Core Concepts: Nucleic Acids Flashcards
What is the general term given to a monomer of a nucleic acid?
nucleotide
What is the general term given to a polymer of a nucleic acid?
poly-nucleotide
What does DNA stand for?
deoxyribonucleic acid
Draw and label a DNA nucleotide
- Phosphate
- Pentose Sugar (Deoxyribose sugar)
- Organic Nitrogenous Base
What are the 4 possible bases in DNA?
Adenine, Thymine, Cytosine, Guanine
Which bases are purines and which are pyrimidines?
Purines: Adenine and Guanine
Pyrimidine: Thymine and Cytosine
What is the bond formed between the parallel bases in DNA?
Hydrogen Bond
What is the complementary base pair rule?
A - T
C - G
pairs are found together
How many bonds form between each of the complementary pairs to join the strands?
A - T = 2 bonds
C - G = 3 bonds
What specifically makes up the sugar phosphate backbone?
deoxyribose sugar and phosphate
Name the bond that forms between the nucleotides and the sugar phosphate backbone
Phosphodiester bond
What type of reaction forms a phosphodiester bond?
condensation
Suggest a function for the sugar phosphate backbone
Protection from things that could cause mutation (radiation, e.g. UV, smoking etc)
What does RNA stand for?
Ribonucleic acid
Draw and label a RNA nucleotide
- Phosphate
- Pentose sugar (ribose sugar)
- Organic nitrogenous base
What are the 4 possible organic nitrogenous bases in RNA?
Adenine, Uracil, Cytosine and Guanine
Which bases are purine or pyrimidine in RNA?
Purine: Adenine and Guanine
Pyrimidine: Uracil and Cytosine
Which base is present in RNA but not DNA?
Uracil
What does mRNA mean?
messenger RNA
What is the shape and structure of mRNA?
Long single stranded molecule formed into a helix
What is the function of mRNA?
- Manufactured in the nucleus
- Carries the genetic code from the DNA in the nucleus to the ribosome
What does tRNA mean?
transfer RNA
What is the shape and structure of tRNA?
Small single stranded molecule which forms a clover leaf shape.
One end is where the amino acid attaches.
At the opposite end of the molecule is a series of 3 bases called anticodon.
What is the function of tRNA?
Bring amino acid molecules to the ribosome so that proteins can be synthesised
What does rRNA stand for?
ribosomal RNA
What is the shape and structure of rRNA?
Long, large complex molecule made up of both double and single stranded helices
What is the function of rRNA?
Ribosome are made up of rRNA and proteins
State the differences between a DNA nucleotide and an RNA nucleotide?
DNA
• deoxyribose sugar • bases: A, T, C, G
RNA
• ribose sugar • bases: A, U, C, G
State how a polymer of DNA would be different from a polymer of RNA?
DNA
• double stranded -> double helix
• has only one type
• larger, as it contains many genes
RNA
• single stranded -> single helix
• has 3 types of RNA: mRNA, tRNA, rRNA
• smaller, e.g. mRNA as it is the copy of only 1 gene
What does ATP stand for?
adenosine triphosphate
Describe the structure of ATP
- base adenine
- sugar ribose
- 3 phosphate groups
What is meant by ATP being the “energy currency of the cell”
- it’s used by all living organisms in every cell
- carries energy from energy-releasing reactions to energy consuming reactions
- used to provide energy for nearly all biochemical reactions in the cell
Describe the reactions that takes place for formation of ADP
When energy is needed…
- ATPase hydrolyses bond between 2nd and 3rd phosphate groups, removing the 3rd phosphate group
- ATP molecule is hydrolysed into adenosine diphosphate (ADP), an inorganic phosphate ion, with release of energy
- exergonic reaction as it releases energy
How much energy is released in the hydrolysis of ATP?
30.6kJ for every mole released when the bond is broken
Describe the reaction that takes place for the formation of ATP
- reverse reaction to the formation of ADP
- the addition of phosphate to ADP is called phosphorylation
- condensation reaction
- requires input of 30.6kJ, endergonic reaction
Write the equation for ATP and ADP
ATP + water ⇌ ADP + Pi + ΔH
- ΔH = -30.6kJ mol^-1
What are the roles of ATP?
- Active transport - to allow molecules to move against concentration gradient
- Synthesise large complex molecules from smaller ones (e.g. protein synthesis)
- Nerve transmission - sodium-potassium pumps actively transport ions across the axon membrane
- Movement - muscle contraction
- Secretion - the packaging & transport of secretory products into vesicles in cells
Describe ATP as a supplier of energy
ATP
• hydrolysis of ATP to ADP requires one enzyme, ATPase
• hydrolysis of ATP is a single step reaction, releases energy immediately
• ATP release energy in small amounts, when and where it’s needed
• small soluble molecules - easily transported within cell and across membrane
Describe glucose as a supplier of energy
Glucose
• many enzymes needed to release energy from glucose
• the breakdown of glucose involves many intermediates and takes longer for energy to be released
• glucose releases energy in large amounts which would be all at once
• large polar molecule
Describe the structure of DNA
- composed of 2 polynucleotide strands wound around each other in a double helix, strands are antiparallel
- deoxyribose sugar and 4 organic bases, the sugar forms the backbone on the outside of the DNA molecule with phosphate groups = backbone
- bases join to complementary base, hydrogen bonds form in between, maintain shape of double helix
- very long and thin (2nm in diameter) and tightly coiled into a chromosome,
What are directions called in a DNA strand
5’ to 3’ = going upwards from C3 to C5
3’ to 5’ -= going downwards from C3 to C5
What are the 2 functions of DNA?
- Replication - each parent strand acts as a template for the synthesis of a new complementary strand
- Protein Synthesis - sequence of bases represents the information carried in DNA and determines the sequence of amino acids in proteins
Why must chromosomes make copies of themselves?
So when cells divide each daughter cell receives an exact copy of the genetic information, this copying of the DNA is called replication
What were the 3 possibilities of how DNA might replicate?
- Conservative replication: where the parental double helix remains intact (it’s conserved and a whole new helix is made)
- Semi-conservative replication: which the parental double helix separates into 2 strands, each act as a template for the synthesis of the new strand
- Dispersive replication: the 2 new double helices contain fragments from both strands of the parental double helix
What is the term for semi-conservative replication?
Mode of DNA replication in which each strand of a parental double helix acts as a template for the formation of a new molecule, each containing an original, parental strand and a newly synthesised complementary daughter strand
What is the process of DNA replication?
- the double helix is untwisted
- hydrogen bonds between complementary bases are broken by DNA helicase, allowing the 2 strands to ‘unzip’, exposing nucleotide bases, each strand acting as a template
- free complementary DNA nucleotides hydrogen bond to the exposed bases according to the complementary base pairing rule, A-T and C-G
- covalent bonds are formed between the nucleotides to join the sugar phosphate back bone using DNA polymerase
- this process is called semi-conservative replication as each DNA molecule consists of one conserved - ‘old’ strand and one newly built strand
Who proposed the model for molecular structure of DNA?
James Watson and Francis Crick in 1953
Who did the experiment to prove the hypothesis of semi-conservative replication?
Meselsohn and Stahl
What was the Meselsohn and Stahl experiment?
- Cultured the bacterium E.coli for many generations in a medium containing the heavy isotope of 15N (instead of the normal light isotope of 14N), so 15N became incorporated into eventually all bacterial DNA. Bacterial DNA was extracted and centrifuged, band of DNA settled low down in the tube (very dense)
- 15N bacterium were then washed and transferred into a medium containing 14N, divided once
- First generation DNA was extracted and centrifuged, had a mid-point density in the tube (band)
- Bacterium allowed to divide again and the DNA from the second generation was extracted and centrifuged showing a mid-point and a high point of equal bands in the tube
Why were the 15N bacterium washed?
prevents contamination of the 14N medium with 15N, so 15N wasn’t incorporated in any new strands
Why does the first generation bacterial DNA disprove conservative replication?
- conservative replication would only produce a band showing the parental molecule that’s entirely heavy in the first generation
- the intermediate position implies that the DNA molecules are made up of one old strand (15N) and one new of DNA (14N) in semi-conservative replication
- OR implies that all strands contain a mixture of light and heavy as in dispersive replication
Why does the second generation disprove dispersive replication?
- if dispersive replication was correct all DNA would have to be a mixture of heavy and light, so only one intermediate band would form, there would be no light band
- the parental strand is conserved (15N), that’s why the intermediate band remains, but will get relatively smaller
What is the process of transcription?
- DNA helicase breaks H-bonds between complementary bases in double helix, unwinds DNA, exposes the unpaired bases on template strand
- RNA polymerase links to the template strand of DNA, inserting free RNA nucleotides one at a time according to the rules of complementary base pairing (C-G & A-U) and forming bonds between them down the sugar phosphate backbone
- Beyond the end of the gene there is a stop sequence where RNA polymerase leaves DNA
- A complementary copy of the base sequence of the template strand of the DNA has been made. Known as pre-messenger RNA (mRNA)
- Called pre-mRNA as it contains both exons and introns . Post-transcriptional modification of pre-mRNA occurs to remove introns, producing mRNA. Small enough to leave the nucleus through the pore to a ribosome in cytoplasm
What is an intron?
Non-coding nucleotide sequence in DNA and pre-mRNA that is removed from pre-mRNA to produce mRNA
Whats is an exon?
Nucleotide sequence in DNA and pre-RNA that remains present in mRNA after introns have been removed
What are the first part of translation?
Initiation: a ribosome attaches to a ‘start’ codon at one end of mRNA molecule
• first tRNA has an anticodon complementary to first codon on mRNA will attach to the small sub-unit of the ribosome
• codon of mRNA bond to complementary bases of anticodon on tRNA with hydrogen bonds
• second tRNA with the complementary anticodon binds to second codon on mRNA with H-bonds
What is the second part of translation?
Elongation: 2 amino acids are close enough for ribosomal enzyme to catalyse formation of a peptide bond between
• first tRNA leaves ribosome, leaves attachment site vacant, returns to cytoplasm to bind to another copy of its specific amino acid
• ribosome moves one codon along on mRNA
• next tRNA binds
What is the third part of translation?
Termination: the sequence repeats until ‘stop’ codon is reached
• ribosome-mRNA-polypeptide complex separates
What is a gene?
A section of DNA on a chromosome which codes for a specific polypeptide
What is the definition for genetic code?
The DNA and mRNA base sequences that determine the amino acid sequences in an organism’s proteins
Describe the genetic code in terms of being a triplet code
4^3 = 64 combinations of amino acids
Enough to code for all 20 amino acids
Therefore 3 bases will code for one amino acid (a triplet code in DNA)
Describe the characteristics of the genetic code
- more than one triplet can encode for an amino acid = degenerate or redundant
- code is punctuated: 3 triplet codes that don’t code for amino acids, in mRNA these are STOP codons
- code is universal: in all known organisms the same triplet codes for the same amino acid
- the code is non-overlapping: each base occurs in only one triplet
What are the types of mutation?
Deletion (a base is lost)
Insertion (extra base added)
- deletion & insertion cause frameshift mutation,
changing the sequence of amino acids from this point
forward
Substitution (one base is substituted for another)
• if it changes the amino acid = missense mutation
• if it doesn’t change the amino acid = silent mutation
• if it changes amino acid to a ‘STOP’ = nonsense mutation
