Nucleotides, Nucleic acids and enzymes Flashcards
What is a nucleotide made from
- Pentose sugar (5 carbon atoms)
- Nitrogenous base (nitrogen containing)
- Phosphate group
What elements are found in nucleotides
C,H, O, N, P
Why are nucleotides important
They are monomers that make up DNA and RNA and therefore a form of nucleic acid. DNA stores genetic information and RNA is used to make proteins
What is the sugar in DNA called
Deoxyribose
What is the pentose sugar in a DNA nucleotide called
Deoxyribose
What does each DNA nucleotide have
Same sugar and a phosphate group but the base can vary
What type of bases are adenine and guanine
Purine
What type of bases are cytosine and thymine
Pyrimidine
What does a purine contain
Two carbon-nitrogen rings joined together
What does a pyrimidine contain
One carbon-nitrogen ring so is smaller than a purine base
What does a molecule of DNA contain
Two polynucleotide chains made up of lots of nucleotides joined together
What is the sugar in RNA called
Ribose
What does RNA contain
A phosphate group and one of four bases
What is an RNA molecule made up form
A single polynucleotide chain
What does it mean to phosphorylate a nucleotide
Adding one or more phosphate groups to it
What is ADP and what does it contain
Adenosine diphosphate and contains adenine, the sugar ribose and two phosphate groups
What is ATP and what does it contain
Adenosine triphosphate and contains adenine, the sugar ribose and three phosphate group
How is ATP synthesized
From ADP and inorganic phosphate (P) using energy from an energy-releasing reaction. ADP is phosphorylated to form ATP and a phosphate bond is formed
Where is energy stored and released
Stored in the phosphate bond and is released when ATP is broken back down into ADP and inorganic phosphate.
What do nucleotides join together to form and how
Polynucleotides are joined between the phosphate group of one nucleotide and the sugar of another through a condensation reaction
What does nucleotides joining together form
Two ester bonds and a phosphate known as a phosphodiester bond
What is the sugars and phosphate known as
Sugar-phosphate backbone
How can polynucleotides be broken down
Hydrolysis
How many hydrogen bonds form between adenine and thymine
2
How many hydrogen bonds form between cytosine and guanine
3
What twists to form a double helix DNA
Two antiparallel polynucleotide strands
How do you purify DNA
Precipitation reaction
1) Break up cells in the sample using a blender
2) Make a solution of detergent, sodium chloride (salt) and distilled water
3) Add cells to beaker in a water bath at 60 degrees for 15 minutes
4) Put the beaker in an ice bath to cool the mixture down and filter into a clean boiling tube
5) Add protease enzymes to break down proteins
6) Dribble some cold ethanol down the side of tube to form a layer on top
7) DNA will form as a white precipitate
Stages of DNA replication
1) DNA helicase breaks the hydrogen bonds between the two nucleotide DNA strands. The helix unzips and forms two single strands
2) Each original single strand acts as a template for a new strand. Free-floating DNA nucleotides join to the exposed bases on each original template strand by complementary base pairing
3) The nucleotides of the new strand are joined together by the enzyme DNA polymerase forming the sugar-phosphate backbone. Hydrogen bonds form between the bases on the original and new strand forming a double-helix
4) Each new DNA molecule contains one strand from the original DNA molecule and one new strand
What is semi-conservative replication
When half of the strands in each new DNA molecule are from the original piece of DNA
Why does DNA need to be replicated accurately
To make sure genetic information is conserved each time the cell is replicated
What does a mutation mean
A random spontaneous change in DNA base sequence as an abnormal protein is produced that may function better or not at all compared to the original one
What is a gene
A sequence of DNA nucleotides that codes for a polypeptide forming the primary structure of a protein
What is RNA
A single polyculeotide strand containing uracil as a base
What is mRNA
- Made in the nucleus
- Three adjacent bases are a codon
- Carries the genetic code from the DNA in the nucleus to the cytoplasm, where it is used to make a protein in translation
What is tRNA
- Found in the cytoplasm
- Has an amino acid binding sit at one end and a sequence of three bases at the other called an anticodon
- It carries the amino acids that are used to make proteins to the ribosomes during translation
What is rRNA
- Forms the two subunits in a ribosome
- The ribosome moves along the mRNA strand during protein synthesis. The rRNA in the ribosome helps to catalyze the formation of peptide bonds between amino acids
What is genetic code
The sequence of base triplets in DNA or mRNA which codes for specific amino acids
Features of genetic code
Non-overlapping = each base triplet is read in sequence separate from the triplet before
Degenerate = there are more possible combinations of triplets than there are amino acids (20 but 64 possible triplets) meaning amino acids are coded for by more than one base triplet
Universal = the same base triplets will code for the same amino acid across all organisms
What happens during transcription
1) This starts when RNA polymerase attaches to the DNA double helix at the start of a gene
2) The hydrogen bonds break separating the strands and the DNA uncoils
3) One of the strands is then used as a template to make an mRNA copy
4) The RNA polymerase lines up free RNA nucleotides along the template strand. Complementary base pairing means that the mRNA strand ends up being a complementary copy of the DNA template strand apart from T is replaced by U
5) Once the RNA nucleotides have paired with their specific bases they are joined together forming an mRNA molecule
6) The RNA polymerase moves along the DNA separating the strands and assembling the mRNA strand
7) The hydrogen bonds between the uncoiled strands of DNA re-form once the RNA polymerase has passed by and the strands coil back into a double-helix
8) When RNA polymerase reaches a stop codon it stops making mRNA and detaches from the DNA
9) The mRNA moves out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm
What happens during translation
1) The mRNA attaches itself to a ribosome and tRNA molecules carry amino acids to the ribosome
2) A tRNA molecule, with an anticodon that’s complementary to the start codon on the mRNA, attaches itself to the mRNA by complementary base pairing
3) A second tRNA molecule attaches itself to the next codon on the mRNA in the same way
4) rRNA in the ribosome catalyzes the formation of a peptide bond between the two amino acids attached to the rRNA molecules. This joins the amino acids together. The first tRNA molecule moves away leaving its amino acid behind.
5) A third tRNA molecule binds to the next codon on the mRNA. Its amino acid binds to the first two and the second tRNA molecule moves away
6) This process continues producing a chain of linked amino acids until there’s a stop codon on the mRNA molecule
7) The polypeptide chain moves away from the ribosome and translation is complete
What are enzymes
Biological catalysts that speed up reactions as the metabolic reactions are sped up. Their action can affect structure in an organism as well as functions
Two type of enzyme action
Intracellular or extracellular
Intracellular examples
Hydrogen peroxide is the toxic by-product of reaction that can kill cells
Catalase is an enzyme that works inside cells to catalase the breakdown of hydrogen peroxide to harmless oxygen and water
Extracellular enzyme examples
Amylase and trypsin work both out of cells in the human digestive system
Amylase is found in saliva and catalyzes the hydrolysis of starch into maltose
Trypsin catalyzes the hydrolysis of peptide bonds turning big polypeptides into smaller ones and is produced in the pancreas secreted into the small intestine
What type of proteins are enzymes
Globular
What type of protein structure is an enzyme
Tertiary
What do enzymes do to the activation energy
It reduces it allowing reactions to occur at lower temperatures speeding up the rate of reaction
Why does the enzyme activation energy change
1) If two substrate molecules need to be joined attaching to the enzyme holds them close together reducing any repulsion between molecules
2) If the enzyme is catalyzing a breakdown reaction, fitting into the active site puts strain on bonds in the substrate meaning the molecule breaks up more easily
Two Theory’s of enzyme fit
1) Lock and Key =They substrate fits perfectly to create an ESC and then when substrate leaves the enzyme is unchanged
2) Induced fit = Substrate does not have to be correct fit as the active site will change shape
Impact of temperature on enzyme activity
The rise in temp means more vibrations between enzyme molecules until it reaches an optimum temp. Then the active site will change and no longer fit leading to the enzyme to denature
What is Q10
The value to show how much the rate of reaction changes when temperature is raised by 10 degrees celcius
Equation for calculating Q10
R2 (rate at higher temperature) /
R1 (rate at lower temperature)
What does a value of 2 mean for Q10
The rate doubles when the temp is changed by 10 degrees
How does pH affect enzyme activity
There is an optimum value most are at 7 except pepsin is 2 as is found in the stomach.
Above and below the optimum pH, H+ and OH- ions found in acids acids and alkalis can mess up the ionic bonds and hydrogen bonds holding the enzymes tertiary structure in place. Making the active site change shape so the enzyme is denatured
How does enzyme concentration affect the rate of reaction
The more enzyme molecules there are in a solution, the more likely a substrate molecule is to collide with one and form an ESC. Therefore increasing Concentration increases ROR
However the amount of substrate is a limiting factor as there comes a point when there’s more than enough enzymes for substrate and has no further effect
How does substrate concentration affect ROR
The higher the substrate concentration, the faster the reaction as more active sites will be used. This is only true until a ‘saturation’ point as there are only so may substrate molecule that the enzymes have and then all the active sites are full.
Substrate concentration decreases with time during a reaction so if all other variable remain the same, the ROR will decrease over time time making the initial ROR the highest
How to measure the Rate of an enzyme controlled reaction using hydrogen peroxide solution
Catalase catalyzes the breakdown of hydrogen peroxide into oxygen and water as it is fed through a delivery tube to an upside down measuring cylinder. The amount of oxygen is then measured or the time for it to stop bubbling
How to measure the Rate of an enzyme controlled reaction using starch solution and amylase enzyme
You can measure the disappearance of the substrate rather than appearance of the product as the mixture sampled is put in a drop of iodine in potassium iodide and timed till when the iodine solution no longer turns blue-black as the start has then been broken down
How to investigate the effect of temperature on catalase activity
1) Set up boiling tubes containing the same volume and concentration of hydrogen peroxide, add equal volumes of a buffer solution to each tube
2) Set up the apparatus to measure the volume of oxygen produced form each boiling tube
3) Put each boiling tube in a water bath set to a a different temp e.g 10-40. And set up another tube of catalase
4) Use a pipette to add the same volume and concentration of catalase to each boiling tube
5) Record how much oxygen is produced in the first 60 seconds
6) Repeat the experiment at each temperature three times and calculate the mean
What are cofactors
Substances that enzymes need to work, another non-protein substance
What are inhibitors
Inhibit enzymes action such as poisons
How do inorganic cofactors work
They help by helping the enzyme and substrate bind together, but do not directly participate in the reaction so are not used up or changed
How do organic cofactors work
They are known as coenzymes and participate in the reaction and are changed by it
What is a cofactor tightly bound to an enzyme
A prosthetic group
What are non-competitive inhibitors
Molecules that bind to all the enzyme away from its active site known as the allosteric site. Causing the active site to change shape so the substrate will no longer be able to fit.
What are competitive inhibitors
Have similar shape to that of the substrate molecules and compete with the substrate molecules to bind to the active site blocking it so that the substrates cannot fit.
How much it is inhibited is dependent on the relative concentrations of the inhibitor and substrate.
What are irreversible inhibitors
Have strong covalent bonds where the inhibitor can’t be removed easily and the inhibition is irreversible
What are reversible inhibitors
Have weaker hydrogen bonds or weak ionic bonds so the inhibitor can be removed and the inhibition is reversible
Examples of drugs and metabolic poisons being enzyme inhibitors
1) Antiviral drugs such as HIV (reverse transcriptase inhibitors) inhibit the enzyme reverse transcriptase which catalyzes the replication of viral DNA preventing the virus replicating
2) Antibiotics such as penicillin inhibits the enzyme transpeptidase which catalyzes the formation of proteins in bacterial cell walls weakening the cell wall and preventing the bacterium from regulating so the cell bursts an the bacterium is killed.
3) Cyanide is an irreversible inhibitor of cytochrome C oxidase that catalyzes respiration reactions
4) Malonate inhibits succinate dehydrogenase
5) Arsenic inhibits the action of pyruvate dehydrogenase and enzyme that catalyzes respiration reactions
What is a metabolic pathway
A series of connected metabolic reactions. The product of the first reaction takes part in the second and so on
What is product inhibition
When enzymes are inhibited by the product of the reaction they catalyse
What is end-product inhibition
When the final product in a metabolic pathway inhibits an enzyme that acts earlier on in the pathway
Why is end-product inhibition useful
It regulates the pathway and controls the amount of end-product that gets made
What are inactive precursors
Used in metabolic pathways to prevent damage to cells such as proteases are synthesized like this to stop protein damage
What happens when the precursor molecule is removed
The enzyme is no longer inhibits and becomes active
