Chapter 1 biochemical similarities
demonstrate the unity of life
Combustion: biological fuels react with oxygen to produce carbon
dioxide and water
Covalent bonds are stable linkages between two atoms within a
molecule due to the sharing of valence electrons
- Strongest bond between atoms
Consequences of stronger bonds
- Greater stability to larger molecules
- More energy is released when these bonds undergo combustion
Proteins: linear array of amino acids joined by peptide bonds
- Translations of genetic information
- Signal molecule
- Receptor for signal molecules
- Catalysts: agents that enhance the rate of a chemical reaction
without being permanently changed -> enzymes
Nucleic acids: composed of nucleotide monomers that stores and
transfers information in cells
- Nucleotide: five carbon deoxyribose or ribose sugar attached to a
nitrogen ring structure (base) and one to three phosphoryl groups
- DNA: adenine, cytosine, guanine and thymine
- RNA: thymine -> uracil and additional -OH group
- mRNA is a template for the synthesis of proteins
Lipids: water-insoluble biomolecules that are soluble in organic solvents
- Storage form of fuel
- Serve as a barrier
- Composed of both hydrophilic and hydrophobic regions
- Structure
Carbohydrates: fuels as well as structural and recognition molecules
that can form branched structures
- Glucose
- Cell-cell communication
,Chapter 2 Water, weak interactions and the
generation of order out of chaos
Distance between twee nonbonded noncovalently atoms -> 4 angstroms
1 angstrom = 0.1 nanometers
Thermal motion: the constant and random movement of all matter due
to inherent kinetic energy
- All substances at temperatures above zero have kinetic energy and
therefore thermal motion
- Brownian motion
Biochemical timescale: the timescale over which most chemical
interactions take place, measured in picoseconds to microseconds
Polar: non-uniform distribution of charge
- Oxygen atoms are slightly negatively charged
- Hydrogen atoms are slightly positively charged
Hydrogen bond: dipole-dipole interaction in which a hydrogen atom is
partially shared by two electronegative atoms
Nonpolar molecules: a molecule that cannot participate in dipole,
hydrogen or ionic interaction
Noncovalent interactions
1. Ionic interactions
2. Dipole-dipole interactions
3. Van der Waals interactions
Ionic interactions: the interactions between distinct electrical charges
on atoms
- Between negative charged and positive charged atoms
- Energy of interaction given Coulomb force:
- F = the force
- Q = the charges of the atoms
- R = the distance between two atoms
- D = the dielectric constant -> intervening
medium
- K = the proportionality constant
,Molecules can be partially negatively charges which leads to electric
dipoles: electrostatic interactions with other dipoles, with ions or with
non-polar groups
Hydrogen-bond donor is the group that includes both
the atom to which the hydrogen is covalently bonded
and the hydrogen atom itself.
Hydrogen-bond acceptor is the lone pair of electrons
Van der Waals interaction: a weak interaction due to fluctuating
dipoles in one group inducing complementary dipoles on a nearby group
- Non specific
- Van der Waals contact distance
Biochemical benefit of weak interactions?
Weak interactions allow repeated interactions among biomolecules
Entropy is a measure of randomness
Hydrophobic effect: the tendency of nonpolar molecules to associate
with one another in aqueous solutions because they are driven together
due to the resulting increase in entropy of water molecules
- Hydrophobic interactions form spontaneously -> no input of energy
is required because when they form, the entropy of water increases
- Membrane formation
Amphipathic molecule: a molecule with both hydrophobic and
hydrophilic parts
pH = a measure of concentration of hydrogen ions in solution, given by
the equation pH = -log [H+]
The species formed by the ionization of acid is its conjugated base
Larger the value of Ka, the stronger the acid
, Henderson-Hasselbalch equation: Relation between pH and the conjugate
acid/base ratio:
pKa is the pH at which the acid is half protonated and half deprotonated
At a pH higher than the pKa less will be protonated than be deprotonated
At a pH lower that pKa there will be more protonated than deprotonated
protein
Buffer: a solution of an acid-base conjugate pair that resists change in pH
upon the addition of acid or base
Chapter 3 amino acids
Proteogenic amino acids: the common set of 20 amino acids used to
build protein by every organism on earth
Essential amino acids: an amino acid that cannot be synthesized and
therefore must be acquired from the diet
Every amino acid
- Central carbon atom -> alfa carbon
- Amino group
- A carboxyl acid group
- Hydrogen atom
- Side chain -> R-group
Alpha amino acids: contain a chiral carbon that is bound to an amino
group, a carboxyl group, a hydrogen atom and a R-group (side chain)
L isomer and D isomer -> only L amino acids are constituent proteins
Zwitterions: an ion carrying both a positive and a negative charge
(dipolar ion)
- Amino group is protonated (NH3+)
- Carboxyl group is deprotonated (COO-)
4 groups of amino acids
1. Hydrophobic amino acids with nonpolar R groups
2. Polar amino acids with neutral R groups but the charge is not evenly
distributed
3. Positively charged amino acids with R groups that have a positive
charge at physiological pH
demonstrate the unity of life
Combustion: biological fuels react with oxygen to produce carbon
dioxide and water
Covalent bonds are stable linkages between two atoms within a
molecule due to the sharing of valence electrons
- Strongest bond between atoms
Consequences of stronger bonds
- Greater stability to larger molecules
- More energy is released when these bonds undergo combustion
Proteins: linear array of amino acids joined by peptide bonds
- Translations of genetic information
- Signal molecule
- Receptor for signal molecules
- Catalysts: agents that enhance the rate of a chemical reaction
without being permanently changed -> enzymes
Nucleic acids: composed of nucleotide monomers that stores and
transfers information in cells
- Nucleotide: five carbon deoxyribose or ribose sugar attached to a
nitrogen ring structure (base) and one to three phosphoryl groups
- DNA: adenine, cytosine, guanine and thymine
- RNA: thymine -> uracil and additional -OH group
- mRNA is a template for the synthesis of proteins
Lipids: water-insoluble biomolecules that are soluble in organic solvents
- Storage form of fuel
- Serve as a barrier
- Composed of both hydrophilic and hydrophobic regions
- Structure
Carbohydrates: fuels as well as structural and recognition molecules
that can form branched structures
- Glucose
- Cell-cell communication
,Chapter 2 Water, weak interactions and the
generation of order out of chaos
Distance between twee nonbonded noncovalently atoms -> 4 angstroms
1 angstrom = 0.1 nanometers
Thermal motion: the constant and random movement of all matter due
to inherent kinetic energy
- All substances at temperatures above zero have kinetic energy and
therefore thermal motion
- Brownian motion
Biochemical timescale: the timescale over which most chemical
interactions take place, measured in picoseconds to microseconds
Polar: non-uniform distribution of charge
- Oxygen atoms are slightly negatively charged
- Hydrogen atoms are slightly positively charged
Hydrogen bond: dipole-dipole interaction in which a hydrogen atom is
partially shared by two electronegative atoms
Nonpolar molecules: a molecule that cannot participate in dipole,
hydrogen or ionic interaction
Noncovalent interactions
1. Ionic interactions
2. Dipole-dipole interactions
3. Van der Waals interactions
Ionic interactions: the interactions between distinct electrical charges
on atoms
- Between negative charged and positive charged atoms
- Energy of interaction given Coulomb force:
- F = the force
- Q = the charges of the atoms
- R = the distance between two atoms
- D = the dielectric constant -> intervening
medium
- K = the proportionality constant
,Molecules can be partially negatively charges which leads to electric
dipoles: electrostatic interactions with other dipoles, with ions or with
non-polar groups
Hydrogen-bond donor is the group that includes both
the atom to which the hydrogen is covalently bonded
and the hydrogen atom itself.
Hydrogen-bond acceptor is the lone pair of electrons
Van der Waals interaction: a weak interaction due to fluctuating
dipoles in one group inducing complementary dipoles on a nearby group
- Non specific
- Van der Waals contact distance
Biochemical benefit of weak interactions?
Weak interactions allow repeated interactions among biomolecules
Entropy is a measure of randomness
Hydrophobic effect: the tendency of nonpolar molecules to associate
with one another in aqueous solutions because they are driven together
due to the resulting increase in entropy of water molecules
- Hydrophobic interactions form spontaneously -> no input of energy
is required because when they form, the entropy of water increases
- Membrane formation
Amphipathic molecule: a molecule with both hydrophobic and
hydrophilic parts
pH = a measure of concentration of hydrogen ions in solution, given by
the equation pH = -log [H+]
The species formed by the ionization of acid is its conjugated base
Larger the value of Ka, the stronger the acid
, Henderson-Hasselbalch equation: Relation between pH and the conjugate
acid/base ratio:
pKa is the pH at which the acid is half protonated and half deprotonated
At a pH higher than the pKa less will be protonated than be deprotonated
At a pH lower that pKa there will be more protonated than deprotonated
protein
Buffer: a solution of an acid-base conjugate pair that resists change in pH
upon the addition of acid or base
Chapter 3 amino acids
Proteogenic amino acids: the common set of 20 amino acids used to
build protein by every organism on earth
Essential amino acids: an amino acid that cannot be synthesized and
therefore must be acquired from the diet
Every amino acid
- Central carbon atom -> alfa carbon
- Amino group
- A carboxyl acid group
- Hydrogen atom
- Side chain -> R-group
Alpha amino acids: contain a chiral carbon that is bound to an amino
group, a carboxyl group, a hydrogen atom and a R-group (side chain)
L isomer and D isomer -> only L amino acids are constituent proteins
Zwitterions: an ion carrying both a positive and a negative charge
(dipolar ion)
- Amino group is protonated (NH3+)
- Carboxyl group is deprotonated (COO-)
4 groups of amino acids
1. Hydrophobic amino acids with nonpolar R groups
2. Polar amino acids with neutral R groups but the charge is not evenly
distributed
3. Positively charged amino acids with R groups that have a positive
charge at physiological pH
