Nucleotides, DNA, RNA, ATP

Question 1

Describe what is meant by a nucleotide

Answer 1

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.

Question 2

FUNCTION OF DNA

Answer 2

used to store genetic information - all the instructions an organism needs to grow and develop from a fertilised egg to a fully grown adult

Question 3

function of RNA

Answer 3

to transfer genetic information from the DNA to the ribosomes

ribosomes themselves are made from RNA and proteins

Question 4

what do nucleotides consist of

Answer 4

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

Question 5

What elements do nucleotides contain

Answer 5

Nitrogen
Oxygen
Phosphorus
Carbon
Hydrogen

Question 6

Draw a diagram of a nucleotide

Answer 6

https://old-ib.bioninja.com.au/_Media/nucleotide-schematic_med.jpeg

oxygen is at point

https://d20khd7ddkh5ls.cloudfront.net/dna_nucleotide_structure.jpg

Question 7

what are nucleotides used to make

Answer 7

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

Question 8

Differences between structure of DNA and RNA

Describe the general structure of nucleotides found in DNA and RNA

Answer 8

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

_________________________

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)
___________________________
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

Question 9

Describe how nucleotides can be joined by a condensation reaction

Describe how polynucleotides are formed

Answer 9

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

Question 10

draw a polynucleotide

Label phosphodiester bond

Answer 10

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

Question 11

what is the sugar-phosphate backbone

Answer 11

Many nucleotides can join in this way to create a chain of phosphates and sugars known as the sugar-phosphate backbone.

Question 12

describe the structure of DNA

Answer 12

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)
__________________________
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
___________________________
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

Question 13

explain why the proportions of Adenine and Thymine AND cytosine and guanine the same

Answer 13

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

Question 14

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

Answer 14

20% guanine
20% cytosine
30% adenine
30% of nucleotides contain thymine

Question 15

Describe the structure of RNA

Answer 15

Like DNA, RNA is a polynucleotide

RNA molecules consist of only one polynucleotide strand

Question 16

further differences between DNA and RNA

Answer 16

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

Question 17

Draw the structure of DNA

Answer 17

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

Question 18

draw a structure of RNA

Answer 18

https://bam.files.bbci.co.uk/bam/live/content/zddngk7/small

Question 19

describe the stages of DNA replication

Answer 19

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

Question 20

DRAW AN ACTIVATED NUCLEOTIDE

Answer 20

NUCLEOTIDE WITH 3 PHOSPHATE GROUPS

Question 21

describe how a mutation can occur

Answer 21

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

Question 22

what happens to a cell every time it undergoes cell division

Answer 22

Every time a cell undergoes cell division all of its DNA is copied - process is called DNA replication

Question 23

describe how scientists determined that DNA replication is semi-conservative

Answer 23

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

Question 24

what would the results of the experiment show if DNA replicates conservatively rather than semi-conservatively

Answer 24

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

Question 25

describe semi-conservative replication

Answer 25

in each of the two copies of DNA one strand is from the original DNA molecule plus one new strand

Question 26

describe conservative replication

Answer 26

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

Question 27

how did the nitrogen in broth solution become a part of the DNA of the bacteria

Answer 27

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

Question 28

examples of long-term energy storage molecules - describe their use

Answer 28

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

Question 29

PROBLEM WITH GLUCOSE REGARDING ENERGY

SOLUTION?

Answer 29

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

Question 30

Describe the structure of the molecule ATP

Answer 30

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

Question 31

state a key property of ATP

Describe how ATP can act as an immediate source of energy

Answer 31

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

Question 32

To break the bond between the second and last phosphate group what is needed

What type of reaction is this?

Answer 32

Breaking this bond requires a water molecule

Therefore this is an example of a hydrolysis reaction

Question 33

state the equation for the hydrolysis of ATP

Answer 33

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

Question 34

what eventually happens to the ADP and phosphate which are released after energy has been used for processes

Answer 34

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

Question 35

atp resynthesis reaction

Answer 35

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.

Question 36

uses of ATP

Answer 36

• 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