5. Core Concepts - Nucleic acids and their functions Flashcards
nucleotide
A nucleoside
a pentose sugar joined to a nitrogenous base: adenosine is composed of ribose bonded to adenine. This nucleoside is a component of ATP (adenosine triphosphate).
bases in DNA
adenine, thymine, guanine or cytosine.
diagram of ATP
how is ATP formed
endergonic reaction (a reaction which uses energy).
ADP and phosphate (Pi) are combined to form ATP. The energy to form the bond comes from exergonic (energy releasing reactions) in cellular respiration. The reaction is a condensation reaction; water is eliminated when the bond is formed. An enzyme that catalyses this reaction is ATP synthetase.
ATP can be hydrolysed to ADP and Pi, this reaction releases energy. The enzyme that catalyses this reaction is ATPase. 30.6 kJmol-1 energy is released when ATP is converted to ADP and Pi.
```
ATP (adenosine triphosphate) is vital to organisms because
it acts as an energy carrier and releases energy efficiently
Importance of ATP Hydrolysis
Single-step Energy Release:
The energy is made available almost immediately because only one reaction is required.
This makes ATP an efficient and rapid energy source for cellular processes.
Controlled Release:
The amount of energy released (~30.5 kJ/mol) is manageable for the cell, preventing wastage or damage that might occur with larger energy releases.
Catalysis by ATPase:
ATPase ensures that the hydrolysis is specific and occurs only when and where the energy is needed in the cell.
This enzymatic control helps direct energy to specific biological processes, like muscle contraction or active transport.
Universal Energy Currency:
ATP is used universally in all types of cells, making it a convenient molecule for transferring energy between different biochemical pathways.
By providing energy in a quick and controlled manner, ATP hydrolysis underpins many essential processes in living organisms, including metabolism, movement, and homeostasis.
hydrolysis of ATP reaction
when in ATP synthesized
when energy is avaliable
this has the advantage of converting the energy into a single useable form.
Cells use energy for active transport, protein synthesis, cell division and muscle contraction.
ATP characteristics
As ATP is relatively small and is soluble, it can easily be transported in cells to where it is required.
ATP hydrolase vs ATPase
For A-level biology, it’s most accurate to refer to the enzyme specifically involved in the breakdown of ATP as ATP hydrolase in the context of simple ATP hydrolysis. However, ATPase is also commonly used when discussing processes where ATP hydrolysis is coupled to specific cellular functions.
ATP AND ADP diagram
two main categories of base in nucleic acids
purines and pyrimidines
purine bases
guanine and adenine; these have a double ring in their structure.
pyrimidines
thymine, cytosine and uracil. They have a single ring.
Edwin Chargaff investigated the proportions of the bases in DNA. His results demonstrated that:
the percentage of purines was always equal to that of pyrimidines
the percentage of adenine was equal to that of thymine
the percentage of guanine was equal to that of cytosine.
G and C bonds
Guanine (G) and cytosine (C) are linked by three hydrogen bonds.
A and T bonds
Adenine (A) and thymine (T) are linked by two hydrogen bonds.
recognise pyrimidine bases
recognise purine bases
DNA has two functions in cells:
DNA contains a base sequence that codes for amino acids in protein synthesis.
replicating prior to cell division so that each daughter cell is genetically identical to the parent cell
polynucleotide
polymer of nucleotides
how are sugar phosphates linked in DNA
sugar-phosphate molecules are joined by condensation reactions, making a phosphodiester linkage.
The sugar-phosphate molecules form the two sugar-phosphate ‘backbones’ of the molecule. T
how are the two strands of DNA joined
The two strands are joined by hydrogen bonds between the complementary base pairs (A-T and C-G).
antiparallel meaning DNA
RNA
is a single stranded polynucleotide. The pentose sugar is ribose, the base uracil is present instead of thymine. RNA is a relatively short-lived molecule and is also shorter than DNA.
There are three types of RNA, each type is involved in protein synthesis:
Ribosomal RNA
Messenger RNA
Transfer RNA
Ribosomal RNA
Messenger RNA
Transfer RNA (tRNA)
Which of these are structural differences between RNA and DNA?
RNA has uracil and DNA has thymine.
RNA has ribose and DNA has deoxyribose.
label
What type of nucleic acid is shown in the image?
tRNA
The main steps in extracting DNA from cells are:
Crush or blend the source cells in detergent, salt and water to release the DNA.
Filter the cell debris and collect the extract.
Pour ice-cold alcohol down the side of the tube containing the extract.
The DNA precipitates at the junction of the extract and alcohol.
DNA can be stained red using acetic orcein.
Risk assessment:
Extracting DNA
**90% alcohol can be a skin irritant and is volatile, so it could affect the nose and throat. Use it in a well-ventilated area and wear safety goggles.
Acetic orcein contains ethanoic acid, and corrosion of skin or eyes is a risk. Transfer it using a dropper and wear safety goggles.**
Meselson and Stahl: models of replication
They proposed three possible mechanisms for DNA replication and tested them out in the experiment. The three possible mechanisms were:
Conservative replication: the DNA molecule would be copied from the original, leaving the original DNA molecule as it was and having a new copy.
Semi-conservative replication: the two polynucleotide chains would part, and new nucleotides attach to each of the chains, leading to each new molecule having one original chain and one new one.
Dispersive replication: sections of the DNA molecule would be copied and spliced together, making each new DNA molecule a mix of original and new DNA.
Meselson and Stahl
Diagram
Meselson and Stahl
Experiment
Intro
used E.coli bacteria as the source of DNA. E.coli are easily grown in a flask of culture medium and replicate their cells (and DNA) every 20 minutes under optimal conditions.
‘New’ and ‘original’ nucleotides were distinguished by the isotope of nitrogen (N) in the nitrogenous bases. 15N is heavier in mass than 14N, so DNA molecules containing bases with 15N and DNA molecules containing 14N can be separated by mass in centrifugation.
Meselson and Stahl
Experiment
First Step
First, the scientists grew E.coli in a culture medium with only 15N isotopes until, after many generations, all of the bases contained 15N. When a sample was centrifuged, the band of DNA molecules was near the bottom of the tube, as shown in the diagram below. This is because 15N is heavier, so it settles at the bottom of the tube.
at the start - bases were ‘normal’ 14N bases
Meselson and Stahl
Experiment
Second Step
Meselson and Stahl
Experiment
Last Step
Meselson and Stahl
Experiment
Conclusion
This first generation showed that replication was not conservative but that each new DNA molecule produced by replication consisted of half new (14N) nucleotides and half original (15N) nucleotides.
Eliminating the dispersive model
Meselson and Stahl Relative Density of DNA
As Meselson and Stahl demonstrated in their experiment, DNA replication happens by a semi-conservative mechanism.
DNA helicase breaks the hydrogen bonds holding the two polynucleotide chains together. The area where the helicase works is a ‘replication fork’.
DNA polymerase joins new nucleotides to their complementary bases by catalysing the formation of phosphodiester bonds between the deoxyribose and phosphate groups working from the 5’ to 3’ direction. The original polynucleotide chains act as a template for the aligning of new nucleotides.
mechanism of DNA replications
trascription
DNA holds the code for proteins in the base sequence. DNA is confined to the nucleus.
The code is transferred from the nucleus to the cytoplasm by means of messenger RNA (mRNA).
The gene is unwound and unzipped by DNA helicase; this means that the hydrogen bonds between the two polynucleotide chains are broken. The bases are exposed. One chain acts as a template for the formation of mRNA.
RNA nucleotides align opposite their complementary base pairs. G on DNA pairs to C RNA nucleotides, C on DNA to G, T on DNA to A and A on DNA to Uracil (U) nucleotides. RNA polymerase joins the nucleotides together, condensing the ribose phosphate backbone. A pre-mRNA molecule is formed. The pre-mRNA leaves the DNA when a stop sequence is reached.
RNA polymerase
RNA polymerase joins the nucleotides together, condensing the ribose phosphate backbone.
catalyses the synthesis of mRNA
what happens to the mRNA before it leaves the nucleus
Genes contain short lengths of nonsense DNA called introns
Introns are copied into the mRNA
but are edited out before the mature mRNA exits the nucleus
✅ 1. Splicing
Introns (non-coding regions) are removed
Exons (coding regions) are joined together
Carried out by the spliceosome
🧠 Think: Introns = Interrupting, Exons = Expressed
bried introns and extrons
exons as regions of DNA that contain the code for
proteins and that between the exons are regions
of non-coding DNA called introns
Eukaryotes and prokaryoes genes
do they contain introns and exons?
Eukaryotic genes are usually discontinuous genes with
coding exons and non-coding introns. Prokaryotic genes
are usually continuous genes, lacking non-coding
sequences.
Post-transcriptional modification
involves the removal of introns (these remain inside the nucleus). The exons are spliced together.
In 1945, the ‘one gene one enzyme hypothesis’ was proposed; it was thought that genes coded only for enzymes which catalysed the production of other proteins. In the 1950s, work on haemoglobin demonstrated that genes also code for other proteins leading to a modification of the hypothesis. The one ‘gene one polypeptide hypothesis’ is that each gene is transcribed and then translated into single polypeptide. This is now thought to be too simplistic, as exons can be spliced in different orders forming different types of mRNA from one pre-mRNA. As the code is different, different proteins will be made, which refutes the one gene one polypeptide hypothesis. Once spliced, the mRNA is called functional mRNA. The exons joined into functional mRNA exit the nucleus through a nuclear pore and attach to ribosomes.
In the diagram below, the exons are represented by boxes.
gene
a section of DNA that codes for a polypeptide
eukaryotes genes vs prokaryotes genes
In eukaryotes, genes contain introns and exons. Exons are the coding parts and introns the non-coding parts. Prokaryotes do not have introns; their genes are continuous.
Translation
Every three bases on mRNA is called a codon. The mRNA joins to a ribosome at the ‘start’ codon. The ribosome can accommodate two codons.
Transfer RNA (tRNA) in the cytoplasm is activated. The correct amino acid is attached to the amino acid binding site. Which amino acid is attached is determined by the anticodon; this is a sequence of three bases, represented by X on the diagram below. This process uses energy from ATP.
tRNA molecules carrying amino acids collide with the codons on mRNA. If the anti-codon and codon are complementary, a codon/anticodon complex can form, as the complementary bases form hydrogen bonds. When two tRNA molecules occupy both ribosome sites, the amino acids are brought close enough to form a peptide bond.
The ribosome moves along the mRNA by one codon. The first tRNA is released from the amino acid and ribosome and returns to the cytoplasm to be reactivated.
Another amino acid is attached, and the ribosome moves on to the next codon. This process happens until a ‘stop’ codon is reached. At the stop codon, the polypeptide chain leaves the ribosome to move to the Golgi body for modification.
In the Golgi body the polypeptide can be folded to make a protein. It may have non-protein (prosthetic) groups joined to it, like carbohydrate, lipid or phosphate. Some polypeptides may be combined to form quaternary structure proteins. Haemoglobin, for example, has four combined polypeptide chains and a prosthetic haem group. The diagram below illustrates transcription and translation.
GCG
triplet code
The genetic code is a triplet code, that means that three bases on DNA code for one amino acid. Codons are three bases on mRNA and anticodons are three bases on tRNA. The anticodon determines which specific amino acid is carried by the tRNA. The code is a triplet code, as three bases in the code give enough combinations to code for all 20 amino acids. Two bases would only give 42 = 16 different codes. Three bases give 43 = 64 codes.
How do mutations alter the DNA sequence
Mutations alter the DNA sequence and therefore the codon sequence. Mutations may not have an effect on the amino acid sequence because the code is degenerate, the new code may code for the same amino acid. If the changed code changes the amino acid, the protein may fold differently and be non-functional.
advantage of the genetic code being universal
The genetic code is universal and is the same in all living things, so each specific codon codes for the same amino acid in all species. It is a linear code with no overlaps, so it can be ‘read’ without any ambiguity.
Properties of the Genetic Code
5
Universal
The same codons code for the same amino acids in almost all organisms.
Example: The codon AUG codes for methionine in humans, bacteria, and plants.
This suggests a common evolutionary origin and allows genes to be transferred between species (e.g., in genetic engineering).
Degenerate
Most amino acids are coded for by more than one codon.
There are 64 possible codons but only 20 amino acids, so some amino acids have multiple codons (e.g., leucine has 6).
This reduces the impact of mutations, as a change in the third base may still code for the same amino acid (called a silent mutation).
Non-overlapping
Each base is read only once as part of a codon.
Codons are read in sequence, one after another, with no overlap.
This ensures that the reading frame is maintained, producing the correct sequence of amino acids in a protein.
Triplet Code
A sequence of three bases (a codon) codes for one amino acid.
Example: GGC codes for glycine.
Contains Start and Stop Codons
Start codon (AUG) signals the start of translation and codes for methionine.
Stop codons (e.g., UAA, UAG, UGA) signal the end of translation and do not code for an amino acid.
EXTRACTING DNA whiteboard
SEMI CONSERVATIVE REPLICATION whiteboard
Meselson and Stahl 3 Models WHITEBOARD
Meselson and Stahl Experiment
diagram of amino acid
2 amino acids join
formation of a peptide bond
elimination reaction
summary of types of bonds between molecules:
Peptide Bond
Peptide Bond
Joins: Two amino acids
Forms by: Condensation reaction
Bond type: Between carboxyl group (-COOH) of one amino acid and amine group (-NH₂) of another
Breaks by: Hydrolysis
Found in: Proteins / polypeptides
summary of types of bonds between molecules:
Glycosidic Bond
Glycosidic Bond
Joins: Two monosaccharides
Forms by: Condensation reaction (removal of H₂O)
Bond type: Between hydroxyl (-OH) groups
Examples:
α-1,4 glycosidic bonds in amylose
α-1,6 glycosidic bonds in amylopectin
Breaks by: Hydrolysis
Found in: Carbohydrates (e.g. starch, glycogen, maltose)
summary of types of bonds between molecules:
Phosphodiester Bond
Phosphodiester Bond
Joins: Nucleotides
Bond type: Between phosphate group of one nucleotide and sugar of the next
Forms the: Sugar-phosphate backbone of DNA/RNA
Forms by: Condensation reaction
Breaks by: Hydrolysis
summary of types of bonds between molecules:
Hydrogen Bond
Hydrogen Bond
Weak bond but important in structure
Occurs between: Slightly positive hydrogen atom and slightly negative atom (often oxygen or nitrogen)
Found in:
Secondary/tertiary structure of proteins
DNA base pairing (A-T = 2 bonds, G-C = 3 bonds)
Cohesion/surface tension in water
summary of types of bonds between molecules:
Disulfide Bond (Disulfide Bridge)
Disulfide Bond (Disulfide Bridge)
Strong covalent bond
Forms between: Two cysteine amino acids (sulfur-containing R groups)
Found in: Tertiary structure of proteins (adds stability)
Ionic Bond (in proteins)
Forms between: Oppositely charged R groups of amino acids
Found in: Tertiary structure of proteins
summary of types of bonds between molecules:
Hydrophobic Interactions
Hydrophobic Interactions (bonus for protein folding)
Non-polar R groups tend to cluster away from water
Helps shape tertiary protein structure
🔁 What is a Mutation?
A mutation is a change in the DNA base sequence. This can alter the sequence of codons, leading to changes in the amino acid sequence of proteins.
Types of mutation:
Substitution
-
Substitution – one base is swapped for another
Silent mutation:
New codon codes for the same amino acid
No change to protein (due to the degenerate genetic code)
Missense mutation:
New codon codes for a different amino acid
May change protein shape/function
Nonsense mutation:
New codon becomes a stop codon
Results in a truncated protein (often non-functional)
Types of mutation:
Addition (Insertion)
- Addition (Insertion) – one or more bases added
Causes a frameshift: all codons downstream are changed
Usually leads to a completely different amino acid sequence
Types of mutation:
Deletion
- Deletion – one or more bases removed
Also causes a frameshift (unless 3 bases are deleted)
Can drastically change the resulting protein
🔧 How Mutations Affect Protein Structure
Changes in the amino acid sequence can:
Alter the position and properties of R groups
Disrupt hydrogen bonds, ionic bonds, or disulfide bridges
Affect folding into secondary and tertiary structure
🧪 Mutation Impact on Protein Function (e.g. enzymes)
The active site of an enzyme is highly specific and depends on the tertiary structure.
If a mutation changes an amino acid in or near the active site:
The active site may no longer fit the substrate (loss of enzyme function)
Or may bind less effectively (reduced activity)
🧬 mRNA vs tRNA
