BIO 110 FINAL EXAM (U of R)
QUESTIONS WITH CORRECT
ANSWERS
The Scientific Method - ANSWERSObservations
Ask questions
Hypothesis to answer the question→ new proposition that is compatible with
observations and facts already known; must result in testable predictions
Make predictions based on your hypothesis
Design experiment to test hypothesis
Designing Controlled Experiments - ANSWERSManipulate one variable at a time
Control group:exposed to the same conditions as the experimental group except for one
independent variable
Experimental group: exposed to the independent variable
hydrophobic effect - ANSWERShighly ordered H2O molecules form "cages" around the
hydrophobic alkyl chains if individual lipids
-entropically driven exclusion from water
- clusters of lipid molecules ; only lipid portions of the edge of the cluster force the
ordering of water;fewer H2O molecules are ordered , and entropy is increased.
-its is not an attraction between lipids that makes them cluster together in water, but the
interactions of water molecules to other water molecules.
how would membranes be affected if water were nonpolar? - ANSWERSwithout the
effect no membrane would exist because there would be nothing keeping the lipids
together , because there is no polarity and no structure would form.
Roles of water - ANSWERS-transport protons (acceptor)
-breaking (hydrolysis) covalent bonds(ATP)
-making(condensation) covalent bonds
-water can ionize (donate protons)
-H2O + H2O → H2O+ +OH-
-the dipole nature of water creates the hydrophobic effect
- can be crucial for the structure and function of an active site of an enzyme
Fluorescence microscopy - ANSWERS-using fluorescent dyes to visualize cellular
structures
-using natural compound with desirable binding properties
-use selective fluorescent dyes that absorbs light at one wavelength and emit light at a
different wavelength
-allows for visualization of specific cell structures at high magnification
,-actin cytoskeleton stained using pahlloida attached to fluorescent dye
-dapi emits blue fluorescence upon binding to DNA
-green fluorescent protein (GFP)
-engineered fluorescent protein
-a version of gfp has been engineered into two different parts , which can be used to
see whether two things within a cell interact
Immunohistochemistry - ANSWERS-a technique used to assess the presence of a
specific protein in cells
-a protein is detected using a specific antibody that binds to it
-antibodies are proteins of the immune system that bind tightly to a specific target
(antigen)
-secondary antibody attached to colorful or glowing molecules
-the antibody allows visualization of the protein under a microscope
endosymbiosis - ANSWERS-may have occurred when larger cells ingested smaller
ones
- mitochondria -- engulfed prokaryotic organisms
-chloroplasts-- larger eukaryotes ingested photosynthetic prokaryotes
carbohydrates - ANSWERSpolysaccharides→ stuff we eat contain glycogen and
starch-- with one type of glycosidic bond plus a branching glycosidic bonds(hydrophilic);
stuff we don't eat contain chitin and cellulose, which have a different type of glycosidic
bond (hydrophobic) (hydrogen bonds); the chains is curved and branches in glycogen ,
rather than linear as in cellulose
-very soluble in water
-glycosidic bond is how to join two sugar
lipids - ANSWERS- energy storage (and insulation)
-basic structural unit of cellular membranes
-light-absorbing pigments
-hormones
Fatty acids - ANSWERS-saturated fatty acid (chains is straight)- single bonds
- unsaturated fatty acid (carbon chain has kinks)- double bonds = less packing
-what are most natural fatty acids ? → cis
Why not only use carbs? - ANSWERSit takes a lt takes up more space to store glucose
than lipids; lipids are less oxidized so they contain more energy per carbon
amino acids - ANSWERS- hydrogen , amino group, r group, carboxyl group
-the building blocks of proteins
- neurotransmitters
-energy source
- precursors for other biomolecules
- the amino acid found in proteins are almost exclusively l-stereoisomer
, why do small proteins have more difficulty folding and holding shape? If you were
designing a protein what elements of structure might you include to increase stability? -
ANSWERSSmall proteins have less ability to bind and don't have enough hydrophilic r
groups to protect hydrophobic groups; I would use a lot of cysteine for small proteins.
our cells create long polypeptides and then cleave them into smaller chains. Why? -
ANSWERSIt is more efficient; large protein has two polypeptides and are already folded
correctly before they are clipped.
Protein folding - ANSWERSthe polypeptide chain goes from a high energy, high entropy
state( unstable, unfolded) to low energy, low entropy state(stable, folded (native))
ribonuclease A - ANSWERSa 124 residue enzyme that breaks down RNA
-4 disulfide bonds
-urea -will denature all but disulfide bonds
-removal of both urea and beta mercapto-ethanol(a reducing agent which will break
disulfide bonds) restores structures and function.
-remove only BME→ restores disulfide bonds, but not correct place
-remove urea(include Bme)--> native ribonuclease
-the structure of one part of the protein (correct disulfide bonds) is not independent of
folding of other parts of protein (cooperativity of folding)
Why do denatured proteins tend to be less soluble? - ANSWERSthe normally
unexposed pieces of protein that are responsible for keeping the folded protein together
are less polar and hence less soluble than the outside of a soluble protein.
x-ray crystallography - ANSWERSget lots of protein, remove water, make a crystal
regular arrangement of proteins
-shoot x-rays through the sample
-most x rays pass through it but some interact with electron cloud of an atom and bend
- looking at how the x rays are bent can tell the structure of a protein
-limitation→ provide little info about molecular motion within the protein
-What do proteins do?
-bind to ligands
-examples: collagen(structural), dna binding(histones), storage(myoglobin)
Ligand - ANSWERSmolecule that binds reversibly to a protein; a ligand may be any
type of molecule, including another protein
-ligands bind to specific sites on the protein-the ligand binding site
-the ligand binding site usually exhibits molecular complementary to the ligand in terms
of size, shape, charge, and hydrophobic or hydrophilic characters.
-protein-ligand binding is very specific
- binding of a ligand to protein will usually change the shape of a protein
-ex. Substrates, signaling molecules, antigens, inhibitor drugs
QUESTIONS WITH CORRECT
ANSWERS
The Scientific Method - ANSWERSObservations
Ask questions
Hypothesis to answer the question→ new proposition that is compatible with
observations and facts already known; must result in testable predictions
Make predictions based on your hypothesis
Design experiment to test hypothesis
Designing Controlled Experiments - ANSWERSManipulate one variable at a time
Control group:exposed to the same conditions as the experimental group except for one
independent variable
Experimental group: exposed to the independent variable
hydrophobic effect - ANSWERShighly ordered H2O molecules form "cages" around the
hydrophobic alkyl chains if individual lipids
-entropically driven exclusion from water
- clusters of lipid molecules ; only lipid portions of the edge of the cluster force the
ordering of water;fewer H2O molecules are ordered , and entropy is increased.
-its is not an attraction between lipids that makes them cluster together in water, but the
interactions of water molecules to other water molecules.
how would membranes be affected if water were nonpolar? - ANSWERSwithout the
effect no membrane would exist because there would be nothing keeping the lipids
together , because there is no polarity and no structure would form.
Roles of water - ANSWERS-transport protons (acceptor)
-breaking (hydrolysis) covalent bonds(ATP)
-making(condensation) covalent bonds
-water can ionize (donate protons)
-H2O + H2O → H2O+ +OH-
-the dipole nature of water creates the hydrophobic effect
- can be crucial for the structure and function of an active site of an enzyme
Fluorescence microscopy - ANSWERS-using fluorescent dyes to visualize cellular
structures
-using natural compound with desirable binding properties
-use selective fluorescent dyes that absorbs light at one wavelength and emit light at a
different wavelength
-allows for visualization of specific cell structures at high magnification
,-actin cytoskeleton stained using pahlloida attached to fluorescent dye
-dapi emits blue fluorescence upon binding to DNA
-green fluorescent protein (GFP)
-engineered fluorescent protein
-a version of gfp has been engineered into two different parts , which can be used to
see whether two things within a cell interact
Immunohistochemistry - ANSWERS-a technique used to assess the presence of a
specific protein in cells
-a protein is detected using a specific antibody that binds to it
-antibodies are proteins of the immune system that bind tightly to a specific target
(antigen)
-secondary antibody attached to colorful or glowing molecules
-the antibody allows visualization of the protein under a microscope
endosymbiosis - ANSWERS-may have occurred when larger cells ingested smaller
ones
- mitochondria -- engulfed prokaryotic organisms
-chloroplasts-- larger eukaryotes ingested photosynthetic prokaryotes
carbohydrates - ANSWERSpolysaccharides→ stuff we eat contain glycogen and
starch-- with one type of glycosidic bond plus a branching glycosidic bonds(hydrophilic);
stuff we don't eat contain chitin and cellulose, which have a different type of glycosidic
bond (hydrophobic) (hydrogen bonds); the chains is curved and branches in glycogen ,
rather than linear as in cellulose
-very soluble in water
-glycosidic bond is how to join two sugar
lipids - ANSWERS- energy storage (and insulation)
-basic structural unit of cellular membranes
-light-absorbing pigments
-hormones
Fatty acids - ANSWERS-saturated fatty acid (chains is straight)- single bonds
- unsaturated fatty acid (carbon chain has kinks)- double bonds = less packing
-what are most natural fatty acids ? → cis
Why not only use carbs? - ANSWERSit takes a lt takes up more space to store glucose
than lipids; lipids are less oxidized so they contain more energy per carbon
amino acids - ANSWERS- hydrogen , amino group, r group, carboxyl group
-the building blocks of proteins
- neurotransmitters
-energy source
- precursors for other biomolecules
- the amino acid found in proteins are almost exclusively l-stereoisomer
, why do small proteins have more difficulty folding and holding shape? If you were
designing a protein what elements of structure might you include to increase stability? -
ANSWERSSmall proteins have less ability to bind and don't have enough hydrophilic r
groups to protect hydrophobic groups; I would use a lot of cysteine for small proteins.
our cells create long polypeptides and then cleave them into smaller chains. Why? -
ANSWERSIt is more efficient; large protein has two polypeptides and are already folded
correctly before they are clipped.
Protein folding - ANSWERSthe polypeptide chain goes from a high energy, high entropy
state( unstable, unfolded) to low energy, low entropy state(stable, folded (native))
ribonuclease A - ANSWERSa 124 residue enzyme that breaks down RNA
-4 disulfide bonds
-urea -will denature all but disulfide bonds
-removal of both urea and beta mercapto-ethanol(a reducing agent which will break
disulfide bonds) restores structures and function.
-remove only BME→ restores disulfide bonds, but not correct place
-remove urea(include Bme)--> native ribonuclease
-the structure of one part of the protein (correct disulfide bonds) is not independent of
folding of other parts of protein (cooperativity of folding)
Why do denatured proteins tend to be less soluble? - ANSWERSthe normally
unexposed pieces of protein that are responsible for keeping the folded protein together
are less polar and hence less soluble than the outside of a soluble protein.
x-ray crystallography - ANSWERSget lots of protein, remove water, make a crystal
regular arrangement of proteins
-shoot x-rays through the sample
-most x rays pass through it but some interact with electron cloud of an atom and bend
- looking at how the x rays are bent can tell the structure of a protein
-limitation→ provide little info about molecular motion within the protein
-What do proteins do?
-bind to ligands
-examples: collagen(structural), dna binding(histones), storage(myoglobin)
Ligand - ANSWERSmolecule that binds reversibly to a protein; a ligand may be any
type of molecule, including another protein
-ligands bind to specific sites on the protein-the ligand binding site
-the ligand binding site usually exhibits molecular complementary to the ligand in terms
of size, shape, charge, and hydrophobic or hydrophilic characters.
-protein-ligand binding is very specific
- binding of a ligand to protein will usually change the shape of a protein
-ex. Substrates, signaling molecules, antigens, inhibitor drugs
