Nucleotides, DNA, RNA, ATP Flashcards
Describe what is meant by a nucleotide
complex chemicals/molecules made up of an organic (nitrogen containing) base, a pentose sugar, and a negatively charged phosphate group
These are the base units/monomers of which the nucleic acids DNA and RNA are made.
FUNCTION OF DNA
used to store genetic information - all the instructions an organism needs to grow and develop from a fertilised egg to a fully grown adult
function of RNA
to transfer genetic information from the DNA to the ribosomes
ribosomes themselves are made from RNA and proteins
what do nucleotides consist of
In the centre - a five carbon sugar molecule (sugars with five carbon atoms are called pentose sugars)
Attached to the sugar - there is a nitrogen-containing molecule/base called a base
(sometimes referred to as nitrogenous bases - as
they contain nitrogen)
Attached to the other side of the sugar molecule there is a negatively charged phosphate group
Phosphate group
Pentose sugar
Base
What elements do nucleotides contain
Nitrogen
Oxygen
Phosphorus
Carbon
Hydrogen
Draw a diagram of a nucleotide
https://old-ib.bioninja.com.au/_Media/nucleotide-schematic_med.jpeg
oxygen is at point
https://d20khd7ddkh5ls.cloudfront.net/dna_nucleotide_structure.jpg
what are nucleotides used to make
Nucleotides are used to make the molecules DNA and RNA
The nucleotides we find in DNA and RNA all share the same general structure
DNA and RNA are formed from nucleotides
Differences between structure of DNA and RNA
Describe the general structure of nucleotides found in DNA and RNA
In DNA, the pentose sugar is called Deoxyribose whereas in RNA, the pentose sugar is called ribose
Deoxyribose has one fewer oxygen atoms than ribose
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In DNA nucleotides, there are 4 different bases. These are called adenine, thymine, guanine and cytosine
Two of these bases have a double carbon ring structure - These are adenine and guanine.
These bases are called purines
The other two bases, thymine and cytosine have a single carbon ring structure. These bases are called pyrimidines (since they have a single ring structure)
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Just like DNA, RNA also contains, the bases adenine, guanine and cytosine. However RNA does not contain the base thymine. Instead, RNA contains the base uracil (Uracil has a single ring structure and is a pyrimidine)
1 hexagon - single ring - pyrimadine
1 hexagon and pentagon = double ring - purine
Describe how nucleotides can be joined by a condensation reaction
Describe how polynucleotides are formed
hydroxyl group on carbon 3 on the pentose sugar
A bond can be formed between the phosphate group on one nucleotide and the hydroxyl group on carbon 3 of the pentose sugar of the other nucleotide
The bond between two nucleotides is called a phosphodiester bond
When the phosphodiester bond forms, water is released so this is an example of a condensation reaction
The molecule formed is called a dinucleotide
The phosphodiester bond can be broken by adding water - this is called a hydrolysis reaction
we can continue to add nucleotides by forming phosphodiester bond
a polymer of nucleotides has been formed - called a polynucleotide
Both DNA and RNA are examples of polynucleotides
nucleotides join by forming phosphodiester bonds
draw a polynucleotide
Label phosphodiester bond
https://study.com/cimages/multimages/16/double_strand_structure.gif
https://s3.eu-west-2.amazonaws.com/elements.cognitoedu.org/5ff74c96-c4bd-42a7-a258-73facbc81b9d/polynucleotide-structure-diagram.png
what is the sugar-phosphate backbone
Many nucleotides can join in this way to create a chain of phosphates and sugars known as the sugar-phosphate backbone.
describe the structure of DNA
DNA consists of two polynucleotide strands
There is the sugar-phosphate backbone on the outside with the bases in the centre
The two polynucleotide strands are held together by hydrogen bonds which form between the bases on opposite strands/(which act between the bases on each of the strands)
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The bases on one strand are complementary to the bases on the other strand
Guanine on one strand always pairs with (hydrogen bonds with) cytosine on the opposite strand
Adenine always pairs with thymine - called complementary base pairing
This complementary base pairing is central to how DNA functions
A purine on one strand always pairs with a pyrimidine on the opposite strand
This means that the distance between the sugar-phosphate backbones is constant all down the DNA molecule
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The two polynucleotide strands in DNA are antiparallel - this means that they run in opposite directions
on the left hand strand - on one strand - the top phosphate group is attached to carbon 5 of the deoxyribose sugar
At the bottom, the hydroxyl group is attached to carbon 3
on the other strand, the carbon 3 hydroxyl is at the top and at the bottom the carbon 5 is attached to the phosphate
3’ end and 5’ end 3 prime and 5 prime
Different base pairs form a different number of hydrogen bonds
Guanine and cytosine form three hydrogen bonds whereas adenine and thymine form two hydrogen bonds
Because of complementary base pairing, the proportions of guanine and cytosine are always the same as each other. The proportions of adenine and thymine are always the same as each other
this means we can calculate the proportion of the different nucleotides
The two polynucleotide strands in DNA twist around each other to form a double helix
The sugar-phosphate backbones are on the outside (can be seen on the outside of the double helix) and the base pairs in the centre
dna - double stranded molecule each strand consists of a polymer of nucleotides joined by a sugar phosphate backbone
explain why the proportions of Adenine and Thymine AND cytosine and guanine the same
Because of complementary base pairing, the proportions of guanine and cytosine are always the same as each other. The proportions of adenine and thymine are always the same as each other
this means we can calculate the proportion of the different nucleotides
Calculate the frequency of nucleotides on DNA strands
e.g. 20% of the nucleotides in a sample of DNA contained the base guanine. Calculate the proportions of the other nucleotides
20% guanine
20% cytosine
30% adenine
30% of nucleotides contain thymine
Describe the structure of RNA
Like DNA, RNA is a polynucleotide
RNA molecules consist of only one polynucleotide strand
further differences between DNA and RNA
DNA is found in chromosomes in the nucleus
RNA is found in the cytoplasm
RNA plays a key role in protein synthesis
DNA is an extremely long molecule (often containing many millions of nucleotides)
RNA molecules are much shorter (many RNA molecules only contain a few hundred nucleotides)
DNA is a double-stranded molecule consisting of Two polynucleotide strands twisted into a double helix
RNA molecules consist of only one polynucleotide strand
Draw the structure of DNA
https://cdn-ilcgdmp.nitrocdn.com/ZNZGaPUCQqgkHHGdlFKJfPiIeULNhire/assets/images/optimized/rev-3977cf1/studymind.co.uk/wp-content/uploads/2022/03/Screen-Shot-2022-03-29-at-3.11.03-PM-308x335.png
draw a structure of RNA
https://bam.files.bbci.co.uk/bam/live/content/zddngk7/small
describe the stages of DNA replication
In the first stage, the enzyme DNA helicase attaches to the DNA molecule
DNA helicase causes the hydrogen bonds between complementary bases (BASE PAIRS) to break
This causes the two polynucleotide strands to separate from each other (CAUSES DOUBLE HELIX TO SEPARATE INTO ITS TWO STRANDS AND UNDWIND)
Now free nucleotides line up with their complementary bases on the DNA strands. At this stage, the free nucleotides are only held in place by hydrogen bonds between the complementary bases. They are not bonded to each other by phosphodiester bonds
These free nucleotides are called activated nucleotides (different from normal nucleotides)
An activated nucleotide contains three phosphate groups while a normal nucleotide only contains one
The activated nucleotides are now lined up held in place by hydrogen bonds between the complementary base pairs.
At this stage a second enzyme now attaches.
This enzyme is called DNA polymerase
DNA polymerase moves down the molecule and catalyses the formation of a phosphodiester bond between the activated nucleotides. This is an example of a condensation reaction
When the phosphodiester bonds form the activated nucleotides lose their extra two phosphate groups
As these two phosphate groups leave, this provides energy for the reaction
There are now two copies of the double stranded DNA molecule
However each of the DNA molecules contains one strand from the original DNA molecule and one strand which is brand new (complementary new strand). This type of DNA replication is called semi-conservative replication
DRAW AN ACTIVATED NUCLEOTIDE
NUCLEOTIDE WITH 3 PHOSPHATE GROUPS
describe how a mutation can occur
its important that DNA is copied accurately
sometimes an incorrect base is inserted into the growing polynucleotide strand
This means that the DNA sequence has changed
This is called a mutation
these can have very serious effects of the organism
Mutations are random and occur spontaneously
what happens to a cell every time it undergoes cell division
Every time a cell undergoes cell division all of its DNA is copied - process is called DNA replication
describe how scientists determined that DNA replication is semi-conservative
experiment to show whether DNA replicated by conservative or semi-conservative replication
All bases in DNA contain the element nitrogen
nitrogen atoms exist in two main isotopes/forms
Nitrogen-14 - light nitrogen - most common isotope
Nitrogen-15 heavy nitrogen
atoms of nitrogen 15 are slightly heavier than atoms of nitrogen 14
A sample of bacteria was taken
under normal conditions, Almost all of nitrogen atoms in the DNA of these bacteria will be nitrogen-14 lighter nitrogen
The scientist now took some of these bacteria and extracted the DNA
They then placed the DNA in a solution and spun this at very high speeds in a centrifuge
The DNA moved down the solution and formed a band which could be detected
The position of the DNA band depends on how heavy the DNA is
Because the nitrogen atoms in this DNA were almost all nitrogen-14 (light nitrogen) this formed a band near the top of the tube - because their DNA was lighter
The bacteria was cultured in a growth medium which contained only nitrogen-15
After the bacteria had reproduced many, many times almost all of the nitrogen atoms in their DNA was nitrogen-15 (heavy-nitrogen)
When this DNA was extracted and centrifuged it formed a band near the bottom of the tube - because their DNA was heavier
At this stage, a sample of the bacteria which had been growing on nitrogen-15 ‘heavy nitrogen’ was taken and transferred these bacteria to nitrogen-14 and allowed them to replicate their DNA only once
The scientists then extracted the DNA and spun it in a centrifuge
What they found was that thisi DNA produced a bad in between the two bands produced before
This told the scientists that this DNA contained one strand with nitrogen-14 and one-strand with nitrogen-15
this means that the DNA must have replicated semi-conservatively
replicated DNA had one strand containing nitrogen-15 (original strand) and one strand containing nitrogen-14 - new strand
The scientists allowed the bacteria to replicate one more time on nitrogen-14
when the DNA was extracted and spun it produced two bands. The band near the top of the tube are two strands of nitrogen -14
lower band is the one strand of N-14 AND ONE STRAND OF N-15
After the second round of replication we have four DNA molecules
two contain a strand with nitrogen-14 and a strand with nitrogen-15
other two DNA molecules both contain two strands with only nitrogen-14
what would the results of the experiment show if DNA replicates conservatively rather than semi-conservatively
Nitrogen-15 bacteria in nitrogen-14 culture growth medium
After one round of replication we would have one DNA molecule containing only nitrogen-15 and one DNA molecule containing only nitrogen-14
After two rounds of replication there would still be one DNA molecule containing only nitrogen-15 but we would now have three DNA molecules containing only nitrogen 14
there would be no DNA molecules contianing both nitrogen 14 and N-15
ORIGINAL BAND - JUST N-15
DNA AFTER 1 REPLICATION LOW BAND N-15 HIGHER BAND N-14
DNA AFTER 2 REPLICATIONS
LOW BAND - N-15 HIGHER BAND N-14
HIGHER BAND THICKER THAN LOWER BAND AS THERE ARE MORE DNA MOLECULES WITH N-14 THAN N-15
describe semi-conservative replication
in each of the two copies of DNA one strand is from the original DNA molecule plus one new strand
describe conservative replication
In conservative replication a DNA double helix is formed containing two new strands
This DNA molecule contains none of the original DNA
end up with one molecule of DNA containingn two original strands and one molecule of DNA containing two new strands
how did the nitrogen in broth solution become a part of the DNA of the bacteria
as the bacteria reproduced they took up nitrogen from the broth to help make nucleotides for new DNA
So the nitrogen gradually became part of the bacteria’s DNA
examples of long-term energy storage molecules - describe their use
Carbohydrates and triglycerides are used as long-term energy storage molecules
glycogen -> glucose
triglyceride -> fatty acids + glycerol
The molecule glycogen can be hydrolysed to produced glucose
This glucose can then be used as a source of energy through respiration
PROBLEM WITH GLUCOSE REGARDING ENERGY
SOLUTION?
problem: glucose contains a lot of stored energy
- infact much more energy than would ever be required by any single process in the cell
this means that cells need a way to transfer the energy from the glucose molecule in smaller, more useful amounts
to do this, cells use the molecule adenosine triphosphate (ATP)
The energy released in the aerobic respiration of one glucose molecule can be transferred to over 30 molecules of ATP
Describe the structure of the molecule ATP
ATP contains the base adenine bonded to the pentose sugar ribose
Together this part of the molecule is called adenosine
On the other side of the ribose, there are three phosphate groups - ribose is also bonded to three phosphate groups on the other side
This means that ATP is a nucleotide
state a key property of ATP
Describe how ATP can act as an immediate source of energy
It only takes a small amount of energy to break the covalent bond holding the last /terminal phosphate group (the furthest one) in place
But when this bond is broken, a large amount of energy is released
This energy can then be used by processes in the cell
Breaking this bond requires a water molecule
ATP not long term energy store like glycogen or triglycerides
ATP is more of an immediate energy source, transferring energy from the sites of respiration to the parts of the cell which require energy
atp hydrolysis provides energy to different processes in the cell
These processes include active transport, muscle contraction and the formation of large molecules such as proteins
To break the bond between the second and last phosphate group what is needed
What type of reaction is this?
Breaking this bond requires a water molecule
Therefore this is an example of a hydrolysis reaction
state the equation for the hydrolysis of ATP
ATP + water –> ADP + Pi + energy
The reaction is catalysed by the enzyme ATPase (above arrow)
Also called ATP hydrolase
In this reaction, we are producing the molecule adenosine diphosphate (ADP)
We are also releasing the phosphate group
Lowercase i tells us that this is inorganic phosphate - in other words not attached to a carbon contianing molecule
what eventually happens to the ADP and phosphate which are released after energy has been used for processes
The ADP and phosphate that are released are then recycled back to ATP
This takes place during respiration in animal cells and in both respiration and photosynthesis in plant cells
Because a phosphate is being added back to ADP, this is called a phosphorylation reaction
This reaction is catalysed by the reaction ATP synthase. Because water is released this is an example of a condensation reaction
atp resynthesis reaction
ADP + Pi —> ATP + water
ATP is resynthesised by the condensation of ADP and Pi
. This
reaction is catalysed by the enzyme ATP synthase during
photosynthesis, or during respiration.
uses of ATP
- The hydrolysis of ATP can be coupled to energy-requiring
reactions within cells. - The inorganic phosphate released during the hydrolysis of
ATP can be used to phosphorylate other compounds, often
making them more reactive
