BCH100 Lecture 3-4

What joins amino acids together in proteins?

Peptide bonds, which are very stable covalent bonds.

Why do different amino acids contribute different properties to proteins?

Each amino acid has an R group with a unique size and chemical character.

Which parts of the peptide backbone form hydrogen bonds?

The C=O and N-H groups of peptide bonds.

Is the peptide-bond C=O group a hydrogen-bond donor or acceptor?

It is a hydrogen-bond acceptor.

Is the peptide-bond N-H group a hydrogen-bond donor or acceptor?

It is a hydrogen-bond donor.

What do disulfide bonds do in proteins?

They covalently connect two cysteines in the same protein or in different proteins.

What is primary protein structure?

The amino-acid sequence of a protein.

What is secondary protein structure?

Common local folding patterns of the polypeptide backbone, especially alpha helices and beta sheets.

What is tertiary protein structure?

The overall three-dimensional shape of a single polypeptide, including any prosthetic groups.

What is quaternary protein structure?

The interaction and arrangement of multiple polypeptide subunits.

Do all proteins have quaternary structure?

No. Only proteins containing multiple polypeptide chains have quaternary structure.

In which direction is a protein sequence read?

From the N-terminus to the C-terminus.

What is found at the N-terminus of a polypeptide?

A free amino group.

What is found at the C-terminus of a polypeptide?

A free carboxyl group.

Why is primary structure important?

It determines the higher-level structures and function of the protein.

How is a peptide bond formed?

The alpha-carboxyl group of one amino acid reacts with the alpha-amino group of another, releasing one H2O.

What type of reaction forms a peptide bond?

A condensation or dehydration reaction.

What is another name for a peptide bond?

An amide bond.

What is a dipeptide?

Two amino acids joined by a peptide bond.

What is a tripeptide?

Three amino acids joined by peptide bonds.

What is a polypeptide?

A chain containing many amino acids joined by peptide bonds.

How stable is an uncatalyzed peptide bond in water?

Its approximate lifetime is 1,000 years.

Why are peptide bonds planar?

Resonance gives the C-N bond partial double-bond character, preventing free rotation.

Which atoms lie in the peptide-bond plane?

The two neighboring alpha carbons, C=O, and N-H.

Why are nearly all peptide bonds in the trans configuration?

The trans configuration minimizes steric interference between neighboring R groups.

Which bonds provide flexibility to the peptide backbone?

The N-Cα bond, described by phi (Φ), and the Cα-C=O bond, described by psi (Ψ).

What does a Ramachandran plot show?

The allowed combinations of phi and psi bond angles for amino-acid residues.

Can amino-acid R groups participate in hydrogen bonding?

Yes. Polar R groups may act as hydrogen-bond donors or acceptors.

What primarily stabilizes protein secondary structure?

Hydrogen bonds between the N-H and C=O groups of peptide bonds.

What are the two major types of secondary structure?

The alpha helix and beta-pleated sheet.

What are the major features of an alpha helix?

It is right-handed, has 3.6 amino acids per turn, rises 5.4 Å per turn, and has R groups pointing outward.

How are hydrogen bonds arranged in an alpha helix?

A C=O group hydrogen-bonds with an N-H group four amino acids away.

How are alpha-helix hydrogen bonds oriented?

They are approximately parallel to the helical axis.

Why does proline disrupt an alpha helix?

Its rigid ring limits backbone movement, and its alpha-amino group is unavailable for normal hydrogen bonding.

What other factors can disrupt an alpha helix?

Repulsion between nearby charged or bulky R groups and competition from side-chain hydrogen-bond donors or acceptors.

What is a beta strand?

A relatively extended section of a polypeptide that participates in a beta sheet.

How is a beta sheet formed?

Beta strands lie side by side and form hydrogen bonds between backbone C=O and N-H groups.

Can the strands in a beta sheet come from different polypeptides?

Yes. They may come from the same polypeptide or different polypeptides.

Where do the R groups point in a beta sheet?

They alternate above and below the plane of the sheet.

How are hydrogen bonds oriented in a beta sheet?

They are approximately perpendicular to the direction of the beta strands.

What is an antiparallel beta sheet?

A beta sheet in which neighboring strands run in opposite N-to-C directions.

What is a parallel beta sheet?

A beta sheet in which neighboring strands run in the same N-to-C direction.

What is a mixed beta sheet?

A sheet containing both parallel and antiparallel strand arrangements.

What are the functions of protein loops and turns?

They reverse the direction of the polypeptide chain, often occur on the surface, and can be functionally regulated.

What primarily stabilizes tertiary protein structure?

Weak noncovalent interactions and covalent disulfide bonds.

Are disulfide bonds covalent?

Yes. They are covalent bonds between two cysteine side chains.

Why are disulfide bonds favored in the endoplasmic reticulum?

The ER has an oxidizing environment that promotes disulfide-bond formation.

How are hydrophobic and hydrophilic amino acids arranged in most globular proteins?

Hydrophobic residues are usually buried inside, while hydrophilic residues are exposed on the surface.

What is a protein domain?

A distinct structural and functional region that may appear in different proteins.

What is alpha-keratin?

A fibrous protein in hair, wool, nails, skin, and teeth containing a coiled coil of two alpha helices.

What stabilizes alpha-keratin?

Van der Waals interactions, ionic interactions, and disulfide bonds.

What is the basic structure of collagen?

A fibrous protein containing a coiled coil of three helices.

What sequence feature is common in collagen?

Every third amino acid is glycine, and glycine-proline-proline sequences occur frequently.

Why is glycine important in collagen?

Its very small side chain fits inside the tightly packed collagen triple helix.

What stabilizes quaternary protein structure?

Weak noncovalent interactions and sometimes disulfide bonds.

What is the subunit composition of adult hemoglobin?

Two alpha subunits and two beta subunits, written α2β2.

What does protein-renaturation evidence demonstrate?

A protein’s primary sequence contains the information needed to form its higher-level structure.

What is usually true about a protein’s native structure?

It is generally the thermodynamically most stable structure under appropriate conditions.

Why is urea used in protein-denaturation experiments?

It disrupts noncovalent interactions, including hydrogen bonding, causing the protein to unfold.

Why is beta-mercaptoethanol used in protein-denaturation experiments?

It reduces and breaks disulfide bonds.

What is a metamorphic protein?

A single amino-acid sequence that can fold into different stable structures with distinct functions.

What are the two major proposed pathways for protein folding?

Local secondary structures may form first, or hydrophobic residues may collapse first to form an internal core.

How can primary protein structure be determined?

Directly by Edman degradation or indirectly through gene sequencing.

How does X-ray crystallography determine protein structure?

X-ray diffraction patterns from protein crystals are analyzed computationally.

How does NMR determine protein structure?

It uses signals from atomic nuclei to determine their identities, environments, and distances in molecules in solution.

How does cryo-electron microscopy determine protein structure?

The sample is rapidly frozen, scanned with an electron beam, and reconstructed computationally.

Where is myoglobin found, and what is its function?

It is found in muscle cells and stores or carries oxygen in muscle.

Where is hemoglobin found, and what is its function?

It is found in red blood cells and carries oxygen from the lungs to other tissues.

What does fractional saturation (Y) measure?

The fraction of all protein oxygen-binding sites that are occupied by O2.

What does pO2 represent?

The partial pressure of oxygen.

What is the structure of myoglobin?

A single 153-amino-acid polypeptide composed mainly of alpha helices.

How many heme groups and oxygen molecules does myoglobin bind?

It contains one heme group and binds one O2 molecule.

How many oxygen molecules can one adult hemoglobin molecule bind?

Four, because each of its four subunits contains one heme group.

What is a prosthetic group?

A nonprotein component that binds tightly to a protein and is required for its function.

What metal ion is found in heme?

Ferrous iron, Fe2+.

What is the role of the proximal histidine in myoglobin and hemoglobin?

Its imidazole ring directly coordinates the Fe2+ ion in heme.

What is the role of the distal histidine?

It forms a hydrogen bond that stabilizes oxygen bound to heme.

What happens to Fe2+ when oxygen binds heme?

The iron moves into the plane of the heme group.

How do the oxygen-binding curves of myoglobin and hemoglobin differ?

Myoglobin has a hyperbolic, noncooperative curve; hemoglobin has a sigmoidal, cooperative curve.

Which has the higher oxygen affinity: myoglobin or hemoglobin?

Myoglobin has the higher oxygen affinity.

At a tissue pO2 of approximately 20 torr, in which direction does oxygen move?

From hemoglobin in the blood to myoglobin in muscle.

Why is hemoglobin’s cooperative behavior physiologically useful?

It allows hemoglobin to load oxygen in the lungs and release a large amount in tissues.

When pO2 falls from 100 to 20 torr, approximately how much oxygen do myoglobin and hemoglobin release?

Myoglobin releases about 7%, while hemoglobin releases about 66%.

What are the T and R states of hemoglobin?

The T state is the low-affinity deoxygenated state; the R state is the high-affinity oxygenated state.

How do the central cavities of T-state and R-state hemoglobin compare?

The T state has a larger central cavity, while the R state has a smaller central cavity.

Which molecules stabilize the T state of hemoglobin?

H+, CO2, and 2,3-BPG.

Why is binding the first oxygen to hemoglobin difficult?

Most deoxygenated hemoglobin subunits begin in the low-affinity T state.

How does oxygen binding produce cooperativity in hemoglobin?

Binding of O2 to one subunit promotes the T-to-R transition in the other subunits, increasing their oxygen affinity.

By approximately how much can cooperativity increase hemoglobin’s oxygen affinity?

Up to approximately 20-fold.

What is an allosteric regulator?

A molecule that changes protein activity by binding somewhere other than the protein’s primary ligand-binding site.

How does 2,3-BPG affect hemoglobin?

It binds and stabilizes the T state, decreases oxygen affinity, and promotes oxygen release.

Why is the effect of 2,3-BPG considered allosteric?

It regulates oxygen binding without binding to the oxygen-binding site.

Why is 2,3-BPG physiologically important?

It allows hemoglobin to release much more oxygen as blood travels from the lungs to tissues.

What is the Bohr effect?

H+ and CO2 decrease hemoglobin’s oxygen affinity and promote oxygen release in metabolically active tissues.

How does increased H+ affect hemoglobin?

H+ binds hemoglobin, stabilizes the T state, and promotes O2 release.

Why does low pH promote oxygen delivery to active tissues?

Active tissues produce acid during metabolism; the increased H+ stabilizes T-state hemoglobin and causes it to release O2.

How does CO2 affect hemoglobin?

CO2 forms carbamate groups on hemoglobin, stabilizing the T state and promoting oxygen release.

What happens to hemoglobin in the lungs?

At higher pH, hemoglobin binds O2 and releases H+ and CO2.

What happens to hemoglobin in active muscle?

At lower pH, hemoglobin releases O2 and binds H+ and CO2.

In what form is most CO2 transported in the blood?

As bicarbonate, HCO3−.