Section 1 - Biological molecules: 2. Nucleic acids Flashcards
What is a nucleic acid
A polymer of nucleotides which store genetic information in biological systems (ie. DNA and RNA)
What is the structure of a nucleotide (3 components)
- Pentose sugar (with 5 carbon atoms)
- A phosphate group
- A nitrogen-containing organic base
Components covalently bonded together in condensation reactions
What is the name of the bond between nucleotides in a polynucleotide
Phosphodiester bonds
What are the 4 bases in DNA
- Adenine
- Thymine
- Cytosine
- Guanine
What are the 4 bases in RNA
- Adenine
- Uracil
- Cytosine
- Guanine
What are the complementary base pairs in the double stranded helix of DNA
Adenine bonds with Thymine (double hydrogen bond)
Cytosine bonds with Guanine (triple hydrogen bond)
How does the structure of DNA relate to it’s function
- Stable (phosphodiester backbone and hydrogen bonds): allows genetic info to be passed on without change
- Two strands joined by hydrogen bonds: allows for separation during replication
- Large molecule: hold more genetic info
- Helix structure: protects the bases from being corrupted by outside forces or chemicals
- Complementary base pairing: allows for the formation of m-RNA
What were the stages of discovering DNA
- 1869: Johann Friedrich discovered nucleic acids
- 1919: Phoebus Levene described the nucleotides within them
- 1944: Oswald Avery discovered that DNA passes on genetic info down generations
- 1950: Erwin Chargaff discovered the complementary base pairing
- 1950: Maurice Wilkins and Raymond Gosling began to collect x-ray diffraction patterns of DNA
- 1952: Rosalind Franklin used improved techniques to produce ‘Photograph 51’, and began evaluating the structure
- 1953: James Watson and Frances Crick published accurate descriptions of the structure of DNA, using Franklin’s work
What was the experiment used to determine the hereditary nature of material in organisms
- Mice injected with living, safe form of bacteria = healthy
- Mice injected with dead, harmful form of bacteria = healthy
- Mice injected with both = infected
This suggests that the dead harmful bacteria can pass on the information needed to make the toxins.
This hereditary material was proven to be DNA, by removing all parts from the living harmful bacteria and adding the individually to living safe bacteria. Only the DNA caused to trait to be passed on.
What was the experiment used to determine that DNA is responsible for passing genetic info down generations.
Viruses infect bacteria to produce more viruses
Viruses only contain DNA and proteins, so one of those must be responsible.
The proteins and DNA in the viruses were labelled with different radioactive elements, and the viruses produced from them only showed signs of radioactive DNA
Where is the 3’ carbon atom located on a pentose sugar
Attached to the hydroxyl group (bottom left when sugar is oriented upright)
Where is the 5’ carbon atom located on a pentose sugar
Attached to the phosphate group (top left when the sugar is oriented upright)
Why can nucleic acids only be synthesised ‘in vivo’
They can only be synthesised in the 5’-3’ direction, as DNA polymerase can only attach nucleotides to the OH group on the 3’ carbon atom
What is semi-conservative replication
The process of DNA replication where one strand of the double helix is conserved, with a new strand attached to it
Describe the process of semi-conservative DNA replication
- The double helix is unzipped by DNA helicase, forming a replication fork
- On the leading strand, leaving the fork with the 3’ end first, the enzyme primase forms a small section of bases attached to it, called a primer
- DNA polymerase binds to this primer, and forms the new strand in the 5’ to 3’ direction as the original strand is passed through in the opposite direction.
- On the lagging strand, leaving the fork with the 5’ end first, the enzyme primase forms multiple primers between which DNA polymerase forms the new strand in the same direction that the original is being passed out, from the 5’ to 3’ end
- These sections of strands formed on the lagging strand are called Okazaki fragments
- The enzyme exonuclease removes all the primers and they are replaced with DNA by DNA polymerase
What is the enzyme that unzips DNA for replication
DNA helicase
What is enzyme that forms primers to begin DNA replication
Primase
What is the enzyme the forms the new strand of DNA replication
DNA polymerase
What is the name of the sections of DNA formed individually on the lagging strand of DNA replication
Okazaki fragments
What direction does the leading strand leave the replication fork in DNA replication
3’ to 5’
What direction does the lagging strand leave the replication fork in DNA replication
5’ to 3’
What is the enzyme that removes the primers after DNA replication
Exonuclease
What were the alternative models of DNA replication instead of semi-conservative replication
- Conservative: original DNA remains intact, and complete new copy is formed
- Dispersive: new and old DNA randomly alternates in both strands
What is the experiment that supports the model of semi-conservative replication (‘the most beautiful experiment’)
- Bacteria grown in 14-N medium
- Bacteria moved and grown in 15-N medium for many generations and when DNA is extracted and centrifuged, all DNA is the heavy, containing 15-N
- After then being grown in 14-N medium for one generation, when extracted and centrifuged, all DNA is in the medium weight band, containing both 14-N and 15-N (disproving conservative replication)
- After 2 generations in 14-N medium, half the DNA was light containing only 14-N, half was medium containing both (disproving dispersive replication)
- After 3 generations, 75% is light and 25% is medium, proving semi-conservative replication, as there is no heavy containing only 15-N, but the proportion containing the original strands halves each generation
What is the structure of ATP
Adenosine Triphosphate:
- Ribose sugar
- Adenine: organic nitrogenous base
- Phosphates: chain of 3 phosphate groups
How does ATP store energy
Bonds between the phosphates are unstable, so have a low activation energy and release lots of energy when broken by hydrolysis, forming ADP
What enzyme catalyses the hydrolysis of ATP into ADP
ATP hydrolase
How is ATP synthesised
A phosphate molecule is added to ADP in a condensation reaction.
What are the 3 ways ATP can be synthesised from ADP
- Happens in plants during photosynthesis (photophosphorylation)
- Happens in plants and animals during respiration (oxidative phosphorylation)
- Happens in plants and animals when phosphate groups are transferred from donor molecules to ADP (substrate-level phosphorylation)
What is photophosphorilation
The synthesis of ATP, by adding a phosphate group to ADP in chlorophyll-containing plant cells during photosynthesis.
What is oxidative phosphorylation
The synthesis of ATP by adding a phosphate group to ADP in plant and animal cells during respiration
What is substrate-level phosphorylation
The synthesis of ATP, when a phosphate group is donated from one ADP to another, in plant and animal cells
What enzyme catalyses the synthesis of ATP
ATP synthase
Why is ATP required as well as glucose
- ATP is unstable, so can’t store energy like glucose
- ATP can be broken down easily for immediate energy release, whereas the breakdown of glucose is a longer process
Where is ATP made
Constantly made in the mitochondria of the cell that it is needed in.
What energy requiring processes is ATP used for
- Metabolic processes
- Movement
- Active transport
- Secretion: formation of lysosomes used for the secretion of cell products
- Activation of molecules: the inorganic phosphate released can phosphorylate other compounds, lowering their activation energy and making them more reactive
What are inorganic ions
Ions that are not directly associated with a biological molecule
Inorganic ions: What are the functions of iron (Fe^2+)
- Forms prosthetic groups in haemoglobin (Haem groups), associating with O2 for transport in the red blood cells
Inorganic ions: What are the functions of Sodium (Na^+)
- Sodium-potassium pumps (in co-transport)
- Important in the nervous system for communication between neurons.
Inorganic ions: What are the functions of Hydrogen (H^+)
- Ion pumps used to maintain pH (digestion)
- Important on respiration and photosynthesis
Inorganic ions: What are the functions of phosphate (PO4^3-)
- Used to form phosphodiester bonds
- Forms part of the sugar-phosphate backbone of DNA and RNA
- Part of ATP molecule that is removed by hydrolysis to release energy
- Used to activate molecules by phosphorylation
- Part of phospholipids within cell membranes
Inorganic ions: What are the functions of Potassium (K^+)
- Regulation of the guard cells, opening and closing the stomata
What is the structure of a water molecule
Two hydrogen atoms are covalently bonded to one oxygen atom
Why is water dipolar
Although it has no overall charge, the arrangement of the electrons within the molecule mean that the oxygen side is slightly negative and the hydrogen end is slightly positive
Why do hydrogen bonds form between water molecules
The negative oxygen of one molecule is attracted to the hydrogen of another, resulting in an electrostatic attraction that forms a hydrogen bond
What are the main properties of water
- High specific heat capacity
- High latent heat of vaporisation
- Cohesive and adhesive nature of the molecules
- Surface tension
- Effective solvent
- Common reactant in metabolism
- Not compressible
- Transparent
Why does water have a high specific heat capacity
The hydrogen bonds between the molecules means that more energy is required to increase their kinetic energy, so increase the temperature
What is an example of the benefits of the high specific heat capacity of water
Allows for sustained ecosystems in water based environments, as the temperature of the water doesn’t fluctuate as much as the air around it
Why does water have a high latent heat of vaporisation
Hydrogen bonds between the molecules mean that more energy is required to change form liquid to gas
What is an example of a benefit of the high latent heat of vaporisation of water
Allows for thermoregulation, as the evaporation of sweat takes in loads of energy, cooling down the skin
Why are water molecules cohesive (and adhesive)
The polarity of the water molecules causes them to be attracted to each other, and other molecules
What is an example of a benefit of the cohesive nature of water molecules
Allows for transpiration to occur, as the cohesion of water causes it to flow up the stem (and adhesives as they are attracted to xylem cells as they pass)
Why does water have surface tension
Hydrogen bonds near the surface allows water droplets to form
What is an example of a benefit of the surface tension of water
Allows droplets to form, and the spherical shape has the minimum surface area, so takes longer to evaporate, supporting ecosystems that rely on the presence of water
Why is water a good solvent
All small and charged particles will dissolve in water as they are attracted to the polar molecules
What is an example of water being used as a solvent
- Ocean
- Blood stream
- Cytoplasm
- Tissue fluid
- Cell sap
- Transpiration flow
Why is water commonly used in metabolic reactions
Readily available, so is commonly present to be used
What is an example of a metabolic reaction that uses water
- Hydrolysis of compounds
- Photosynthesis
Why is water not compressible
Sides of the molecules with the same charge will repel if too close, stopping the water from being compressed
What is an example of a benefit of water being non-compressible
- Turgid pressure in plants
- Hydrostatic pressure differences
Why is water transparent
The constant breaking and forming of hydrogen bonds allows light to pass through the gaps between molecules
What is an example of a benefit of water being transparent
- Allows for photosynthesis in underwater plants
- Vital for eyesight
