Biochemistry

99 flashcards by MentisLibrary

The chemistry of living systems: water and buffers, the four classes of biomolecule, protein structure and enzyme kinetics, membranes, the central metabolic pathways, bioenergetics and gene expression.

Why is water polar, and what does that let it do?
Oxygen pulls the shared electrons harder than hydrogen and the molecule is bent, so one end carries a partial negative charge and the other a partial positive one. That lets water hydrogen bond with itself and dissolve ions and polar molecules.
How does hydrogen bonding explain water's high heat capacity and high heat of vaporization?
Warming or evaporating water requires breaking many hydrogen bonds, so a large amount of energy goes in before the temperature rises or a molecule escapes.
What is the hydrophobic effect and what drives it?
Nonpolar groups cluster together in water not because they attract each other strongly, but because doing so releases ordered water molecules from around them and raises the entropy of the water.
How does the bicarbonate buffer keep blood pH near 7.4?
Carbon dioxide and water interconvert with carbonic acid, which dissociates into hydrogen ion and bicarbonate. Added acid is mopped up by bicarbonate, and added base drives more carbon dioxide into solution.
Why does an ionizable group's pKa matter in biochemistry?
A group is roughly half ionized at its pKa, so comparing pKa with cellular pH tells you the charge that group carries in the cell.
Name the functional groups that appear repeatedly in biomolecules.
Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate and methyl.
Contrast condensation and hydrolysis reactions.
Condensation, also called dehydration synthesis, joins two monomers and releases a water molecule. Hydrolysis splits a bond using a water molecule.
Why does chirality matter so much in biochemistry?
Enzymes and receptors have chiral binding sites, so they discriminate between mirror-image forms. Proteins are built from L amino acids and most biological sugars are D.
Draw the general structure of an amino acid.
A central alpha carbon bonded to an amino group, a carboxyl group, a hydrogen, and a variable R group that distinguishes the twenty standard amino acids.
How are the twenty standard amino acid side chains classified?
Nonpolar and hydrophobic, polar and uncharged, acidic and negatively charged, and basic and positively charged.
What is a zwitterion and what is the isoelectric point?
At physiological pH an amino acid carries both a protonated amino group and a deprotonated carboxyl group, so it has a positive and a negative charge at once. The isoelectric point is the pH at which its net charge is zero.
How is a peptide bond formed and what is unusual about it?
A condensation reaction joins the carboxyl group of one amino acid to the amino group of the next, releasing water. The resulting amide bond has partial double bond character, so it is planar and cannot rotate.
What is a protein's primary structure and what determines it?
The linear sequence of amino acid residues, determined by the gene that encodes the protein.
Describe the alpha helix and the beta sheet.
Both are secondary structures held by hydrogen bonds between backbone atoms. The alpha helix is a right-handed coil with about 3.6 residues per turn, hydrogen bonded from each carbonyl to the amide four residues along. Beta sheets are extended strands hydrogen bonded side by side, parallel or antiparallel.
What interactions hold tertiary structure together?
Hydrophobic clustering of nonpolar side chains in the core, hydrogen bonds and ionic bonds between side chains, and covalent disulfide bridges between cysteines.
What is quaternary structure?
The assembly of two or more folded polypeptide subunits into one functional protein, held by the same non-covalent forces as tertiary structure.
What does denaturation do to a protein?
Heat, extreme pH, organic solvents or detergents disrupt the weak interactions holding the fold, so the protein unfolds and loses function while its primary sequence stays intact.
What did Anfinsen's ribonuclease experiment establish?
That denatured ribonuclease spontaneously refolds into its active form when the denaturant is removed, showing that the amino acid sequence contains all the information needed to specify the three-dimensional structure.
What do molecular chaperones do?
They bind exposed hydrophobic surfaces on unfolded or partly folded proteins, preventing incorrect aggregation and giving the chain repeated chances to reach its correct fold.
What is a prosthetic group?
A non-protein component permanently bound to a protein and required for its function.
Why is haemoglobin's oxygen binding curve sigmoidal?
Binding oxygen at one subunit shifts the whole tetramer toward a higher-affinity conformation, so the next oxygen binds more easily. That cooperativity produces an S-shaped curve.
What is the Bohr effect?
Falling pH and rising carbon dioxide reduce haemoglobin's oxygen affinity, so oxygen is released where metabolism is most active.
Why are glycine and proline structurally special?
Glycine's side chain is a single hydrogen, so it is small and unusually flexible. Proline's side chain loops back to the backbone nitrogen, which rigidifies the chain and disrupts helices.
How is collagen built and why does it need vitamin C?
Three polypeptides with a repeating glycine-X-Y pattern wind into a triple helix. Hydroxylation of proline residues stabilizes the helix, and the hydroxylating enzyme requires vitamin C.
What does an enzyme actually do to a reaction?
It lowers the activation energy by stabilizing the transition state, so a far larger fraction of collisions succeeds. It is not consumed and it does not change the equilibrium position or the free energy change.
Compare the lock and key model with induced fit.
Lock and key pictures a rigid active site precisely complementary to the substrate. Induced fit recognizes that binding changes the enzyme's shape, tightening around the substrate and aligning catalytic groups.
Write the Michaelis-Menten equation and define its terms.
$v_0 = \frac{V_{max}[S]}{K_m + [S]}$, where $v_0$ is the initial rate, $V_{max}$ the maximum rate at saturating substrate, and $K_m$ the substrate concentration giving half of $V_{max}$.
What does a low Km tell you about an enzyme?
That it reaches half its maximum rate at a low substrate concentration, so it binds substrate tightly and works efficiently when substrate is scarce.
What are kcat and catalytic efficiency?
kcat, the turnover number, is the number of substrate molecules one active site converts per second when saturated. Catalytic efficiency is $k_{cat}/K_m$ and rates the enzyme under physiological, non-saturating conditions.
How does a competitive inhibitor affect Km and Vmax?
It binds the active site and competes with substrate, so the apparent Km rises while Vmax is unchanged, because enough substrate can still outcompete it.