DNA,RNA and protein synthesis Flashcards
Nucleotides
Consist of 3 parts:
- A five carbon sugar molecule called a
PENTOSE SUGAR.
- A nitrogen-containing molecule called a
BASE.
- Negatively charge PHOSPHATE GROUP.
- The covalent bond between the sugar and the phosphate group is also called a PHOSPHODIESTER BOND.
Contain the ELEMENTS:
- Carbon
-Hydrogen
- Oxygen
- Nitrogen
- Phosphorus
- Used to make both the molecules DNA and RNA.
Polynucleotide
A PHOSPHODIESTER BOND is formed between:
- PHOSPHATE GROUP of nucleotide
- The HYDROXYL GROUP on carbon 2 of the pentose sugar of the other nucleotide.
Water is released ~ CONDENSATION reaction.
- The molecule we have formed between TWO nucleotides is called a DINUCLEOTIDE
- If we continue to add nucleotides by forming phosphodiester bonds we will form a polymer of nucleotides known as a POLYNUCLEOTIDE.
- Both DNA and RNA are examples of polynucleotides.
- We can BREAK the phosphodiester bond by adding back water known as a HYDROLYSIS reaction.
DNA & its structure
A nucleic acid and one of the important MACROMOLECULES that make up the structure of living organisms.
- consists of two POLYNUCLEOTIDE strands which twist around each other to form a DOUBLE HELIX.
- A 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.
COMPLEMENTARY bases
- 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.
- This complementary base pairing is 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.
What does it mean that the two polynucleotide strands in DNA are ANTIPARALLEL?
- 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.
The number of HYDROGEN BONDS formed between complementary pairs and the PROPORTIONS of different nucleotides.
GUANINE & CYSTOSINE ~ 3
ADENINE & THYMINE ~ 2
- Because of complementary base pairing, the proportion of G & C are always the same and the proportions of A&T are always the same.
- This means 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
DNA nucleotides
- the pentose sugar is called DEOXYRIBOSE which has one fewer OXYGEN atoms than ribose.
- LONG polynucleotide chain
- FOUR different bases ~ adenine , cytosine guanine and THYMINE.
RNA nucleotides
- Have the pentose sugar RIBOSE
- SHORT polynucleotide chain.
- FOUR different bases ~ adenine , guanine , cytosine and URACIL.
Differences in DNA and RNA
(not already mentioned)
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.
DNA replication STEPS
GYRASE ~ Unwinds the DNA
HELICASE :
- This enzyme attaches to the DNA molecule.
- 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:
- This enzyme now attaches to the DNA molecule.
- Moves down the molecule and catalyses the formation of a PHOSPHODIESTER bond between the activated nucleotides.
- This is an example of a CONDENSATION reaction.
- 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.
Mutations
- Sometimes an INCORRECT BASE is inserted into the growing polynucleotide strand.
- This means the DNA sequence has CHANGED.
- This is called a MUTATION which are RANDOM and occur SPONTANEOUSLY.
- Can have very SERIOUS EFFECTS on the organism.
TRANSLATION in 8 steps
- Once the mRNA moves from the nucleus into the cytoplasm, a ribosome binds with the mRNA at the START CODON.
- 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. - Now a second tRNA molecule moves into place.
The anticodon on this tRNA is complementary to the second codon on the mRNA. - 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. - Now the ribosome moves to the next codon and forms a peptide bond to the next amino acid.
- The first tRNA molecule is released and later attaches to their amino acid by enzymes in the CYTOPLASM.
- The ribosome continues moving down the mRNA forming the POLYPEPTIDE.
- When the ribosome comes to a STOP CODON , it DETATCHES and the polypeptide chain is released.
mRNA nucleotides
- The nucleotide sequence of the mRNA is used to determine the amino acid sequence of the polypeptide.
- the mRNA nucleotides are read as a series of TRIPLETS known as the GENETIC CODE.
tRNA
- 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.
3 featured of the genetic code
- DEGENERATE ~ most amino acids have more than one triplet, usually FOUR.
- NON-OVERLAPPING ~ no base is read more than once.
- UNIVERSAL ~ the same triplets encode the same amino acids in the vast majority of organisms on planet earth.
START & STOP triplets
START ~ determine where to start translating the mRNA molecule.
STOP ~ determines where translation stops.
Why can a large number of polypeptide molecules be produced rapidly?
- 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.
DNA in PROKARYOTES
- Circular DNA with no free ends.
- Relatively short
- Not bound to histones
DNA in EUKARYOTES
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.
How do chromosomes become VISIBLE in the cell?
- In the nucleus of a eukaryotic cell, the dark material is the DNA bound to histones.
- It is not possible to see any distinct chromosomes because at this stage, the chromosomes have a relatively 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.
Why is DNA replication a SEMI-CONSERVTIVE replication?
- 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.
What if DNA replicated CONSERVATIVELY?
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.
Which ELEMENT was used to test that DNA replicated semi-conservatively?
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 .
How scientists SHOWED that DNA replicates semi-conservatively - STEP 1
- 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.
How scientists SHOWED that DNA replicates semi-conservatively - STEP 2
- 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.
How scientists SHOWED that DNA replicates semi-conservatively - STEP 3
- 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.
What happened when the scientist allowed the bacteria to replicate one more time on NITROGEN-14?
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.
Why is ATP needed?
- 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.
- This means that cells need a way to transfer the energy from the glucose molecule , into SMALLER & 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 THIRTY molecules of ATP
- Also PHOSPHORYLATES molecules to make them more REACTIVE.
What is ATP ?
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.
The STRUCTURE of 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.
- 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.
- Breaking this bond requires a water molecule so is a HYDROLYSIS REACTION.
- This energy can then be used by processes in the cell.
GENE
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)
TRANSCRIPTION
The process of DNA being copied into mRNA.
- The enzyme 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.
RNA splicing
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.
