Nucleic Acids and Protein Synthesis
Nucleic Acids and Their Functions
Nucleotide Structure
Nucleic acids (DNA and RNA) are polymers called polynucleotides.
Monomers of nucleic acids are nucleotides.
A nucleotide comprises:
A phosphate group.
A 5-carbon sugar molecule (pentose sugar).
An organic nitrogenous base.
Components are linked by covalent bonds formed during condensation reactions.
Pentose Sugar
In DNA, the 5-carbon sugar is deoxyribose.
In RNA, the 5-carbon sugar is ribose.
Deoxyribose lacks an oxygen atom at the C2 position (has a Hydrogen atom).
Ribose has a hydroxyl group (OH) at the C2 position.
Nitrogenous Bases
Each nucleotide contains an organic nitrogenous base attached to the pentose sugar at carbon 1.
DNA has four possible bases: Adenine (A), Thymine (T), Guanine (G), and Cytosine (C).
RNA has Adenine (A), Guanine (G), and Cytosine (C), but Thymine (T) is replaced by Uracil (U).
Nitrogenous bases are classified by the number of rings in their structure:
Pyrimidines: single-ring structures (Cytosine, Uracil, Thymine).
Purines: double-ring structures (Adenine, Guanine).
Phosphate Group
A phosphate group (PO_4^-) is bound to the pentose sugar at the C5 position.
Key Terms
Nucleotide = Pentose sugar + Nitrogenous base + Phosphate group.
Nucleoside = Pentose sugar + Nitrogenous base.
Mnemonic: "As Pure As Gold" (Adenine and Guanine are Purines).
Adenosine Triphosphate (ATP)
Structure of ATP
ATP is a mononucleotide.
Made of:
Adenine (nitrogenous base).
Ribose (pentose sugar).
Three phosphate groups.
Adenosine = Adenine + Ribose
Adenosine Triphosphate = Adenine + Ribose + 3 Phosphate groups
Energy and ATP
Photoautotrophs convert light energy into chemical energy (organic molecules) during photosynthesis.
Heterotrophs convert chemical energy from food into other forms of energy.
Chemical energy within food is converted into ATP during respiration.
ATP is an energy carrier molecule within cells.
Energy is the ability to do work.
Energy cannot be created or destroyed, only converted (light, heat, sound, kinetic, chemical, electrical, etc.).
Energy is measured in Joules (J).
Cells cannot directly use energy from glucose.
Respiration releases energy from glucose to produce ATP.
ATP releases small, manageable amounts of energy to prevent waste and fatal temperature increases.
ATP Synthesis
Occurs across the inner membrane of the mitochondria.
Catalyzed by ATP synthetase.
Involves phosphorylation of ADP (endergonic reaction).
Equation: ADP + P_i \xrightarrow{ATP \ synthetase} ATP
ATP Hydrolysis
ATP has unstable phosphate bonds with low activation energy, easily broken.
Breaking these bonds releases energy.
Usually, only the terminal phosphate is released.
Hydrolysis of ATP to ADP and P_i is catalyzed by ATPase (exergonic reaction).
One mole of ATP releases 30.6 KJ of energy.
Equation: ATP \xrightarrow{ATPase} ADP + P_i
Chemical energy change (ΔH) = -30.6kJ (exergonic reaction).
Extension
Bonds holding the 3rd and 2nd phosphates are phosphoanhydride bonds.
The bond holding the first phosphate to the ribose sugar is a phosphoester bond.
Phosphorylation: addition of a phosphate group.
ADP can be further hydrolyzed to AMP (adenosine monophosphate).
ATP \rightarrow ADP + Pi \rightarrow AMP + Pi
ATP as Energy Currency
ATP is the universal energy currency of cells.
Used by all organisms for biochemical reactions.
Good energy donor due to unstable phosphate bonds but not a good energy store.
Carbohydrates and fats are used for energy storage.
ATP is an intermediate energy source.
Advantages of Using ATP
Releases smaller, more manageable energy amounts (30.6 KJ) compared to glucose.
Requires only one enzyme (ATPase) for energy release, unlike glucose.
Hydrolysis is a one-step reaction, unlike glucose breakdown.
Only one ATP molecule is needed to transfer energy to reactions.
Different energy types are converted into a common form.
Easily transported across organelle membranes.
Cannot exit the cell, ensuring immediate energy source.
Processes Requiring ATP
Active transport: movement of ions and molecules against concentration gradients.
ATP changes the shape of carrier proteins in plasma membranes.
Synthesis of organic molecules: building macromolecules from smaller molecules (monosaccharides to polysaccharides, amino acids to polypeptides, nucleotides to polynucleotides).
Muscle contraction: requires 2 million ATP molecules per second in contracting muscle cells.
Maintenance, repair, and division: needed by cells and organelles.
Maintaining body temperature: used by birds and mammals (endothermic organisms).
Secretion: required for lysosome production and exocytosis.
Nervous transmission: generation of action potentials requires ATP for sodium-potassium pumps.
Deoxyribonucleic Acid (DNA) Structure
DNA is a polynucleotide made of DNA nucleotides.
A DNA nucleotide consists of:
A phosphate group.
Deoxyribose sugar (5C).
Nitrogenous base (Adenine, Thymine, Cytosine, Guanine).
Nucleotides join via condensation reactions, forming phosphodiester bonds between the phosphate group and the pentose sugar of neighboring nucleotides, creating the sugar-phosphate backbone.
DNA is a double-stranded polynucleotide with antiparallel strands:
One strand runs 5’ to 3’, the other 3’ to 5’.
Nitrogenous bases point inward.
Bases pair up in a specific manner (complementary base pairing):
A purine (2 rings) always pairs with a pyrimidine (1 ring), maintaining uniform distance between backbones.
Adenine pairs with Thymine (A=T) via 2 hydrogen bonds.
Cytosine pairs with Guanine (C≡G) via 3 hydrogen bonds.
Hydrogen bonds are weak individually but strong collectively.
The double-stranded polynucleotide twists into a double helix.
DNA coils around histone proteins in the nucleus.
In eukaryotes:
Loosely coiled DNA forms chromatin (non-dividing cell).
Tightly coiled DNA forms chromosomes (dividing cell).
DNA Functions
DNA has two major functions:
Replication in dividing cells.
Carrying information for protein synthesis in all cells.
DNA is a long molecule capable of carrying a vast amount of genetic information.
Essential for DNA to be inherited accurately across generations, therefore, it needs to be protected.
Complementary base pairs are held inside the molecule for protection.
Strands are held together by weak hydrogen bonds, easily broken during transcription.
Ribonucleic Acid (RNA)
General Structure
RNA is a single-stranded polynucleotide.
Each nucleotide comprises:
Ribose (5C pentose sugar).
A phosphate group.
An organic nitrogenous base (A, G, C, and Uracil instead of Thymine).
RNA twists into a single helix with nitrogenous bases projecting outwards.
Types of RNA
Messenger RNA (mRNA):
Made in the nucleus during transcription.
mRNA code is complementary to DNA code.
The nucleotide sequence on mRNA = genetic code.
Long, single strand, wound into a helix.
Transfers DNA code from the nucleus to the cytoplasm.
Acts as a messenger.
Small enough to leave the nucleus through nuclear pores.
Determines the sequence of amino acids.
Associates with a ribosome in the cytoplasm.
Acts as a template for protein synthesis.
Easily broken down after use.
Transfer RNA (tRNA):
Small (around 80 nucleotides long).
Folded into a cloverleaf shape with complementary base pairing within the strand.
The 3’ end has the sequence C-C-A, the amino acid binding site.
Has an anticodon, a sequence of three adjacent nucleotides.
Each amino acid has a different anticodon sequence.
The anticodon is complementary to a codon on mRNA.
Found in the cytoplasm and carries amino acids to the ribosome during translation.
Ribosomal RNA (rRNA):
Found free in the cytoplasm or bound to the RER.
A component of ribosomes (along with proteins).
Folded into a spherical shape.
Ribosomes are the site of translation (protein synthesis).
Base Pairing
RNA can base pair with RNA or DNA:
G ≡ C
A = U or A = T
Differences Between DNA and RNA
Property | DNA | RNA |
|---|---|---|
Pentose sugar | Deoxyribose | Ribose |
Number of strands | Two | One |
Nitrogenous bases | A, T, C, G | A, U, C, G |
Length | Longer than RNA | Shorter than DNA |
DNA Replication
Functions of DNA
Replication: the base sequence of one strand determines the sequence of the other.
Each parent strand serves as a template for a new complementary strand.
Protein Synthesis: the sequence of bases carries information and determines the amino acid sequence.
Theories of DNA Replication
DNA must be copied precisely before cell division.
Occurs during the interphase stage of the cell cycle.
Creates identical sister chromatids.
Three theories proposed:
Conservative replication: the parental double helix remains intact, and a new helix is made.
Dispersive replication: new double helices contain fragments of old and new DNA.
Semi-conservative replication: the parental double helix separates, and each strand acts as a template for a new strand (correct mechanism).
Demonstrated by Meselson and Stahl.
Semi-Conservative Replication
Requirements:
Four types of nucleotides (A, G, C, T) with deoxyribose.
Both DNA strands must act as templates (needs to be single-stranded).
DNA polymerase is required to catalyze the reaction.
Chemical energy (ATP) is needed to drive the reaction.
Free nucleotides in the nucleus are required to build new strands.
DNA ligase and DNA helicase are also needed.
Process:
Occurs in the nucleus.
DNA helicase breaks hydrogen bonds, unzipping the double helix.
The double helix unwinds and separates into two strands.
Exposed bases attract free DNA nucleotides present in the nucleus. ATP is used to activate the nucleotides.
Free DNA nucleotides pair with complementary exposed bases under the control of DNA polymerase.
DNA polymerase forms phosphodiester bonds between adjacent nucleotides on the newly formed strands.
Each DNA molecule rewinds into a double helix resulting in two genetically identical DNA molecules, each with one old and one new strand.
Enzymes Involved In DNA Replication
Enzyme | Action |
|---|---|
DNA helicase | Unwinds and unzips the DNA by breaking hydrogen bonds between bases. |
DNA polymerase | Links the newly arrived DNA nucleotides by forming covalent bonds. |
DNA Ligase | Joins together small sections of polynucleotide (Ozaki fragments). |
Extension
Replication starts simultaneously at multiple sites (replication forks) due to the length of the DNA molecule.
DNA ligase joins fragments of newly formed DNA (Okazaki fragments).
The template strands are read by DNA polymerase in the 3’ → 5’ direction. The new strands are synthesized in the 5’ → 3’ direction due to the anti-parallel nature of DNA.
Evidence of Semi-Conservative Replication: The Meselson-Stahl Experiment
Conducted in 1958 to determine the mechanism of DNA replication.
Cultured Escherichia coli in a medium containing ^{15}N (heavy isotope of nitrogen) instead of ^{14}N (light isotope).
Bacteria incorporated ^{15}N into their nucleotides.
^{15}N bacteria were transferred to a medium of lighter ^{14}N.
DNA was extracted and spun in an ultracentrifuge in caesium chloride solution.
Denser DNA settles further down the tube.
DNA bands were visualized with UV light.
Results:
Generation 0: Single heavy band at the bottom of the tube.
Generation 1: Single intermediate band.
Ruled out conservative replication (would have two bands – one heavy and one light).
Could be semi-conservative or dispersive.
Generation 2: Two bands – one light and one intermediate.
Ruled out dispersive replication (would have only one intermediate band).
Confirmed semi-conservative replication.
Relating Structure to Function in DNA
The sequence of bases stores information in the form of codes to build proteins.
Long molecules can store vast amounts of information.
Base pairing rules allow the replication of complementary information.
The double helix structure provides stability.
Hydrogen bonds allow easy unzipping for copying and reading information.
The Genetic Code
Features of the Genetic Code
Triplet Code:
A group of three bases codes for one amino acid.
A triplet of bases is known as a codon.
An mRNA codon is complementary to its DNA codon.
Degenerate Code:
More than one codon usually codes for an amino acid.
There are 64 codons and only 20 amino acids.
Punctuated Code:
Three mRNA codons (UAA, UAG, UGA) do not code for amino acids (stop codons).
These mark the end of translation.
The first codon of a gene is usually AUG (start codon), coding for Methionine.
Non-Overlapping Code:
Each base in a sequence is only read once.
Universal Code:
The same codons code for the same amino acids in all species (evidence for a common origin of life).
Genetic code: The DNA and mRNA sequences that determine the amino acid sequences used in an organism’s proteins.
Introns and Exons
Genes are found on one strand of DNA, the coding strand.
The opposite strand is the non-coding strand.
The location of a gene on DNA is called a locus.
Alleles of a gene arise from mutations in the base sequence.
Eukaryotic genes are usually discontinuous, containing:
Exons: coding regions.
Introns: non-coding regions.
Introns are removed during protein synthesis.
Key Terms
Gene: a sequence of DNA that codes for a polypeptide.
Introns: non-coding nucleotide sequences in DNA and pre-mRNA, removed from pre-mRNA to produce mature mRNA.
Exons: nucleotide sequences in DNA and pre-mRNA that remain in the final, mature mRNA.
Extension
Eukaryotic DNA contains multiple repeats outside genes.
These are DNA sequences that repeat over and over (e.g., CCTTCCTTCCTT).
These areas do not code for amino acids.
Used as the basis of genetic fingerprinting.
Prokaryotic genes are continuous and do not contain introns.
Protein Synthesis
Overview
The DNA code is transcribed into messenger RNA (mRNA).
mRNA travels from the nucleus to ribosomes.
Transfer RNA (tRNA) carries amino acids to the ribosomes.
The mRNA code is translated, and amino acids are assembled into a polypeptide via peptide bonds on the ribosomes.
Transcription
Occurs in the nucleus (eukaryotic cells).
DNA helicase breaks hydrogen bonds between DNA strands in the specific gene.
Only one DNA strand, the coding or sense strand, acts as a template.
RNA polymerase attaches to the template strand of DNA and moves along it.
Free RNA nucleotides align opposite their complementary DNA bases:
Guanine (DNA) pairs with Cytosine (RNA).
Cytosine (DNA) pairs with Guanine (RNA).
Thymine (DNA) pairs with Adenine (RNA).
Adenine (DNA) pairs with Uracil (RNA).
RNA Types
mRNA – messenger RNA
tRNA – transfer RNA
rRNA - ribosomal RNA
Transcription Details
Transcription occurs when a segment of DNA (gene) acts as a template to direct the synthesis of a complimentary sequence of mRNA, with the enzyme RNA polymerase.
DNA and mRNA nucleotides form temporary hydrogen bonds.
About 12 base pairs are exposed at a time.
RNA polymerase detaches at the stop codon.
Free mRNA nucleotides join to form a sugar-phosphate backbone via phosphodiester bonds, forming pre-mRNA.
The pre-mRNA detaches from the DNA strand.
The DNA rezips and rewinds.
In prokaryotes, mRNA attaches directly to the ribosome in the cytoplasm.
Post-Transcriptional Modifications
In eukaryotic cells, introns are removed from the pre-mRNA (splicing).
Functional exons join to form mature mRNA.
Mature mRNA passes out of the nucleus via nuclear pores and attaches to a ribosome.
Extension
Mutations can affect splicing, causing disorders like Alzheimer’s disease.
Translation
Ribosomes
Composed of two subunits (one large and one small).
Subunits are made of protein and rRNA.
Ribosomes can be attached to the RER or free in the cytoplasm.
The larger subunit has two tRNA attachment sites.
The smaller subunit binds to the mRNA.
Extension: Factors Affecting Transcription Rate
*Transcription factors: protein molecules which control the transcription of genes.
*Activators: increase rate of transcription.
*Suppressors: decrease the rate of transcription.
*Oestrogen: binds to a transcription factor (oestrogen receptor) and forms an oestrogen-oestrogen receptor complex. Act as an activator or as a repressor.
*Small interfering RNA (siRNA): short and double stranded and can interfere with the expression of some genes
Stages of Translation
Initiation
Energy from ATP is required to attach the amino acid to the tRNA (amino acid activation).
The mRNA attaches to a ribosome at the start codon (AUG).
The first tRNA molecule with complementary anticodon (UAC) pairs with the start codon, carrying Methionine.
Hydrogen bonds form between complementary base pairs.
The next tRNA-amino acid complex arrives at the next attachment site and the anti-codon and codon form hydrogen bonds.
Elongation
Peptide bond forms between amino acids, catalyzed by a ribosomal enzyme and energy from ATP.
The first tRNA leaves the ribosome, leaving its attachment site vacant.
The ribosome moves one codon along the mRNA, releasing the first tRNA from its amino acid, which however remains attached via the peptide bonds.
The next tRNA binds.
tRNA can be reused with its specific amino acid.
The ribosome moves along the mRNA, together with two more tRNA molecules, each pairing up with their two complementary codons on the mRNA.
Termination
The process continues until a stop codon is reached (UGA).
The polypeptide chain is complete.
The ribosome-mRNA-polypeptide complex separates.
Up to 50 ribosomes can simultaneously make polypeptide chains (polysome).
Post-Translational Modifications
The polypeptide chain (primary structure) is coiled or folded into secondary structures.
Further folded into a tertiary structure.
Bonded to other polypeptide chains to form a quaternary structure.
The protein is passed to the Golgi apparatus for modification and packaging.
Modifications include:
Glycoproteins – protein and carbohydrate.
Lipoproteins – protein and lipid.
Phospho-proteins – protein and phosphate.
One Gene – One Polypeptide Hypothesis
Experiments on Neurospora crassa showed radiation damage prevented a single enzyme from being made, leading to the hypothesis “one gene – one enzyme”.
Later modified to “one gene – one protein”.
Then, considering proteins like hemoglobin are made of more than one polypeptide it follows “one gene – one polypeptide”.
Extension: it has now been shown that with splicing possible in different regions of pre-mRNA, one gene can code for more than one polypeptide. The theory was important in establishing our understanding of the processes of transcription and translation.Example – Hemoglobin:
Secondary structure - α helix
Tertiary structure - further folding to give 3D shape.
Quaternary structure - 4 polypeptide chains bonded together.
Prosthetic group- the protein is modified by four non-protein haem groups to make the functional protein.
Glossary
Nucleic acids: Polymers such as DNA and RNA.
Nucleotides: Monomers of nucleic acids, consisting of a phosphate group, a 5-carbon sugar, and a nitrogenous base.
Pentose sugar: A 5-carbon sugar molecule; deoxyribose in DNA and ribose in RNA.
Nitrogenous base: An organic base containing nitrogen, such as adenine, guanine, cytosine, thymine (DNA), or uracil (RNA).
Purines: Nitrogenous bases with a double-ring structure (adenine and guanine).
Pyrimidines: Nitrogenous bases with a single-ring structure (cytosine, thymine, and uracil).
ATP (Adenosine Triphosphate): A nucleotide that serves as the primary energy carrier in cells.
Phosphodiester bond: The covalent bond that links nucleotides together in DNA or RNA, forming the sugar-phosphate backbone.
Antiparallel strands: The arrangement in DNA where one strand runs 5’ to 3’ and the other runs 3’ to 5’.
Complementary base pairing: The specific pairing of nitrogenous bases in DNA: adenine with thymine (A=T) and cytosine with guanine (C≡G).
DNA helicase: An enzyme that unwinds the DNA double helix by breaking hydrogen bonds.
DNA polymerase: An enzyme that synthesizes new DNA strands by adding nucleotides to the 3’ end of a template strand.
DNA ligase: An enzyme that joins DNA fragments together by forming phosphodiester bonds.
Replication fork: The point at which the DNA double helix is unwound during replication.
Okazaki fragments: Short DNA fragments synthesized on the lagging strand during DNA replication.
Transcription: The process by which the DNA sequence of a gene is copied into mRNA.
Translation: The process by which the sequence of codons in mRNA
Here are the functions of DNA, mRNA, rRNA, and tRNA:
DNA (Deoxyribonucleic Acid):
Replication: DNA replicates ensuring genetic information is accurately passed to new cells.
Protein Synthesis: DNA carries the genetic information that determines the amino acid sequence of proteins.
mRNA (Messenger RNA):
Transfers DNA code from the nucleus to the cytoplasm.
Acts as a messenger carrying genetic information.
Determines the sequence of amino acids.
Acts as a template for protein synthesis.
rRNA (Ribosomal RNA):
A component of ribosomes (along with proteins).
Ribosomes are the site of translation (protein synthesis).
tRNA (Transfer RNA):
Found in the cytoplasm and carries amino acids to the ribosome during translation
Transcription:
DNA helicase breaks hydrogen bonds between DNA strands in the specific gene.
Only one DNA strand, the coding or sense strand, acts as a template.
RNA polymerase attaches to the template strand of DNA and moves along it.
Free RNA nucleotides align opposite their complementary DNA bases:
Guanine (DNA) pairs with Cytosine (RNA).
Cytosine (DNA) pairs with Guanine (RNA).
Thymine (DNA) pairs with Adenine (RNA).
Adenine (DNA) pairs with Uracil (RNA).
Free mRNA nucleotides join to form a sugar-phosphate backbone via phosphodiester bonds, forming pre-mRNA.
The pre-mRNA detaches from the DNA strand.
The DNA rezips and rewinds.
In eukaryotic cells, introns are removed from the pre-mRNA (splicing).
Functional exons join to form mature mRNA.
Mature mRNA passes out of the nucleus via nuclear pores and attaches to a ribosome.
Translation:
Energy from ATP is required to attach the amino acid to the tRNA (amino acid activation).
The mRNA attaches to a ribosome at the start codon (AUG).
The first tRNA molecule with complementary anticodon (UAC) pairs with the start codon, carrying Methionine.
Hydrogen bonds form between complementary base pairs.
The next tRNA-amino acid complex arrives at the next attachment site and the anti-codon and codon form hydrogen bonds.
Peptide bond forms between amino acids, catalyzed by a ribosomal enzyme and energy from ATP.
The first tRNA leaves the ribosome, leaving its attachment site vacant.
The ribosome moves one codon along the mRNA, releasing the first tRNA from its amino acid, which however remains attached via the peptide bonds.
The next tRNA binds.
tRNA can be reused with its specific amino acid.
The ribosome moves along the mRNA, together with two more tRNA molecules, each pairing up with their two complementary codons on the mRNA.
The process continues until a stop codon is reached (UGA).
The polypeptide chain is complete.
The ribosome-mRNA-polypeptide complex separates.