Nucleic Acid Stucture Flashcards
Nucleic Acids
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What is DNA?
Nucleic Acid
What is a nucleic acid?
Biological macromolecules containing; Oxygen, hydrogen, carbon, nitrogen and phosphorus
What are the two types of nucleic acids?
Ribonucleic acid (RNA)
Deoxyribonucleic acid (DNA)
What are the basic units that make up nucleic acids?
Nucleotides
What components make up a nucleotide?
Phosphate
Ribose sugar
Nitrogen containing base
How do nucleotides bind together?
Condensation reaction - forms a polynucleotide
DNA
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Why is DNA a polymer?
It’s made of repeating units of repeating nucleotides
What is a double helix in DNA?
Two stands that are coiled around each other
What does it mean for DNA strands to be anti-parallel?
One strand runs in one direction, while the other runs in the opposite direction
What is the physical structure of DNA?
A polymer of nucleotides
What is the backbone of DNA made of?
Sugar and phosphate
What are the four different bases in DNA?
Thymine (T)
Adenine (A)
Guanine (G)
Cytosine (C)
What is complementary base pairing in DNA?
Thymine pairs with Adenine (T-A) Guanine pairs with Cytosine (G-C)
Which bases are classified as purines?
Adenine (A)
Guanine (G)
Which bases are classified as pyrimidines?
Thymine (T)
Cytosine (C)
What is the result of complementary base pairing in a DNA molecule?
Equal amounts of A and T, and equal amounts of C and G
(Makes DNA stronger)
What type of bond links nucleotides together in a DNA strand?
Phosphodiester bond
What type of bond holds the two strands of DNA together? (between bases)
Hydrogen bonds
Lots of hydrogen bonds provides strength
Which base pair has more hydrogen bonds, and what does this imply?
Cytosine and Guanine; they provide greater stability to the DNA molecule
Why is DNA being very stable help it be adapted for its job?
It can pass from generation to generation without change (so info is not changed and is passed to the next gen)
How does DNA having 2 separate strands that are joined by H bonds help it be adapted for its job?
H bonds can separate to allow DNA replication to take place (and protein synthesis)
Each strand acts as a template for replication
How does DNA being an extremely large molecule help it be adapted for its job?
Can store a large amount of information
How does the base pairs being protected help the DNA be adapted for its job?
Base pairs are made of the molecules and protected by the sugar/phosphate back bone, increases the stability of genetic information
RNA
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How many stands does RNA have?
1 - its a single standed molecule and is simpler than DNA
What is the structure of RNA?
RNA is a single strand that contains the bases A, C, G, and U (uracil) instead of T (thymine)
What sugar does RNA use?
Ribose sugar
What are the two different kinds of RNA?
messenger RNA (mRNA)
transfer RNA (tRNA)
(mRNA carries messages, while tRNA helps in the translation process)
What are the differences between RNA (1) and a DNA nucleotide (2) ?
(1) has ribose sugar (2) has deoxyribose sugar
(2) has Thymine (1) has Uracil instead
(1) is single stranded (2) is double stranded
(1) is shorter/smaller (2) is larger/longer
ATP
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What is the full name of ATP?
Adenosine triphosphate
What is the structure of ATP?
Ribose sugar
Adenine base
3 phosphate groups
Has a very similar structure to a nucleotide
Why do cells require ATP?
For cell reactions - main energy source without ATP the cells can not use energy from food
How is ATP adapted for it’s function?
Has instable phosphate bonds which means they can easily break to release energy
What processes require ATP?
Metabolic processes
Movement
Active transport
Secretion
Activation of molecules
How does ATP help in metabolic processes?
- ATP provides the energy needed to build up macromolecules from their basic units
- For example, making starch from glucose or polypeptides from amino acids.
How does ATP help in movement?
- ATP provides the energy for muscle contraction
- In muscle contraction, ATP provides the energy for the filaments of muscle to slide past one another and therefore shorten the overall length of a muscle fibre.
How does ATP help in active transport?
- ATP provides the energy to change the shape of carrier proteins in plasma membranes
- This allows molecules or ions to be moved against a concentration gradient
How does ATP help in secretion ?
- ATP is needed to form the lysosomes necessary for the secretion of cell products
How does ATP help in activation of molecules
- The inorganic phosphate released during the hydrolysis of ATP can be used to phosphorylate other compounds in order to make them more reactive, thus lowering the activation energy in enzyme-catalysed reactions
- For example - the addition of phosphate to glucose molecules at the start of glycolysis.
Where is energy stored in the ATP molecule?
It is stored in the bonds between the phosphates, when hydrolysed the energy is released
What happens during the hydrolysis of ATP?
ATP is converted to ADP and an inorganic phosphate group (Pi) and is catalysed by the enzyme ATP hydrolase
What can the inorganic phosphate released during the hydrolysis of ATP be used for?
Can be used to phosphorylate other components - often making them more reactive
What is phosphorylation?
The process of adding a phosphate group to a molecule, making it more reactive
What is the equation for the formulation of ATP?
ADP + Pi → ATP
( reversible reaction, energy is created during it)
What is the equation for the hydrolysis of ATP?
ATP + H2O → ADP + Pi.
What is the difference between ATP (1) and a DNA nucleotide (2) ?
(1) has ribose sugar (2) has deoxyribose sugar
(1) has 3 phosphate groups (2) has 1 phosphate group
What is the significance of the high-energy phosphate bonds in ATP?
They store energy that can be released during hydrolysis for cellular work
This energy release is crucial for driving biochemical reactions.
Pauling and Corey and Watson and Crick
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What was Pauling and Corey’s model of the structure of DNA?
3 intertwined chains, with phosphates near the fibre axis and the bases on the outside
Why is Pauling and Corey’s model of the structure of DNA unsatisfactory in Watson and Cricks opinion?
Believe the material which gives the X-ray diagrams is the salt, not the free acid, without the acidic H atoms, it’s not clear what forces hold the structure together, especially as negatively charged phosphates near axis repel
Some of van der Waals distances appear too small
Who else suggested a three chain structure?
Fraser
In his model the phosphates are on the outside and the bases on the inside, linked by H bonds
What was Watson and Cricks model of the structure of DNA?
2 helical chains coiled round the same axis (right-handed helices) but owing the dyad the sequences of the atom in the two chains - run in opposite directions
Each chain consists of phosphate diester groups joining β-D-deoxyribofuranose residues with 3’5’ linkage
Bases on the inside of the helix, phosphates on the outside
Sugar roughly perpendicular to base
Configuration of sugar and atoms = close to Furberg’s ‘standard config’
What did Watson and Crick expect to happen to DNA in a lower water content?
Expect the bases to tilt so that the structure would become more compact
What was the experimental evidence for base pairing that Watson and Crick found?
The ration of the amounts of adenine to thymine, and the ratio to guanine and cytosine, always very close to unity for DNA
Why can the double helix structure not be formed using a ribose sugar instead of deoxyribose?
The extra oxygen atom would make it too close to Van der Waals contact
What is the directional structure of DNA?
Each DNA strand has a directional structure due to the ends of each strand behind either a sugar thats attached to the 5’ end or a hydroxyl group attached to the 3’ end
DNA replication
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Why does DNA replicate?
Has to replicate itself every time a cell divides so both cells have identical copies of the entire genome
What type of replication does DNA replicate by?
Semi conservative replication
What does semi conservative replication of DNA mean?
Half of each double helix is a strand that has come from the double helix of the original DNA molecule - conserved from parent cell
1 stand from template strand
1 strand newly synthesised
What does DNA helicase do in DNA replication?
‘Unwinds’ the double helix - breaks H bonds between bases of the DNA strands
What does DNA polymerase do in DNA replication?
Joins free nucleotides to the new strand with condensation reactions catalysed by the DNA polymerase which forms H bonds between bases of the two stands
How does DNA polymerase work in DNA replication?
Each DNA strand has a directional structure due to the ends of each strand beind either a sugar thats attached to the 5’ end or a hydroxyl group attached to the 3’ end
Only complimentary to the 3’ end of the template so can only move along the template strand - add nucleotides to the 3’ to 5’ direction. New strand is built 5’ to 3’ as strands are anti -parallel.
What is the 1st step of DNA replication?
- Enzyme DNA helicase ‘unwinds’ the double helix - breaks H bonds between bases of the DNA strands
What is the 2nd step of DNA replication?
- Each original strand then acts as a template to build a new strand . Free DNA nucleotides are attracted to the exposed bases on the template strands and they attach to the correct bases through complementary base pairing. (A-T, G-C)
What is the 3rd step of DNA replication?
3.The free nucleotides to the new strand with condensation reactions catalysed by the DNA polymerase which forms H bonds between the bases of the two stands
What is the 4th step of DNA replication?
- Each new DNA molecule contains one strand from the original DNA molecule and one new strand
How is the structure of DNA adapted to allow replication?
H bonds between the bases can be easily broken to allow both strands to be a template and complimentary base pairing means the replication of the new strands should be accurate as the correct bases can ONLY pair with each other due to their structure
Meselson and Stahl
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What was ‘the most beautiful experiment’?
An investigation to find out what type of replication DNA used - conservative, dispersive or semi-conservative
What does dispersive replication mean?
In the dispersive model, DNA replication results in two DNA molecules that are a mixture of parental and daughter DNA. Each strand of the daughter molecule is a hybrid of old and new DNA.
What does conservative replication mean?
In conservative replication, two DNA copies are produced from one original DNA, which serves as a template. Out of these two, one is entirely new DNA, and the other is made of old DNA strands.
What does semi-conservative replication mean?
1 stand from template strand
1 strand newly synthesised
Who conducted the ‘Most beautiful experiment’?
Matthew Meselson and Franklin Stahl
How did they do the experiment?
-Used E-coli bacteria
-Grew in presence of N15 which would make one batch heavier/denser
-Grew the other batch in the presence of N14 to make it lighter/less dense
-They then started growing the two batches together to see how the DNA replicated - samples taken after 1&2 cycles of replication
- Use centrifugation to tell the difference between the new and old DNA - Pellet formed - N15 DNA settled closed to bottom
How did they prove that DNA replication was semi-conservative?
After 1 cell division -
DNA = half heavy/denser (N15) and half lighter/less dense (N14)
Rules out conservative replication (1 molecule would be heavy, 1 would be light)
After 2 cell divisions -
DNA = either entirely light/less dense or half heavy/denser (N15) and half lighter/less dense (N14)
Only left semi - conservative as an option
Dispersive model ruled out (DNA would all be half and half|)
How did centrifugation separate the different kinds of DNA in ‘the most beautiful experiment’?
The N15 grown DNA was denser so during centrifugation it would settle closer to the bottom of the tube where as the N14 grown DNA would be closer to the top due to it being less dense
N14 & N15 would e in the middle as it has a medium density
Transcription - Protein synthesis
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What is transcription?
Where the DNA code is copied (transcribed) into a single strand of RNA called messenger RNA
Where does transcription take place?
In the nucleus of a cell
Why does transcription occur?
Because DNA is a large molecule that cannot get through nuclear pores, so smaller mRNA is used to ‘copy’ a section of DNA which codes for a protein - mRNA leaves nucleus and joins with a ribosome where protein synthesis occcurs
What is the 1st stage of transcription?
- RNA polymerase binds at start codon. DNA Helicase binds break the H bonds on the section of DNA containing the gene for the desired protein. Bases are exposed.
What is the 2nd stage of transcription?
- RNA polymerase moves along one strand out of the two DNA strands (template strand). Joins free RNA nucleotides that are complementary to the exposed template strand to form pre-mRNA
What is the 3rd stage of transcription?
- DNA bases re-join behind the RNA polymerase as it moves along
What is the 4th stage of transcription?
4.The RNA polymerase will stop and detach when it. reaches a particular DNA sequence at the end of the gene - stop codon
What is the 5th stage of transcription?
- Pre-mRNA is then spliced before leaving the nuclear pore to find a ribosome
What is splicing?
DNA contains regions which code for proteins (exons) and regions of DNA that do not (introns)
In pre - mRNA both are present - introns must be removed or ‘spliced out’ to only leave exons
Only happens in eukaryotes - prokaryotes only contain exons
Translation - Protein synthesis
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What is a genome?
The entire set of genes or genetic material present in a cell or organism
What is a codon?
A group of 3 bases that code for a particular amino acid
What is a proteome?
The entire complement of proteins that can be expressed from the genes in the genome
What do the bases in a gene code for?
Which amino acids are needed to build a protein
What is the ribosome structure?
Mostly rRNA (ribosomal RNA) and some proteins
Have two parts - a large and a small subunit which fit either side of the mRNA strand
No membrane
Found free in the cytoplasm or bound to the RER
Several can be attached the the same mRNA strand at once
What is translation?
The mRNA is read by a ribosome and the code is ‘translated’ into a polypeptide chain - 2nd stage to protein synthesis
What is the first step for translation?
- A ribosomes attaches to the start codon on the mRNA. A tRNA molecule with a complimentary anticodon to the start codon binds to the mRNA. It has a specific amino acid attached (always Methionine)
What is the second step for translation?
- The ribosome moves along to the next codon, it can fit around two at a time. Process is repeated and the enzyme catalyses the condensation reaction between amino acids to join them with a peptide bond, forming a polypeptide
What are the third step for translation?
- The ribosome continues to move along the mRNA and tRNAs arrive with ribosomes at each codon until a stop codon is reached. The ribosome, mRNA and tRNA all separate and the polypeptide is
What is a mutation?
A change to the DNA sequence e.e one base is substituted or deleted
If a base is changed in a codon could then code a different amino acid - sequence of amino acids then altered - protein made differently or damaged
Genetic code
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What is the genetic code?
The sequence of bases in the DNA which determines the sequence of amino acids in the polypeptide
3 bases (triplet codon) codes for each amino acid
Why is genetic code degenerate? (importance)
Because most amino acids are coded for by more than one triplet codon - reduces effect of mutations
What are the main features of the genetic code?
Non-overlapping - each base is only read once
Each is coded for by 3 bases/nucleotides on mRNA
A few only have 1 codon - also start and stop codon - some have more than one codon
Degenerate
3 codons do not code for any amino acid - code for stop
Universal code - codon codes for some amino acid in all organisms
What is the structure of mRNA?
Single strand - linear
Varies in length
Contains codons
Smaller than DNA
Contains uracil instead of thymine
Mirror image of DNA molecule to be translated into a polypeptide
What is the function of mRNA?
Messenger RNA -
Carries genetic information from the DNA in the nucleus to the cytoplasm for ribosomes
Acts as a template for proteins to be built
What is the structure of tRNA?
‘Clover leaf’ shape
One end extends beyond the other - where amino acid attaches (amino acid binding site)
Contains anti-codon area (3 base sequence) - complimentary to mRNA codons
Small molecule - 80 nucleotides
H bonds hold shape
What is the function of tRNA?
Transfer RNA-
Carries specific amino acids to the ribosomes for protein synthesis
What are the differences between tRNA (1) and mRNA (2)?
(1) is a ‘clover leaf’ shape (2) is linear
(1) is 80 nucleotides - fixed length (2) varies in length depending on the gene
(1) has an amino acid binding site (2) does not
(1) has an anticodon (2) doesn’t - has codons instead
Water
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What is the structure of water?
2 atoms of hydrogen
1 atom of water
Covalent bonds join them
Why is water considered a polar molecule?
It has no overall charge but the oxygen atom has a slight positive charge
Its both positive and negative poles, therefore dipolar
What are 3 properties of water that explain its significance in the cytoplasm?
transparent - sunlight can reach chloroplasts
readily dissolves substances - would break down complex substances for the cell & dissolves required substances into cell
high specific heat capacity - would need a lot of energy to increase temp, stable heat for cell
Properties of water and significance to life
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What is the significance that ice is less dense than water?
Ice forms an insulating layer over water
What is the significance that water has a high surface tension?
The high surface tension of water means it can form a habitat on the surface of the water
What is the significance that water has strong cohesive properties and high tensile strength?
Water can be pulled through plants in a column as the water molecules are held together by H-bonds
What is the significance that water is colourless with a high transmission?
Light can pass through cells for photosynthesis
What is the significance that water is a liquid at room temperature?
Can be used for transport and a medium for reactions
What is the significance that in order for water to evaporate it must absorb a large amount of energy (high latent heat of vaporisation)?
Can be used for cooling organisms by evaporation e.g sweat
What is the significance that water can absorb a lot of energy for only a small rise in temperature (high specific heat capacity)?
Conditions are stable in cells and aquatic environments
Ions
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Why are calcium ions (Ca²⁺) vital in animals?
Muscle contraction, nerve impulse transmission and blood clotting
Why are calcium ions (Ca²⁺) vital in plants?
Help strengthen cell walls by forming calcium pectate in the middle lamella
Why are sodium ions (Na⁺) and potassium ions (K⁺) vital in animals and plants?
- It’s involved in the generation of action potentials in neurons
- The sodium-potassium pump actively transports Na⁺ out of the cell and K⁺ into the cell to maintain the resting membrane potential
- Essential for nerve impulses and muscle function
(Na⁺) - important in the transport of glucose and amino acids across plasma membranes
Why are iron ions (Fe²⁺) vital in animals?
- Are a key component of haemoglobin, the oxygen-carrying molecule in red blood cells
- Each haemoglobin molecule contains four iron ions, which bind reversibly to oxygen, enabling oxygen transport around the body
- A deficiency in iron leads to anaemia, a condition where oxygen transport is reduced
Why are iron ions (Fe²⁺) vital in plants?
- Crucial for the generation of ATP, influencing energy availability in cells
Why are phosphate ions (PO₄³⁻) vital in animals?
- Have multiple biological roles
- They are key components of ATP (adenosine triphosphate), which stores and releases energy for cellular processes
- Phosphate ions are also found in DNA and RNA, linking nucleotides together in a phosphodiester bond
Why are phosphate ions (PO₄³⁻) vital in plants?
- Phosphate is a major nutrient required for root development, cell membrane formation, and energy transfer in respiration and photosynthesis
- It is also a component of phospholipids, which are essential for cell membrane structure
Why are magnesium ions (Mg²⁺) vital in animals?
- Maintains the conformation of nucleic acids and is essential for the structural function of proteins and mitochondria
Why are magnesium ions (Mg²⁺) vital in plants?
- Essential for chlorophyll production, allowing plants to carry out photosynthesis
- Without sufficient magnesium, plants develop chlorosis, where leaves turn yellow due to the lack of chlorophyll
Why are hydrogen ions (H⁺) vital in animals?
- Hydrogen ions help maintain the pH of body fluids, which is important for metabolic processes
- The concentration of H+ ions determines the pH of a solution (In digestion)
- Hydrogen ions are important for ATP synthesis in the mitochondria during cellular respiration
Why are hydrogen ions (H⁺) vital in plants?
- Play a crucial role in the process of photosynthesis, specifically in the light-dependent reactions, where they are used to create a proton gradient across the thylakoid membrane, which then drives the synthesis of ATP
- The movement of hydrogen ions through ATP synthase generates the energy needed to produce ATP
Why are chlorine ions (Cl⁻) vital in animals?
Keeps the pH level of blood constant when gas exchange occurs
Responsible for transmitting certain nerve impulses
Why are chlorine ions (Cl⁻) vital in plants?
- The primary role of chloride ions in plants is to act as a cofactor for enzymes like amylase, which breaks down starch
- Chloride ions can also contribute to maintaining a suitable pH level within the plant cell
- Chloride ions can be transported across cell membranes through specific channels, enabling their uptake and distribution within the plant
What are inorganic ions?
Charged atoms or groups of atoms that do not contain carbon
