process of division

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20
Q

what are the two main stages of cell division

A
  • nuclear division is the process by which the nucleus divides
    there are tow types of nuclear division, mitosis, meiosis

-cytokinesis follows nuclear division and is the process by which the whole cell divides

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21
Q

what must happen before a nucleus divides

A

before a nucleus divides its DNA must be replicated (copied)

This ensures that all daughter cells have a genetic information to produce the enzymes and other proteins that they need

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22
Q

how can we tell that the process of DNA replication is precise

A

the precise of DNA replication is clearly very precise because all the new cells are more or less genetically identical to the original one.

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23
Q

what is the semi-conservative replication

A

The process in which DNA replicates is called semi - conservative replication

  1. enzyme DNA helicase breaks the hydrogen bonds linking the base pairs
  2. As a result of the double helix separates into its two strands and unwind
  3. each exposed polynucleotide strand acts as a template to which the free nucleotides bind to complementary specific base pairings
  4. nucleotides are joined together in a condensation reaction by the enzyme DNA polymerase to form the “missing” polynucleotide strands of DNA
  5. each new DNA molecule contains one stand from the original DNA molecule and one new strand

This process is called “semi conservative replication”

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24
Q

what are the four requirements needed for semi - constructive replication

A
  • four types of nucleotide, each with their bases of A, G, C, T must be present
  • Both strands of the DNA molecule acts as a template for the attachment of these nucleotides
  • the DNA polymerase
  • a source of chemical energy is required to drive the process
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25
Q

what was the other theory of how DNA replicated

A

conservative

before Meselson and Stahl’s experiment, people were unsure whether DNA replicated was semi - conservative / conservative

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26
Q

what did Meselson and Stahl’s experiment show

A

Meselson and Stahl’s experiment showed that DNA is replicated using the semi-conservative method

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27
Q

what was the method behind Meselson and Stahl’s experiment

A
  1. Two samples of bacteria were grown from many generations one in a nutrient broth containing light nitrogen and one in a broth with heavy nitrogen
  2. a sample of DNA was taken from each batch of bacteria and spun in a centrifuge
    - the DNA from heavy nitrogen settled lower down the centrifuge tube
    - DNA from the light nitrogen bacteria settle higher up
  3. bacteria grown in heavy nitrogen broth were taken out and put in a broth containing only light nitrogen.
    - the bacteria were left for one round of DNA replication, and then another DNA sample was taken out and spun in the centrifuge
  4. as it turned out, the DNA settled in the middle showing that DNA molecules contained a mixture of heavy and light nitrogen
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28
Q

what should have happened in Meselson and Stahl’s experiment if DNA replicated conservatively

A

If replication was conservative, the original heavy DNA, which would still be together, would settle at the bottom and the new light DNA would settle at the top

-conservative replication the the parent DNA remains unchanged and is copied to form a daughter DNA

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29
Q

what should have happened in Meselson and Stahl’s experiment if DNA replicated semi -conservatively

A

if replication was semi - conservative, the new bacterial DNA molecules would contain one strand of the old DNA (containing N15) and one containing new DNA (N14)

therefore the DNA would settle between the light nitrogen DNA and heavy nitrogen (in the middle)

30
Q

why is energy important

A

plant and animal cells need energy for biological processes e.g. DNA replication

31
Q

what is ATP

A

ATP is an energy storing molecule

ATP is made from the nucleotide base adenine combined with a ribose sugar and three phosphate groups

32
Q

how is ATP made

A

ATP is made during respiration

33
Q

how is ATP used to provide energy

A

the bonds between the phosphate groups are unstable and so have a low activation energy which means they are easily broken in a hydrolysis reaction

when they do break, they release a considerable amount of energy.
Usually in living cells, it is only terminal phosphate that is removed

The ATP hydrolysis can be coupled to other energy requiring reactions in the cell - this means that the energy released can be used to make the coupled reaction happen

this forms:
ATP + H2O - ADP +Pi

This reaction is catalyzed by the enzyme ATP hydrolase

34
Q

how can ATP be re -synthesised

A

ATP can be re- synthesised in a condensation reaction between ADP and Pi

this happens during both:
photosynthesis
respiration

This reaction is catalysed by the enzyme ATP synthase

35
Q

why is ATP a bad long term energy store

A

the instability of its phosphate bonds (which make it a good donor of energy ) is the reason why it is not a good long term energy store

ATP is therefore the immediate energy source for a cell.
Therefore cells do not store large quantities of ATP but rather just maintain a few seconds worth supply .

36
Q

cells do not store large quantities of ATP but rather just a few seconds worth supply - why is this not a problem

A

ATP is rapidly re- formed from ADP and inorganic phosphate and therefore a little goes a long way

37
Q

what is a better long term energy store than ATP

A

fats and carbohydrates e.g. glycogen work better as a long term energy store

38
Q

why is ATP a better immediate energy source than glucose

A
  • each ATP molecule releases less energy than each glucose molecule.
    The energy for reactions is therefore released in smaller more manageable quantities rather than the much greater, and therefore less manageable release of energy from glucose
  • the hydrolysis of ATP is a single reaction that releases immediate energy. The breakdown of glucose is a long series of reactions and therefore, the energy released takes longer
  • ATP cannot be stored therefore it is continuously made within the mitochondria of cells. This means that cells that require a lot of energy will have a lot of mitochondria
39
Q

what are some of the uses of ATP

A

-metabolic processes
ATP provides energy needed to build up macromolecules (polymers) from their basic sub unit

-movement
provides energy for muscle contraction. ATP provides energy needed for the filaments of muscle to slide past one another and therefore shorten the overall length of the muscle

-active transport
provides energy to change shape of the carrier proteins in the plasma membranes . This allows molecules or ions to be moved against a concentration

-secretion
ATP is needed to form lysosomes necessary for the secretion of all procedures

-activation of molecules
the organic phosphate released during the hydrolysis of ATP can be use to phosphorylate other compounds in order to make therm more reactive. This lowers the activation energy in enzyme catalyses reactions

-

40
Q

what are the three different ways that the synthesis of ATP from ADP can occur

A
  • in chlorophyll - containing plant cells during photosynthesis
    (photophosphoryllation)
  • in plant and animal cells during repsiration (phosphorylation)
  • in plant and animal cells when phosphate groups are transferred from ions or molecules to ADP ( substrate- level phosphorylation)
41
Q

why is water important

A

water is vital to living organisms because:

  • it makes up 80% of a cell’s content and has a lot of important functions, inside and outside cells
  • water is a metabolite
  • water is a good solvent
  • helps with temperature control
  • water molecules are cohesive
42
Q

what is the structure of water

A

in a molecule of water (H2O) there is one oxygen joined to two atoms of hydrogen (H2) by shared electrons ( a covalent bond

43
Q

why is water a polar molecule

A
  • because the shared negative hydrogen electrons are pulled towards the oxygen atom, the other side of each hydrogen atom is left with a slight positive charge
  • the unshared negative electrons on the oxygen atom give it a slight negative charge

This makes water a polar molecule - it has a slight (partial ) negative charge on one side and a slight ( partial) positive charge on the other side

44
Q

what are hydrogen bonds

A

hydrogen bonds are weak bonds between a slightly positively charged hydrogen atom in one molecule and a slight negatively shared atom in another molecule

45
Q

why do hydrogen bonds form between water molecules

A

hydrogen bonds form between water molecules because the slightly negatively charged oxygen atoms of water attract the slightly positively charged hydrogen atoms of other water molecules

46
Q

what can the useful properties of water be attributed too

A

the hydrogen bonding between water molecules

47
Q

why is water an important metabolite

A
  • water is used to breakdown many complex molecules by hydrolysis e.g. proteins to amino acids
    water is also produced in a condensation reaction as a new bond is formed
  • chemical reactions take place in an aqueous medium (cytoplasm)
  • energy is released by a hydrolysis reaction ( the breakdown of ATP)
  • water is a major raw material in photosynthesis
48
Q

how is water a good solvent

A

a lot of important substances in biological reactions are ionic (e.g. salt)

  • one positively charged atom/ molecule
  • one negatively charged atom/ molecule
    e. g. salt is made from positive sodium ion and a negative negatively charged ion

because water is polar, the slightly positively charged end of water molecule will be attracted to the negative ion and the slightly negatively charged end of a water molecule will be attracted to the positive ion

This means the ions will get totally surrounded by water molecules - essentially they will dissolve

49
Q

why is it important that water is a good solvent

A

water being a good solvent is important to living organism as it means they can take up useful substances (e.g. mineral ions) in the water and these dissolved substances can be transported around the organisms

50
Q

why does water have high latent heat of vaporisation

A 
water evaporates (vaporises) when the hydrogen bonds holding water molecules together are broken
- this allows the water molecules on the surface to escape into the air as a gas

it takes a lot of energy (heat) to break the hydrogen bonds between water molecules - so a lot of energy is used when water evaporates

this means water has a high latent heat of vaporisation

51
Q

why is water having a high latent heat of vaporisation useful

A

body heat can be used to evaporate the water, a living organism can use the water loss through evaporation to cool down without losing too much water ( due to water having a high latent heat of vaporisation)

this allows the body to control its temperature

52
Q

why does water have a high specific heat capacity

A

the hydrogen bonds give water a high specific heat capacity ( the energy needed to raise 1 gram of a substance by 1C)

53
Q

why is water having a high specific heat capacity useful

A

when water is heated, a lot of heat energy is used to break the hydrogen bonds between the water molecules

This means there is less heat energy available to actually increase the temp of the water
- so water has a high specific capacity - it takes a lot of energy to heat up

This is useful for living organisms because:
-water doesn’t experience rapid changes. This makes water a good habitat because the temp under water is likely to be more stable than on land

  • water inside organisms also remain a fairly constant temperature helping them to maintain a constant internal body temperature
54
Q

what is cohesion

A

cohesion is the attraction between molecules of the same type ( tendency of molecules sticking together)

55
Q

why are water molecules very cohesive

A

water molecules are very cohesive because they’re polar

56
Q

why is it important that water molecules are cohesive

A

strong cohesion helps water to flow , making it great for transporting substances
e.g. water travels in columns up the xylem in plants

water cohesion is why sweat forms droplets which evaporates from the skin to cool an organism down
- it is also the reason why pond skaters, can walk on the surface of a pond

57
Q

what are ions

A

an ion is an atom ( or group of atoms) that has an electric charge

58
Q

what is a positive ion called

A

cation

59
Q

what is a negative ion called

A

anion

60
Q

what is an inorganic ion

A

an inorganic ion is one which doesn’t contain carbon (although there are a few exceptions to this rule)

there are inorganic ions in solutions, in the cytoplasm of cells and in the body fluid of organisms

61
Q

why are inorganic molecules important

A

each ion has a specific role, depending on it properties

  • an ions role determines whether it is found in high or low concentrations in a cell
62
Q

what are examples of inorganic ions

A
  1. iron ions in haemoglobin
  2. hydgrogen ions
  3. sodium ion
  4. phosphate ions
63
Q

why are iron ions important in hemoglobin

A

its the Fe2+ ions that actually bind to the oxygen in haemoglobin so it’s a key component

when oxygen is bound, the Fe2+ temporarily becomes an Fe3+ ion, until oxygen is released

64
Q

what is haemoglobin

A

haemoglobin is a large protein that carries oxygen around the body in the red blood cells

65
Q

what is the structure of haemoglobin

A

it is made up of four different polypeptide chains each with an iron ion (Fe2+) in the centre

66
Q

why are hydrogen ions important

A

pH is calculated based on the concentration of hydrogen ions (H+) in the environment

more H+ the lower the pH ( the environment is more acidic)

this is important as enzyme controlled reactions are affected by pH

67
Q

why are sodium ions important

A

sodium ions are important in the transport of glucose and amino acids across the plasma membranes

this is called co- transport

68
Q

why are phosphate ions important

A

PO4-3

DNA, RNA and ATP all contain phosphate groups

It’s the bonds between phosphate groups that store energy in ATP

the phosphate groups in DNA and RNA allow nucleotides to join up to form the polypeptides

69
Q

what are the different ends of a DNA structure

A

each end of a DNA strand is slightly different in its structure
One end is called the 3’ (pronounced “three prime”)
end and one end is called the 5’ (five prime)

70
Q

what is the action of DNA - polymerase

A

during DNA replication the active site of DNA polymerase is only complementary to the 3’ end of the newly forming DNA strand - so the enzyme can only add nucleotide to the new strand 3’ end.

This means that the new strand is made in a 5’ to 3’ direction and that DNA polymerase moves down the template in a 3’ to 5’ direction

71
Q

what does the nature of the antiparrelel strands of DNA mean for polymerase working on the template strands

A

Because the strands in the double helix are antiparallel to each other, the DNA polymerase working on one of the temple strands moves in the opposite direction of the DNA polymerase working on the other template

biology a levels (9 decks)

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