BMSC 200 Final Exam Questions with
Complete Answers
Membranes and Cellular Functions - ANSWER-Eukaryotes contain membrane-
enclosed compartments inside the cell. Prokaryotes lack intracellular membranes.
Lipids make up bilayers.
Plasma Membrane - ANSWER-Separates the inside of the cell from the outside. Is
impermeable to most biomolecules but is selectively permeable because of the
proteins associated with it. In a plant cell, it is surrounded by a cell wall composed of
cellulose and glucose.
Vacuoles - ANSWER-Large, unique to plants, store water, ions, and various
nutrients.
Chloroplasts - ANSWER-Abundant in photosynthetic organisms such as plants and
algae. It is where sunlight is utilized to synthesize carbohydrates. They reflect green
light and primarily contain chlorophyll. Are responsible for making sugars instead of
ATP.
Cytoplasm - ANSWER-Part of the cell surrounded by the plasma membrane but are
not enclosed by any intracellular membranes. Organized by a series of structural
filaments of proteins called the cytoskeleton.
Cytoskeleton - ANSWER-Maintains cell shape and volume, seems invisible until
really high resolution.
Mitochondria - ANSWER-Oxidization plant. Produces ATP and contains two
membranes. Curved inner membrane increases surface area.
Cellular Compartments - ANSWER-Biochemical functions are sequestered in these
structures. The nucleus is the information centre. The lysosome is in charge of lysis
and contains digestive enzymes so that the entire cell isn't digested. Some
organelles process and sort proteins and exchange material with the environment.
Endoplasmic Reticulum - ANSWER-A series of membranous sacs in the cytoplasm.
There are two types:
1. Rough- has ribosomes associated with it and plays a role in protein processing.
2. Smooth- no ribosomes and plays a variety of biochemical roles.
Golgi Complex - ANSWER-A series of stacked membranes that play a role in protein
sorting. Carbohydrates are attached to this structure. Proteins move from the RER to
this complex via transport vesicles. Is another very folded membrane.
,Exocytosis - ANSWER-Secretes biomolecules in this process.
Endocytosis - ANSWER-A means of bringing crucial biomolecules into the cell. An
endosome is the structure that forms when the plasma membrane invaginates and
buds off. Is transported to the lysosome.
Phagocytosis - ANSWER-The intake of large amounts of material
Human Proteins - ANSWER-A human has about 1/4 million.
Lysosomes - ANSWER-These contain a variety of digestive enzymes. They fuse
with endosomes to digest material brought into the cell.
Weak Bonds - ANSWER-Covalent bonds. These bonds allow for dynamic
interactions that form the basis of biochemistry.
Angstrom - ANSWER-10^-10m. The shortest covalent bond is R-H.
Brownian Motion - ANSWER-the movement of molecules powered by random
fluctuations of environmental energy. This means that they bump into each other at
certain times more. This principle in water creates many biochemical interactions.
This whole idea was discovered by Einstein and he learned that the higher the
temperature the more reactions in fact 5-25x greater.
Water - ANSWER-A polar molecule, with the oxygen atom carrying a slightly
negative charge and the hydrogen atoms carrying slightly positive charges. Any
polar molecule therefore is hydrophillic and the more non-polar a molecule is the
more hydrophobic it becomes. Water is quite unique in the way that its oxygen atom
has two lone pairs of electrons and two hydrogen atoms attached. Can form 4 H-
bonds.
Hydrogen Bonds - ANSWER-An acceptor is an F,O,N with a lone pair with no
attached H. A donor is one of those atoms with a H attached. In ice strong hydrogen
bonds tend to form when the hydrogen atom is aligned with the lone pair of electrons
and this leads to the most stability. In a molecule like ammonia that has 1 donor and
3 acceptors it is not able to form quite as many bonds.
Importance of Water - ANSWER-It is polar which allows the formation of hydrogen
bonds and accounts for how cohesive it is. It is also able to dissolve many
biomolecules also because of how polar it is. The inability to dissolve non-polar
molecules is also super important as it allows for hydrophobic collapse.
electrostatic interactions - ANSWER-Between electrical charged- full charged ions.
Also called ionic bonds or salt bridges. They are the interactions between distinct
electrical charges on atoms. Stronger than a hydrogen bond. The energy between
can be measure by coulombs law which is E=Kq₁q₂/Dr where E is the energy
constant, q are the ion charges, D is the dielectric constant which is the amount the
charge is diluted compared to a vacuum. r is the distance between ions and k is the
proportionality constant. If E is negative then the forces are attractive but if it is
,positive then there is great repulsion. D is 80 in water which means that it weakens
electrostatic interactions.
Ionic Compounds Dissolving - ANSWER-They can only dissolve and break out of the
lattice if they are surrounded by molecules that will interact with them like water. In
salt the Na+ breaks away and is surrounded by the negative dipole in the water (O)
the chloride ion does the same thing except is surrounded by the positive dipoles.
Hydrogen bonds outside of water - ANSWER-These bonds are not unique to water
and can occur whenever a hydrogen is bonded to an electronegative atom. Water
disrupts hydrogen bonds by competing for hydrogen bonding capability.
Vander waal forces - ANSWER-Nonpolar and uncharged molecules can interact
electrostatically with these interactions. The basis of interaction is that transient
asymmetry in the electron distribution of on molecule will induce complementary
asymmetry in a nearby molecule. These interactions are distant dependent. The
molecules will attract until they hit a point called the contact distance which is
between 3-4 angstroms. At this point the electron clouds overlap and become
extremely repulsive. The greater the number of atoms involved the stronger the
interaction. Spontaneous reactions increase entropy which is usually released as
heat.
Advantage of Weak Bonds - ANSWER-Are easily broken which means that the
interactions can be repeated rapidly. A good example of this is DNA the bonds that
hold it together are weak enough that the strands can be opened up but are strong
enough to protect it. It can go in both the forward and reverse directions without
harming the molecule.
Hydrophobic Cluster - ANSWER-When a non-polar molecule is introduced to a polar
solute the polar molecule surrounds it but has no ability to break it down. The polar
molecules surrounding the non-polar ones are much more organized which in order
to maintain the second law of thermodynamics the NP must become organized as
the P disorganizes and that is exactly what happens.
Membrane Formation - ANSWER-Powered by the hydrophobic effect as the head
orients its self towards the water and the tails orient themselves toward each other.
VDW stabilize the two tails in a bilayer.
Protein Folding and Hydrophobicity - ANSWER-Form complex 3-D structures that
are able to fold spontaneously under the correct circumstances. The hydrophobic
effect increases order in the protein because some of the amino acids have non-
polar groups and they want to associate together and fold into the inside of the
protein. This allows water to be freed and increase in entropy. Hydrogen bonds and
van der waal forces form within a protein structure to stabilize it.
Functional Group Properties - ANSWER-All functional groups of which they are a
part act similarily in all molecules. There is a limited number and have an array of
atoms which have distinctive chemical properties. All of the groups have to ability to
either form hydrogen bonds or ionic bonds except the strictly hydrophobic groups.
, Hydrophobic-Hydrocarbons - ANSWER-Chain: R-CH₃
Aromatic R-benzene
Hydroxyl (alcohol) - ANSWER-R-OH
Aldehyde - ANSWER-
Keto-ketone - ANSWER-
Carboxyl-carboxylic acid - ANSWER-
Amino-Amines - ANSWER-R-NH2
Phosphates (organic phosphates) - ANSWER-
Sulfhydryl (Thiols) - ANSWER-R-SH
pH - ANSWER-The measure of H+ (proton) concentration of a solution. Being able to
control this is a crucial function in biological systems.
gastroesophageal reflux disease (GERD) - ANSWER-A digestive disease that
develops when stomach acid refluxes into the esophogus and irritates the lining of
the esophagus. Smokers and people with obesity are at an increased risk.
Water Ionization - ANSWER-Very small amounts are able to dissociate and form
hydronium and hydroxyl ions with the concentration being 1E10^-7. The dissociation
equation is H₂O⇌H₃O⁺+OH⁻ which means that the Keq is [H⁺][OH⁻]/[H₂O]. Water is
essentially unchanged by the small amount of ionization so we are able to define a
new constant Kw=Keqx[H₂O] which in the most simplified form is Kw=[H⁺][OH⁻]
Kw=1.0E10⁻¹⁴.
pH Equation - ANSWER-=-log₁₀[H⁺] This means that pure water has a pH of 7. pOH
is the opposite of pH and they add up to 14 total always.
Proton Donor and Acceptor - ANSWER-Acids ionize to form a proton and a base.
The chemical formed upon ionization of an acid is called its conjugate base. The
base conversely can accept a proton and it is called a conjugate acid.
Ka - ANSWER-The equation is [H⁺][A⁻]/[HA] and the larger the value the stronger
the acid. It is possible to convert this equation into logarithms for convenience. This
gives us the relationship between pH and the ration of acid to base.
PKa - ANSWER-Is found by taking the log of Ka in the Henderson-Hasselbalch
equation which is pH=pKa + log([A⁻]/[HA]) When the acid and conjugate base are
equal then the pKa is 0. A positive pKa value means that the base is dominant and a
negative value means the acid. In dissociation, only the H associated with O can be
released.
Complete Answers
Membranes and Cellular Functions - ANSWER-Eukaryotes contain membrane-
enclosed compartments inside the cell. Prokaryotes lack intracellular membranes.
Lipids make up bilayers.
Plasma Membrane - ANSWER-Separates the inside of the cell from the outside. Is
impermeable to most biomolecules but is selectively permeable because of the
proteins associated with it. In a plant cell, it is surrounded by a cell wall composed of
cellulose and glucose.
Vacuoles - ANSWER-Large, unique to plants, store water, ions, and various
nutrients.
Chloroplasts - ANSWER-Abundant in photosynthetic organisms such as plants and
algae. It is where sunlight is utilized to synthesize carbohydrates. They reflect green
light and primarily contain chlorophyll. Are responsible for making sugars instead of
ATP.
Cytoplasm - ANSWER-Part of the cell surrounded by the plasma membrane but are
not enclosed by any intracellular membranes. Organized by a series of structural
filaments of proteins called the cytoskeleton.
Cytoskeleton - ANSWER-Maintains cell shape and volume, seems invisible until
really high resolution.
Mitochondria - ANSWER-Oxidization plant. Produces ATP and contains two
membranes. Curved inner membrane increases surface area.
Cellular Compartments - ANSWER-Biochemical functions are sequestered in these
structures. The nucleus is the information centre. The lysosome is in charge of lysis
and contains digestive enzymes so that the entire cell isn't digested. Some
organelles process and sort proteins and exchange material with the environment.
Endoplasmic Reticulum - ANSWER-A series of membranous sacs in the cytoplasm.
There are two types:
1. Rough- has ribosomes associated with it and plays a role in protein processing.
2. Smooth- no ribosomes and plays a variety of biochemical roles.
Golgi Complex - ANSWER-A series of stacked membranes that play a role in protein
sorting. Carbohydrates are attached to this structure. Proteins move from the RER to
this complex via transport vesicles. Is another very folded membrane.
,Exocytosis - ANSWER-Secretes biomolecules in this process.
Endocytosis - ANSWER-A means of bringing crucial biomolecules into the cell. An
endosome is the structure that forms when the plasma membrane invaginates and
buds off. Is transported to the lysosome.
Phagocytosis - ANSWER-The intake of large amounts of material
Human Proteins - ANSWER-A human has about 1/4 million.
Lysosomes - ANSWER-These contain a variety of digestive enzymes. They fuse
with endosomes to digest material brought into the cell.
Weak Bonds - ANSWER-Covalent bonds. These bonds allow for dynamic
interactions that form the basis of biochemistry.
Angstrom - ANSWER-10^-10m. The shortest covalent bond is R-H.
Brownian Motion - ANSWER-the movement of molecules powered by random
fluctuations of environmental energy. This means that they bump into each other at
certain times more. This principle in water creates many biochemical interactions.
This whole idea was discovered by Einstein and he learned that the higher the
temperature the more reactions in fact 5-25x greater.
Water - ANSWER-A polar molecule, with the oxygen atom carrying a slightly
negative charge and the hydrogen atoms carrying slightly positive charges. Any
polar molecule therefore is hydrophillic and the more non-polar a molecule is the
more hydrophobic it becomes. Water is quite unique in the way that its oxygen atom
has two lone pairs of electrons and two hydrogen atoms attached. Can form 4 H-
bonds.
Hydrogen Bonds - ANSWER-An acceptor is an F,O,N with a lone pair with no
attached H. A donor is one of those atoms with a H attached. In ice strong hydrogen
bonds tend to form when the hydrogen atom is aligned with the lone pair of electrons
and this leads to the most stability. In a molecule like ammonia that has 1 donor and
3 acceptors it is not able to form quite as many bonds.
Importance of Water - ANSWER-It is polar which allows the formation of hydrogen
bonds and accounts for how cohesive it is. It is also able to dissolve many
biomolecules also because of how polar it is. The inability to dissolve non-polar
molecules is also super important as it allows for hydrophobic collapse.
electrostatic interactions - ANSWER-Between electrical charged- full charged ions.
Also called ionic bonds or salt bridges. They are the interactions between distinct
electrical charges on atoms. Stronger than a hydrogen bond. The energy between
can be measure by coulombs law which is E=Kq₁q₂/Dr where E is the energy
constant, q are the ion charges, D is the dielectric constant which is the amount the
charge is diluted compared to a vacuum. r is the distance between ions and k is the
proportionality constant. If E is negative then the forces are attractive but if it is
,positive then there is great repulsion. D is 80 in water which means that it weakens
electrostatic interactions.
Ionic Compounds Dissolving - ANSWER-They can only dissolve and break out of the
lattice if they are surrounded by molecules that will interact with them like water. In
salt the Na+ breaks away and is surrounded by the negative dipole in the water (O)
the chloride ion does the same thing except is surrounded by the positive dipoles.
Hydrogen bonds outside of water - ANSWER-These bonds are not unique to water
and can occur whenever a hydrogen is bonded to an electronegative atom. Water
disrupts hydrogen bonds by competing for hydrogen bonding capability.
Vander waal forces - ANSWER-Nonpolar and uncharged molecules can interact
electrostatically with these interactions. The basis of interaction is that transient
asymmetry in the electron distribution of on molecule will induce complementary
asymmetry in a nearby molecule. These interactions are distant dependent. The
molecules will attract until they hit a point called the contact distance which is
between 3-4 angstroms. At this point the electron clouds overlap and become
extremely repulsive. The greater the number of atoms involved the stronger the
interaction. Spontaneous reactions increase entropy which is usually released as
heat.
Advantage of Weak Bonds - ANSWER-Are easily broken which means that the
interactions can be repeated rapidly. A good example of this is DNA the bonds that
hold it together are weak enough that the strands can be opened up but are strong
enough to protect it. It can go in both the forward and reverse directions without
harming the molecule.
Hydrophobic Cluster - ANSWER-When a non-polar molecule is introduced to a polar
solute the polar molecule surrounds it but has no ability to break it down. The polar
molecules surrounding the non-polar ones are much more organized which in order
to maintain the second law of thermodynamics the NP must become organized as
the P disorganizes and that is exactly what happens.
Membrane Formation - ANSWER-Powered by the hydrophobic effect as the head
orients its self towards the water and the tails orient themselves toward each other.
VDW stabilize the two tails in a bilayer.
Protein Folding and Hydrophobicity - ANSWER-Form complex 3-D structures that
are able to fold spontaneously under the correct circumstances. The hydrophobic
effect increases order in the protein because some of the amino acids have non-
polar groups and they want to associate together and fold into the inside of the
protein. This allows water to be freed and increase in entropy. Hydrogen bonds and
van der waal forces form within a protein structure to stabilize it.
Functional Group Properties - ANSWER-All functional groups of which they are a
part act similarily in all molecules. There is a limited number and have an array of
atoms which have distinctive chemical properties. All of the groups have to ability to
either form hydrogen bonds or ionic bonds except the strictly hydrophobic groups.
, Hydrophobic-Hydrocarbons - ANSWER-Chain: R-CH₃
Aromatic R-benzene
Hydroxyl (alcohol) - ANSWER-R-OH
Aldehyde - ANSWER-
Keto-ketone - ANSWER-
Carboxyl-carboxylic acid - ANSWER-
Amino-Amines - ANSWER-R-NH2
Phosphates (organic phosphates) - ANSWER-
Sulfhydryl (Thiols) - ANSWER-R-SH
pH - ANSWER-The measure of H+ (proton) concentration of a solution. Being able to
control this is a crucial function in biological systems.
gastroesophageal reflux disease (GERD) - ANSWER-A digestive disease that
develops when stomach acid refluxes into the esophogus and irritates the lining of
the esophagus. Smokers and people with obesity are at an increased risk.
Water Ionization - ANSWER-Very small amounts are able to dissociate and form
hydronium and hydroxyl ions with the concentration being 1E10^-7. The dissociation
equation is H₂O⇌H₃O⁺+OH⁻ which means that the Keq is [H⁺][OH⁻]/[H₂O]. Water is
essentially unchanged by the small amount of ionization so we are able to define a
new constant Kw=Keqx[H₂O] which in the most simplified form is Kw=[H⁺][OH⁻]
Kw=1.0E10⁻¹⁴.
pH Equation - ANSWER-=-log₁₀[H⁺] This means that pure water has a pH of 7. pOH
is the opposite of pH and they add up to 14 total always.
Proton Donor and Acceptor - ANSWER-Acids ionize to form a proton and a base.
The chemical formed upon ionization of an acid is called its conjugate base. The
base conversely can accept a proton and it is called a conjugate acid.
Ka - ANSWER-The equation is [H⁺][A⁻]/[HA] and the larger the value the stronger
the acid. It is possible to convert this equation into logarithms for convenience. This
gives us the relationship between pH and the ration of acid to base.
PKa - ANSWER-Is found by taking the log of Ka in the Henderson-Hasselbalch
equation which is pH=pKa + log([A⁻]/[HA]) When the acid and conjugate base are
equal then the pKa is 0. A positive pKa value means that the base is dominant and a
negative value means the acid. In dissociation, only the H associated with O can be
released.
