Chapter 1- The Chemical Foundations of Biochemistry
1. What is “biochemistry”? Biochemistry is the chemical systems that happen in all living
organisms
1.1. General Chemical Principles
2. Provide a biological example of the first law of thermodynamics
The first law is that all energy is conserved (it canted be created only converted)
- Ex: we can pump ions across an impermeable barrier and the heat energy can
be released INTO the system, which increases the temperature of the organism
and chemical energy may be converted into a photon of light by bioluminescent
organisms
3. Thought question: How do the first and second laws of thermodynamics support the
statement “there is no free lunch!”?
- first law = energy is conserved
- second law = spontaneous processes are characterized by the conversion of order to
disorder
- essentially, nothing is free
4. Gibbs Free Energy: why is the notion of “ΔG” more useful than simply using “G” in
biological systems? Compare a reaction going in forward and reverse directions in terms
of free energy
Delta G is more useful than just using G in biological systems as free energies are
compared to one another
5. Distinguish between a state of chemical equilibrium, and a non-equilibrium steady state.
This is a key concept for biochemistry!
Chemical equilibrium: the state where the rate of the fwds rxn is equal to the reverse
rxn. There is no net change in concentrations of reactants and products.
non-equilibrium steady state: a state in a system where external forces maintain a
constant state of imbalance, leading to properties that do not change with time despite
being out of thermal equilibrium
6. Does maintaining homeostasis break the laws of thermodynamics—does Le Châtelier’s
principle apply in biological systems?
- Le chateliers principle (a state in a system where external forces maintain a
constant state of imbalance, leading to properties that do not change with time
despite being out of thermal equilibrium) applies in all systems including
biochemical ones.
- Homeostasis maintenance DOES NOT break the laws of thermodynamics. Living
things are in OPEN systems( can only reach equilibrium when the flow of matter
and energy has stopped) having equilibrium for living things = death and
living things maintain a non-equilibrium steady state
7. In your own words, what is “kinetics” in chemistry?
Kinetics in chemistry is the rate of a chemical reaction (how/the rate of atoms moving)
1.2. Fundamental Concepts of Organic Chemistry
8. What is a “functional group” in organic chemistry?
, Parts of a molecule (like hydroxyl groups) that react specifically enabling us to better
understand how molecules work and what their properties are.
9. How do functional groups affect the solubility of organic molecules?
Polar or charged functional groups have higher solubility in water. So when molecules
have more polar/charged groups they become more soluble (ex. hydroxyl groups and
thiols, or charged groups, such as amine and carboxylate salts; phosphates; and, in
some instances, sulfates.)
10.Why is it important that you remember organic reaction mechanisms when we are
studying biochemistry?
Because they explain how reactions within our bodies occur. It can help us to
understand how enzymes work as catalysts, understand how drugs work, and the
metabolic pathways of our bodies.
11. What is a polymer? Provide two or three examples of important biological molecules
that are polymers—what are their building blocks, and what is their overall structure?
- macromolecular assemblies of building blocks known as monomers which may
be attached in a linear way or in a branched way (ex. DNA or RNA)
- DNA: the building blocks are nucleotides and the overall structure is a double
helix
- RNA: the building blocks are nucleotides and the overall structure is a single
strand
- Proteins: the building blocks are amino acids and their overall structure is an
alpha helices or a beta sheet
- Carbohydrates: building blocks are monosaccharides (CH2O) there overall
structure is dependant on how big it is
1.3. The Chemistry of Water
12.How does the structure of water molecules affect its properties:
- Water is uncharged, so why is it polar? Because of the unequal sharing of electrons
between the highly electronegative oxygen and the very low electronegative hydrogen.
There are 2 L.P’s on the oxygen atom so it has a tetrahedral bond angle which allows for
a dipole moment in the water molecule (ie. one side is positive and the other is
negative), which allows for water to be polar.
- How can water molecules form hydrogen bonds? The negative end of one water
molecule is attracted to the positive end of another molecule creating a hydrogen bond.
13.Provide a simple definition of Brønsted-Lowry acids and bases—this will be important for
understanding many biochemical interactions!
Acids are protons donors (loses protons) and Bases are proton acceptors (gains
protons)
14.Why is water important for defining acid/base interactions?
Water is able to act as an acid or a base. This is important in acid/base interactions as
water may make a solution more basic or more acidic.
15.How can water be both a solvent and a reactant?
Water may act as a solvent in a situation where it causes a compound like NaCl to
dissociate and dissolve into the solution by using its polar nature. Or it may act as a
1. What is “biochemistry”? Biochemistry is the chemical systems that happen in all living
organisms
1.1. General Chemical Principles
2. Provide a biological example of the first law of thermodynamics
The first law is that all energy is conserved (it canted be created only converted)
- Ex: we can pump ions across an impermeable barrier and the heat energy can
be released INTO the system, which increases the temperature of the organism
and chemical energy may be converted into a photon of light by bioluminescent
organisms
3. Thought question: How do the first and second laws of thermodynamics support the
statement “there is no free lunch!”?
- first law = energy is conserved
- second law = spontaneous processes are characterized by the conversion of order to
disorder
- essentially, nothing is free
4. Gibbs Free Energy: why is the notion of “ΔG” more useful than simply using “G” in
biological systems? Compare a reaction going in forward and reverse directions in terms
of free energy
Delta G is more useful than just using G in biological systems as free energies are
compared to one another
5. Distinguish between a state of chemical equilibrium, and a non-equilibrium steady state.
This is a key concept for biochemistry!
Chemical equilibrium: the state where the rate of the fwds rxn is equal to the reverse
rxn. There is no net change in concentrations of reactants and products.
non-equilibrium steady state: a state in a system where external forces maintain a
constant state of imbalance, leading to properties that do not change with time despite
being out of thermal equilibrium
6. Does maintaining homeostasis break the laws of thermodynamics—does Le Châtelier’s
principle apply in biological systems?
- Le chateliers principle (a state in a system where external forces maintain a
constant state of imbalance, leading to properties that do not change with time
despite being out of thermal equilibrium) applies in all systems including
biochemical ones.
- Homeostasis maintenance DOES NOT break the laws of thermodynamics. Living
things are in OPEN systems( can only reach equilibrium when the flow of matter
and energy has stopped) having equilibrium for living things = death and
living things maintain a non-equilibrium steady state
7. In your own words, what is “kinetics” in chemistry?
Kinetics in chemistry is the rate of a chemical reaction (how/the rate of atoms moving)
1.2. Fundamental Concepts of Organic Chemistry
8. What is a “functional group” in organic chemistry?
, Parts of a molecule (like hydroxyl groups) that react specifically enabling us to better
understand how molecules work and what their properties are.
9. How do functional groups affect the solubility of organic molecules?
Polar or charged functional groups have higher solubility in water. So when molecules
have more polar/charged groups they become more soluble (ex. hydroxyl groups and
thiols, or charged groups, such as amine and carboxylate salts; phosphates; and, in
some instances, sulfates.)
10.Why is it important that you remember organic reaction mechanisms when we are
studying biochemistry?
Because they explain how reactions within our bodies occur. It can help us to
understand how enzymes work as catalysts, understand how drugs work, and the
metabolic pathways of our bodies.
11. What is a polymer? Provide two or three examples of important biological molecules
that are polymers—what are their building blocks, and what is their overall structure?
- macromolecular assemblies of building blocks known as monomers which may
be attached in a linear way or in a branched way (ex. DNA or RNA)
- DNA: the building blocks are nucleotides and the overall structure is a double
helix
- RNA: the building blocks are nucleotides and the overall structure is a single
strand
- Proteins: the building blocks are amino acids and their overall structure is an
alpha helices or a beta sheet
- Carbohydrates: building blocks are monosaccharides (CH2O) there overall
structure is dependant on how big it is
1.3. The Chemistry of Water
12.How does the structure of water molecules affect its properties:
- Water is uncharged, so why is it polar? Because of the unequal sharing of electrons
between the highly electronegative oxygen and the very low electronegative hydrogen.
There are 2 L.P’s on the oxygen atom so it has a tetrahedral bond angle which allows for
a dipole moment in the water molecule (ie. one side is positive and the other is
negative), which allows for water to be polar.
- How can water molecules form hydrogen bonds? The negative end of one water
molecule is attracted to the positive end of another molecule creating a hydrogen bond.
13.Provide a simple definition of Brønsted-Lowry acids and bases—this will be important for
understanding many biochemical interactions!
Acids are protons donors (loses protons) and Bases are proton acceptors (gains
protons)
14.Why is water important for defining acid/base interactions?
Water is able to act as an acid or a base. This is important in acid/base interactions as
water may make a solution more basic or more acidic.
15.How can water be both a solvent and a reactant?
Water may act as a solvent in a situation where it causes a compound like NaCl to
dissociate and dissolve into the solution by using its polar nature. Or it may act as a
