2.3 - Nucleotides and Nucleic Acids Flashcards
What is a nucleotide?
The monomer from which nucleic acids are made
What are the types of nucleic acid?
DNA
RNA
ATP
What are nucleotides made up of?
- a pentose sugar (with 5 carbons)
- a nitrogen-containing organic base
- a phosphate group
What are the components of a DNA nucleotide?
- deoxyribose sugar (hydrogen at 2’ position)
- a phosphate groups
- nitrogenous base either adenine, cytosine, guanine or thymine
What are the components of an RNA nucleotide?
- a ribose sugar (OH group on 2’ position)
- a phosphate group
- nitrogenous base either adenine, cytosine, guanine or uracil
How does the difference in structure between DNA and RNA alter their function?
- presence of OH on 2’ in ribose makes RNA more susceptible to hydrolysis
- this is why DNA is a storage molecule and RNA is the transport molecule with a shorter molecular lifespan
What are purines and pyrimidines?
PURINES:
• double ring structure
• adenine and guanine
PYRIMIDINES:
• single ring structure
• cytosine, thymine and uracil
What reaction forms polynucleotides?
- condensation reaction
* forms phosphodiester bonds between phosphate group of one nucleotide and the pentose sugar of another (3’ carbon)
What reaction breaks down polynucleotides?
- condensation reactions
* breaks down phosphodiester bonds
What is the sugar-phosphate backbone?
The chain of alternating phosphate groups and pentose sugars
Produced as a result of many phosphodiester bonds
Why do organisms require energy?
ALL:
• anabolic reactions (building larger molecules from smaller ones
• moving substances within cells/active transport
ANIMALS:
• muscle contraction
• conduction of nerve impulses
What is ATP?
- adenosine triphosphate
- a phosphorylated nucleotide
- universal energy currency - used to transfer energy in all known forms of life
Describe the structure of ADP and ATP
ADP (adenosine diphosphate):
• adenine (nitrogenous base)
• ribose (pentose sugar)
• 2 phosphate groups
ATP (adenosine triphosphate):
• adenine (nitrogenous base)
• ribose (pentose sugar)
• 3 phosphate groups
Describe the structure of a DNA molecule
There are 2 antiparallel DNA strands
• each DNA molecule has a 3’ end and a 5’ end, (depending on which one isn’t bonded to another nucleotide)
• the strands run in opposite directions, so one is the 5’ to 3’ strand and the other is the 3’ to 5’
The antiparallel strands are held together by hydrogen bonds between complimentary base pairs
• A bonds to T
• C bonds to G
The DNA molecules twist to form a double helix
What is complimentary base pairing?
- hydrogen bonds formed between to nitrogenous bases (one purine and one pyrimidine)
- adenine and thymine are complementary, forming 2 hydrogen bonds between them
- guanine and cytosine are complementary, forming 3 hydrogen bonds between them
Describe the process of purifying DNA by precipitation
1) Cut up the onion into small pieces (5 mm × 5 mm)
2) Add the washing-up liquid to 90 cm³ of tap water in a beaker, then add some of the onion pieces to the beaker
3) Place the beaker in a water bath at 60 °C for 15 minutes
• the detergent and the heat disrupt the phospholipid bilayer of the onion cell membranes and nuclear membranes, releasing the DNA
• the heat also denatures enzymes released from the cell that would otherwise begin to digest the DNA
4) Cool the mixture in an ice-water bath for 5 minutes, stirring it continually
• Lowering the temperature prevents the DNA itself from breaking down
• Continual stirring ensures the whole mixture is cooled
5) Use a pestle and mortar to grind the mixture
• this breaks down the cell walls and cell membranes of the onion cells even further, releasing more DNA
6) Using the filter paper, filter the mixture into another beaker
• Filtering removes cell debris and membrane fragments
• The filtrate now contains the DNA and its associated proteins
7) Pour 10 cm³ of the filtrate into a test tube and add 2-3 drops of protease enzyme, mixing well
• The protease denatures and removes the proteins, leaving just the DNA
8) Carefully add the ice-cold ethanol to the test tube and wait 2-3 minutes
• Nucleic acids are insoluble in ice-cold ethanol and so the DNA forms a precipitate (white layer) at the top of the test tube mixture
What is semi-conservative replication?
When DNA replicates, each new DNA molecule has one original strand of DNA and one newly synthesised strand
This is important to maintain genetic continuity between generations of cells (ensuring new cells inherit all their genes from parent cells)
What are the stages of DNA replication?
1) enzyme gyrase untwists the DNA
2) DNA helicase breaks hydrogen bonds between complementary base pairs, exposing nitrogenous bases
3) Each strand of DNA acts as a template for the formation of a new molecule
4) The enzyme primase adds a few RNA nucleotides to the DNA strand, forming a primer
5) free activated DNA nucleotides align with exposed bases according the the complimentary base pairing rule (A-T, G-C), forming hydrogen bonds.
6) DNA polymerase attaches to the primer and moves from the 3’ end of the template strand to the 5’ end, forming phosphodiester bonds between adjacent nucleotides. This forms the sugar phosphate backbone.
7) each DNA molecule has 1 old and 1 new strand - semi conservative replication
How can mutations occur during DNA replication?
- bases being inserted into the complementary strand in the wrong order
- an extra base being inserted by accident
- a base being left out by accident
These result in the occurence of random, sponatneous mutations
What is a codon?
- a triplet of 3 bases
- each codon codes for 1 amino acid
- the order of codons in a gene determines the order of the amino acids in a protein (the primary structure)
What does the genetic code being non-overlapping mean?
• DNA is sequentially read in groups of three, so a nucleotide that forms part of one codon will not be read as part of another codon
What does the genetic code being degenerate mean?
Multiple codons can code for the same amino acid
The degenerate nature of DNA can limit the effect of mutations
What does the genetic code being universal mean?
- almost evergy organism uses the same code - the same codons code for the same amino acids
- this is why genetic engineering is possible
What are the 2 stages of protein synthesis?
TRANSCRIPTION
• occurs in the nucleus
• DNA is transcribed and an mRNA molecule is produced
TRANSLATION
• occurs on the ribosomes
• mRNA is translated and an amino acid sequence is produced
What are the stages of transcription?
1) the section of DNA containing the gene unwinds, and the hydrogen bonds between complementary base pairs are broken by DNA helicase.
2) Free RNA nucleotides form hydrogen bonds between with exposed bases on the antisense (3’-5’) strand of the DNA according to the complementary base-pairing rule
3) RNA polymerase forms phosphodiester bonds between adjacent RNA nucleotides. An mRNA molecule is formed.
4) the mRNA detaches from the template strand and leaves the nucleus via a nuclear pore. It travels to ribosomes in cytoplasm. DNA helix reforms.
What are the sense and antisense strand?
SENSE
• runs from 5’ to 3’
• contains the code for the DNA to be synthesised
ANTISENSE
• runs from 3’ to 5’
• a complementary copy of the sense strand
• acts a template during transcription, so that the mRNA strand formed has the same base sequence as the sense strand
What are the stages of translation?
1) the mRNA binds to the small subunit of the ribosome at its start codon
2) a tRNA with the complementary anticodon binds to the mRNA start codon.
3) another tRNA binds to the next codon on the mRNA
4) Peptidyl transferase forms a peptide bond between the 2 amino acids on the tRNA molecules.
5) the ribosome moves along the mRNA molecule, and first tRNA molecule is released from the ribosome
6) stages 3-5 repeat until a stop codon is reached and the polypeptide is released.
What is tRNA?
- transfer RNA
- a strand of RNA folded into a cross shape, so that 3 bases (anticodon) are at on end of the molecule
- the anticodon binds to a complementary codon on mRNA molecule
- each tRNA molecule carries an amino acid corresponding to that codon
What is rRNA?
- ribosomal RNA
- makes up part of the ribosomes
- maintains structural stability of the protein protein synthesis sequence
- plays a biochemical role in catalysing the reaction
