2:1:3 Nucleotides and Nucleic Acids Flashcards
What are nucleic acids
Polymers that are made up of repeating units (monomers) called nucleotides (e.g. DNA and RNA)
What is the structure of a nucleotide
- Pentose sugar (5 carbons)
- Nitrogenous base
- Phosphate group
What are the components of a DNA nucleotide
- Deoxyribose sugar with hydrogen at the 2’ carbon
- Phosphate group
- 1 nitrogenous base: adenine (A), cytosine (C), guanine (G) or thymine (T)
- Double stranded (double helix)
What are the components of a RNA nucleotide
- Ribose sugar with a hydroxyl (OH) group at the 2’ carbon (allows it to be susceptible to hydrolysis allowing it to be the transport molecule as opposed to the storage molecules (DNA))
- Phosphate group
- 1 nitrogenous base: adenine (A), cytosine (C), guanine (G) or uracil (U)
- Single stranded
What are purines
The structure of nitrogenous bases with a double ring (e.g. adenine and guanine)
What are pyrimidines
The structural formula of nitrogenous bases with a single ring (e.g. cytosine, thymine and uracil)
What are phosphodiester bonds
The bond that makes the sugar-phosphate backbone of DNA/RNA and that joins nucleotides together via a condensation reaction between the phosphate group and the pentose sugar of the other nucleotide (one phosphate group and two ester bonds)
What is ATP
Adenosine Triphosphate is a phosphorylated nucleotide produced in respiration that are used to transfer energy in all energy requiring processes in cells of organisms, it’s the universal energy currency
What is Adenosine
A nucleoside that can be combined with 1,2, or 3 phosphate groups to make adenosine monophosphate (AMP), adenosine diphosphate (ADP), and adenosine triphosphate (ATP)
What is the structure of DNA molecules
- Two polynucleotide strands side by side running in opposite directions (antiparallel)
- Strands made of alternating deoxyribose sugars and phosphates joined with phosphodiester bonds making the sugar phosphate backbone
- Phosphodiester bond links 5’ carbon of one molecules to the phosphate of another that is bonded to the 3’ carbon
How is DNA antiparallel
On strange runs in the 5’ to 3’ direction, and the other in the 3’ to 5’ direction
How are the two strands of DNA bonded together
- Held together by hydrogen bonds between nitrogenous bases
- Adenine (A) always makes 2 hydrogen bonds with thymine (T)
- Guanine (G) always makes 3 hydrogen bonds with cytosine (C)
- The pairings are called complementary base pairs
What shape is DNA
It is the three dimensional shape of a helix
How is DNA purified
- Isolating DNA occurs from the precipitation process
- Isolating DNA is used in molecular biology
- Involves the cells and membranes being broken, and enzymes denature and remove proteins in the DNA so it can be formed into an insoluble solid by an organic solvent
Describe the process of DNA purification
- Cut up sample into small pieces and place in a beaker with washing up liquid and water
- Place beaker in water bath at 60 degrees for 15 mins
- Cool beaker in ice bath for 5 mins whilst stirring
- Blend mixture for 5 seconds
- Filter (with filter paper) the mixture into another beaker
- Pour 10cm3 filtrate into a test tube and add few drops of protease enzyme and mix
- Add ice-cold ethanol to the test tube and wait 2 mins
- Layer of white precipitate containing DNA will sit upon the solution
Why is detergent used in the DNA purification process
It disrupts the phospholipids bilayer of the sample cell membranes which releases the DNA
Why is a water bath used in the DNA purification process
The heat disrupts the phospholipid bilayer of the sample cell membrane and releases the DNA, as well as denaturing the enzymes released for the cells which would otherwise digest the DNA
Why is an ice-water bath used in the DNA purification process
Lowering the temperature prevents the DNA from breaking down
Why is the mixture blended for a short time in the DNA purification process
Blending breaks down the cell walls can cell membranes in the sample so further DNA can be released, but only for seconds as otherwise the DNA strands could be broken
Why is filtering part of the DNA purification process
To remove cell debris and membrane fragments so the filtrate consists of only DNA and it’s associated proteins
Why is protease enzyme added in the DNA purification process
It denatures and removed the proteins, leaving only the DNA
Why is ice cold ethanol added in the DNA purification process
Nucleic acids are insoluble in ice cold ethanol so the DNA can form a precipitate at the top of the solution
Why does DNA have to replicate before cell division
To ensure that the daughter cells from the cell division have full copies of the parental DNA
What is semi-conservative replication
The way DNA is copied, where in each new DNA molecule, one of the polynucleotide strand is from the original DNA molecule, so the new molecule has conserved half of the original DNA
Why does one original DNA strand have to be conserved in semi-conservative replication
To ensure there is genetic continuity between generations of cells, so new cells inherit all their genes from the parent cells during cell division, as cells are replaced regularly and have to complete the same function as previously
Describe the process of semi-conservative DNA replication
- Occurs in S phase in preparation for mitosis so the number of DNA molecules in parent cells must be doubled
- Helicase enzyme breaks the hydrogen bonds between base pairs to unwind the double helix
- The separated strands act as templates for the new strand, where free nucleotides in the nucleus join to their complementary base pair by DNA polymerase enzyme which catalyses the condensation reactions
- The two strands come together as hydrogen bonds form between the base pairs
How does DNA polymerase work
- DNA polymerase enzyme synthesises new DNA strands from the template strands by catalysing condensation reactions between the sugar and phosphate groups
- It then cleaves (breaks off) the two extra phosphates and uses the energy released to create the phosphodiester bonds between nucleotides
- Hydrogen bonds form between the base pairs
What are Okazaki fragments
DNA polymerase travels up the DNA strand from the 3’ to 5’ direction. This is the leading strand which undergoes continuous replication. The lagging strand undergoes discontinued replication where the DNA polymerase waits for the DNA to unzip before producing another strand in fragments (Okazaki)
Why must the formation of DNA strands be highly accurate
To create exact copies of the parent DNA molecule,
What possible mutations can occur during DNA replication
- Bases being inserted in the complementary strand in the wrong order
- Extra bases being inserted
- Bases being left out
What is the cause of mutations in DNA replication
Occurrence of random spontaneous mutations (errors in genetic code)
What is a gene
A sequence of nucleotides that forms part if a DNA molecule which codes for the production of a specific polypeptide, by controlling protein structure through determining the exact amino acid sequence
What determines the shape and behaviour of a protein (polypeptide) molecule
Depends on the sequence of amino acids (primary structure of protein molecule)
What is the triplet code
The sequence of three DNA bases that codes for one amino acid (e.g. CAG codes for the amino acid valine)
What are start and stop signals in cells
Signals coded by triplet bases that tell the cell where the individual gene starts (by coding for methionine ATG) and stops in order for the DNA to be read correctly and produce the right sequence of amino acids. Stop signals don’t code for amino acids
Why is the genetic code non-overlapping
Each base in a codon is only read once
Why is the genetic code degenerate
The are 4 bases, so 64 different possible triplets (4^3=64), but only 20 commonly occurring amino acids, so the code is degenerate as multiple codons code for the same amino acids. The degenerative nature can limit mutations
Why is the genetic code universal
Every organism uses the same code and the same triplet codes for the same amino acids in all organisms, meaning genetic information is transferable (enabling genetic engineering)
What is a codon
Each triplet within the mRNA code
What is an anti codon
Complementary to the codons on mRNA, but are present on tRNA
What is protein synthesis
Where genes in DNA molecules code for specific sequences of amino acids, that in turn make a specific polypeptide (protein)
What are the two stages of protein synthesis
- Transcription
- Translation
What is transcription
The first stage of protein synthesis which occurs in the cell nucleus, where the base sequences of genes are copied and transported to ribosomes
Describe the process of transcription
- DNA molecule unwinds an DNA polymerase enzyme moves along (hydrogen bonds break between complementary base pairs)
- Sense strand (5’ to 3’) codes for the protein to be synthesised
- Complimentary copy of sense strand is made by building a single stranded molecule that acts as the template strand (antisense strand 3’ to 5’)
- Free RNA nucleotides pair up with complementary bases on the template strand (with thymine being replaced by uracil (U) on the mRNA strand)
- Sugar-phosphate groups in the RNA nucleotides form phosphodiester bonds by DNA polymerase enzyme forming mRNA molecule
- Gene is transcribed when mRNA molecule is complete, causing hydrogen bonds between DNA template strand and mRNA strand break and the DNA strand reforms
- mRNA has a guanine ‘cap’ added to the beginning of the molecule, and a series of 100 adenine molecules ‘tail’ added to the end
- Splicing occurs and the mRNA strand leaves the nucleus via pores in the nucleic envelope
Describe the process of translation
- Occurs in the cytoplasm
- mRNA attaches to a ribosome which consists of rRNA which is stable so the mRNA is prepared for synthesis
- Free tRNA molecules in the cytoplasm have triplets of unpaired bases at the anticodon where a specific amino acid can attach
- tRNA molecules bind with the specific amino acid and bring them to the mRNA molecules so the complementary codons can pair
- 2 tRNA molecules can fit onto the ribosome at one time
- A peptide bond is formed via condensation reactions between the amino acids which is catalysed by rRNA
- Process continues until a stop codon on the mRNA molecule is reached and an amino acid chain is formed
What is splicing
Removing the non-coding regions (introns) and joining the coding regions (extrons) of the mRNA strand together, before it leaves the nucleus
