DNA,RNA & Protein Synthesis

Question 1

Nucleotides

Answer 1

MONOMERS from which nucleic acids, such as DNA & RNA are formed

Consist of 3 parts:
- A five carbon sugar molecule called a
PENTOSE SUGAR.
- A nitrogen-containing molecule called a
BASE.
- Negatively charge PHOSPHATE GROUP.

Contain the ELEMENTS:
- Carbon
- Hydrogen
- Oxygen
- Nitrogen
- Phosphorus

Question 2

Polynucleotide

Answer 2

PHOSPHODIESTER BOND is formed between:
- PHOSPHATE GROUP of nucleotide
- The HYDROXYL GROUP on carbon 2 of the pentose sugar of the other nucleotide.

CONDENSATION REACTION ~ a water molecule is formed.

TWO nucleotides joined together~ DINUCLEOTIDE

POLYNUCLEOTIDE ~ 3 or more phosphodiester bonds formed between nucleotides.
Examples ~ DNA & RNA

HYDROLYSIS REACTION ~ addition of a water molecule to break the phosphodiester bond

Question 3

DNA & its structure

Answer 3

• NUCLEIC ACID

-MACROMOLECULE that make up the structure of living organisms.

• TWO POLYNUCLEOTIDE strands which twist around each other to form a DOUBLE HELIX.
• SUGAR-PHOSPHATE BACKBONE on the outside with the BASES in the centre.
• HYDROGEN BONDS ~ hold the two polynucleotide strands together, form between the bases on opposite strands.

Question 4

COMPLEMENTARY base pairing

Answer 4

• The bases on one strand are complementary to the bases on the other strand.
• GUANINE on one strand always pairs with CYSTOSINE on the opposite strand.
• ADENINE always pair with THYMINE.
• CENTRAL to how DNA functions.
• A PURINE (two rings) base always pairs with a PYRAMIDINE (one ring) base on the opposite strand.
• This means the DISTANCE between the sugar phosphate backbones is CONSTANT all down the DNA molecule.

Question 5

What does it mean that the two polynucleotide strands in DNA are ANTIPARALLEL?

Answer 5

• They run in OPPOSITE directions.

ONE STRAND:
- The top phosphate group will be attached to carbon 5 of the deoxyribose sugar.

• At the bottom , the hydroxyl group will be attached to carbon 3.

OTHER STRAND:
- The carbon 3 hydroxyl group is at the top.

• At the bottom we have the carbon 5 attached to the phosphate group.

Question 6

The number of HYDROGEN BONDS formed between complementary pairs and the PROPORTIONS of different nucleotides.

Answer 6

GUANINE & CYSTOSINE ~ 3
ADENINE & THYMINE ~ 2

• PROPORTION of G&C and A&T are always the same.
• We can CALCULATE the proportions of different nucleotides.

Proportions of a base can change in different species due to different :
- proteins
- genes
- DNA bae sequences

Question 7

DNA nucleotides

Answer 7

• Pentose sugar ~ DEOXYRIBOSE, one fewer OXYGEN atoms than ribose.
• LONG polynucleotide chain
• FOUR different bases ~ adenine , cytosine guanine and THYMINE.

Question 8

RNA nucleotides

Answer 8

• Pentose sugar RIBOSE
• SHORT polynucleotide chain.
• FOUR different bases ~ adenine , guanine , cytosine and URACIL.

Question 9

Differences in DNA and RNA
(not already mentioned)

Answer 9

DNA:
- Found in CHROMOSOMES in the nucleus
- TWO polynucleotide strands in a double helix.

RNA:
- Found in the CYTOPLASM where it plays a key role in protein synthesis.
- ONE polynucleotide strand.

Question 10

DNA replication STEPS

Answer 10

GYRASE ~ Unwinds the DNA

HELICASE :
- Causes the hydrogen bonds between complementary bases to BREAK.

-This causes the two polynucleotide strands to separate from one another.

• Both strands act as a TEMPLATE
• The ACTIVATED nucleotides (contain 3 phosphate group rather than one) now line up with their complementary bases on the DNA strands and are held in place by HYDROGEN BONDS only.

DNA POLYMERASE:

• Catalyses the formation of a PHOSPHODIESTER bond between the activated nucleotides.
• CONDENSATION REACTION ~ a water molecule is formed
• The activated nucleotides now lose their EXTRA TWO phosphate groups which leave and provide ENERGY for the reaction.
• We have now got TWO copies of our double stranded DNA molecule.

Question 11

Mutations

Answer 11

• When an INCORRECT BASE is inserted into the growing polynucleotide strand.
• Caused DNA base sequence to CHANGE
• Occur RANDOM and occur SPONTANEOUSLY.
• Can have very SERIOUS EFFECTS on the organism.

Question 12

TRANSLATION in 8 steps

Answer 12

1. Once the mRNA moves from the nucleus into the cytoplasm, a ribosome binds with the mRNA at the START CODON.
2. A tRNA molecule with an ANTICODON complementary to the start codon attaches.
   The tRNA delivers 1 SPECIFIC amino acid.
   This is held in place by HYDROGEN BONDS between the complementary base pairs on the mRNA and tRNA.
3. Now a second tRNA molecule moves into place.
   The anticodon on this tRNA is complementary to the second codon on the mRNA.
4. A PEPTIDE BOND is formed between the two amino acids using energy provided by ATP.
   This is catalysed by the enzyme peptidyl transferase which is part of the rRNA.
5. Now the ribosome moves to the next codon and forms a peptide bond to the next amino acid.
6. The first tRNA molecule is released and later attaches to their amino acid by enzymes in the CYTOPLASM.
7. The ribosome continues moving down the mRNA forming the POLYPEPTIDE.
8. When the ribosome comes to a STOP CODON , it DETATCHES and the polypeptide chain is released.

Question 13

mRNA nucleotides

Answer 13

• The mRNA nucleotid is used to determine the amino acid sequence of the polypeptide.
• Read as a series of TRIPLETS known as the GENETIC CODE.

Question 14

tRNA

Answer 14

• TRANSFER RNA
• Single stranded
• Clover shaped
• Larger than mRNA
• TOP of molecule is a BINDING SITE for an amino acid.
• BOTTOM is a TRIPLET of bases called the ANTICODON.
• The anticodon is COMPLEMENTARY to the triplet of bases in the mRNA called the CODON for that amino acid.
• Many amino aids are encoded by SEVERAL triplets , each one of these will have a corresponding tRNA.

Question 15

3 featured of the genetic code

Answer 15

1. DEGENERATE ~ most amino acids have more than one triplet, usually FOUR.
2. NON-OVERLAPPING ~ no base is read more than once.
3. UNIVERSAL ~ the same triplets encode the same amino acids in the vast majority of organisms on planet earth.

Question 16

START & STOP CODONS

Answer 16

START ~ determine where to start translating the mRNA molecule.

STOP ~ determines where translation stops.

Question 17

Why can a large number of polypeptide molecules be produced rapidly?

Answer 17

• Once the first ribosome has started moving along, another ribosome can attach to the start codon and begin translating.
• This may cause a whole line of ribosomes making their way along the mRNA, allowing the process to occur quickly.

Question 18

DNA in PROKARYOTES

Answer 18

• Circular DNA with no free ends.
• Relatively short
• Not bound to histones

Question 19

DNA in EUKARYOTES

Answer 19

In the NUCLEUS:
- Linear DNA with two ends.
- Much longer
- Tightly wrapped around histone proteins.

Also find DNA in the MITOCHONDRIA & CHLOROPLASTS:
- This DNA is very similar to the DNA found in prokaryotes.
- Relatively short, circular and not attached to histones.

Question 20

How do chromosomes become VISIBLE in the cell?

Answer 20

• In the nucleus of a eukaryotic cell, the dark material is the DNA bound to histones.
• Chromosomes are NOT visible ~ OPEN STRUCTURE.
• At this point, we refer to the DNA and histones as CHROMATIN.
• Before a cell divides, all of the chromosomes are COPIED.
• These two copies remain attached at a point called the CENTROMERE.
• Now the DNA molecules are called CHROMATIDS.
• At this stage we refer to the entire structure as a CHROMOSOME.
• The chromosomes CONDENSE , the DNA and histones form densely packed loops and coils.
• The chromosomes are now VISIBLE in the cell.

Question 21

Why is DNA replication a SEMI-CONSERVTIVE replication?

Answer 21

• The DNA double helix separates into TWO polynucleotide strands.
• Each strand is then REPLICATED into a complementary NEW strand.
• So at the end, ONE molecule of DNA has been copied into TWO molecules of DNA.
• Each of the two copies contains one strand from the ORIGINAL DNA molecule and one NEW strand.

Question 22

What if DNA replicated CONSERVATIVELY?

Answer 22

This would produce:
- One molecule of DNA containing TWO ORIGINAL strands.
- One molecule of DNA containing TWO NEW strands.

ONE ROUND OF REPLICATION :
- One DNA molecule containing only nitrogen-15 .
- One DNA molecule containing only nitrogen-14.

TWO ROUNDS OF REPLICATION:
- One DNA molecule containing only nitrogen-15.
- THREE DNA molecules containing only nitrogen -14.

This means we would have NO DNA molecules containing BOTH nitrogen-14 and nitrogen-15.

Question 23

Which ELEMENT was used to test that DNA replicated semi-conservatively?

Answer 23

NITROGEN:
- All the bases in DNA contain the element nitrogen which exists in two main forms or isotopes:
- Nitrogen-14 (lighter)
- Nitrogen-15 (heavier)

• Due to their difference in MASSES , they form a BAND in different positions .

Question 24

How scientists SHOWED that DNA replicates semi-conservatively - STEP 1

Answer 24

• Took a sample of BACTERIA .
• Under normal conditions , almost all of the NITROGEN atoms in the DNA of these bacteria will be N-14 (lighter)
• EXTRACTED the DNA , placed in a SOLUTION, and spun this at very high speeds in a CENTRIFUGE.

-The DNA moved down the solution and formed a BAND which the scientists could detect.

• As it mostly contained the lighter isotope, the band formed near the TOP of the tube.

Question 25

How scientists SHOWED that DNA replicates semi-conservatively - STEP 2

Answer 25

- Next the scientist cultured the bacteria in a growth medium which only contained NITROGEN-15. - After the bacteria had REPRODUCED many times, almost all the nitrogen atoms in the DNA were N-15. - When this DNA was extracted and centrifuged , it formed a band near the BOTTOM due to be the HEAVIER isotope.

Question 26

How scientists SHOWED that DNA replicates semi-conservatively - STEP 3

Answer 26

- The scientist took a sample of the bacteria which had been growing on NITROGEN-15. - TRANSFERRED these bacteria to a NITROGEN-14 and allowed them to REPLICATE their DNA only ONCE. - DNA was EXTRACTED and spun in a CENTRIFUGE. - This DNA produced a band IN BETWEEN the two bands produced before. - This shows that this DNA contained one strand with NITROGEN-14 and one strand with NITROGEN-15. - This means that DNA must have replicated SEMI-CONSERVATIVELY.

Question 27

What happened when the scientist allowed the bacteria to replicate one more time on NITROGEN-14?

Answer 27

It produced a band pattern: - One band~ same position as the band shown when DNA has replicated once. - Second band~ same position as the band shown with only NITROGEN-14. This is because the second round of replication produces FOUR DNA molecules: - TWO contain a strand with N-14 and a strand with N-15. - TWO both contain two strands with only N-14.

Question 28

Why is ATP needed?

Answer 28

- Carbohydrates and triglycerides are used as LONG-TERM storage molecules. - For example, the molecule GLYCOGEN can be hydrolysed to produce GLUCOSE. - This glucose can then be used as a source of energy through respiration. - PROBLEM~ glucose contains a great deal of stored energy , much more than would ever be required by any single process in the cell. ATP: - transfers the energy from the glucose, into SMALLER & USEFUL amounts. - IMMEDIATE energy source - PHOSPHORYLATES molecules to make them more REACTIVE.

Question 29

What is ATP ?

Answer 29

ATP: - A nucleotide - Acts as an IMMEDIATE energy source - Transfers energy from the site of RESPIRATION , to the parts of the cell which require energy. Processes that require this energy: - Active transport -Muscle contraction - Formation of larger molecules such as proteins.

Question 30

The STRUCTURE of ATP

Answer 30

- 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. - It only takes a SMALL AMOUNT of energy to break the covalent bond holding the last phosphate group in place. - But when this bond is broken, a GREAT DEAL OF ENERGY is released ( converted to ADP) - Breaking this bond requires a water molecule so is a HYDROLYSIS REACTION. - This energy can then be used by processes in the cell.

Question 31

GENE

Answer 31

A length of DNA that codes for a polypeptide or for a length of RNA that is involved in regulating gene expression. - Within each gene , there is a sequence of DNA BASE TRIPLETS that determines the amino acid sequence , or primary structure of a polypeptide. - Some do NOT encode for polypeptides but instead functional RNA molecules such as TRANSFER RNA (tRNA) and RIBOSOMAL RNA ( rRNA)

Question 32

TRANSCRIPTION

Answer 32

The process of DNA being copied into mRNA. - DNA HELICASE breaks the hydrogen bonds between the bases - The DNA helix UNWINDS - ONE strand acts as a TEMPLATE - RNA POLYMERASE joins the RNA nucleotides by forming PHOSPHODIESTER BONDS. - These nucleotides line up by complementary base pairing, A-T,C-G,A-U. - The enzymes continue making their way along the DNA until they reach the end of a gene. - The mRNA has now been SYNTHESISED and the RNA polymerase DETATCHES from the DNA and the DNA goes back to its normal double helix structure. - The mRNA now moves out of the nucleus through a NUCLEAR PORE ,where it enters the cytoplasm, ready to take part in TRANSLATION.

Question 33

RNA splicing

Answer 33

Converts the pre-mRNA into FUNCTIONAL mRNA. - Non-coding and coding regions DNA are found both between and within GENES. Non-coding regions ~ INTRONS Coding regions ~ EXONS - In humans , many genes contain a large number of INTRONS. - During transcription, both EXONS and INTRONS are copied into RNA. - This means RNA contains non-coding regions called PRE -mRNA. - Once the pre-mRNA is formed , the INTRONS on then REMOVED and the ends of the EXONS connected ( splicing). - This process does not take place in PROKARYOTES as INTRONS are UNCOMMON.