Module 2 - Nucleotides Flashcards
What is DNA?
- Deoxyribose nucleic acid
-double stranded polymer - contains the genetic code used by the cell to make proteins
What is RNA?
- Ribonucleic acid
-single stranded polymer of nucleotide - used to make proteins
What are the 3 types different types of RNA?
- messenger
- transfer
- Ribosomal
what is the structure of RNA nucleotide?
- Phosphate group
- nitrogenous bases (A,C,G,U)
- Ribose sugar
what is the structure of DNA nucleotide?
- Phosphate group
- nitrogenous bases (A,C,G,T)
- deoxyribose sugar
What are purines?
large bases
What are the two types of purines?
- Adenine
- Guanine
What are pyrimidines?
smaller bases
what are the 3 types of pyrimidines?
- cytosine
- thymine
- uracil
How many rings are pyrimidines?
They are single rings
How many rings are purines?
They are double rings
Do purines and pyrimidines contain nitrogen in both?
yes
What are polynucleotides?
Nucleotides joined by condensation reactions to form polymers
What is a phosphodiester bond?
Bonds that form between the phosphate groups of one nucleotides and the sugar of another.
What is the 3’ and the 5’?
It is the number of carbon atoms in the sugar molecules
What is DNA composed of?
It is composed on 2 polynucleotide strands, joined together and twisted to form a double helix structure
What bonds are the DNA strands joined by?
Hydrogen binds between the specific pairs of bases
What is complementary base pairing?
How many bonds they are able to form when binded together.
What does adenine pair with and how many bonds do they form?
- thymine
- 2 hydrogen bonds
What does Guanine pair with and how many bonds do they form?
- cytosine
- 2 hydrogen bonds
What does cytosine pair with and how many bonds do they form?
- Guanine
- 3 hydrogen bonds
What does Guanine pair with and how many bonds do they form?
- cytosine
- 3 hydrogen bonds
What is the base pairing rule with purines and pyrimidines?
- smaller pyrimidines always pair up with larger purines
What is the rule between A & T or G & C ?
The number of A & T molecules will always be equal and the number of C & G will always be equal.
What does it mean if 2 strands are antiparallel?
The two strands are arranged so that they run in opposite directions.
Is DNA twisted into a double helix?
- Yes
- the 2 joined polynucleotide strands are then twisted into a double helix and held by hydrogen bonds.
How does coiled DNA relate to its function?
- It has a compact shape
- can be stored in a small space - nucleus
How does base sequence relate to its function?
It acts as the genetic code
How does the double stranded DNA structure relate to its function?
Allows for accurate replication of DNA when needed
How does the double helix DNA structure relate to its function?
Makes it a more stable structure and this protects the genetic code from damage
Why do we grind the sample in a mortar and pestle?
This breaks down the cell wall
Why do we mix the sample with the detergents?
- This breaks the cell membrane, releasing the cell contents into solutions
Why do we add salt to the sample?
This breaks the hydrogen bonds between the DNA and the water molecules
Why so we add a layer of ethanol on top of the sample?
alcohol causes the DNA to precipitate out of the solution
What does ATP stand for?
Adenosine Tri Phosphate
Structure of ATP?
- always has the base ADENINE
- sugar ribose
- 3 phosphate heads
Why does the cell require energy?
-synthesis - e.g. for large molecules like proteins
- transport - pumping molecules across the cell membrane
- movement - e.g. protein fibres cause muscle contraction
What happens when ATP is broken down?
- Forms ADP and Pi
- by hydrolysis reaction
- releases energy
Where is ATP made in the cell?
In the mitochondria
Where does aerobic respiration produce ATP from?
glucose and oxygen
How does the structure of ATP make it a good energy source? (1)
- small molecule - easy to move around within a cell
- water solution - reactions that require energy in cells occur in aqeuous solutions
How does the structure of ATP make it a good energy source? (2)
- releases small amounts of energy - hydrolysis of a single ATP molecule releases a suitable amount of energy to dive on cellular respiration
How does the structure of ATP make it a good energy source? (3)
Easily regenerated: when ATP is used, it is quickly regenerated by aerobic respiration in the cell
Why does DNA need to replicate itself?
- Cells carries out Mitosis, forms 2 daughter cells genetically identical to the original.
- Before a cell carries out Meiosis it needs to replicate the DNA to be shared against the 4 daughter cells.
(DNA replication) - What is the first step of DNA replication?
2 strands in the DNA double helix unwinds and separates, exposing the bonds?
(DNA replication) - How does the DNA double helix wind?
It uses the enzyme DNA helicase
(DNA replication) - What bonds are broken when the helix unwinds?
Hydrogen bonds
which are broken between the complementary bases so the 2 strands separate
(DNA replication) - Are there any free nucleotides in the cell?
Yes, there are free DNA nucleotides in the cell nucleus
(DNA replication) - What happens when the 2 strands separate?
The free nucleotides will line up next to the exposed bases, by complementary base pairing
(DNA replication) - What bonds form between the exposed bases?
New hydrogen bonds form between the exposed bases on the original strand and the new ones
(DNA replication) - as well as bonds, what else is formed?
New sugar phosphate back bones are formed (phosphodiester bonds form) - involves enzyme DNA polymerase
(DNA replication) - what enzyme forms the sugar phosphate back bones?
DNA polymerase
Why is it called semi conservative DNA replication?
It has one original strand and has one new strand
Does DNA in all organisms replicate the same way?
yes it does
What direction can the DNA polymerase move?
One direction (3’ to 5’)
What is the leading strand?
One of the strands is continuously replicated
What is the lagging strand?
The other strand that has to be copied in sections as it unwinds.
What is a mutation?
A change in the DNA base sequences
what are the consequences of a mutation?
- Changes in the primary structure of the protein.
- may result in a change to the protein being coded for or may no longer function properly.
What is a gene?
A section of DNA that contains the complete sequence of bases to code for a protein.
What 3 types of RNA are there?
- mRNA
- tRNA
- rRNA
What is mRNA?
- (messenger RNA)
- single polynucleotide strand
- made in the nucleus during transcription
What is mRNA main role?
- carries the genetic code from the DNA in the nucleus to the cytoplasm, where it is used to make a protein during translation
What are codons?
groups of three adjacent bases in mRNA
what is tRNA?
- transfer mRNA
- single polynucleotide strand that is folded into a clove shape
- hydrogen bonds between specific base pairs hold the molecule in shape.
What is an anticodon?
when a tRNA molecule has a specific sequence of three bases at one end.
What is the main role of tRNA?
-found in the cytoplasm
- involved in translation
- carries the amino acids that are used to make proteins to the ribosomes.
Are anticodons on the tRNA complementary to codons on mRNA?
yes
What is rRNA?
- ribosomal rna
- forms 2 subunits in a ribosome, along with proteins.
- ribosomes move along the mRNA strand during protein synthesis.
What is the main role of rRNA?
It helps catalyse the formation of peptide bonds between the amino acids.
Why is it called ribosomal RNA?
it makes up the ribosomes
What does it mean the genetic code is a triplet code?
Each amino acid is coded for by a sequence of 3 bases.
What are the two stages of protein synthesis?
Transcription and Translation
Why does protein synthesis occur?
The DNA is too big to leave the nucleus and cannot travel to a ribosome, so the DNA is coverted to mRNA.
Which stage of protein synthesis occurs first?
Transcription
Where does transcription occur?
Nucleus
(Transcription) - stage 1 - what is the first stage of transcription which involves the enzyme DNA helicase?
- DNA helicase attaches to the DNA at the beginning of the gene.
- Causes the unwinding of the DNA helix and breaks the hydrogen bonds.
(Transcription) - stage 2 - what happens after the unwinding of the DNA helix?
- The two strands separate
- one strand is the coding strand
- the other strand is the template strand
(Transcription)- stage 3 - What does the template strand do?
It is used to make the a mRNA copy of DNA.
(U replaces T)
(Transcription)- stage 4 - What do the free nucleotides do?
- The free nucleotides are present in the cell nucleus
- they line up by complementary bases pairing next to the exposed DNA bases on the template strand.
(Transcription)- stage 5 - what does RNA polymerase do?
RNA polymerase joins the sugar phsophate back bones of the new mRNA molecules being made, until its complete.
(Transcription)- stage 6 - What happens when the enzyme has passed a section?
The DNA molecule reforms
(2 strands re-join)
(Transcription)- stage 7 - what is the final step of transcription?
the mRNA carries the same code as the DNA coding strand
- except U has replaced T)
What are introns?
the non-coding part of the amino acids
What happens to the introns/ how is pre-mRNA produced?
- introns are copied from the DNA to mRNA
producing pre-mRNA
What happens to the introns/ how is functional mRNA produced?
they cut out of the mRNA using enzyme before it leaves the nucleus
- produces functional mRNA
- mRNA is capped before it leaves the nucleus to prevent it from being damaged in the cytoplasm
What happens when the functional mRNA leaves the nucleus?
- it travels to the ribosomes
Where does translation occur?
In the ribosomes
(Translation) - stage 1 - what is the first step of translation?
- The genetic code on the mRNA will be used to assemble a corresponding chain of amino acids
(Translation) - stage 2 - what happens when the mRNA attaches to the ribosomes?
-the mRNA attaches to the ribosomes, every group of 3 bases on the mRNA is called a codon
(Translation) - stage 3 - what does the tRNA molecules contain?
It contains triplets at one end called anticidons.
- these line up next to the codons on the mRNA complementary base pairing (temporary hydrogen bonds)
(Translation) - stage 4 - what does the the end of the tRNA molecule have attached?
the other end of the tRNA molecule has a specific amino acid attached
(Translation) - stage 5 - what happens after the ribosomes hold the two RNA molecules?
- The ribosomes hold the tRNA molecules in position at the same time, allowing their amino acids to join by a peptide bond
(Translation) - stage 6 - what happens when the first tRNA molecule leaves the ribosome?
- the tRNA molecule leaves the ribosomes, leaving its amino acids behind and another tRNA arrives with its amino acid.
(Translation) - stage 7 - how do the amino acids join?
- the ribosomes move along so that the next two tRNA molecules are in position, allowing their amino acids to join, peptide bonds forms, then the second tRNA molecule moves away
- the process continues
(Translation) - stage 8 - How long does the process go on for?
Happens until the a “STOP” codon on the mRNA is reached, signalling that the polypetide is now complete.
(Translation) - stage 9 - where is the polypetide released?
Tje polypeptide is released into the cyoplasm, this is the primary protein structure, and then build up further into a complete functionin protein
What does it mean the code is degenerate?
there are more possible triplet codes (64) than there are amino acids (20)
What does it mean that the code is non-overlapping?
The base code does not share their bases, each triplet is distinct from the next
what does it mean the code is universal?
All organisms use the same code although the sequences of base coding for each individual protein will be different
What are some differences between RNA and DNA
DNA
- double stranded
- thymine
- deoxyribose
- double helix of 2 antiparallel polynucleotide chains
- one type of DNA with numerous variations
- used as a long term storage of genetic information
- long lived stable molecule
RNA
- single stranded
- uracil
- ribose
- one polynucleotide chain twists into a helix
three types of RNA (mRNA, tRNA, rRNA)
- role - protein syntheis
- short- lived and not stable
