Case 3 Lost in translation
vrijdag 12 september 2025 11:26
Point of interest
- If a protein is made, does it survive forever
--> preserving bodies (after death)
- How does a cell translate nucleic acids to a complex 3D structure of a protein
- Different 3D structures
- What changes do proteins undergo after formation.
- Amino acids
- Rough Er and Smooth Er
- Ribosomes
- Steps of translation
- Codons, anticodons and tRNA
- Imaging techniques
Learning goals
- What is a protein - function
- What is translation
- What is the life span of a protein (after death)
--> degradation
- What is the structure of a protein
- What changes does a protein undergo after formation
- Structure and function of ribosomes
- Control of protein synthesis & destruction
What is a protein? - function
A protein is a large, complex biological molecule essential for life, made of long chains of amino acids linked together by peptide bonds. Proteins perform a vast range of functions in the body, including acting as enzymes to speeds
up reactions, providing structure to tissues like skin and muscle.
What are proteins made of
Amino Acids - The building blocks of proteins are amino acids, of which there are about 20 different types that the body uses.
Peptide bonds - Amino acids are linked together in chains by peptide bonds, forming long structures called polypeptides.
Protein Synthesis
- Cells constantly produce new proteins trough a process calls protein synthesis.
- This process uses information encoded in DNA to assemble the correct sequence of amino acids.
- After assembly, the amino acid chain folds into a specific three-dimensional shape, which is crucial for its function.
Function
Catalysis - Proteins called enzymes speed up the chemical reactions necessary for life, making them essential for processed like digestion and energy production.
Structure - They provide structural support for cells, tissues, and organs, much like the building blocks of a house.
Transport - Proteins transport vital molecules like oxygen (hemoglobin) and nutrients throughout cells.
Immunity - Proteins called antibodies are crucial components of the immune system, identifying and neutralizing foreign invaders like bacteria and viruses.
Metabolism - They are involved in metabolic reactions and help maintain fluid and pH balance within the body.
Movement and regulation - Some proteins are involved in the movement of cells and help regulate gene expression, controlling how genes are used to build new molecules.
Repair and Energy - Proteins also play a role in repairing damaged tissues and can be used as an energy source when carbohydrates and fats are insufficient.
Process RNA translation.
Translation involves 'decoding' a messenger RNA and using its information to build a polypeptide, or chain of amino acids. For most purposes, a polypeptide is
basically just a protein.
In an mRNA, the instructions for building a polypeptide come in groups of three nucleotides called codons.
• There are 61 different codons for amino acids
• Three stop codons mark the polypeptide as finished
• One codon, AUG is a start signal to kick off translation.
In translation, the codons of an mRNA are read in order from the 5' end to the 3' end by molecules called transfer RNAs or tRNAs
Each tRNA has an anticodon, a set of three nucleotides that binds to a matching mRN'a codon through base pairing.
tRNAs bind to mRNAs inside of a protein-and-RNA-structure called the ribosome. As the tRNAs enter slots in the ribosome and bind to codons, their amino acids
are links to the growing polypeptide chain in a chemical reaction
Stages of translation
Initiation - In order to start translation you need a few things.
• A ribosome
• An mRNA with instructions for the protein we'll build
• An "initiator" tRNA carrying the first amino acid in the protein, which is almost always methionine.
During initiation, these pieces must come together in just the right way. Together, they form the initiation complex.
Inside the cells of eukaryotes, translation initiation goes like this - first, the tRNA carrying methionine (start codon) attaches to the small ribosomal subunit.
Together they bind to the 5' end of the mRNA by recognizing the 5' GTP cap. Then, they walk along the mRNA in the 3' direction, stopping when they reach the
start codon.
In bacteria, the initiation is a little different. Here the small ribosomal subunit doesn't start at the 5' end of the mRNA and travel toward the 3' end. Instead,
sequences come just before start codons and point them out to the ribosome.
Elongation - Is when the polypeptide chain gets longer.
Our first, methionine-carrying tRNA starts out in the middle slot of the ribosome, called the P site. Next to it a fresh codon is exposed in another slot, called the A
site. The A site will be the landing site for the next tRNA, one whose anticodon is a perfect complementary match for the exposed codon.
Non matching tRNAs may also enter the A site, but they don't get to stay there. Each tRNA is escorted by helper proteins, and only a tRNA that's a perfect match
for the codon will be released into the A slot.
Once the matching tRNA has landed in the A site, the formation of the peptide bond that connects one amino acid to another. This transfers the methionine from
the first tRNA onto the amino acid of the second tRNA in the A site Once the peptide bond is formed, the mRNA is pulled onward through the ribosome by exactly
one codon. This allows the first tRNA to drift out via the E site. It then exposes a new codon in the A site, so the whole cycle can repeat.
Termination - Polypeptides must eventually come to and end. Translation ends in a process called termination. Termination happens when a stop codon in the
mRNA (UAA, UAG, or UGA) enters the A site.
Stop codons are recognized by proteins called release factors, which fit neatly into the p site (though they aren't tRNAs). Release factors mess with the enzyme
that normally forms peptide bonds: they make it add a water molecule to the last amino acid of the chain. This reaction separates the chain from the tRNA, and
the newly made protein is released.
Translation equipment is very reusable. After the small and large ribosomal subunits separate from the mRNA and from each other, each element can take part in
another round of translation.
What is the life span of a protein (after death) and degradation
A proteins lifespan, or half-life varies greatly, ranging from minutes to several years, depending on its type and cellular function. Most cellular proteins have
relatively short half-lives of hours to a few days, ensuring rapid replacement to maintain cell health and function. However, some structural or specialized proteins
can persist for month or even years without being degraded.
Factors influencing protein lifespan
Function - Regulatory molecules like transcription factors often have very short half-lives, while structural components of cell nuclei or mitochondria may be long-
lived.
Cellular Localization - Proteins found in specialized organelles like mitochondria and the endoplasmic reticulum tend to have longer lifespans compared to other
cellular proteins.
Protein Quality Control - Cells actively degrade misfolded or damaged proteins, which influences their overall lifespan.
Organismal lifespan - There is a correlation between an organism's lifespan and the turnover rate of its abundant proteins - longer-lived organisms often have
slower protein turnover.
Measuring
Half-Life - The most common way to measure a protein's lifespan is its half-life (t1/2), which is the time it takes for half of an initial amount of the protein to be
degraded.
Examples of differing lifespans
Short-lived proteins - Many regulatory proteins are degraded within minutes to hours to allow for rapid changes in cellular processes.
Long-lived Proteins - Proteins in structures like the nuclear pore complex can persist for the entire life of the cell, and some specialized proteins can extist for moth
or even years.
What happens with a protein after death
After death, the body's own enzymes break down proteins in a process called autolysis, while environmental factors like bacteria and temperature promote further
protein breakdown. These processes convert proteins into smaller molecules like amino acids, which are then broken down into simpler compounds.
vrijdag 12 september 2025 11:26
Point of interest
- If a protein is made, does it survive forever
--> preserving bodies (after death)
- How does a cell translate nucleic acids to a complex 3D structure of a protein
- Different 3D structures
- What changes do proteins undergo after formation.
- Amino acids
- Rough Er and Smooth Er
- Ribosomes
- Steps of translation
- Codons, anticodons and tRNA
- Imaging techniques
Learning goals
- What is a protein - function
- What is translation
- What is the life span of a protein (after death)
--> degradation
- What is the structure of a protein
- What changes does a protein undergo after formation
- Structure and function of ribosomes
- Control of protein synthesis & destruction
What is a protein? - function
A protein is a large, complex biological molecule essential for life, made of long chains of amino acids linked together by peptide bonds. Proteins perform a vast range of functions in the body, including acting as enzymes to speeds
up reactions, providing structure to tissues like skin and muscle.
What are proteins made of
Amino Acids - The building blocks of proteins are amino acids, of which there are about 20 different types that the body uses.
Peptide bonds - Amino acids are linked together in chains by peptide bonds, forming long structures called polypeptides.
Protein Synthesis
- Cells constantly produce new proteins trough a process calls protein synthesis.
- This process uses information encoded in DNA to assemble the correct sequence of amino acids.
- After assembly, the amino acid chain folds into a specific three-dimensional shape, which is crucial for its function.
Function
Catalysis - Proteins called enzymes speed up the chemical reactions necessary for life, making them essential for processed like digestion and energy production.
Structure - They provide structural support for cells, tissues, and organs, much like the building blocks of a house.
Transport - Proteins transport vital molecules like oxygen (hemoglobin) and nutrients throughout cells.
Immunity - Proteins called antibodies are crucial components of the immune system, identifying and neutralizing foreign invaders like bacteria and viruses.
Metabolism - They are involved in metabolic reactions and help maintain fluid and pH balance within the body.
Movement and regulation - Some proteins are involved in the movement of cells and help regulate gene expression, controlling how genes are used to build new molecules.
Repair and Energy - Proteins also play a role in repairing damaged tissues and can be used as an energy source when carbohydrates and fats are insufficient.
Process RNA translation.
Translation involves 'decoding' a messenger RNA and using its information to build a polypeptide, or chain of amino acids. For most purposes, a polypeptide is
basically just a protein.
In an mRNA, the instructions for building a polypeptide come in groups of three nucleotides called codons.
• There are 61 different codons for amino acids
• Three stop codons mark the polypeptide as finished
• One codon, AUG is a start signal to kick off translation.
In translation, the codons of an mRNA are read in order from the 5' end to the 3' end by molecules called transfer RNAs or tRNAs
Each tRNA has an anticodon, a set of three nucleotides that binds to a matching mRN'a codon through base pairing.
tRNAs bind to mRNAs inside of a protein-and-RNA-structure called the ribosome. As the tRNAs enter slots in the ribosome and bind to codons, their amino acids
are links to the growing polypeptide chain in a chemical reaction
Stages of translation
Initiation - In order to start translation you need a few things.
• A ribosome
• An mRNA with instructions for the protein we'll build
• An "initiator" tRNA carrying the first amino acid in the protein, which is almost always methionine.
During initiation, these pieces must come together in just the right way. Together, they form the initiation complex.
Inside the cells of eukaryotes, translation initiation goes like this - first, the tRNA carrying methionine (start codon) attaches to the small ribosomal subunit.
Together they bind to the 5' end of the mRNA by recognizing the 5' GTP cap. Then, they walk along the mRNA in the 3' direction, stopping when they reach the
start codon.
In bacteria, the initiation is a little different. Here the small ribosomal subunit doesn't start at the 5' end of the mRNA and travel toward the 3' end. Instead,
sequences come just before start codons and point them out to the ribosome.
Elongation - Is when the polypeptide chain gets longer.
Our first, methionine-carrying tRNA starts out in the middle slot of the ribosome, called the P site. Next to it a fresh codon is exposed in another slot, called the A
site. The A site will be the landing site for the next tRNA, one whose anticodon is a perfect complementary match for the exposed codon.
Non matching tRNAs may also enter the A site, but they don't get to stay there. Each tRNA is escorted by helper proteins, and only a tRNA that's a perfect match
for the codon will be released into the A slot.
Once the matching tRNA has landed in the A site, the formation of the peptide bond that connects one amino acid to another. This transfers the methionine from
the first tRNA onto the amino acid of the second tRNA in the A site Once the peptide bond is formed, the mRNA is pulled onward through the ribosome by exactly
one codon. This allows the first tRNA to drift out via the E site. It then exposes a new codon in the A site, so the whole cycle can repeat.
Termination - Polypeptides must eventually come to and end. Translation ends in a process called termination. Termination happens when a stop codon in the
mRNA (UAA, UAG, or UGA) enters the A site.
Stop codons are recognized by proteins called release factors, which fit neatly into the p site (though they aren't tRNAs). Release factors mess with the enzyme
that normally forms peptide bonds: they make it add a water molecule to the last amino acid of the chain. This reaction separates the chain from the tRNA, and
the newly made protein is released.
Translation equipment is very reusable. After the small and large ribosomal subunits separate from the mRNA and from each other, each element can take part in
another round of translation.
What is the life span of a protein (after death) and degradation
A proteins lifespan, or half-life varies greatly, ranging from minutes to several years, depending on its type and cellular function. Most cellular proteins have
relatively short half-lives of hours to a few days, ensuring rapid replacement to maintain cell health and function. However, some structural or specialized proteins
can persist for month or even years without being degraded.
Factors influencing protein lifespan
Function - Regulatory molecules like transcription factors often have very short half-lives, while structural components of cell nuclei or mitochondria may be long-
lived.
Cellular Localization - Proteins found in specialized organelles like mitochondria and the endoplasmic reticulum tend to have longer lifespans compared to other
cellular proteins.
Protein Quality Control - Cells actively degrade misfolded or damaged proteins, which influences their overall lifespan.
Organismal lifespan - There is a correlation between an organism's lifespan and the turnover rate of its abundant proteins - longer-lived organisms often have
slower protein turnover.
Measuring
Half-Life - The most common way to measure a protein's lifespan is its half-life (t1/2), which is the time it takes for half of an initial amount of the protein to be
degraded.
Examples of differing lifespans
Short-lived proteins - Many regulatory proteins are degraded within minutes to hours to allow for rapid changes in cellular processes.
Long-lived Proteins - Proteins in structures like the nuclear pore complex can persist for the entire life of the cell, and some specialized proteins can extist for moth
or even years.
What happens with a protein after death
After death, the body's own enzymes break down proteins in a process called autolysis, while environmental factors like bacteria and temperature promote further
protein breakdown. These processes convert proteins into smaller molecules like amino acids, which are then broken down into simpler compounds.
