2.1.4 Nucleic Acids

What does DNA stand for? (recap of GCSE)

Deoxyribose Nucleic Acid

What does RNA stand for? (recap of GCSE)

Ribose Nucleic Acid

What is a double helix?

- Main shape of DNA.

- Coiling of two sugar-phosphate backbone strands

- Right-handed configuration

What does a nucleotide it consist of?

Consists of;

- One five-carbon based sugars

- One phosphate group

- One nitrogenous base

Is a nucleotide a monomer or a polymer?

Monomer.

What is the polymer of a nucleotide?

Nucleic acid.

Which carbon atom is a nitrogenous base linked to on a pentose sugar?

On the carbon one atom.

Which carbon atom is the phosphate group linked to?

On the carbon five or carbon three atom.

What molecules are nucleotides used in?

- Nucleic acids (RNA and DNA)

- AMP, ADP and ATP

What different coenzymes are nucleotides part of?

- NADP

- NAD

-FAD

- CoA

What are the differences between adenosine monophosphate and adenosine diphosphate?

AMP contains one phosphate group whereas ADP contains two phosphate groups

What is the difference between a nucleoside and a nucleotide?

- Nucleosides contains NO phosphate groups

- Nucleotides have one or more phosphate groups

DNA is a large molecule, what group is it associated with, that are known as "large molecules"?

DNA is part of the macromolecule umbrella term

What other macromolecules are there?

Lipids, carbohydrates and proteins

What is the structure of DNA? (Scroll!)

- DNA is a polymer made up of nucleotides

- Two stands run anti parallel

- Each DNA nucleotide has a phosphate group, deoxyribose sugar and one of four organic nitrogenous bases

- Contains phosphodiester bonds

- DNA is long and can carry a lot of information

What are the four nitrogenous organic bases in DNA?

Adenine

Thymine

Guanine

Cytosine

You do not need to draw these nitrogenous bases however the next following cards will have pictures of each base; remember to link each with their base!

Adenine nucleotide (as with the next cards, just remember which organic nitrogenous base links to which picture structure)

Guanine nucleotide

Cytosine nucleotide

Thymine nucleotide

Uracil nucleotide

What nitrogenous organic bases are part of the purines?

Adenine and guanine nitrogenous bases

What nitrogenous organic bases are part of the pyrimidines?

Thymine and cytosine nitrogenous bases

How many rings does purines have?

Two rings.

How many rings does pyrimidines have?

One ring.

How are the two antiparallel DNA strands held together?

Hydrogen bonds between the nitrogenous organic bases.

What nitrogenous organic base pairs with Thymine in DNA?

Adenine.

What nitrogenous organic base pairs with Guanine?

Cytosine.

How many hydrogen bonds are involved between Adenine and Thymine?

Two hydrogen bonds

How many hydrogen bonds are involved between Guanine and Cytosine?

Three hydrogen bonds.

Does one purine bond with themselves or with a pyrimidine?

A single purine unit will only bind with a pyrimidine.

Why is it that a purine binds only with a pyrimidine? (How does this relate to DNA coiling to form a helix)

1) Equal size rungs on the DNA ladder will be formed.

2) This therefore allows twisting of the DNA molecule

3) DNA molecules forms a double helix coil.

What does a double helix coil provide in DNA?

Stability to the nucleotide chain.

What will hydrogen bonds allow the molecule of DNA to do?

- Breaking hydrogen bonds for transcription and replication.

What is breaking hydrogen bonds also known as?

Unzipping (DNA/RNA)

Why is the phosphate backbone regarded as anti-parallel?

- One of the two DNA strands are always facing the opposite of its adjacent strand.

- 3' to 5' direction

- 5' to 3' direction

How are the two polynucleotide chains of DNA held together?

- Phosphodiester bonds in the backbone

- Hydrogen bonds between the bases

- Purines bind to pyrimidines

- 2 hydrogen bonds A and T

- 3 bonds between G and C

How is DNA organised in cells that are eukaryotic?

- Majority of DNA content is in the nucleus

- Each large molecule of DNA is tightly wound around special histone proteins

What is the purpose of tightly wound histone proteins?

Location of each molecule of DNA is secured in chromosomes.

Other than the nucleus, what other organelles can DNA be found in? (still eukaryotes)

- Mitochondria

- Chloroplasts

How is DNA arranged the mitochondria and the chloroplast?

Loop of DNA without histone proteins

How many molecules of DNA are/is in one chromosome

ONE molecule of DNA.

How is DNA organised in prokaryotic cells?

- DNA is in a loop within the cytoplasm and not in a nucleus

- NOT wound around histone proteins

- DNA is therefore regarded as "naked"

How does viruses contain DNA information? (repeated question)

Through loops of naked DNA

How do you extract and purify DNA?

1. If there is a cell wall (i.e cellulose), macerate the tissue

2. Add a strong detergent (i.e. washing-up liquid)

3. Add enzyme hydrolytic protease

3. Filter the culture

4. Place the culture in ice cold ethanol

Why do we macerate the tissue in step one?

To break down the cell walls

Why do we add a detergent?

To break down the cell surface membrane and nuclei double membrane

Why do we add a hydrolytic protease enzyme?

To break down histone proteins wrapped around chromosomes.

Why do we filter the culture?

To remove any excess matter solution detergent and salts

Why do we add ice-cold ethanol?

To precipitate the DNA.

What is a DNA polymerase?

An enzyme that catalyses the formation of DNA from activated deoxyribose nucleotides.

What does DNA polymerase use as a template to form DNA?

Uses single-stranded DNA as a template.

What is DNA helicase?

An enzyme that catalyses the breaking of hydrogen bonds between nitrogenous organic bases (DNA molecule)

What is semi-conservative replication?

How DNA replicates;

- Two new molecules are formed, both containing

- One old strand

- One new strand.

What happens in the first "stage" of semi-conservative replication?

1. The DNA molecule unwinds

2. Double helix is "untwisted" relatively slowly by DNA gyrase

3. DNA helicase unzips DNA breaking hydrogen bonds between nucleotide bases

4. Two single strands of DNA are left with exposed bases.

What happens in the second "stage" of semi-conservative replication?

5. Phosphorylated "activated" nucleotides that are free in the nucleoplasm attach to the exposed complementary organic nitrogenous bases.

6. DNA polymerase catalyses free nucleotides that are now attached to the exposed nitrogenous bases.

* DNA polymerase only does this in the 5' to 3' direction on the leading strand

* DNA polymerase only does this to a single strand of DNA

Before step 3, if you are still confused about this explanation. flip this card

1) Imagine two separate DNA old stands with free nucleotides on them that need to have their phosphodiester bonds catalysed to form two complete DNA strands

2) DNA polymerase joins nucleotides together.

3) Another enzyme called DNA ligase helps with what DNA polymerase does in this process but on one stand

For a reason that I will say later, our bodies has decided to use another enzyme that helps DNA polymerase (Imagine, for this process, DNA ligase helps DNA polymerase do the same thing).

Why is there a DNA polymerase that doesn't need a ligase on one strand and another strand that has polymerase and ligase to do the same job but needs a ligase enzyme I hear you ask ? Because the specification is lying to us. However for now believe that DNA ligase helps DNA polymerase only one one strand and on another strand DNA polymerase doesn't need ligase

4) DNA ligase + DNA polymerase works slower than just DNA polymerase.

5) One old strand is the "leading strand" and one strand is the "lagging strand"

6) DNA polymerase is faster therefore when attached to a old strand, will be the leading strand

7) DNA ligase + DNA polymerase is slower therefore when attached to a old strand, will be the lagging strand

8) Look at the next card with a picture

Picture for those still confused.

What happens in the final "stage" of semi-conservative replication?

7. Leading strand in synthesised continuously and the lagging strand is in fragments.

8. Lagging strand is later joined by DNA ligase enzymes

9. Hydrolysis of activated nucleotides releases phosphate ions and supplies energy to form phosphodiester bonds

Where else does semi-conservative occur?

- Loop of DNA in prokaryotes

- Inside mitochondria's loop of DNA

- Inside chloroplasts loop of DNA

How frequent is a mutation?

1 in every 100,000,000 possibility of a mutation

What reduces the rate of mutation?

Enzymes that proofread and edit out incorrect nucleotides

What is known as a different version of a gene?

Allele

Are all mutations harmful?

No, however;

- Many provide no difference of an advantage/disadvantage

- Some are harmful

- Few are beneficial.

Name the three different enzymes used in semi-conservative DNA replication

1. DNA Gyrase

2. DNA Helicase

3. DNA polymerase

What does gyrase do?

Unwinds the double branded helix of DNA

What does the enzyme helicase do?

Breaks hydrogen bonds between organic nitrogenous bases in DNA (DNA helicase) and RNA (RNA helicase)

What does the enzyme DNA polymerase do?

Joins free nitrogenous bases to the template stands nucleotides.

What is a gene?

- A length of DNA that codes for a polypeptide(s)

- A length of RNA that is involved in regulating gene expression.

What is a polypeptide?

- A polymer made of multiple amino acids joined by peptide bonds.

- Multiple polypeptides form proteins

What is a protein?

A large polypeptide made of 100 or more amino acids.

Sometimes multiple polypeptides can form a protein (quaternary structure)

What is transcription?

- Process of making messenger RNA from a DNA template

- Exportation of RNA out of the nucleolus and nucleus into the cytoplasm

What is translation?

Formation of a polypeptide at ribosomes through the assembling of amino acids in a particular sequence

Assembly depends on the gene transcript from the DNA

How is RNA structurally different to DNA?

- Sugar molecule in RNA is a ribose instead of deoxyribose

- Organic nitrogenous base Uracil replaces thymine (pyrimidine)

- Polynucleotide chain is single stranded compared to double stranded DNA

- Polynucleotide of RNA is shorter than DNA

- Three forms of RNA exist compared to one DNA form

How is ATP/ADP different to DNA nucleotide?

- ATP contains three phosphate groups, DNA nucleotide contains one phosphate group

- DNA contains deoxyribose, ATP/ADP contains a ribose

How is ATP/ADP the same to DNA nucleotide?

- Both contain a phosphate group

- Both contain adenine as an organic nitrogenous base

How does organic nitrogenous bases pairing allow identical copies of DNA to be made? (give the obvious paring of bases first)

- Adenine pairs only with Thymine

-Guanine pairs only with cytosine

- Purines only bind with pyrimidines do balance out the rings with hydrogen bonds

What are the three forms of RNA?

- mRNA / messenger RNA

- tRNA / transfer RNA

- rRNA / ribosomal RNA

What does a DNA base triplet determine of a protein from each gene?

- The R group of an amino acid, therefore;

- The protein's entire primary structure

Where are proteins made?

In ribosomes in the cytoplasm (and RER)

Why must a copy of each gene be transcribed?

As the instructions inside the gene cannot pass out of the nucleus to the ribosome (DNA is too big)

How does the cell pass information to the ribosome?

1. Transcribes a copy of the gene into a length of mRNA

2. Coded instructions are translated into the ribosome

* This is a complex of mRNA, tRNA and a ribosome

In mRNA form, what are the the sequence of base triplets called?

Codons

If DNA has a base sequence of CATG, what would be the complementary mRNA sequence?

CUAG

What are three constant rules of genetic code?

Genetic code is:

1. Universal

2. Degenerate

3. Non-overlapping

What is the Universal rule?

All living organisms use the same base triplets to code for the same amino acid.

What is the Degenerate rule?

There is more than one base triplet to code for the same amino acid.

i.e for Protein X there are 17 base triplets. One base change is less likely to cause a significant change to the protein.

What is the non-overlapping rule?

1. If one base is added or deleted the total number of bases changes, a "frame shift" occurs

2. Every triplet after that frame shift will be different.

3. The entire amino acid code changes.

What is the exact definition of non-overlapping and degenerate code?

Each nucleotide is only part of one triplet of bases and more than one triplet codes for a specific acid

What are the stages of transcription (5)

1. Gene unwinds and unzips

2. Hydrogen bonds between complementary organic nucleotide bases break

3. RNA polymerase catalyses the formation of temporary hydrogen bonds between RNA molecules and complementary unpaired DNA bases. DNA is the template strand

4. Length of RNA complementary to the template strand is produced (coding strand) and is a copy of the DNA stranded gene

5. mRNA passes out of the nucleus through the nuclear envelope and the nuclear pores and attaches to a ribosome.

Where are ribosomes made? What is produced?

Nucleolus, as two smaller subunits

How does the ribosomal subunits leave the nucleus?

Through the pores in the nuclear envelope.

What happens after the two smaller subunits leave the nuclear envelope?

The join to form a ribosome with the addition of magnesium ions.

Where are transfer RNA molecules made in? How do they leave?

The nucleolus. Exit via the double envelope through the nuclear pores

What is as the end of a tRNA? What do they do?

A trio of nucleotide bases that recognises and attaches to a specific amino acid.

What is at the other end of the loop of a tRNA molecule?

An anti-codon.

What are the feature of an anticodon?

It is complementary to a specific codon of bases on the mRNA

What is the process of the transfer RNA molecules and messenger RNA in the ribosome?

1. Transfer RNA molecules bring the amino acids to the ribosome and use their anticodons to temporarily bind (via hydrogen bonds) to a codon on the mRNA molecule

2 After many tRNA and mRNA molecules bond, the amino acids opposite side on the tRNA molecules bind to other amino acids on other tRNA molecules.

3. Peptide bonds form. This is helped by the ribosome.

4. Newly synthesised polypeptide is helped by chaperone cells to fold correctly into its tertiary structure

After polypeptide is assembled, what happens to the unneeded mRNA molecules?

mRNA breaks down and it's components molecules are recycled for new lengths of RNA.

Where does the energy needed for translation come from?

ATP.