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IB DP Biology D1.2 Protein synthesis Study Notes

IB DP Biology D1.2 Protein synthesis Study Notes - New Syllabus -2025

IB DP Biology D1.2 Protein synthesis Study Notes – New syllabus 2025

IB DP Biology D1.2 Protein synthesis Study Notes at  IITian Academy  focus on  specific topic and type of questions asked in actual exam. Study Notes focus on IB Biology syllabus with guiding questions of

  • How does a cell produce a sequence of amino acids from a sequence of DNA bases?
  • How is the reliability of protein synthesis ensured?

Standard level and higher level: 3 hours
Additional higher level: 3 hours

IBDP Biology 2025 -Study Notes -All Topics

D1.2.1—Transcription as the synthesis of RNA using a DNA template

Transcription is the synthesis of RNA, using DNA as a template. Because RNA is single-stranded, transcription only occurs along one of the two strands of DNA.1 Genes can be transcribed repeatedly to provide as many copies of a base sequence as needed.

The enzyme RNA polymerase has multiple roles in transcription:

  • binding to a site on the DNA at the start of the gene that is being transcribed
  • unwinding the DNA double helix and separating it into two single strands (template and coding strands)
  • moving along the template strand
  • positioning RNA nucleotides on the template strand with bases complementary to those of the template
  • linking the RNA nucleotides by covalent sugar-phosphate bonds to form a continuous strand of RNA
  • detaching the assembled RNA from the template strand and allowing the DNA double helix to reform.

Transcription stops when a sequence is reached that indicates the end of the gene. The completed RNA molecule is then released. Because the RNA has a base sequence complementary to the template strand, its sequence is identical to the sense strand of the DNA, apart from one difference: uracil replaces thymine. There is no thymine in RNA. During transcription uracil not thymine pairs with adenine on the template strand.

D1.2.2—Role of hydrogen bonding and complementary base pairing in transcription

The copying of base sequences during transcription depends on complementary base pairing. Each nucleotide added to the growing RNA strand by RNA polymerase must have a base that is complementary to the corresponding base on the template DNA strand. Pairs of bases are complementary because they form hydrogen bonds with each other but not with other bases. Cytosine and guanine will only pair with each other. Thymine on the template strand will only pair with adenine on the RNA strand. Adenine on the template strand only pairs with uracil on the RNA strand.

Transcription is used to copy the base sequence of one of the two strands in a DNA molecule. The DNA strand with the base sequence to be copied into RNA is called the sense strand (or the coding strand). The other strand, which has a complementary base sequence to the sense strand, is called the template strand (or the antisense strand). Transcription of this strand results in a strand of RNA with the same base sequence as the sense strand of DNA except that uracil is replaced by thymine.

  • Complementary Base Pairing: During transcription, RNA polymerase synthesizes an RNA strand using a DNA strand as a template. The process relies heavily on complementary base pairing.
  • Base Pairing Rules:
    • Adenine (A) on the DNA template strand pairs with uracil (U) in the RNA strand.
    • Thymine (T) on the DNA template strand pairs with adenine (A) in the RNA strand.
    • Guanine (G) on the DNA template strand pairs with cytosine (C) in the RNA strand.
    • Cytosine (C) on the DNA template strand pairs with guanine (G) in the RNA strand.
  • Hydrogen Bonding: Complementary base pairs form hydrogen bonds with each other. These hydrogen bonds stabilize the interaction between the DNA template strand and the growing RNA strand.
  • Sense and Antisense Strands: The DNA strand that serves as the template for RNA synthesis is called the antisense strand or template strand. The other DNA strand, which has a base sequence complementary to the template strand, is called the sense strand or coding strand. The RNA strand produced during transcription has the same base sequence as the sense strand of DNA, except that uracil replaces thymine.

D1.2.3—Stability of DNA templates

  • Maintaining DNA Sequence Integrity: During transcription, when RNA polymerase splits DNA into single strands to use one as a template, it’s crucial that the original DNA base sequence remains unchanged. After transcription, the two DNA strands must correctly re-pair, with each base forming hydrogen bonds with its complementary base on the opposite strand.

  • Minimizing Mutation Risk: The DNA strands are only separated for a brief period as RNA polymerase transcribes the gene. This short exposure window minimizes the vulnerability of the bases to chemical changes that could lead to mutations.

  • Importance of Template Stability: The stability of DNA templates is paramount because they are often transcribed repeatedly throughout a cell’s lifespan.

  • Consequences of Template Mutations: If mutations were frequent, frequently used templates would accumulate errors. This would result in RNA copies with increasing numbers of mistakes.

  • Impact on Protein Synthesis: These flawed RNA copies would then be translated into proteins with progressively more amino acid substitutions. Such alterations are highly likely to impair protein function.

D1.2.4—Transcription as a process required for the expression of genes

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D1.2.4 Transcription as a process required for the expression of genes

Gene expression is the process by which information carried by a gene has observable effects on an organism. The sequence of the bases in genes does not determine the observable characteristics in an organism. The function of most genes is to specify the sequence of amino acids in a particular polypeptide.1 It is the proteins produced that directly or indirectly determine the observable characteristics of an individual. Two processes are needed to produce a specific polypeptide using the base sequence of a gene: transcription and translation.

Transcription is the first stage in gene expression and the key stage at which it can be switched on or off. Only some genes are switched on in a cell at any particular time. Some genes may never be switched on during the life of a cell. For example, the gene for making insulin is only expressed in pancreatic cells. In all other cells this gene is never normally transcribed. There are also genes that are always expressed because the proteins they code for are always required. These are the housekeeping genes with functions such as cell respiration.

The full range of RNA types made in a cell is its transcriptome. Within an individual, different cells or tissue types have different transcriptomes. Over time, the transcriptome changes as the activity of the cell changes.

D1.2.5—Translation as the synthesis of polypeptides from mRNA

To make a specific polypeptide, amino acids must be linked together in the correct sequence. A typical polypeptide is a chain of hundreds of amino acids; each amino acid could be any one of the 20 amino acids. The information needed to make a polypeptide is held in the base sequence of an RNA molecule, copied from a gene by transcription. RNA holds the information in the form of the genetic code. To make an amino acid sequence from a base sequence this code is translated. The process of polypeptide synthesis is therefore called translation.

Translation happens in the cytoplasm. In eukaryotes, RNA is produced in the nucleus and then passes out to cytoplasm via nuclear pores. Distances are shorter in prokaryotes but transcription and translation happen in different parts of the cell. The RNA with the information for making a polypeptide travels from one place to another within a cell, so is known as messenger RNA (mRNA). Translation in biology is synthesis of polypeptides from mRNA.

D1.2.6—Roles of mRNA, ribosomes and tRNA in translation

Three components work together to synthesize polypeptides by translation.

mRNA has a site to which a ribosome can bind and a sequence of codons that specifies the amino acid sequence of the polypeptide, with a start and a stop codon to indicate where translation should begin and end. One mRNA molecule can be translated many times but is broken down if it becomes damaged or if more copies of the polypeptide it codes for are not required.

Transfer RNA (tRNA) translates the base sequence of mRNA into the amino acid sequence of a polypeptide. To do this tRNA molecules have an anticodon at one end consisting of three bases and at the other end an attachment point for the amino acid corresponding to the anticodon. Each type of tRNA molecule has a distinctive shape that is recognized by a dedicated activating enzyme which attaches the correct amino acid onto the tRNA.

Ribosomes are complex structures consisting of a small and a large subunit. The small subunit has a binding site for mRNA and the large subunit has three binding sites for tRNA. The large subunit also has a catalytic site that makes peptide bonds between amino acids, to assemble the polypeptide.

D1.2.7—Complementary base pairing between tRNA and mRNA

The faithfulness of translation depends on complementary base pairing. The three bases of an anticodon on a tRNA must be complementary to the three bases of the next codon on mRNA for the tRNA to be able to bind to the ribosome and deliver its amino acid. Adenine and uracil are complementary and also cytosine and guanine.

D1.2.8—Features of the genetic code

DNA is singularly well suited to data storage because it can hold long sequences of bases (A, C, G and T) which can be arranged in any order. The sequences can be accurately copied. The data commonly stored in DNA base sequences is the amino acid sequences of polypeptides. It is stored in a coded form. There are four different bases and twenty amino acids, so one base cannot code for one amino acid. There are 16 combinations of two bases, which is still too few to code for all 20 amino acids. Living organisms therefore use a triplet code, with groups of three bases coding for an amino acid. There are 64 combinations of three bases.

A sequence of three bases on the mRNA is called a codon. All but three of these codons cause a specific amino acid to be added to a growing polypeptide. Table 1 shows all 64 codons. The left-hand column indicates the first base in a codon, the second base is indicated by the row of bases at the top of the table, and the right-hand column indicates the third base of the codon. The coloured cells of the table tell you what amino acid is coded for. So, for example, the codon AUG codes for the amino acid methionine (often abbreviated to Met) and also acts as the start codon in translation. The codon CAU codes for histidine. There are also three stop codons that end the process of translation.

Two notable features of the genetic code are degeneracy and universality. The code is said to be degenerate because different codons can code for the same amino acid. For example, the codons GUU and GUC both code for the amino acid valine.1 The code is universal because it is used by all living organisms and viruses, with only very minor changes in some cases.

D1.2.9—Using the genetic code expressed as a table of mRNA codons

Three letters are used to indicate each amino acid in the table of the genetic code. Each of the 20 amino acids has between one and six codons. Read off the three letters of each codon for the amino acid. For example, the amino acid tryptophan has one codon which is UGG.

The first three bases in the mRNA sequence are the codon for the first amino acid, the next three bases are the codon for the second amino acid and so on. Look down the left-hand side of the table to find the first base of a codon, across the top of the table to find the second base and down the right-hand side to find the third base. For example, GCA codes for the amino acid alanine.

A strand of mRNA is produced by transcribing the template or antisense strand of the DNA. This therefore has a base sequence complementary to the mRNA. For example, the codon AUG in mRNA is transcribed from the base sequence TAC on the template or antisense strand of the DNA. A longer example is that the base sequence GUACGUACG in mRNA is transcribed from CATGCATGC on the template strand of DNA. Note that adenine pairs with thymine in DNA but with uracil in RNA.

D1.2.10—Stepwise movement of the ribosome along mRNA and linkage of amino acids by peptide bonding to the growing polypeptide chain

Translation of an mRNA molecule is done by a repeating cycle of steps. Each cycle results in the addition of one amino acid to the growing polypeptide chain. Once in each cycle the ribosome moves three bases along the mRNA, which is one codon. The cycle is shown in Figure 13. The process can also be considered by following what happens to one tRNA molecule during the process.

  1. An activating enzyme with an active site that fits the tRNA binds to it and attaches the specific amino acid corresponding to the anticodon of the tRNA.

  2. The tRNA carrying a single, attached amino acid binds to the A (amino acyl) site on the ribosome, with its anticodon linked by complementary base pairing to the next codon on mRNA.

  3. The single amino acid on the tRNA is linked to the end of the growing polypeptide by formation of a peptide bond. The tRNA is now holding the whole of the growing polypeptide.

  4. The tRNA moves from the A to the P (peptidyl) site as the ribosome moves along the mRNA by one codon. The anticodon of the tRNA is still paired with the codon on the mRNA.

  5. The polypeptide held by the tRNA is transferred to another tRNA that has
    arrived at the A site.
  6. The tRNA moves from the P to the E (exit) site as the ribosome moves
    along the mRNA by one more codon. This causes the anticodon of the
    tRNA to separate from the codon on the mRNA and the tRNA to separate
    from the ribosome.
  7. The cycle starts again with an amino acid being linked to a tRNA.

D1.2.11—Mutations that change protein structure

  • A gene mutation is a change in the base sequence of a gene.

  • A single base substitution can change a codon, potentially coding for a different amino acid.

  • This can alter the protein structure and function.

  • Sickle cell disease is caused by a single base substitution in the gene for beta-globin.

  • The mutation changes the sixth codon from GAG to GTG.

  • This results in valine being incorporated instead of glutamic acid.

  • The altered hemoglobin molecules clump together in low oxygen conditions.

  • This distorts red blood cells into a sickle shape.

  • Sickle cells can block capillaries, reducing blood flow and causing damage.

  • The mutation can be inherited.

  • In some regions, the HbS allele is common.

  • Individuals with two copies of the allele have sickle cell anemia.

  • Individuals with one copy have mild anemia.

D1.2.12—Directionality of transcription and translation

  • DNA and RNA strands have directionality because their ends are different.

  • This directionality, along with enzyme specificity, makes transcription and translation unidirectional.

  • In transcription, RNA nucleotides are added to the growing strand by linking the phosphate group of a free nucleotide to the ribose sugar at the end of the strand.

  • Transcription proceeds in the 5′ to 3′ direction.

  • In translation, the ribosome moves along the mRNA towards its 3′ end.

  • Translation also proceeds in the 5′ to 3′ direction.

D1.2.13—Initiation of transcription at the promoter

  • A promoter is a DNA sequence that initiates gene transcription.

  • Promoters are typically 100-1000 bases long and located adjacent to genes.

  • The promoter sequence allows RNA polymerase and transcription factors to bind.

  • Repressor sequences within the promoter prevent RNA polymerase binding, inhibiting transcription.

  • Activator sequences within the promoter enhance RNA polymerase binding, promoting transcription.

  • Promoters are upstream of the gene, near the 5′ end of the sense strand.

  • RNA polymerase binds to the promoter and transcribes the template (antisense) strand.

  • Cells regulate gene expression by controlling which transcription factors bind to promoters.

  • Genes with similar promoters can be expressed together.

  • Some transcription factors require cofactors to bind to the promoter.

D1.2.14—Non-coding sequences in DNA do not code for polypeptides

We often think of DNA as a strict instruction manual for building proteins. But what if I told you that’s only part of the story? Hidden within our genetic code is a vast, unexplored territory of non-coding DNA – sequences that don’t directly translate into proteins, yet play crucial roles in the drama of life. Think of them as the stage directions, the lighting cues, and the behind-the-scenes crew that bring the protein “play” to life.

  • Non-coding DNA sequences are parts of an organism’s DNA that do not encode protein sequences. 
     
  • Some non-coding DNA sequences are known to have functional roles, such as regulating gene expression. 
     
  • Other non-coding DNA sequences have no known function. 
     
  • Non-coding DNA sequences are also known as “junk DNA”. 
     
  • Non-coding DNA sequences are transcribed into functional non-coding RNA molecules. 
     
  • Non-coding DNA sequences are important for the function of cells, particularly the control of gene activity. 
     
Examples of non-coding DNA sequences Promoter and operator regions, Satellite DNA sequences, Telomeres, Introns, and Non-coding genes. 

D1.2.15—Post-transcriptional modification in eukaryotic cells

Post-transcriptional modification (PTM) in eukaryotic cells is a process that chemically alters RNA to create mature mRNA. This process is essential for the correct translation of eukaryotic genomes. 
 
Steps of PTM 
 
  • Capping
    A methyl group is added to the 5′ end of the RNA transcript. This protects the transcript from degradation and helps the cell’s translational machinery recognize it.
  • Polyadenylation
    A long chain of adenine nucleotides, called a poly-A tail, is added to the 3′ end of the transcript. This improves the stability of the transcript and helps it leave the nucleus.
  • Splicing
    Non-coding sequences called introns are removed from the transcript. The coding regions, called exons, are then fused together.
Types of PTM
  • N6-methyladenosine (m6A): The most common PTM in eukaryotic cells. It regulates biological processes and is involved in human diseases like cancer. 
     
  • Cleavage: A type of PTM that involves the cleavage of the RNA transcript. 
     
  • Thiolation: A type of PTM that involves the thiolation of the RNA transcript. 
     
  • Isopentenylation: A type of PTM that involves the isopentenylation of the RNA transcript. 
     
  • Pseudouridine formation: A type of PTM that involves the formation of pseudouridine in the RNA transcript. 
     
PTM is a dynamic process that can be reversed. This allows cells to quickly adapt to environmental changes. 

D1.2.16—Alternative splicing of exons to produce variants of a protein from a single gene

  • Alternative splicing allows multiple polypeptides to be produced from a single gene.

  • The primary transcript is the same, but post-transcriptional modifications differ.

  • Exon skipping is a common mechanism, where certain exons are removed in some mRNA variants but retained in others.

  • Many other alternative splicing methods exist.

  • Alternative splicing increases protein diversity without gene duplication.

  • It allows for tissue- or developmental-specific protein isoforms.

  • Example 1: Troponin T gene (TNNT2) in heart muscle:

    • Troponin T regulates muscle contraction.
    • The TNNT2 gene has 17 exons and 16 introns.
    • Exons 4 and 5 are alternatively spliced, producing four troponin T isoforms.
    • These isoforms are expressed at different developmental stages (fetal vs. adult heart).
    • They also exhibit different sensitivities to calcium ions.

  • Example 2: Tropomyosin gene in mammals:

    • Tropomyosin has 11 exons.
    • Alternative splicing in different tissues yields five tropomyosin isoforms.
    • Different exon combinations are included or excluded in different tissues (e.g., skeletal vs. smooth muscle).

  • Example 3: Dscam gene in fruit flies:

    • Dscam protein guides nerve cell growth.
    • Alternative splicing of the Dscam gene could potentially produce 38,000+ mRNA variants due to the large number of introns.

  • Broad impact: Alternative splicing significantly expands the proteome (all proteins in an organism).

D1.2.17—Initiation of translation

Translation initiation is the first step in protein synthesis, where the ribosome and messenger RNA (mRNA) are assembled to begin the process of translation. 
Steps
  1. The small (40S) and large (60S) ribosomal subunits assemble to form an 80S ribosome. 
     
  2. The initiator transfer RNA (tRNA) binds to the start codon of the mRNA in the ribosomal P site. 
  3. The tRNA anticodon binds to the start codon of the mRNA. 
     
Factors
  • eIF1 and eIF1A: These factors bind to the small ribosomal subunit in eukaryotes. They help position the tRNA and start codon, and maintain the accuracy of the start codon recognition. 
     
  • SD sequence: This sequence base pairs with the anti-SD sequence in the 16S rRNA. This interaction attaches the mRNA to the 30S ribosomal subunit. 
     
  • GTP binding: GTP binding is involved in the initiation process. 
     
Other factors 
 
  • The distance between the SD sequence and the start codon
  • The strength of the SD interaction
  • The presence of mRNA secondary structure in the RBS
  • Small metabolites
  • RNA binding proteins
  • Antisense RNAs
  • Temperature

D1.2.18—Modification of polypeptides into their functional state

Polypeptides are modified into functional proteins through post-translational modifications. These modifications include cleavage, phosphorylation, and chemical modifications. 
Cleavage
  • Polypeptide chains are split to create smaller chains that form a functional protein 
  • For example, the C-peptide is removed from proinsulin to create insulin 
Phosphorylation 
  • Phosphate groups are added to the protei
Chemical modifications 
  • Disulfide bridges are formed between cysteine residues
  • Other proteins or inorganic cofactors are conjugated to the protein
  • Glycosylation is performed to improve structural stabilit
Other modifications 
  • Amino acids are removed from the polypeptide chain
  • The formyl group of the first amino acid, methionine, is remove
Examples 
 
  • Insulin: Synthesized as pre-proinsulin, which is then modified into proinsulin and finally into insuline
Process 
  1. Hsp70 chaperone stabilizes the polypeptide chain until protein synthesis is complete
  2. The polypeptide chain is transferred to an Hsp60 chaperonin, where it folds into its functional shape

D1.2.19—Recycling of amino acids by proteasomes

Proteasomes are protein complexes that break down unwanted or damaged proteins to recycle amino acids. This process is called proteolysis. 
How it works
  • Marking proteins: Enzymes patrol the cell and mark proteins for destruction with a chemical tag. 
     
  • Degrading proteins: The proteasome breaks the peptide bonds within the protein, breaking it down into amino acids. 
     
  • Recycling amino acids: The recycled amino acids can be used to build new proteins. 
     
Why it’s important 
  • Proteasomes help regulate protein expression levels.
  • They control almost every cellular process.
  • They are essential for maintaining a functional proteome
What they degrade 
  • Signaling molecules
  • Tumor suppressors
  • Cell-cycle regulators
  • Transcription factors
  • Inhibitory molecules
  • Anti-apoptotic proteins
Structure
  • The proteasome is a large, barrel-shaped complex.
     
  • It consists of two sub-complexes: a 20S core particle and a 19S regulatory particle. 

 

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