Chapter 2 Nucleic Acids Flashcards
What does ATP stand for
Adenosine triphosphate
Key properties of ATP that makes it a suitable source of energy for cells
- releases energy instantaneously (immediate energy source) transfers energy from the sites of respiration to the parts of the cell which require energy
- does not leave cells
- releases small amounts of energy
What type of reaction occurs when breaking the covalent bond of the last phosphate group of the ATP molecule
Hydrolysis reaction
Hydrolysis of ATP equation and catalyst
ATP + water → ADP (adenosine diphosphate) + Pi (inorganic phosphate) + energy
Catalyst: ATPase
Explain how ATP releases energy to be used by processes in cells
- The covalent bonds between last phosphate groups are very unstable
- This means it requires a low activation energy and hence a small amount of energy to break the covalent bond holding the last phosphate group in place
- Once the covalent bond is broken the terminal phosphate group (last phosphate group) is removed releasing energy which is used by processes in cells
energy-requiring processes that use ATP
- active transport
- metabolic reactions
- muscle contraction
- secretion of molecules using vesicles
- activation of molecules (transfers energy to molecules )
How can atp activate molecules
Through phosphorylation - By transferring a Phosphate group to other molecules making them more reactive and lowering their activation energy
Where is ADP and phosphate turned back into ATP
- Respiration in plants and animals (oxidative phosphorylation)
- In chlorophyll containing plants during the LIR in photosynthesis (photophosphorylation)
- In animals and plants when phosphate groups are transferred from donor molecules to ADP (substrate level phosphorylation)
Name of reaction of ATP synthesis
phosphorylation reaction or condensation reaction
Advantages of ATP over glucose
- ATP releases less energy than glucose meaning that smaller and more manageable quantities of energy is used for reactions so less energy is lost by heat
- Hydrolysis of ATP happens in a single reaction releasing energy whilst hydrolysis of glucose occurs over a long series of reactions to release energy, so ATP is less time consuming
What is the synthesis of ATP (ADP and phosphate conversion to ATP) catalysed by
ATP synthase
What is ATP
An immediate source of energy for biological processes
How does ATP synthesis work
During respiration from ADP by the addition of an inorganic phosphate group through a condensation reaction (or phosphorylation) and using the enzyme ATP synthase
Why is ATP an immediate source for energy
- Requires a small amount of energy to break the covalent bond holding the last phosphate group in place which releases a lot of energy when broken, which is used by processes in the cell
How is ATP used in metabolic reactions
It provides energy needed to build up macromolecules from their basic units
How is ATP used in movement
It provides energy for muscle contraction by providing energy for the filaments to slide past each other
How is ATP used in active transport
Provides energy to change shape of the carrier proteins in the plasma membrane allowing molecules to move against the concentration gradient
Function of DNA
- codes for the sequence of amino acids in the primary structure of a protein which in turn determines the final 3d structure and function of a protein
- responsible for passing genetic information from cell to cell and generation to generation
- creates genetic diversity and speciation due to its variety of sequences of bases
Why is DNA important
- So that every cell contains a copy of genetic code and that it can be passed on to new cells without being damaged
Types of nitrogenous bases and their base pairs
Guanine, cytosine, adenine thymine, uracil (only RNA and usually binds with adenine as rna does not contain thymine)
A- T
G -C
Name of pentose sugar in DNA and RNA
DNA – deoxyribose sugar
RNA - ribose sugar
Monomer that makes up DNA
Nucleotide
Polymer of the nucleotide
Polynucleotide
How do polynucleotide form
Through condensation reactions and the formation of a phosphodiester bond between a phosphate of one nucleotide and Carbon 3 of the deoxyribose sugar of the next nucleotide
How does the strong phosphodiester bonds(covalent bonds) became an advantage in a DNA molecule
They help ensure that the genetic code is not broken down
What is a sugar phosphate backbone
The phosphodiester bonds between the sugar and phosphate group that hold the polymer together and provides structural support to the molecule
How are double helix’s formed
When two polynucleotides are joined together by their complimentary base pairs through hydrogen bonding, which they then twist around each other to form a double helix
(The two dna strands are anti parallel to each other)
Why is DNA a stable molecule
- adenine and thymine form 2 hydrogen bonds whilst cytosine and guanine form 3 hydrogen bonds, so the more GC pairing the more stable the molecule is
- there are other interactive forces between base pairs
- the reactive bases are protected by the sugar phosphate backbone inside the double helix making the molecule stable and protecting the bases from damage
EXPLAIN how the structure of DNA is related to its function
- sugar-phosphate (backbone) so provides stability and protects bases
- long molecule so can store lots of information
- coiled into a helix so compact
- weak hydrogen bonds so it is easy to seperate strands
- double stranded so replication can occur semi-conservatively and complementary base pairing so identical copies can be made
- base sequence allows information to be stored
differences between dna and rna
DNA found in chromosomes - rna found in cytoplasm
DNA is extremely long - rna is very short
DNA has a double helix - rna only has kne polynucleotide strand
Types of rna and their functions
mRNA (messenger) - transfers information from DNA to ribosomes
tRNA (transfer) - transfers the amino acid to the ribosome and places it into the correct sequence in the peptide
Ribosomal rna - ribosomes made from rna and proteins
Process of semi conservative dna replication
1) the enzyme DNa helicase attaches to the DNA molecule
2) the DNA helicase causes the hydrogen bond between complimentary base pairs to break undwinding the DNA helix , causing the two polynucleotide strands to separate and each strand acts as a template for a new strand
3) free nucleotides join up along the template strand by complimentary base pairing and are held in place by hydrogen bonds between complimentary base pairs and are not bonded to each other by phosphodiester bonds
4) dna polymerase moves down the molecule and joins the free nucleotides by catalysing the formation of a phophodiester bond between the free nucleotides through a condensation reaction and the strands twist to form a double helix and two identical dna molecules are produced with each molecule containing a single strand from the original dna and a single new strand
What causes mutations in dna
When an incorrect base is inserted into the growing polynucleotide strand so the DNA sequence is changed
What happens in conservative dna replication
A dna double helix is formed contains two new strands with none of the original dna in it
Evidence for semi conservative dna replication experiment (Meselson and Stahl)
1) the scientist took a sample of bacteria and grew it on a median only containing nitrogen -14 (the lighter isotope) and a median containing only nitrogen -15 (the heavier isotope) and extracted its both of its DNA
2) they placed the DNA in a solution and spun it in a centrifuge so the scientists could detect the DNA and found that the sample which only had n-14 formed a band of DNA near the top of the tube whilst the sample only contains n-15 formed a band of DNA at the bottom of the tube
3) the scientist then transferred a sample of the bacteria growing on n-15 to the bacteria growing in n-14 and allowed the DNA to replicate once
4) the scientist then extracted the DNA and placed it in the centrifuge and found that the DNA produce a band between the two bands formed from the lighter and heavier isotopes, proving that the DNA contained one strand of n-14 and one strand of n-15 so it must of replicated semi conservatively
Why does the DNA polymerase work along the dna molecule from 5 prime to 3 prime
As the active site of the enzyme is complimentary to the 5 prime end of the dna nucleotide being used for the new strand so can only bind to 5’ and not 3’ as has a different shape
What direction does the dna polymerase move in along the template strand to
5’ to 3’
Direction of dna helicase
3’ to 5’
Structure of water molecule
- dipolar molecule as it has two different regions that is charged
- has an uneven distribution of charge due to the O2 being electronegative causing the H to be positive causing hydrogen bonds to form between o and h
Key properties of water
- it is a metabolite
- a solvent
- has a high specific heat capacity
- has a large of specific latent heat of vaporisation
- strong cohesion between water molecules which supports the water and provide surface tension
- transparent
What is a metabolite
A molecule involved in lots of chemical reactions or metabolism
Why is water a metabolite
Water is involved in many reactions such as photosynthesis, hydrolysis and condensation reactions
Why is water a good solvent
As polar molecules can dissolve in water due to it being dipolar. This is because the positive charge in the hydrogen atoms will attract any negative ions and the negative charge of the oxygen will attract any positive ions in the solutes
(That why these molecules are described as hydrophilic as they are attracted to water)
Why does water have a high specific heat capacity
As it requires a lot of energy to raise the temperature of water as some of the heat energy is used to break the hydrogen bonds between water molecules
How does the high specific heat capacity in water help organisms
- The temperature remains relatively stable even if the surrounding temperature fluctuates so the water acts as a temperature buffer this means that the internal temperature on plants and animal should remain the same despite the outside temperature due to the fact that a large proportion of the organism is made out of water
- this helps enzymes not denature or reduce activity with temperature fluctuations in organism and helps provide a stable environment for aquatic organism
Why does water have a large latent heat of vapourisation
As a lot of energy is required to convert water in its liquid state to a gaseous state due to the hydrogen bonds as energy is needed to break the hydrogen bonds between water molecules to turn it into a gas
How does water having a large latent heat of vapourisation help organism
- As it provides a significant cooling effect
- In humans a large amount of body heat is used to evaporate the sweat from the surface of the skin, cooling down the organism and taking the heat energy away
- plants - transpiration
What is cohesion
Water molecules sticking together by hydrogen bonds
How does cohesion help organism
- due to water molecules sticking together when the water moves up the xylem in plants due to transpiration it is a continuous column of water. This is easier to draw up as it is in a column rather than individual molecules
- cohesion also provides surface tension to the water allowing small invertebrates to move and live on the surface providing them a habitat away from predators within the water
What are the inorganic ions
Sodium
Iron
Hydrogen
Phosphate
Function of iron
- found in haemoglobin by binding to oxygen and plays a role in the transport of oxygen
Function of phosphate
- stores energy in phosphate molecules
- structural role in DNA
Function of hydrogen
- determines ph of solutions and functions of ions
Function of sodium
Transports glucose and amino acids across membrane s through co transport
Nerve transmissions
What is adhesion
When water molecules stick to the walls of a container
How does water being transparent help organism
- aquatic plants can still get light for photosynthesis
- light can pass through fluid filled eye to the retina
During replication, the two DNA strands separate and each acts as a template for the production of a new strand. As new DNA strands are produced, nucleotides can only be added in the 5’ to 3’ direction
Explain why new nucleotides can only be added in the 5’ to 3’ direction.
- DNA strands are antiparallel
- Nucleotides have different shapes due to their different positions
- The DNA polymerase active site is complementary to the 5’ end of the DNA molecule
- So can only catalyse DNA strands in that direction as the active site is a different shape to the 3’ end
give two ways in which ATP hydrolysis is used in cells
- to add phosphate to other substances and making them more reactive
- to provide energy for reactions
The new antibiotic is safe to use in humans because it does not inhibit the ATP
synthase found in human cells.
Suggest why human ATP synthase is not inhibited and bacterial synthase is
inhibited.
Human ATP synthase has a different tertiary
structure to bacterial ATP synthase
OR
Human ATP synthase has a different shape
active site to bacterial ATP synthase
OR
Antibiotic cannot enter human cells/mitochondria
OR
Antibiotic not complementary (to human ATP
synthase)
