1.4 DNA and Protein synthesis

Question 1

What are nucleic acids?

Answer 1

Organic compounds that include important macromolecules such as deoxyribonucleic acid (DNA).

Question 2

What are the essential roles and features of DNA in organisms?

Answer 2

• Contains genetic material: the info needed for the development and function of every organism.
• It is hereditary material- the molecule used to pass genetic information to offspring.
• It is a polynucleotide- polymer made up of nucleotide monomers.

Question 3

What is a nucleotide?

Answer 3

A single nucleotide (mono nucleotide) is the monomer used to build up polynucleotides like DNA. Made up of three components: pentose sugar (in DNA this is deoxyribose), phosphate group, and a nitrogen-containing organic base.

DIAGRAM GOES HERE ONCE YOU HAVE PRO

Question 4

What are the four organic bases in DNA?

Answer 4

Adenine, Guanine, Cytosine and Thymine.

Question 5

What are the purine and pyrimidine bases?

Answer 5

Purine (bigger bases with two carbon rings):
Guanine and Adenine
Pyrimidine (smaller bases with one carbon ring):
Thymine and Cytosine

Question 6

How do nucleotides join?

Answer 6

Via a condensation reaction that occurs between hydroxyl groups on the phosphate group and pentose sugar.

DIAGRAM GOES HERE AFTER PRO

Question 7

How are polynucleotides formed?

Answer 7

Many nucleotides can be joined together in a series of condensation reactions to form a polynucleotide.

Question 8

How are phosphodiester bonds broken in polynucleotides?

Answer 8

Hydrolysis: a molecule of water enters, breaks the phosphodiester bond to form two mononucleotides.

Question 9

What is the general structure of DNA?

Answer 9

-Composed of two very long polynucleotide chains twisted into a double helix.
- The sides of the double helix are made from pentose sugar and phosphate groups, forming a sugar-phosphate backbone.
- Two strands of DNA are held together by hydrogen bonds between the bases, creating the ‘rungs’ of the ladder.
- Double helix of DNA is antiparallel- strands of DNA run in opposite directions to each other.

Question 10

What are the base pairings in DNA?

Answer 10

A+T, G+C

Question 11

Why do the correct bases pair up?

Answer 11

The number of hydrogen bonds each pair of bases can form:
- A+T form 2 hydrogen bonds, G+C form 3 hydrogen bonds.
And the size of the bases, a larger purine must always pair with a smaller pyrimidine.

Question 12

What are the percentages of the base pairings in DNA?

Answer 12

Due to base pairing, there will always be the same percentage of complementary bases in a DNA molecule.
C=30%
G=30%
= 60%

A=20%
T=20%
=40%
Known as Chargaff’s rule.

Question 13

How are the polynucleotide strands positioned in DNA?

Answer 13

• Run in opposite directions to each other- they are antiparallel.
• One of the strands runs 5’ to 3’ while the other runs 3’ to 5’. These directions are named according to the position number of the carbon atoms in the pentose sugar of each nucleotide.

-In a mononucleotide, carbon five is bonded to the phosphate group and carbon three has a hydroxyl group.
-However, in a polynucleotide, carbon three is instead bonded to the phosphate group of the next nucleotide, creating a 5’ to 3’ strand.

Question 14

What is RNA, what are it’s roles?

Answer 14

Ribonucleic acid which:
- Acts as a messenger molecule, helps to transfer information from DNA to proteins.
- Has roles in the regulation and synthesis of proteins.
- Is also a polynucleotide, polymer made up of nucleotide monomers.

Question 15

What is the structure of RNA?

Answer 15

• Composed of one polynucleotide chain unlike DNA.
• RNA polynucleotide chains are also shorter than DNA chains.
• RNA nucleotides differ in molecular structure; the pentose sugar in RNA is ribose.

Question 16

What bases are used by RNA?

Answer 16

Adenine, Guanine, Cytosine, Uracil

(U, no T)

Guanine and Adenine are the purine bases

Uracil and Cytosine are the pyrimidine bases.

Question 17

What is the importance of DNA replication?

Answer 17

• The function of DNA is to contain the genetic information needed for the development and functioning of an organism.
• Each cell needs to contain a full set of DNA.
• During the lifetime of an organism, cells must divide for growth, reproduction and to replace old or damaged cells.
• When a cell divides into two cells, both daughter cells must also contain the full set of DNA, therefore DNA must first be replicated.

Question 18

When does DNA replication take place in the cell cycle?

Answer 18

During interphase: the phase before the cell starts to divide.

Question 19

Where is DNA stored in Eukaryotes?

Answer 19

• Stored in long, linear molecules called chromosomes which are found in the nucleus. Before a cell divides, every chromosome must first make a copy of itself.
• Eukaryotes also have circular DNA found in mitochondria and chloroplasts, which must also be replicated.

Question 20

Where is DNA found in Prokaryotes?

Answer 20

Found in a long, circular loop of DNA in the nucleiod with many smaller circular strands called plasmids.

Question 21

What is the role of DNA helices in replication?

Answer 21

Two polynucleotide strands are held together by hydrogen bonds between complementary base pairs, in order for DNA replication to occur, helix must first be ‘unzipped’ and hydrogen bonds broken. This is catalysed by the enzyme DNA helicase which moves along the DNA molecule. This creates a replication fork with two exposed single strands. THIS BIT NEEDS AJDUSTIVE PLESSE.

Question 22

What is the role of DNA polymerase in replication?

Answer 22

These DNA strands then act as a template for the new strands as free activated nucleotides pair with their complementary bases. New nucleotides are then joined to adjacent nucleotides by phosphodiester bonds in a condensation reaction. This is catalysed by DNA polymerase.
New DNA molecules fold into double helices as hydrogen bonds form within the molecules. THIS BIT NEEDS ADJSUYTIBEV PLEASE

Question 23

What is the role of ligase in DNA replication?

Answer 23

ADJUSTIVE PLEASE!

Question 24

What is semi-conservative replication?

Answer 24

Method in which DNA replicates, creating two molecules of DNA that consist of one original DNA strand and one newly synthesised DNA strand.

Question 25

What models were proposed for DNA replication by the scientific community?

Answer 25

Semi-conservative replication: the original DNA molecule is separated and the two new strands are synthesised.

Conservative replication: the original DNA molecule remains intact and a new copy is synthesised from new nucleotides.

Question 26

What did Mendelssohn and Stahl realise?

Answer 26

The distribution of old and new strands would be different depending on the model of replication.

Question 27

What was their method for labelling strands for testing?

Answer 27

-DNA is composed of two long chains of nucleotides, which each have a nitrogen-containing organic base.
-Nitrogen naturally occurs in two forms: the more abundant 14N and the less abundant 15N isotope.
- Mendelssohn and Stahl grew E.coli bacteria in a medium containing the heavier 15N for many generations.
-The bacteria incorporated the 15N into the new DNA molecules synthesised during replication.
- Resulted in a colony of bacteria that contained heavier DNA, providing a label for original strands. They also grew a control colony with the lighter 14N.
- The heavy DNA from the parent colony collected in a band near the bottom of the centrifuge tube. There were heavy and light strands, thus proving the theory of semi-conservative replication.

Question 28

What are genes?

Answer 28

Every molecule of DNA contains sections of DNA that are used to code for a specific polypeptide- these are called genes.
Some proteins are made up of multiple polypeptides and therefore are coded for by multiple genes.
Genes can also code for functional RNA- RNA that has a functional role in an organism other than coding for proteins.

Question 29

What processes must be carried out in order for a gene to code for a polypeptide?

Answer 29

1) Transcription: a section of the DNA molecule is transcribed into an RNA molecule called messenger RNA (mRNA).
2) Translation: the RNA molecule is then translated into a specific amino acid sequence.

Question 30

How is the primary structure (sequence of amino acids) determined in a gene?

Answer 30

By the sequence of bases. Primary structure determines tertiary shape, so DNA indirectly codes for the shape of proteins, and therefore their function.

Question 31

What is the genetic code?

Answer 31

The specific sequence of bases in DNA or RNA that codes for a sequence of amino acids during protein synthesis.

Question 32

What are the features of the genetic code?

Answer 32

Triplet code: three bases for one amino acid.
Degenerate: more than one triplet codes for the same amino acid. This reduces the effects of mutations: a change in the base sequence may not affect the amino acid sequence as the new triplet may still code for the amino acid.
Non-overlapping: each triplet only read once and triplets don’t share any bases.
Universal: the same in all organisms and species.
Contains ‘start’ and ‘stop’ codons which either start or stop protein synthesis. Start codon: methianine represented by one codon. There are three stop codons that are used to stop translation.

Question 33

What is a codon?

Answer 33

A codon is a sequence of three bases of RNA or DNA that codes for a specific amino acid.

Question 34

What is mRNA?

Answer 34

A smaller molecule used to transfer genetic information from the nucleus into the cytoplasm- messenger RNA.
Much smaller than a chromosome, so can be transported from the nucleus to the cytoplasm through nuclear pores.
mRNA is then able to associate with ribosomes in order to carry out the next stage of protein synthesis.

Question 35

What is the structure of mRNA?

Answer 35

A single stranded polynucleotide that coils into a single helix. Can be of varying length depending on the length of the gene that has been transcribed.
Although mRNA is single-stranded, RNA bases are able to temporarily form hydrogen bonds with complementary DNA bases.

Question 36

How does transcription occur?

Answer 36

1)Hydrogen bonds between complementary bases of the DNA double helix break and DNA uncoils, separating the two strands. This is catalysed by DNA helicase.
2)One of the DNA strands is used as a template to move the mRNA molecule. The template strand is referred to as the ‘antisense’ strand. The coding strand is referred to as the ‘sense’ strand, and has the same nucleotide sequence as the strand being synthesised.
3)Free nucleotides line up on the template strand by complementary base pairing and adjacent nucleotides are joint together by phosphodiester bonds, forming an mRNA molecule. Catalysed by RNA polymerase.
4) mRNA then moves out of the nucleus via a nuclear pore and attaches to a ribosome in the cytoplasm, the site of the next stage of protein synthesis.

Question 37

How does translation occur?

Answer 37

Amino acids join together to form a polypeptide chain:
1) mRNA attaches to a ribosome one the rough endoplasmic reticulum.
2) A tRNA molecule, which has a specific amino acid attached to its amino acid binding site, binds to the mRNA via it’s anticodon.
3) Hydrogen bonds form between the anticodon of the tRNA and the codon of the mRNA.
4) A second tRNA molecule binds to the next codon of the mRNA and the two amino acids form a peptide bond.
5) A third tRNA molecule joins and the first one leaves the ribosome.
This process is repeated thus leading to the formation of a polypeptide chain until a stop codon is reached on the mRNA.

Question 38

What is the structure of tRNA?

Answer 38

DIAGEAN HERE OKS

Question 39

What are mutations?

Answer 39

Changes to the genetic material of a cell. They can be small scale (gene mutations) or large scale (chromosome mutations)
Gene mutations occur spontaneously during the process of DNA replication.
Chromosome mutations are changes to the structure or number of whole chromosomes. These only occur during the process of meiosis.

Question 40

How are mutations inherited?

Answer 40

If it occurs during the formation of gametes it may be inherited by offspring. This is important for evolution as it increases genetic variation within a species.

Question 41

What happens when mutations occur during mitotic division of somatic cells?

Answer 41

It will not be inherited by offspring. Mutations that occur in somatic cells can often result in cancers.

Question 42

What are some of the causes of mutation?

Answer 42

They mainly occur spontaneously during the process of DNA replication. The rate of mutation is increased by mutagens: a chemical, physical or biological agent that causes mutations.

Question 43

Give some types of mutagens, examples and effects.

Answer 43

Type of mutagen: Example: Effect:
Physical Ionising radiation Breaks DNA strands
Chemical
TABLE HERE AFTER PRO OK
Mutagens that cause mutations in DNA that lead to the cell becoming cancerous are known as carcinogens.

Question 44

What is a point mutation?

Answer 44

When a mutation only involves a change to one or a few nucleotides.

Question 45

What is a substitution mutation?

Answer 45

Occurs when a nucleotide is replaced with another nucleotide that contains a different organic base. This changes the base sequence of the DNA strand and therefore changes the codon the nucleotide is present in.
As genetic code is degenerate, this may not change which amino acid is coded for by the new codon. Therefore sometimes there will be no change in the amino sequence of the protein.

Question 46

What are deletion mutations?

Answer 46

The removal of one or more nucleotides from the DNA sequence. This usually results in a frameshift mutation- where the reading frame for decoding the DNA sequence moves, meaning a change to every successive codon from the point of the deletion mutation.

Question 47

What is an insertion mutation?

Answer 47

Occurs when an additional nucleotide is inserted into the DNA sequence. This also usually results in a frameshift mutation; changes every codon from the point of the insertion mutation.

Question 48

What is the rule of frame shifting?

Answer 48

If the inserted or deleted number of nucleotides is a a multiple of three, a frameshift will not occur.

Question 49

What is meant by a ‘silent’ mutation?

Answer 49

Mutations that occur that do not effect protein structure and therefore maintain protein function- they are silent mutations.
Mutations can be silent for two different reasons:
- Mutation may have occurred in non-coding region of gene (intron)
- The genetic code is degenerate: the new codon may code for the same amino acid as the original to the original codon.

Question 50

What is a missense mutation?

Answer 50

Occurs due to a substitution of one nucleotide; only one amino acid will be changed.

Question 51

What is a conservative mutation?

Answer 51

If the amino acid changed has similar properties to the original amino acid, the structure of the protein may only slightly change. This means that the protein remains functional.

Question 52

What is a non-conservative missense mutation?

Answer 52

These significantly impact protein structure and function. They can occur when the changed amino acid has different properties, and/or if the changed amino acid is located in an important position in the protein. This can also occur when many amino acids are changed due to a frameshift mutation.

Question 53

What are nonsense mutations?

Answer 53

These occur when a mutation causes a codon which previously coded for an amino acid to become a stop codon. This premature stop results in the formation of a shortened protein, making it non-functional.