Module 2 Section 3: Nucleotides and Nucleic Acids

Question 1

What is used to make nucleic acids

Answer 1

Nucleotides

Question 2

What is the structure of nucleotides

Answer 2

A nucleotide is a type of biological molecule
It’s made from:
A pentose sugar ( sugar with 5 carbon atoms )
A nitrogenous ( nitrogen-containing ) base
A phosphate group
All nucleotides contain the elements C, H, O, N and P

Question 3

Why are nucleotides important

Answer 3

They’re monomers that make up DNA and RNA
DNA and RNA are both types of nucleic acid
DNA I used to store genetic information - the instructions an organism needs to grow and develop
RNA is used to make proteins from the instructions in DNA

ATP and ADP are special types of nucleotide as they’re used to store and transport energy in cells

Question 4

What is the sugar in DNA

Answer 4

The pentose sugar in a DNA nucleotide is called deoxyribose
DNA stands for DeoxyriboNucleic Acid

Question 5

Structure of DNA nucleotides

Answer 5

Each DNA nucleotide has the same sugar and a phosphate group
The base on each nucleotide can vary
There are four possible bases: adenine (A), thymine (T), cytosine (C) and guanine (G)

Question 6

What are the two bases in DNA

Answer 6

Adenine and Guanine are a type of base called a purine
Cytosine and Thymine are a type of base called a pyrimidine

Question 7

What are the structures of purine and pyrimidine

Answer 7

A purine base contains two carbon-nitrogen rings joined together
A pyrimidine base only has one carbon-nitrogen ring - a pyrimidine base is smaller than a purine base

Question 8

What does a molecule of DNA contain

Answer 8

A molecule of DNA contains two polynucleotide chains
Each chain is made up of lots of nucleotides joined together

Question 9

What is the sugar in RNA called

Answer 9

RNA ( RiboNucleic Acid) contains nucleotides with a ribose sugar

Question 10

Structure of RNA

Answer 10

An RNA nucleotide has a phosphate group and one of 4 bases
In RNA Uracil ( a pyrimidine ) replaces thymine as a base
An RNA molecule is made up of a single polynucleotide chain

Question 11

What are ATP and ADP

Answer 11

ADP and ATP are phosphorylated nucleotides
To phosphorylate a nucleotide, you add one or more phosphate groups to it
ADP ( Adenosine Diphosphate ) contains the base adenine, the sugar ribose and two phosphate groups
ATP ( Adenosine Triphosphate ) contains the base adenine, the sugar ribose and three phosphate groups

Question 12

Function of ATP

Answer 12

ATP provides energy for chemical reactions in the cell
ATP is synthesised from ADP and inorganic phosphate ( Pi ) using energy from an energy-releasing reaction, e.g. the breakdown of glucose in respiration
The ADP is phosphorylated to form ATP and a phosphate bond is formed
Energy is stored in the phosphate bond
When this energy is needed by a cell, ATP is broken back down in ADP and inorganic phosphate ( Pi )
Energy is released from the phosphate bond and used by the cell

Question 13

How do nucleotides join together to form polynucleotides

Answer 13

The nucleotides join up between the phosphate group of one nucleotide and the sugar of another via a condensation reaction
This forms a phosphodiester bond ( consisting of the phosphate group and two ester bonds )
The chain of sugars and phosphates is known as the sugar-phosphate backbone
Polynucleotides can be broken down into nucleotides again by breaking down the phosphodiester bonds ( using hydrolysis reactions )

Question 14

How do DNA molecules join together to form a double helix

Answer 14

Two DNA polynucleotides strand join together by hydrogen bonding between the bases
Each base can only join with one particular partner - complimentary base pairing
Adenine always pairs with Thymine ( A - T ) and Cytosine always pairs with Guanine ( C - G )
A purine ( A or G ) always pairs with a pyrimidine ( T or C )
Two hydrogen bonds form between A and T, and three hydrogen bonds form between C and G
Two antiparallel ( running in opposite directions ) polynucleotide strands twist to form the DNA double helix

Question 15

How is computer modelling used to study DNA

Answer 15

You can use computer modelling to investigate the structure of DNA and other nucleic acids

Question 16

How to purify DNA using precipitate reaction

Answer 16

Break up cells in sample ( slice of onion ) using a blender

Make up solution of detergent, salt and distilled water

Add cells to beaker with detergent solution

Incubate for 15 mins at 60° water bath

Then put in ice bath to cool down

Filter mixture and transfer to clean boiling tube

Add protease enzymes to filtered mixture, these will break down some proteins in mixture e.g. histone proteins bound to the DNA.
Adding RNase enzymes will break down any RNA in the mixture

Add cold ethanol slowly down side of the tube, so it forms layer on top of DNA-detergent mixture

Leave tube for a few minutes and DNA will form white precipitate which can be removed using glass rod

Question 17

How does the precipitate reaction work with DNA

Answer 17

The detergent in the mixture breaks down cell membranes
Salt binds to the DNA and causes it to clump together
The temperature of the water bath should stop enzymes in the cell from working properly and breaking down the DNA

Question 18

How does DNA self replication work

Answer 18

DNA helicase ( an enzyme ) breaks the hydrogen bonds between the two polynucleotide DNA strands
The helix unzips to form two single strands

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 - A with T and C with G

The nucleotides of the new strand are joined together by the enzyme DNA polymerase
This forms the sugar-phosphate backbone
Hydrogen bonds form between bases on the original and new strand
Strand twists to form double helix

Each new DNA molecule contains one strand from original DNA molecule and one new strand

Question 19

Why is it called semi conservative replication

Answer 19

This type of copying is called semi-conservative replication because half of the strands in each new DNA molecule are from original piece of DNA - the new molecule contains one old strand and one new strand

Question 20

Why is DNA replication accurate

Answer 20

DNA replication is accurate because it has to make sure genetic information is conserved each time the DNA in a cell is replicated

Question 21

What does a DNA mutation do

Answer 21

Sometimes a random mutation occurs
This is a change to the DNA base sequence
Mutations don’t always have an effect, but can alter the sequence of amino acids in a protein
Can cause abnormal protein to be produced
This may function better than a normal protein or might not work at all

Question 22

What is a gene

Answer 22

A gene is a sequence of DNA nucleotides that that codes for a polypeptide
The sequence of amino acids in a polypeptide forms the primary structure of a protein

Question 23

What determines the order of amino acids in a particular protein

Answer 23

Different proteins have different numbers and orders of amino acids
It’s the order of nucleotide bases in a gene that determines the order of amino acids in a particular protein

Question 24

What codes for amino acids in genes

Answer 24

Each amino acid is coded for by a sequence of three bases ( called a triplet ) in a gene
Different sequences of bases code for different amino acids
So the sequence of bases in a section of DNA is a template that’s used to make proteins during protein synthesis

Question 25

How is DNA is copied into RNA for protein synthesis ( simple overview )

Answer 25

Used for protein synthesis
DNA molecules found in nucleus, but ribosomes found in cytoplasm
DNA is too large to fit out of nucleus, so a section is copied into mRNA
This process is called transcription
mRNA leaves nucleus and joins with a ribosome in the cytoplasm, where it can be used to synthesis a protein
This is called translation

Question 26

Three main types of RNA

Answer 26

Three main types of RNA:
mRNA
tRNA
rRNA

Question 27

What is messenger RNA (mRNA)

Answer 27

Made in the nucleus
Three adjacent bases are called a codon
Carries the genetic code from the DNA in the nucleus to the cytoplasm, where it’s used to make a protein during translation

Question 28

What is transfer RNA (tRNA)

Answer 28

Found in cytoplasm
Has an amino acid binding site at one end and a sequence of three bases at the other end called an anticodon
Carries amino acids that are used to make proteins to the ribosomes during translation

Question 29

What is ribosomal RNA (rRNA)

Answer 29

Forms two subunits in a ribosome (along with proteins)
The ribosome moves along the mRNA strand during protein synthesis
The rRNA in the ribosome helps to catalyse the formation of peptide bonds between the amino acids

Question 30

What is genetic code

Answer 30

It is the sequence of base triplets ( codons ) in DNA or mRNA which codes for specific amino acids

Question 31

How is the genetic code non overlapping

Answer 31

In the genetic code, each base triplet is read in sequence, separate from the triplet before it and after it
Base triplets don’t share their bases - the code is non overlapping
E.g. GUC ( mRNA base triplet ) = valine

Question 32

How is genetic code degenerate

Answer 32

There are more possible combinations of triplets than there are amino acids ( 20 amino acids but 64 possible triplets )
This means that some amino acids are coded for by more than one base triplet

Question 33

What can some triplets be used for other than protein synthesisn

Answer 33

Some triplets can be used to tell the cell when to start and stop production of the protein
These are called start and stop signals/ codons
Found at the beginning and end of the gene

Question 34

How is genetic code universal

Answer 34

The same specific base triplets code for the same amino acids in all living things

Question 35

Transcription 1: How is a template made in transcription

Answer 35

Transcription starts when RNA polymerase attaches to the DNA double helix at the beginning of a gene
The hydrogen bonds between the two DNA strands in the gene break, separating the strands, and the DNA molecule uncoils at that point
Strands are separated into non-coding/antisense strand (where template is made off) and coding/sense strand
One of the strand is then used as a template to make an mRNA copy

Question 36

Transcription 2: How is an mRNA molecule made in transcription

Answer 36

The RNA polymerase lines up free RNA nucleotides alongside the template strand (non-coding strand/anti sense strand)
mRNA strand ends up as complementary copy of DNA template strand ( complementary base pairing ) apart from A and T is replaced with A and U in RNA strand
Once the RNA nucleotides have paired up with their specific bases on the DNA strand they’re joined together, forming an mRNA molecule

The RNA polymerase moves along the DNA, separating the strands and assembling the mRNA strand
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
When RNA polymerase reaches a stop codon it stops making mRNA and detaches from the DNA

Question 37

Transcription 3: Final stage of transcription

Answer 37

The mRNA movess out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm, where the next stage of protein synthesis takes place

Question 38

Process of translation ( long one )

Answer 38

The mRNA attaches itself to a ribosome and transfer RNA (tRNA) molecules carry amino acids to the ribosome

A tRNA molecule, with an anticodon that’s complementary to the start codon on mRNA, attaches itself to the next codon on the mRNA in the same way

Ribosomal RNA in the ribosome catalyses the formation of a peptide bond between the two amino acids attached to the tRNA molecules
This joins the amino acids together

The first tRNA molecule moves away, leaving the amino acid behind

A third tRNA molecule binds to the next codon on the mRNA
It’s amino acid binds to the first two and the second tRNA molecule moves away

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

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

Question 39

Why must only plant cells be crushed in the DNA precipitation experiment

Answer 39

They have cell walls that must be broken down

Question 40

Structure of purine and pyrimidine

Answer 40

(Pyramidine single hexagon)

Question 41

Difference between RNA polymerase and DNA polymerase

Answer 41

RNA polymerase:
Makes mRNA, tRNA or rRNA by transcription
Uses one strand of DNA and forms one strand

DNA polymerase:
Uses in DNA replication
Semi conservative replication where both strands are used and 2 strands are formed
Used before cell division