10/16/24, 11:29 BISC 2202 Notes Lectures
AM 9-14
Lecture 10/2/18
Prions continued
➢ Misfolded proteins (prions) are resistant to proteases, heat, radiation, and
formaldehyde
which would normally degrade proteins
○ Once unfolded, they will not refold
○ Rise due to misfolding
■ Prevented normally by chaperone proteins which
encourage proper folding
■ Example chaperone proteins: those that respond to heat
➢ Protein domains - a single functional unit of a protein
➢ Forces that act on proteins
○ Hydrophobic forces
○ Hydrogen bonds
○ Disulfide bonds
■ Can be broken with hydrolysis - added a water to separate
the S and make SH groups
➢ Quaternary structure - multiple proteins connected and interacting with each other
○ Tend to be connected by disulfide bonds or non-covalent bonds (ie
hydrogen bonds, hydrophobic forces)
○ Example: hemoglobin
○ Proteins join in arrangements that create a meaningful structure,
such as a tube for the cytoskeleton
➢ Fun fact: curly hair is the result of coiled coils of alpha helices. Straightening curly
hair
requires breaking disulfide bonds
➢ Protein family - a group of similar proteins
○ Example - proteases for digestion, immune proteins, clotting proteins
➢ Protein function
○ Proteins bind to other molecules with noncovalent bonds
○ Folding allows any active sites to be present in an accessible place
➢ Enzymes are also subclassified into categories such as proteases
➢ Allosteric inhibition - using an inhibitor to reduce enzymatic activity
➢ Feedback inhibition - a negative feedback loop - when a product will
regulate its own synthesis (ie tryptophan)
➢ Positive regulation - where a product increases production
➢ Phosphorylation - good for energy, reversible. Can either activate or
deactivate a protein, either way is possible depending on the protein
➢ Example of enzyme effect
○ Pain killers being used for inhibition of pain signaling pathways COX 1 and
2
○ Insecticide malathion by targeting insect nervous systems
○ Antibiotics target bacterial development: cell wall development, for
instance
○ Antiviral drugs target the viral life cycle
○ Poisons (chemical warfare) targets neurotransmitters causing muscle
failure and suffocation
○ Cyanide binds to the electron transport chain causing irreversible inhibition
of the
about:blan 1/
k 10
, 10/16/24, 11:29 BISC 2202 Notes Lectures
AM 9-14
ATP creation process, killing cells
➢ Proteins can be modified covalently with things like acetyl groups,
phosphates, and ubiquitin
➢ Motor proteins are regulated by ATP, which fuels movement
➢ Most protein complexes are coordinated by ATP
➢ Protein study
○ Sources -
■ A grown tissue/cell
■ Producing artificially
○ Homogenization - breaks cells/tissue and essentially makes a bio smoothie
■ High frequency sound to break cell wall
■ Detergent to poke holes in a cell wall
■ High pressure
■ Using a well fitted plunger to mechanically break cell walls
■ Products are things like free proteins, nucleuses, mitochondria, etc
○ Isolating proteins - use affinity purification (attracting proteins)
○ Column chromatography - sample goes on top and gets filtered by
size by the media in the column
■ Ion exchange - proteins of one charge fall through the tube and the
other
are attracted to the solvent and stay in the tube
■ Gel-filtration - small particles will stay in the gel and large
molecules will fall through
■ Affinity chromatography - using a substrate that a protein is
attracted
while everything else passes through
○ Crystallography - a way to see structure
■ Only useful for highly structure proteins
■ Relies on ability to crystalize a protein
○ Antibodies can be used to isolate antigens and proteins tho
○ Western blot - separating proteins using electrophoresis
Lecture 10/4/18
➢ Evolution of the genome
○ Mechanisms of evolution
■ Mutations in genes
● Environmental damage (toxins, UV)
● Replication errors
■ Mutations in regulatory DNA (which then alters how a gene is
expressed)
● I.e. repressors, activators
■ Gene duplication (accidental copying of an entire section of DNA)
■ Exon shuffling (switching places in DNA, happens during
homologous recombination such as in meiosis
■ Mobile genetic elements (pieces of DNA that catalyze, jump
around in the genome)
■ Horizontal gene transfer (less common in eukaryotes, but a form of
about:blan 2/
k 10
AM 9-14
Lecture 10/2/18
Prions continued
➢ Misfolded proteins (prions) are resistant to proteases, heat, radiation, and
formaldehyde
which would normally degrade proteins
○ Once unfolded, they will not refold
○ Rise due to misfolding
■ Prevented normally by chaperone proteins which
encourage proper folding
■ Example chaperone proteins: those that respond to heat
➢ Protein domains - a single functional unit of a protein
➢ Forces that act on proteins
○ Hydrophobic forces
○ Hydrogen bonds
○ Disulfide bonds
■ Can be broken with hydrolysis - added a water to separate
the S and make SH groups
➢ Quaternary structure - multiple proteins connected and interacting with each other
○ Tend to be connected by disulfide bonds or non-covalent bonds (ie
hydrogen bonds, hydrophobic forces)
○ Example: hemoglobin
○ Proteins join in arrangements that create a meaningful structure,
such as a tube for the cytoskeleton
➢ Fun fact: curly hair is the result of coiled coils of alpha helices. Straightening curly
hair
requires breaking disulfide bonds
➢ Protein family - a group of similar proteins
○ Example - proteases for digestion, immune proteins, clotting proteins
➢ Protein function
○ Proteins bind to other molecules with noncovalent bonds
○ Folding allows any active sites to be present in an accessible place
➢ Enzymes are also subclassified into categories such as proteases
➢ Allosteric inhibition - using an inhibitor to reduce enzymatic activity
➢ Feedback inhibition - a negative feedback loop - when a product will
regulate its own synthesis (ie tryptophan)
➢ Positive regulation - where a product increases production
➢ Phosphorylation - good for energy, reversible. Can either activate or
deactivate a protein, either way is possible depending on the protein
➢ Example of enzyme effect
○ Pain killers being used for inhibition of pain signaling pathways COX 1 and
2
○ Insecticide malathion by targeting insect nervous systems
○ Antibiotics target bacterial development: cell wall development, for
instance
○ Antiviral drugs target the viral life cycle
○ Poisons (chemical warfare) targets neurotransmitters causing muscle
failure and suffocation
○ Cyanide binds to the electron transport chain causing irreversible inhibition
of the
about:blan 1/
k 10
, 10/16/24, 11:29 BISC 2202 Notes Lectures
AM 9-14
ATP creation process, killing cells
➢ Proteins can be modified covalently with things like acetyl groups,
phosphates, and ubiquitin
➢ Motor proteins are regulated by ATP, which fuels movement
➢ Most protein complexes are coordinated by ATP
➢ Protein study
○ Sources -
■ A grown tissue/cell
■ Producing artificially
○ Homogenization - breaks cells/tissue and essentially makes a bio smoothie
■ High frequency sound to break cell wall
■ Detergent to poke holes in a cell wall
■ High pressure
■ Using a well fitted plunger to mechanically break cell walls
■ Products are things like free proteins, nucleuses, mitochondria, etc
○ Isolating proteins - use affinity purification (attracting proteins)
○ Column chromatography - sample goes on top and gets filtered by
size by the media in the column
■ Ion exchange - proteins of one charge fall through the tube and the
other
are attracted to the solvent and stay in the tube
■ Gel-filtration - small particles will stay in the gel and large
molecules will fall through
■ Affinity chromatography - using a substrate that a protein is
attracted
while everything else passes through
○ Crystallography - a way to see structure
■ Only useful for highly structure proteins
■ Relies on ability to crystalize a protein
○ Antibodies can be used to isolate antigens and proteins tho
○ Western blot - separating proteins using electrophoresis
Lecture 10/4/18
➢ Evolution of the genome
○ Mechanisms of evolution
■ Mutations in genes
● Environmental damage (toxins, UV)
● Replication errors
■ Mutations in regulatory DNA (which then alters how a gene is
expressed)
● I.e. repressors, activators
■ Gene duplication (accidental copying of an entire section of DNA)
■ Exon shuffling (switching places in DNA, happens during
homologous recombination such as in meiosis
■ Mobile genetic elements (pieces of DNA that catalyze, jump
around in the genome)
■ Horizontal gene transfer (less common in eukaryotes, but a form of
about:blan 2/
k 10
