Biochem (v2) condensed

Ch 1-3

What is biochemistry?

The chemistry of life; the study of the molecular nature of life processes.

What are the four major types of biomacromolecules?

Proteins, nucleic acids, carbohydrates, and lipids.

What is a monomer?

A single molecular unit that can combine with others to form a polymer.

What is a polymer?

A large molecule made of many repeating monomers.

What are the monomers of proteins?

Amino acids.

What are proteins made of?

Polypeptide chains of amino acids.

What are the monomers of nucleic acids?

Nucleotides.

What are nucleic acids made of?

Nucleotides.

What are the monomers of carbohydrates?

Monosaccharides.

What are polysaccharides made of?

Monosaccharides.

What components form many lipids?

Fatty acids and glycerol.

What is the general formula for many carbohydrates?

(CH2O)n.

In what forms can monosaccharides exist?

Linear or ring forms.

Why do fatty acids have poor solubility in water?

Their hydrocarbon regions are hydrophobic.

What functional group is found in alcohols?

Hydroxyl group (−OH).

What functional group is found in ethers?

Ether group (−O−).

What functional group is found in amines?

Amino group.

What functional group is found in thiols?

Sulfhydryl group (−SH).

What functional group is found in aldehydes and ketones?

Carbonyl group (C=O).

What functional group is found in carboxylic acids?

Carboxyl group (−COOH).

What functional group is found in esters?

Ester group.

What functional group is found in amides?

Amide group.

What important linkage is found between phosphates in molecules such as ATP?

Phosphoric acid anhydride linkage.

What end of a protein has the free amino group?

The N-terminus or amino-terminal end.

What end of a protein has the free carboxyl group?

The C-terminus or carboxyl-terminal end.

What is free at the 5′ end of a nucleic acid?

A phosphate group.

What is free at the 3′ end of a nucleic acid?

A hydroxyl group.

What does prokaryote mean?

Before the nucleus.

What defines a prokaryotic cell?

A single-celled organism without a definite membrane-bound nucleus.

What are examples of prokaryotes?

Bacteria and cyanobacteria.

What does eukaryote mean?

True nucleus.

What defines a eukaryotic cell?

A cell containing a well-defined nucleus surrounded by a nuclear membrane.

Can eukaryotes be single-celled or multicellular?

Both.

Do prokaryotes have a nucleus?

No definite nucleus.

Do eukaryotes have a nucleus?

Yes.

Do both prokaryotes and eukaryotes have cell membranes?

Yes.

Do prokaryotes have mitochondria?

No.

Do eukaryotes have mitochondria?

Yes.

Do both prokaryotes and eukaryotes have ribosomes?

Yes.

Do prokaryotes have endoplasmic reticulum?

No.

Do eukaryotes have endoplasmic reticulum?

Yes.

What is the function of the nucleus?

Contains the main genome and is the site of most DNA and RNA synthesis.

What is the function of mitochondria?

Site of energy-yielding oxidation reactions.

What is the function of chloroplasts?

Site of photosynthesis in green plants and algae.

What is the function of the rough endoplasmic reticulum?

Protein synthesis; it is studded with ribosomes.

What is the function of the Golgi apparatus?

Protein secretion and modification.

What is the function of lysosomes?

Contain hydrolytic enzymes.

What is the function of peroxisomes?

Contain enzymes involved in hydrogen peroxide metabolism.

What is the function of the cell membrane?

Separates cell contents from the outside environment.

What does ΔG represent?

Change in free energy.

What does ΔG < 0 mean?

Spontaneous/exergonic; energy is released.

What does ΔG = 0 mean?

Equilibrium.

What does ΔG > 0 mean?

Nonspontaneous/endergonic; energy is required.

Does spontaneous mean fast?

No.

Can a nonspontaneous reaction occur?

Yes, if energy is supplied.

What is the Gibbs free-energy equation?

ΔG = ΔH − TΔS.

What does ΔH represent?

Change in enthalpy or heat.

What does ΔS represent?

Change in entropy.

What does entropy measure?

Molecular disorder or randomness.

What does ΔH > 0 mean?

Endothermic; heat enters the system.

What does ΔH < 0 mean?

Exothermic; heat leaves the system.

What does ΔS > 0 mean?

The system becomes more disordered/random.

What does ΔS < 0 mean?

The system becomes less disordered/random.

What is an open system?

Exchanges both matter and energy.

What is a closed system?

Exchanges energy but not matter.

What is an isolated system?

Exchanges neither matter nor energy.

What type of system is a living cell?

An open system.

Is ATP hydrolysis spontaneous?

Yes; ΔG < 0.

Why is ATP hydrolysis favorable with respect to entropy?

The products are more disordered than the reactants, so ΔS > 0.

What type of molecule is water?

A polar covalent molecule.

What is a covalent bond?

A bond formed by sharing electrons.

What makes a covalent bond polar?

Electrons are shared unequally because of differences in electronegativity.

What is electronegativity?

The attraction a nucleus has for electrons.

Which atoms commonly pull electrons strongly in biomolecules?

Oxygen and nitrogen.

What is the most electronegative element?

Fluorine.

What is a dipole moment?

Separation of partial positive and partial negative charge.

What is a nonpolar bond?

A bond in which electrons are shared nearly equally.

Can a molecule contain polar bonds but be nonpolar overall?

Yes; its geometry can cause the dipoles to cancel, as in CO2.

Do noncovalent interactions involve sharing electrons?

No.

What major interactions stabilize biomolecules?

Ionic interactions, hydrogen bonds, dispersion forces, hydrophobic interactions, and disulfide bonds.

Which of these is covalent?

Disulfide bonds.

How do you recognize an ion-ion interaction?

Both interacting groups have full charges.

What is an ion-ion interaction?

Electrostatic attraction between oppositely charged species.

What is a salt bridge?

An ion-ion attraction between oppositely charged groups in close proximity.

How do you recognize an ion-dipole interaction?

One participant has a full charge and the other is a polar molecule.

What is an ion-dipole interaction?

An interaction between an ion and a permanent dipole.

What common molecule forms ion-dipole interactions with ions?

Water.

What is a hydration shell?

Water molecules surrounding an ion.

How do you recognize a dipole-dipole interaction?

Both molecules are neutral but polar.

What is a dipole-dipole interaction?

Attraction between partial positive and partial negative regions of polar molecules.

What is a hydrogen bond?

A special type of dipole interaction involving H attached to an electronegative atom and another electronegative atom with a lone pair.

How do you recognize a hydrogen bond?

Look for H bonded to O or N interacting with O or N.

What are common hydrogen-bonding atoms in biological molecules?

Oxygen and nitrogen.