Lectures TRAD
Lecture 1 Processes of gene expression and protein turnover
Cachexia
Severe muscle wasting (cachexia) occurs during aging and in many chronic diseases →
causing disuse. Worsens prognosis of recovery.
Limited physical activity in the elderly → high risks of falls and fractures. Exercises increases
mobility, reduces risk of fractures and improves musculoskeletal health.
Architecture of skeletal muscle
A muscle consists of a muscle belly with 1000 thousand muscle fibers. They are organized in
a tube. One single fiber is one single cell. The muscle fibers are full of protein. Skeletal
muscle fiber is a multinucleated cell and contain stem cells below their basal lamina. The
muscle cell is big and a continuous breakdown of protein. The nucleus consists of DNA so the
recipe for all the proteins. The nucleus helps with the protein turnover.
Maximal force is proportional to the cross-sectional area. # muscle fibers are set after birth.
There is no change in the number of muscle fibers during lifetime. The number of muscle
fibres differs between people.
Muscle activity
The only way to change the muscle is changing the number of sarcomeres in parallel or in
series. Skeletal muscle has the ability to hypertrophy and increase the number of
sarcomeres in response to immobilization at extended length.
Strength is determined by the cross-sectional of the fibers. Power is determined by the
number of sarcomeres in series.
The volume of the muscle determined by the number of fibers and the volume of the fibers
tell us what the maximal power is.
Power = the force x velocity.
There are different myosin forms:
- MHC-IIX
- MHC-IIA
- MHC-I → the maximal force is minimal
Cyclists have a low peak power, due to the slow myosin fibers.
Determinants of maximal muscle power
- Muscle volume
- Physiological cross-sectional area
- Optimum muscle fiber length
- Myosin composition
,Determinants of endurance
- Mitochondrial density
- Slow myosin heavy chains
- Capillary density → More capillaries lead to more oxygen to the cell.
- Myoglobin concentration → → is an oxygen binding molecule. So, mitochondria,
capillaries and myoglobin are determinants of endurance.
Adaptation of muscle size is a change in balance of protein synthesis and degradation.
Overview of the major steps in the regulation of protein synthesis
It all starts in the nucleus. There are a lot of myosin in the nucleus. In order to get a new
protein. The DNA must open and copy this. Bring the copy to the cytoplasm → this leads to a
mRNA. mRNA is a single strand. mRNA is translated and this ends with a protein. A ribosome
can read the sequence and translated it to a sequence of amino acids.
Transcription → information transcribed (copying) from DNA
into mRNA. This occurs in the nucleus.
Translation → information in mRNA translated the mRNAs
into primary sequence of a protein. Translation occurs in the
cytoplasm.
Post-translational modification → folding and connections at
certain location
In the muscle there are many nuclei.
There is a strong relationship between the number of nuclei
and the length. There is a proportional relationship. The
bigger cells have more nuclei.
How can you increase the number of nuclei?
- By the satellite cells. The satellite cells are outside of the membrane. They circle
around the myofiber. The satellite cells are activated when there is a breakdown
(injury). They can proliferate and fuse to the membrane and get into the cytoplasm.
They can add up to the pole of the myonuclei. The satellite cells can become a
myonuclei.
Proteins synthesis starts with the DNA. The nucleus is a library with recipes for the synthesis
of proteins.
DNA and RNA
Human DNA → 22.000 genes
DNA
- Double-stranded helix and H-bonds between
strands
RNA
- 3 kinds (mRNA, tRNA, rRNA)
- All single strands
- H-bonds within strands
By reading the anti-sense, it copies the proper sense
strand (mRNA)
,Nucleic acids
Nucleic acids made up of chains of nucleotides
Nucleotides consist of:
- A nitrogenous base
- A sugar (deoxy)ribose
- Hydroxyl group
Two types of nucleic acids in cells:
- Deoxyribonucleic acid (DNA)
- Ribonucleic acid (RNA)
Complementarity of bases
The different bases in the nucleotides which make up DNA and RNA
are:
- Adenine & Thymine (or Uracil)
- Guanine & Cytosine
Chemical structure only allows bases to bind with specific other bases due to chemical
structure.
5’ is defined as the nucleic acid of which the 5 carbon is attached to a phosphate group and
not to another nucleic acid.
3’ is defined as the nucleic acid of which the 3 carbon is attached to a hydroxyl and not to
another nucleic acid.
RNA
Three types of RNA
- Messenger RNA (mRNA) → carries the code for the protein
- Transfer RNA (tRNA) → carries amino acids from amino acid pool to mRNA
- Ribosomal RNA (rRNA) → joins with ribosomal proteins in ribosome where amino
acids are joined to form the protein primary structure
Transcription of RNA
Initiation → the transcription starts at a certain point. In front of the gene there is a
promoter. This is the place where the transcription starts. There needs to be binding of
certain proteins → general transcription factors. Specific transcription factors are required
for the opening of the DNA. There are also proteins that block the transcription →
repressors
Transcriptional regulatory elements
- Promotor
o TATATA or TATAAA sequences – 25-35 nucleotides upstream of the start
codon.
- Promotor-proximal elements and enhancer sites
Transcriptional control
Each cell nucleus contains all genes for that organism, but most genes are only expressed as
needed. Transcription regulated by transcription factors. Proteins produced by their own
genes
- Transcription factors promoting transcription → activators
- Transcription factors inhibiting transcription → repressors
Regulation of transcription
- Activation domains of transcription factors by e.g., phosphorylation
- Modulation of concentration of transcription factors
, o Transcriptional regulation
o Translation regulation
o Regulation of degradation
Posttranscriptional modifications of mRNA: splicing
The introns are spliced out of the mRNA and the
exons stay in the mRNA.
Modifications of the mRNA:
5’ cap is methylated, 3’ poly-adenylation (poly(A)tail
and splicing of introns. There are several ways to
splice the introns: constitutive splicing, exon skipping,
intron retention etc.
Amino acids are coded by sequence of 3 nucleic
acids
Start codon is AUG. There are 3 stopcodons →
UAA, UAG and UGA
A small mutation can give you a completely
different protein.
The effect of a point mutation
- Base pair substitution
- Base pair insertion or deletion
Translation (protein synthesis)
Activation
- Each amino acid activated by reaction
with ATP
- Aminoacetyl tRNA synthetase enzyme
attaches activated amino acid to own
particular rRNA
There are 4 steps:
- Activation
- Initiation
- Elongation
- Termination
Initiation
Eukaryotic initiation factors control the initiation translation:
eIF1: stabilizer
eIF2: directs the S40 complex to mRNA
eIF3: separates the 40S from 60S
eIF4: regulates binding of 40S to mRNA and movement to start codon
eIF5: regulates tight binding of 40S with 60S
eIF6: regulates separation of 60S form 40
Elongation
eEF1: directs tRNA to the ribosome
eEF2: regulates thee translocation of the ribosome 3 nucleotides in the
direction of the 3’ end.
Lecture 1 Processes of gene expression and protein turnover
Cachexia
Severe muscle wasting (cachexia) occurs during aging and in many chronic diseases →
causing disuse. Worsens prognosis of recovery.
Limited physical activity in the elderly → high risks of falls and fractures. Exercises increases
mobility, reduces risk of fractures and improves musculoskeletal health.
Architecture of skeletal muscle
A muscle consists of a muscle belly with 1000 thousand muscle fibers. They are organized in
a tube. One single fiber is one single cell. The muscle fibers are full of protein. Skeletal
muscle fiber is a multinucleated cell and contain stem cells below their basal lamina. The
muscle cell is big and a continuous breakdown of protein. The nucleus consists of DNA so the
recipe for all the proteins. The nucleus helps with the protein turnover.
Maximal force is proportional to the cross-sectional area. # muscle fibers are set after birth.
There is no change in the number of muscle fibers during lifetime. The number of muscle
fibres differs between people.
Muscle activity
The only way to change the muscle is changing the number of sarcomeres in parallel or in
series. Skeletal muscle has the ability to hypertrophy and increase the number of
sarcomeres in response to immobilization at extended length.
Strength is determined by the cross-sectional of the fibers. Power is determined by the
number of sarcomeres in series.
The volume of the muscle determined by the number of fibers and the volume of the fibers
tell us what the maximal power is.
Power = the force x velocity.
There are different myosin forms:
- MHC-IIX
- MHC-IIA
- MHC-I → the maximal force is minimal
Cyclists have a low peak power, due to the slow myosin fibers.
Determinants of maximal muscle power
- Muscle volume
- Physiological cross-sectional area
- Optimum muscle fiber length
- Myosin composition
,Determinants of endurance
- Mitochondrial density
- Slow myosin heavy chains
- Capillary density → More capillaries lead to more oxygen to the cell.
- Myoglobin concentration → → is an oxygen binding molecule. So, mitochondria,
capillaries and myoglobin are determinants of endurance.
Adaptation of muscle size is a change in balance of protein synthesis and degradation.
Overview of the major steps in the regulation of protein synthesis
It all starts in the nucleus. There are a lot of myosin in the nucleus. In order to get a new
protein. The DNA must open and copy this. Bring the copy to the cytoplasm → this leads to a
mRNA. mRNA is a single strand. mRNA is translated and this ends with a protein. A ribosome
can read the sequence and translated it to a sequence of amino acids.
Transcription → information transcribed (copying) from DNA
into mRNA. This occurs in the nucleus.
Translation → information in mRNA translated the mRNAs
into primary sequence of a protein. Translation occurs in the
cytoplasm.
Post-translational modification → folding and connections at
certain location
In the muscle there are many nuclei.
There is a strong relationship between the number of nuclei
and the length. There is a proportional relationship. The
bigger cells have more nuclei.
How can you increase the number of nuclei?
- By the satellite cells. The satellite cells are outside of the membrane. They circle
around the myofiber. The satellite cells are activated when there is a breakdown
(injury). They can proliferate and fuse to the membrane and get into the cytoplasm.
They can add up to the pole of the myonuclei. The satellite cells can become a
myonuclei.
Proteins synthesis starts with the DNA. The nucleus is a library with recipes for the synthesis
of proteins.
DNA and RNA
Human DNA → 22.000 genes
DNA
- Double-stranded helix and H-bonds between
strands
RNA
- 3 kinds (mRNA, tRNA, rRNA)
- All single strands
- H-bonds within strands
By reading the anti-sense, it copies the proper sense
strand (mRNA)
,Nucleic acids
Nucleic acids made up of chains of nucleotides
Nucleotides consist of:
- A nitrogenous base
- A sugar (deoxy)ribose
- Hydroxyl group
Two types of nucleic acids in cells:
- Deoxyribonucleic acid (DNA)
- Ribonucleic acid (RNA)
Complementarity of bases
The different bases in the nucleotides which make up DNA and RNA
are:
- Adenine & Thymine (or Uracil)
- Guanine & Cytosine
Chemical structure only allows bases to bind with specific other bases due to chemical
structure.
5’ is defined as the nucleic acid of which the 5 carbon is attached to a phosphate group and
not to another nucleic acid.
3’ is defined as the nucleic acid of which the 3 carbon is attached to a hydroxyl and not to
another nucleic acid.
RNA
Three types of RNA
- Messenger RNA (mRNA) → carries the code for the protein
- Transfer RNA (tRNA) → carries amino acids from amino acid pool to mRNA
- Ribosomal RNA (rRNA) → joins with ribosomal proteins in ribosome where amino
acids are joined to form the protein primary structure
Transcription of RNA
Initiation → the transcription starts at a certain point. In front of the gene there is a
promoter. This is the place where the transcription starts. There needs to be binding of
certain proteins → general transcription factors. Specific transcription factors are required
for the opening of the DNA. There are also proteins that block the transcription →
repressors
Transcriptional regulatory elements
- Promotor
o TATATA or TATAAA sequences – 25-35 nucleotides upstream of the start
codon.
- Promotor-proximal elements and enhancer sites
Transcriptional control
Each cell nucleus contains all genes for that organism, but most genes are only expressed as
needed. Transcription regulated by transcription factors. Proteins produced by their own
genes
- Transcription factors promoting transcription → activators
- Transcription factors inhibiting transcription → repressors
Regulation of transcription
- Activation domains of transcription factors by e.g., phosphorylation
- Modulation of concentration of transcription factors
, o Transcriptional regulation
o Translation regulation
o Regulation of degradation
Posttranscriptional modifications of mRNA: splicing
The introns are spliced out of the mRNA and the
exons stay in the mRNA.
Modifications of the mRNA:
5’ cap is methylated, 3’ poly-adenylation (poly(A)tail
and splicing of introns. There are several ways to
splice the introns: constitutive splicing, exon skipping,
intron retention etc.
Amino acids are coded by sequence of 3 nucleic
acids
Start codon is AUG. There are 3 stopcodons →
UAA, UAG and UGA
A small mutation can give you a completely
different protein.
The effect of a point mutation
- Base pair substitution
- Base pair insertion or deletion
Translation (protein synthesis)
Activation
- Each amino acid activated by reaction
with ATP
- Aminoacetyl tRNA synthetase enzyme
attaches activated amino acid to own
particular rRNA
There are 4 steps:
- Activation
- Initiation
- Elongation
- Termination
Initiation
Eukaryotic initiation factors control the initiation translation:
eIF1: stabilizer
eIF2: directs the S40 complex to mRNA
eIF3: separates the 40S from 60S
eIF4: regulates binding of 40S to mRNA and movement to start codon
eIF5: regulates tight binding of 40S with 60S
eIF6: regulates separation of 60S form 40
Elongation
eEF1: directs tRNA to the ribosome
eEF2: regulates thee translocation of the ribosome 3 nucleotides in the
direction of the 3’ end.
