UWCSEA - IB Biology 2025 - Topic D1.2 Protein synthesis

D1.2.1—What is transcription?

Transcription is the synthesis of RNA;

using a DNA template;

RNA polymerase attaches to a sequence of DNA known as the promoter;

separates the DNA strands;

and synthesizes a complementary mRNA strand;

identical to the coding strand of DNA (the sense strand);

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

RNA polymerase binds to the promoter region on the DNA; unwinds the DNA;

and synthesizes a complementary RNA strand by matching RNA nucleotides to the antisense strand;

using complementary base pairing;

adenine to uracil; guanine to cytosine;

This process occurs in the 5' → 3' direction.

D1.2.3—Stability of DNA templates

Single DNA strands are used as the template for transcribing a base sequence and can be used many, many times;

therefore the DNA base sequence needs to be stable and remain the same, without changing;

if it changed through mutation or degradation, this could lead to non-functional proteins and to cancer and other metabolic issues;

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

Not all genes in a cell are expressed at any given time; many are "switched off";

Transcription is the first stage of gene expression;

Transcription is a key stage at which expression of a gene can be switched on and off;

allowing cells to respond to environmental changes and developmental signals;

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

The base sequence of mRNA is translated into the amino acid sequence of a polypeptide, which then folds into a functional protein;

Translation occurs in the cytoplasm of the cell, where ribosomes carry out the assembly of amino acids into polypeptides;

The sequence of nucleotides in mRNA determines the specific order of amino acids, which in turn dictates the structure and function of the resulting protein;

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

mRNA binds to the small subunit of the ribosome;

the mRNA is as a template for protein synthesis;

Two tRNAs can bind at the same time to the large subunit;

bringing specific amino acids to the ribosome based on the codon sequence of the mRNA;

Ribosomes allow the correct matching of tRNA anticodons with mRNA codons;

D1.2.7—Complementary base pairing between tRNA and mRNA

A codon is a sequence of three nucleotides in mRNA that codes for a particular amino acid;

An anticodon is a sequence of three nucleotides in tRNA that is complementary to a specific mRNA codon;

Complementary base pairing between codons and anticodons ensures the correct amino acids are incorporated into the growing polypeptide chain;

D1.2.8—Features of the genetic code

The genetic code is a triplet code, meaning each codon consists of three nucleotides;

Degeneracy refers to the fact that multiple codons can code for the same amino acids;

providing redundancy and reducing the impact of mutations;

Universality indicates that the genetic code is nearly identical across all organisms,

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

Split the code into 3 bases;

Use the table to look up each letter and work out the amino acid coded for;

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

Elongation occurs in a series of repeated steps;

the ribosome translocates (moves) 3 bases along the mRNA;

(the tRNA which was in the A site moves to the P site;)

(the tRNA which was in the P site moves to the E site and is released;)

a peptide bond then forms between the amino acids

(which are attached to the tRNAs in the P and the A site);

the process repeats, in a step-wise fashion, moving 3 bases at a time, bonding one new amino acid at at time

D1.2.11—Mutations that change protein structure

A point mutation is a change in a single nucleotide in the DNA sequence,

which can alter the corresponding mRNA and amino acid sequence;

Changes in the amino acid sequence can affect the folding and function of the protein; potentially leading to diseases or altered phenotypes;

e.g. sickle cell anaemia, where a single mutation causes valine to replace glutamic acid;

causing haemoglobin to join together into long strands causing abnormal red blood cell shapes;

HL Only - D1.2.12 - What is the direction of transcription and translation?

transcription proceeds in the 5' to 3' direction;

RNA polymerase reads the DNA template strand in the 3' to 5' direction;

the newly synthesized mRNA strand grows from the 5' end to the 3' end;

translation also occurs in the 5' to 3' direction;

the ribosome reads the mRNA from the 5' end to the 3' end, synthesizing the polypeptide chain accordingly;

HL Only - D1.2.13 - Where does transcription begin? What helps this process to occur?

transcription begins at the promoter region of a gene;

transcription factors bind to the promoter to facilitate the binding of RNA polymerase;

these factors help position RNA polymerase correctly to start transcription;

HL Only - D1.2.14 - What are non-coding sequences in DNA? What are their functions?

non-coding sequences in DNA do not code for polypeptides;

examples include regulators of gene expression, introns, telomeres, and genes for rRNAs and tRNAs in eukaryotes;

regulatory sequences control when and where genes are expressed;

introns are non-coding regions within genes that are removed during RNA processing;

telomeres protect the ends of chromosomes;

rRNAs and tRNAs are essential for protein synthesis but do not code for proteins themselves;

HL Only - D1.2.15 - What is post-transcriptional modification?

post-transcriptional modification involves processing of pre-mRNA into mature mRNA;

introns are removed, and exons are spliced together;

a 5' cap is added to the 5' end of the mRNA;

a 3' polyA tail is added to the 3' end;

these modifications stabilise the mRNA and stops it being broken down;

HL Only - D1.2.16 - What is alternative splicing? How does it increase complexity?

alternative splicing allows one gene to code for different polypeptides;

different combinations of exons are spliced together to produce different mRNA transcripts;

this process allows different proteins to be made from a single gene; making organisms more complex;

HL Only - D1.2.17 - How is translation initiated? What is the role of the binding sites on the ribosome?

translation begins with the attachment of the small ribosome subunit to the 5' end of the mRNA;

the ribosome moves along the mRNA to the start codon;

the initiator tRNA binds to the start codon;another tRNA binds to the next codon;

the large ribosome subunit attaches to form a complete ribosome;

the ribosome has three binding sites for tRNA: A site, P site, and E site;

the A site is where new tRNA carrying amino acids bind;

The P site is where the first tRNA binds;

The E site is where tRNAs leave;

D1.2.18—How can polypeptides be modified before they function? Give an example

Modification of polypeptides into their functional state;

many polypeptides must be modified before they can function;

an example is the two-stage modification of pre-proinsulin to insulin;

pre-proinsulin is cleaved to form proinsulin, which is further processed to produce active insulin;

D1.2.19 Recycling of amino acids by proteasomes

A proteasome is a protein complex responsible for the breakdown and recycling of unneeded or damaged proteins;

It functions by hydrolysing the proteins fed into it;

it breaks the peptide bonds between amino acids so they can be reused;

It provides cells with a reliable supply of amino acids to synthesise new proteins;

It actively removes non-functional or damaged proteins;