nucleic acids Flashcards
what are nucleic acids
nucleic acids are the most important molecules of which the best known are ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)
what is deoxyribonucleic acid (DNA)
DNA carries genetic information
The double helix structure of deoxyribonucleic acid makes it immediately recognisable
what is the monomer sub unit that makes up DNA
Despite its complex structure, DNA is made up of nucleotides that have just three basic compounds
what is the structure of a nucleotide
Individual nucleotides are made up of three component:
- a pentose sugar ( so called as it has five carbon atoms - glucose is a hexose sugar as it has six carbons)
- a phosphate
- a nitrogen - containing organic base.
These are: cytosine C, thymine T, uracil U, adenine A and guanine G
how is the pentose sugar, phosphate group and organic base joined together
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
what is the bond that is formed between two mononucleotides called
bond formed is called a phosphodiester bond
what is the new structure called when two mononucleotides bond together
dinucleotides
The continued linking of mononucleotides in this way forms a long chain known as a polynucleotide
what is the difference between DNA and proteins
- DNA is a sequence of bases
- proteins are a sequence of amino acids
- nucleotides join to form a polynucleotide
- amino acids join to form a polypeptide
what is ribonucleic acid/ what is its structure
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
what is the function of ribonucleic acid (RNA)
- 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
- another type of RNA is involved in protein synthesis
who worked out the structure of DNA
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
what is the structure of DNA
- 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)
what are the base pairings
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
what is the double helix structure of a DNA
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
what is the structure of DNA and how does it relate to its function
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
what does the function of the DNA molecule depend on
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
how does the molecule DNA remain stable
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)
what makes DNA molecules differ from one and other
-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
how do other cells replicate
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
what are the two main stages of cell division
- 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
what must happen before a nucleus divides
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
how can we tell that the process of DNA replication is precise
the precise of DNA replication is clearly very precise because all the new cells are more or less genetically identical to the original one.
what is the semi-conservative replication
The process in which DNA replicates is called semi - conservative replication
- enzyme DNA helicase breaks the hydrogen bonds linking the base pairs
- As a result of the double helix separates into its two strands and unwind
- each exposed polynucleotide strand acts as a template to which the free nucleotides bind to complementary specific base pairings
- nucleotides are joined together in a condensation reaction by the enzyme DNA polymerase to form the “missing” polynucleotide strands of DNA
- each new DNA molecule contains one stand from the original DNA molecule and one new strand
This process is called “semi conservative replication”
what are the four requirements needed for semi - constructive replication
- 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
what was the other theory of how DNA replicated
conservative
before Meselson and Stahl’s experiment, people were unsure whether DNA replicated was semi - conservative / conservative
what did Meselson and Stahl’s experiment show
Meselson and Stahl’s experiment showed that DNA is replicated using the semi-conservative method
what was the method behind Meselson and Stahl’s experiment
- 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
- 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 - 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 - as it turned out, the DNA settled in the middle showing that DNA molecules contained a mixture of heavy and light nitrogen
what should have happened in Meselson and Stahl’s experiment if DNA replicated conservatively
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
what should have happened in Meselson and Stahl’s experiment if DNA replicated semi -conservatively
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)
why is energy important
plant and animal cells need energy for biological processes e.g. DNA replication
what is ATP
ATP is an energy storing molecule
ATP is made from the nucleotide base adenine combined with a ribose sugar and three phosphate groups
how is ATP made
ATP is made during respiration
how is ATP used to provide energy
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
how can ATP be re -synthesised
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
why is ATP a bad long term energy store
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 .
cells do not store large quantities of ATP but rather just a few seconds worth supply - why is this not a problem
ATP is rapidly re- formed from ADP and inorganic phosphate and therefore a little goes a long way
what is a better long term energy store than ATP
fats and carbohydrates e.g. glycogen work better as a long term energy store
why is ATP a better immediate energy source than glucose
- 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
what are some of the uses of ATP
-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
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what are the three different ways that the synthesis of ATP from ADP can occur
- 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)
why is water important
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
what is the structure of water
in a molecule of water (H2O) there is one oxygen joined to two atoms of hydrogen (H2) by shared electrons ( a covalent bond
why is water a polar molecule
- 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
what are hydrogen bonds
hydrogen bonds are weak bonds between a slightly positively charged hydrogen atom in one molecule and a slight negatively shared atom in another molecule
why do hydrogen bonds form between water molecules
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
what can the useful properties of water be attributed too
the hydrogen bonding between water molecules
why is water an important metabolite
- 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
how is water a good solvent
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
why is it important that water is a good solvent
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
why does water have high latent heat of vaporisation
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
why is water having a high latent heat of vaporisation useful
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
why does water have a high specific heat capacity
the hydrogen bonds give water a high specific heat capacity ( the energy needed to raise 1 gram of a substance by 1C)
why is water having a high specific heat capacity useful
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
what is cohesion
cohesion is the attraction between molecules of the same type ( tendency of molecules sticking together)
why are water molecules very cohesive
water molecules are very cohesive because they’re polar
why is it important that water molecules are cohesive
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
what are ions
an ion is an atom ( or group of atoms) that has an electric charge
what is a positive ion called
cation
what is a negative ion called
anion
what is an inorganic ion
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
why are inorganic molecules important
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
what are examples of inorganic ions
- iron ions in haemoglobin
- hydgrogen ions
- sodium ion
- phosphate ions
why are iron ions important in hemoglobin
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
what is haemoglobin
haemoglobin is a large protein that carries oxygen around the body in the red blood cells
what is the structure of haemoglobin
it is made up of four different polypeptide chains each with an iron ion (Fe2+) in the centre
why are hydrogen ions important
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
why are sodium ions important
sodium ions are important in the transport of glucose and amino acids across the plasma membranes
this is called co- transport
why are phosphate ions important
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
what are the different ends of a DNA structure
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)
what is the action of DNA - polymerase
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
what does the nature of the antiparrelel strands of DNA mean for polymerase working on the template strands
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
