Chapter 2: Cell Chemistry and Bioenergetics
Life hinges on the chemical properties of water. H2O is highly polar because the O is strongly
attractive for electrons, which gives it a negative charge.
hydrogen bond: noncovalent bond in which an electropositive hydrogen atom is partially
shared by two electronegative atoms.
- Each water molecule can form these bonds through it’s two H atoms to two other water
molecules, which forms a network in which bonds are continually broken and formed
hydrophilic: dissolving readily in water (water-loving)
- Alcohols, most proteins, sugars
Hydrophobic: not dissolving readily in water (water-fearing)
- Hydrocarbons
There are three types of noncovalent bonds: electrostatic attractions, hydrogen bonds and van
der Waals attractions; and a fourth factor which pushes molecules together, the hydrophobic
force. Their energies working together can create a strong force, individually the forces are
weak.
electrostatic attractions: a noncovalent, ionic bond between two molecules carrying groups
of opposite charge
Van der Waals attractions: type of (individually weak) noncovalent bond that is formed at
close range between nonpolar atoms
Hydrophobic force: force exerted by the hydrogen-bonded network of water molecules
that brings two nonpolar surfaces together by excluding water
between them. (also happens in RNA and DNA)
When a polar molecule becomes surrounded by water, the proton will be attracted to the partial
negative charge on the O atom creating a hydronium ion.
proton: Positively charged subatomic particle that forms part of an atomic
nucleus. Hydrogen has a nucleus composed of a single proton
hydronium ion: Water molecule associated with an additional proton. The form generally
taken by protons in aqueous solution.
acids: A proton donor. Substance that releases protons when dissolved in water,
forming hydronium ions and lowering the pH.
- characterized as strong or weak, depending on how readily they give up protons
- the concentration of the H3O+ in cells has to be regulated closely because of how readily
they give up protons.
base: A substance that can reduce the number of protons in solution, either by
accepting H+ ions directly or by releasing OH- ions which then combine
with H+ to form H2O
buffers: Solution of weak acid or weak base that resists the pH change that would
otherwise occur when small quantities of acid or base are added.
- weak bases are important in living cells because they have a weak tendency to
reversibly accept a proton from water.
,chemical group: Certain combinations of atoms, such as methyl (-CH3), hydroxyl (-OH_),
carboxyl (-COOH), carbonyl (-C=O), phosphate (-PO32-), sulfhydryl (-SH) and amino (-NH2), that
have distinct chemical and physical properties and influence the behavior of the molecule in
which the group occurs.
macromolecules: Polymers constructed of long chains of covalently linked, small organic
(carbon containing) molecules. The principal building blocks from which a
cell is constructed and the components that confer the most distinctive
properties of living things.
- example: proteins, they act as enzymes, structural components, molecular motors
- each polymer grows by the addition of a monomer onto the end of a growing chain with
a condensation reaction.
- the shape of macromolecules are highly constrained because of the many weak
noncovalent bonds that form between different parts of the same molecule. → gives
enzymes their specific task because of their unique shape. (determined by the sequence
of the monomers)
IN BOOK: Panel 2-3, 2-4, 2-5, 2-6
monosaccharides: either contain an aldehyde (H-C=O) group (aldoses) or a ketone (-C=O)
group (ketoses)
- in aqueous solution aldehyde or ketone group reacts with a hydroxyl group of the same
molecule and forms a ring.
- beta hydroxyl: upwards, alpha hydroxyl: downwards
disaccharides: the carbon that carries the aldehyde or ketone group can react with any
hydroxyl group on a second sugar molecule
- maltose (glucose + glucose), lactose (galactose + glucose), sucrose (glucose + fructose)
polysaccharides: name for long chains, short chains are called oligosaccharides.
fatty acids: unsaturated (double bond, liquid) and saturated (no double bond, solid)
- stored as an energy reserve, linked to glycerol
- phospholipides are the major constituents of cell membranes (hydrophilic head and
hydrophobic tail)
bases: pyrimidine (C,U,T) or purine (A,G)
nucleoside: sugar + base
nucleotide: sugar + base + phosphate (<-- makes it negatively charged)
- buildingblocks for DNA
, Chapter 3: Proteins
Proteins, apart from building blocks, execute the majority of the cell’s functions:
- enzymes → provide the intricate molecular surfaces inside a cell that catalyze its many
chemical reactions.
- in the plasma membrane → form channels and pumps that control the passage of small
molecules into and out of the cell.
- providing information for mechanisms in and outside the cell
- antibodies, toxins, hormones, antifreeze molecules, elastic fibers, ropes or sources of
luminescence
The shape of a protein is specified by its amino acid sequence. There are 20 different amino
acids.
protein: the major macromolecular constituent of cells. A linear polymer of
amino acids linked together by peptide bonds in a specific
sequence.
polypeptide backbone: Repeating sequence of atoms along the core of the polypeptide
chain
side chains: The part of an amino acid that differs between amino acid types.
The side chains give each type of amino acid its unique physical
and chemical properties.
- side chains can be nonpolar, uncharged polar, acidic or basic
- many weak bonds acting in parallel can hold two regions of a polypeptide chain tightly
together.
- the single bonds between the amino acids allow for rotation (psi and phi rotation)
- basic side chains: at neutral pH they will be positively charged. (histidine is only partly
neutral, very weak)
- acidic: at neutral pH they are negatively charged.
- nonpolar side chains tend to cluster in the interior of the molecule (hydrophobic forces),
polar groups tend to arrange themselves near the outside.
Life hinges on the chemical properties of water. H2O is highly polar because the O is strongly
attractive for electrons, which gives it a negative charge.
hydrogen bond: noncovalent bond in which an electropositive hydrogen atom is partially
shared by two electronegative atoms.
- Each water molecule can form these bonds through it’s two H atoms to two other water
molecules, which forms a network in which bonds are continually broken and formed
hydrophilic: dissolving readily in water (water-loving)
- Alcohols, most proteins, sugars
Hydrophobic: not dissolving readily in water (water-fearing)
- Hydrocarbons
There are three types of noncovalent bonds: electrostatic attractions, hydrogen bonds and van
der Waals attractions; and a fourth factor which pushes molecules together, the hydrophobic
force. Their energies working together can create a strong force, individually the forces are
weak.
electrostatic attractions: a noncovalent, ionic bond between two molecules carrying groups
of opposite charge
Van der Waals attractions: type of (individually weak) noncovalent bond that is formed at
close range between nonpolar atoms
Hydrophobic force: force exerted by the hydrogen-bonded network of water molecules
that brings two nonpolar surfaces together by excluding water
between them. (also happens in RNA and DNA)
When a polar molecule becomes surrounded by water, the proton will be attracted to the partial
negative charge on the O atom creating a hydronium ion.
proton: Positively charged subatomic particle that forms part of an atomic
nucleus. Hydrogen has a nucleus composed of a single proton
hydronium ion: Water molecule associated with an additional proton. The form generally
taken by protons in aqueous solution.
acids: A proton donor. Substance that releases protons when dissolved in water,
forming hydronium ions and lowering the pH.
- characterized as strong or weak, depending on how readily they give up protons
- the concentration of the H3O+ in cells has to be regulated closely because of how readily
they give up protons.
base: A substance that can reduce the number of protons in solution, either by
accepting H+ ions directly or by releasing OH- ions which then combine
with H+ to form H2O
buffers: Solution of weak acid or weak base that resists the pH change that would
otherwise occur when small quantities of acid or base are added.
- weak bases are important in living cells because they have a weak tendency to
reversibly accept a proton from water.
,chemical group: Certain combinations of atoms, such as methyl (-CH3), hydroxyl (-OH_),
carboxyl (-COOH), carbonyl (-C=O), phosphate (-PO32-), sulfhydryl (-SH) and amino (-NH2), that
have distinct chemical and physical properties and influence the behavior of the molecule in
which the group occurs.
macromolecules: Polymers constructed of long chains of covalently linked, small organic
(carbon containing) molecules. The principal building blocks from which a
cell is constructed and the components that confer the most distinctive
properties of living things.
- example: proteins, they act as enzymes, structural components, molecular motors
- each polymer grows by the addition of a monomer onto the end of a growing chain with
a condensation reaction.
- the shape of macromolecules are highly constrained because of the many weak
noncovalent bonds that form between different parts of the same molecule. → gives
enzymes their specific task because of their unique shape. (determined by the sequence
of the monomers)
IN BOOK: Panel 2-3, 2-4, 2-5, 2-6
monosaccharides: either contain an aldehyde (H-C=O) group (aldoses) or a ketone (-C=O)
group (ketoses)
- in aqueous solution aldehyde or ketone group reacts with a hydroxyl group of the same
molecule and forms a ring.
- beta hydroxyl: upwards, alpha hydroxyl: downwards
disaccharides: the carbon that carries the aldehyde or ketone group can react with any
hydroxyl group on a second sugar molecule
- maltose (glucose + glucose), lactose (galactose + glucose), sucrose (glucose + fructose)
polysaccharides: name for long chains, short chains are called oligosaccharides.
fatty acids: unsaturated (double bond, liquid) and saturated (no double bond, solid)
- stored as an energy reserve, linked to glycerol
- phospholipides are the major constituents of cell membranes (hydrophilic head and
hydrophobic tail)
bases: pyrimidine (C,U,T) or purine (A,G)
nucleoside: sugar + base
nucleotide: sugar + base + phosphate (<-- makes it negatively charged)
- buildingblocks for DNA
, Chapter 3: Proteins
Proteins, apart from building blocks, execute the majority of the cell’s functions:
- enzymes → provide the intricate molecular surfaces inside a cell that catalyze its many
chemical reactions.
- in the plasma membrane → form channels and pumps that control the passage of small
molecules into and out of the cell.
- providing information for mechanisms in and outside the cell
- antibodies, toxins, hormones, antifreeze molecules, elastic fibers, ropes or sources of
luminescence
The shape of a protein is specified by its amino acid sequence. There are 20 different amino
acids.
protein: the major macromolecular constituent of cells. A linear polymer of
amino acids linked together by peptide bonds in a specific
sequence.
polypeptide backbone: Repeating sequence of atoms along the core of the polypeptide
chain
side chains: The part of an amino acid that differs between amino acid types.
The side chains give each type of amino acid its unique physical
and chemical properties.
- side chains can be nonpolar, uncharged polar, acidic or basic
- many weak bonds acting in parallel can hold two regions of a polypeptide chain tightly
together.
- the single bonds between the amino acids allow for rotation (psi and phi rotation)
- basic side chains: at neutral pH they will be positively charged. (histidine is only partly
neutral, very weak)
- acidic: at neutral pH they are negatively charged.
- nonpolar side chains tend to cluster in the interior of the molecule (hydrophobic forces),
polar groups tend to arrange themselves near the outside.
