Nucleic Acids (Chapter 2) Flashcards
STRUCTURE OF RNA AND DNA
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What are the two examples of nucleic acids ?
DNA + RNA
What does DNA stand for and what is the function of it ?
- deoxyribonucleic acid
- It stores genetic information
What is the sugar in DNA?
Deoxyribose
What does RNA stand for?
Ribonucleic acid
What is the function of RNA?
It transfers genetic information from the nucleus to the ribosome
What is the sugar in RNA?
Ribose
What are DNA and RNA (apart from nucleic acids, they are also …) ?
They are polymers
What is the basic structure of nucleotides
- A phosphate group
- A Pentose sugar
- A nitrogen- containing base (nitrogenous base)
What are polynucleotides?
Nucleotides join together to form polynucleotides
What type of reaction do nucleotides join together by?
A condensation reaction
What is formed between the sugar of one nucleotide and the phosphate of another nucleotide (what type of bond) ? , and what is the new structure called ?
Type of bond :Phosphodiester bond
New structure: dinucleotide
The bases on the two strands of DNA attach to each other by what type of bonds?
by hydrogen bonds (E.g. cytosine and guanine)
What is the chain of sugars and phosphates referred to as?
The sugar phosphate backbone
What causes a double helix in DNA?
Coiling in the polymer due to interactions between nearby DNA monomers
As the two DNA strands run in opposite directions, they are referred to as …
As being antiparallel to one another.
Is specifically asked, why are the DNA strands being synthesised in opposite directions?
- DNA has antiparallel strands
2, Nucleotides aligned different,y on each strand - Enzymes such as polymerase have active sites with specific shape
- Only 3 carbon ends can bind with active site of DNA polymerase ,the polymerase enzymes therefore travel in opposite directions
Complementary base pairing
2 polynucleotides can join together by what type of bond ?
Hydrogen bond, each base can only join one other base
What are the four types of nitrogenous bases in DNA ?
Adenine [A], Thymine [T] , Guanine [G], Cytosine [C]
What is the base pairing for the four nitrogenous bases in DNA ?
Adenine will always join with thymine, forming two hydrogen bonds.
Guanine will always join with cytosine, forming three hydrogen bonds
There will be equal amounts of ? in the polynucleotide ?
Complementary bases
RNA has some differences to DNA which are :
- the sugar in RNA is ribosome rather than deoxyribose
- The base uracil (U) replaces thymine.
Uracil pairs with adenine in the formation of RNA
-RNA polynucleotides are single stranded
What are the four types of nitrogenous bases in RNA ?
Adenine [A], Uracil [U], Guanine [G], Cytosine [C]
What is the base pairing for the four nitrogenous bases in RNA ?
Adenine will always join with uracil, forming two hydrogen bonds.
Guanine will always join with cytosine, forming three hydrogen bonds
The DNA molecule is adapted to carry its functions in a number of different ways:
- very stable structure which normally passes from generation to generation without significant change
- its two separate strands are joined only by hydrogen bonds, which allow them to separate during DNA replication and protein synthesis
- it is an extremely large molecule, so carries an immense amount of genetic information
- By having the base pairs within the helical cylinder of the deoxyribose-phosphate backbone, the genetic information is protected from being corrupted by outside chemical + physical forces
- Base pairing leads to DNA being able to replicate and transfer information ad mRNA
MITOSIS
When cells divide, the daughter cells produced must be …
genetically identical to the parent cell - they must have 23 pairs of chromosomes
What happens to the DNA before a nucleus divides?
It replicates (copied)
Why does the DNA replicate before the nucleus divides ?
To ensure that all the daughter cells have the genetic information to produce enzymes and other proteins that they need
Semi -conservative replication
For semi-conservative replication to take place, there are 4 requirements :
- The four types of nucleotide (each with their bases of adenine, guanine, cytosine or thymine, must be present)
-Both strands of the DNA molecule act as a template for the attachment of these nucleotides
-The enzyme DNA polymerase - A source of chemical energy is required to drive the process
The process of semi-conservative replication:
- The enzyme DNA helicase breaks the hydrogen bonds between the complementary base pairs. This causes the double helix to separate into two strands and unwind (leaving the bases exposed)
- Free nucleotides that have been activated bind specifically to their complementary base pairs in the template strand of the parental DNA.
( They form hydrogen bonds between their complementary bases in the template strand) - Once the activated nucleotides are bound, they are joined together by DNA polymerase which forms phosphodiester bonds between the adjacent (next to) nucleotides (nucleotides are joined together in a condensation reaction ) forming the sugar phosphate backbone on the new strand.
[The remaining unpaired bases continue to attract their complementary nucleotides] - Finally, all the nucleotides are joined to form a complete polynucleotide chain using DNA polymerase. In this way, two identical strands of DNA are formed. 2 sets of daughter DNA contains one strand of the parental DNA + one newly synthesised strand, this method of replication is called the semi-conservative method.
Discovering of method of DNA replication theories
What is conservative replication ?
DNA molecule would get copied and make a new molecule
What is dispersive replication ?
The DNA molecule would be cut various parts, each part would get copied then reattached to produce 2 DNA molecules
What is a semi-conservative replication ?
DNA strands would separate, and each strand would be a template to produce a second strand
Meselson and Stahl experiment -1958:
Evidence for semi-conservative replication
What is the Meselson and Stahl experiment?
1) The scientists grew ecoli bacteria on a petri dish in a lab in the presence of N15 (nitrogen 15) which would be in the DNA. This made the DNA very heavy
2) They used centrifugation to separate the DNA according to its weight. This produced heavy DNA.
3) Then they started growing the cells in the presence of N14 (nitrogen 14), which is light nitrogen. This meant that the DNA made in subsequent cell divisions would be lighter. After one cell division, the DNA was half heavy and half light
4) After the second division, the DNA was half heavy and half light, and entirely light
—> is in line with semi-conservative model
Why is the Meselson and Stahl experiment not in line with the conservative model (After the first cell division, in step 3, why is the experiment not in line with the conservative model) ?
This is not in line with the conservative model since that would depict one molecules as being all light and one as being all heavy
Why is the Meselson and Stahl experiment in line with dispersive and semi-conservative models after the first cell division in step 3?
It is line with dispersive and semi-conservative models as they would both have light and heavy DNA mixed together
Why is the Meselson and Stahl experiment not in line with the dispersive model (After the second cell division, in step 4, why is the experiment not in line with the dispersive model) ?
This is not in line with dispersive model which would depict the molecules staying as half heavy/ half light after 2nd division.
Why is the Meselson and Stahl experiment in line with the semi-conservative model (after 2nd cell division) ?
This is in line with semi-conservative model since after 1st division, the DNA would be half 1 heavy strand and 1 light strand. After the 2nd division, the DNA would have 1 heavy and 1 light strand or two light strands.
ATP AND ADP
What is the structure of ATP?
-Phosphate X3 ~~> a chain of three phosphate groups
- ribose (Pentose sugar) ~~~> a sugar molecule with a 5-carbon ring structure that acts as the backbone to which the other parts are attached
- Adenine ~~~> a nitrogen-containing organic base
Describe how an ATP molecules is formed from its component molecules ?
Three components : 3X phosphate groups, ribosome + adenine via condensation reaction by ATP synthase
What is the function of ATP?
ATP is an immediate energy source of energy for biological process
What is a phosphorylated nucleotide?
Adding a phosphate to a something
What does ATP stand for ?
Adenosine triphosphate
What does ATP provide energy for ?
Chemical reactions within cells - cells can’t get their energy directly from glucose
What is ATP synthesised from?
ATP is synthesised from ADP and inorganic phosphate using energy from reactions such as breakdown of glucose in respiration
It is resynthesised :
[by ATP synthase, during respiration/photosynthesis]
What is the respiration reaction which forms ATP?
ADP + Pi ~~> ATP+ H2O
[Adenosine diphosphate +inorganic phosphate = adenosine triphosphate +water ]
What type of reaction is this, and where is phosphorylation shown in the reaction ?
ADP + Pi ~~> ATP+ H2O
-It is a condensation reaction
- ADP is phosphorylated during these respiration reactions to form ATP. This involves adding another Pi group via a phosphate bond.
What is the respiration reaction that forms ADP ?
ATP + H20 —> ADP +Pi
What type of reaction is this ?
A hydrolysis reaction
- When energy is needed by a cell, ATP is broken down into ADP and Pi. This is a hydrolysis reaction. A phosphate bond is broken and energy is released. The reaction is catalysed by the enzyme ATP hydrobase.
How can ATP be re-synthesised in a condensation reaction ?
ATP can be re-synthesised in a condensation reaction from ADP and Pi by ATP synthase during respiration/photosynthesis
What is the reaction catalysed by ATP synthase ?
ADP + Pi ~> ATP + H20
What can the released inorganic phosphate be added to ?
Another compound (called phosphorylation, which often makes compounds reactive)
ATP properties (the body uses ATP as its immediate source of energy rather than glucose due to its properties) :
- Unstable phosphate bonds - low activation energy, so are easily broken, releasing a considerable amount of energy
- Only one hydrolysis reaction needed to release energy (lots more needed to break down glucose)
- Releases a small, manageable amount of energy
- Does not need to be stored - quick to synthesise
Why do unstable phosphate bonds in ATP release considerable amounts of energy?
These bonds are unstable so have low activation energy
Where is ATP made?
It is continuously made in cells via the mitochondria, as ATP cannot be stored
Roles of ATP:
- metabolic processes such as building macromolecules
- movement - muscle contraction requires ATP
- Active transport of molecules across the plasma membrane via carrier proteins
- Secretin - ATP is needed to form lysosomes necessary for the secretion of cell products
- Activation molecules - the inorganic phosphate released during the hydrolysis of ATP can be used to make them more reactive, thus lowering the activation energy in enzyme-catalysed reactions
Give two ways in which the hydrolysis of ATP is used in cells ?
- To provide energy for other reactions
- To add phosphate to other substances and make them more reactive
5 properties of ATP vs glucose :
- ATP release energy is small, manageable amount so no energy is wasted.
In comparison to glucose, this would release large amounts of energy that could result in wasted energy. - It is a small + soluble molecule to easily be transported around the cell.
Glucose also does this.
Useful : provides energy for chemical reactions within the cell - Only one bond is hydrolysed to release energy (why it is immediate).
Glucose would need several bonds to be broken down to release all its energy. - It can transfer energy to another molecule by transferring one of its phosphate groups.
~> ATP enables Phosphorylation, making other compounds reactive, glucose can’t. - ATP can’t pass out of the cell, cell always has immediate supply of energy .
~> ATP can’t leave cell, glucose can means cells have constant supply of ATP, but can run out of glucose.
WATER AND ITS FUNCTIONS
What is the structure of water (H20) ?
2 atoms of hydrogen are covalently bonded to a molecule of oxygen
What type of molecule is water ?
A polar molecule - electrons not evenly distributed across the molecule (hydrogen slightly positive, oxygens slightly negative)
What bond forms when between the charges from the attraction in water ?
Hydrogen bond
Attraction between these charges forms hydrogen bond between water molecules
Types of properties in water
What are the five properties in water ?
- High heat capacity
- High latent heat of vaporisation
- Strong cohesion between water molecules
- An important solvent
- A metabolite
Why is high heat capacity a property of water ?
[The heat needed to raise the temperature of 1kg of water by 1°C is specific heat capacity / the amount of energy needed to change the temperature]
- Water acts as a buffer to aquatic organisms, temperatures don’t change rapidly.
(It buffers changes in temperature)
What is high heat capacity’s significance to life?
- Allows water to act as a habitat for aquatic organisms
E.g. controlling the temperature in the arctic, so the ice doesn’t melt as quickly
Why is large latent heat of vaporisation a property of water ?
- the amount of heat energy needed to evaporate water, providing a cooling effect
What is large latent heat of vaporisation’s significance to life?
Allows animals to cool themselves without losing a great deal of water e.g sweating
Why is strong cohesion between water molecules a property of water ?
- produces surface tension (where water meets air).
What is strong cohesion between water molecules’ significance to life?
Surface tension is useful as it allows the surface of water to act as a habitat for small organisms
E.g. for insects such as pond skaters
Why is water being an important solvent a property of water ?
Contains dissolved substances.
Helps transport dissolved substances.
Why is water being an important solvent significant to life?
Water transports dissolved substances, mineral ions, up the xylem
Why is water being an a metabolite a property of water ?
-water molecules can also be involved in chemical reactions directly:
Condensation -> makes up molecules
Hydrolysis-> breaks down molecules
Why is water being a metabolite significant to life?
Water is produced in condensation reactions.
Water is a reactant in photosynthesis + hydrolysis reactions
-condensation reactions are important in synthesis of important molecules such as proteins in living organisms
- hydrolysis reactions are important in digestion of large molecules in animals
State and explain the property of water that can help to buffer changes in temperature.
High specific heat capacity,
So can gain energy without changing temperature/ takes a lot of heat to change temperature.
Give two properties of water that are important in the cytoplasm of cells. For each property of water, explain its importance in the cytoplasm.
- Polar molecule, acts as a universal solvent
- Reactive, takes place in hydrolysis/condensation reactions
DISCOVERY OF DNA
Who discovered DNA?
Watson + Crick
What did Watson + Crick discover about DNA?
They discovered the structure of DNA and were the first to describe a method of replication
What was originally doubted about DNA?
DNA could be the hereditary material due to its relatively simple structure
The Griffith experiment
What did the Griffith experiment hope to prove ?
That DNA is a hereditary material
What was used in the Griffith experiment?
Used a bacterium that causes pneumonia in mice
What 2 forms did the Griffith experiment exist in ?
- A safe form that does not cause pneumonia (R-strain)
- A harmful strain that does cause pneumonia (S-strain)
What was the method of the Griffith experiment
What was the method and result of the Griffith experiment?
1) Living S strain (Virulent) ~> mouse dies
2) Living R strain (Non-virulent) ~> mouse lives
3) Dead S strain (Heated) ~> mouse lives
4) Mix living R strain and Dead S strain ~> Mouse dies
Why did the R strain + S strain kill the mouse?
-experimental error: not all the harmful bacteria really died
- The safe form had mutated to become harmful
-Pneumonia is caused by a toxin, the code for which remained in the dead bacteria and was used by the living bacteria
What were the further investigations of the Griffith experiment ?
- the living harmful bacteria that were found in the mice with pneumonia were collected
- Various substances were isolated from them + purified
- each substance was added to suspensions of living safe bacteria to see if it would transform them into the harmful form
- The only substance that produced this transformation was purified DNA
- when an enzyme (DNAase) that breaks down DNA was added, the ability to carry out the transformation ceased
