Bio E1 redo

What are proteins structurally?

Linear polymers made from amino acid monomers linked by peptide bonds.

How do amino acids give proteins functional diversity?

Their side chains contain different functional groups, which determine properties such as charge, polarity, binding, and chemical reactivity.

How do proteins form complex cellular structures?

Proteins interact with other proteins, nucleic acids, lipids, and small molecules to form larger functional assemblies.

What flexibility can proteins be?

Rigid or Flexible

What Charge DNA have?

Negative

What type of amino acids can interact with DNA

Positive amino acids can interact with negative charge DNA

What can binding induce in a conformationally flexible protein?

A conformational change.

What is an α-amino acid made of?

An α carbon linked to an amino group, a carboxylic acid group, a hydrogen atom, and a distinctive R group (side chain).

What makes an amino acid chiral?

Four different groups are bonded to the α carbon.

What are the two mirror-image forms of chiral amino acids?

L and D isomers

Which amino acid isomers are found in proteins?

Only L isomers.

In what form do free amino acids exist at neutral pH?

As zwitterions, with a charged amino group (NH₃⁺) and carboxyl group (COO⁻).

What are the four groups of amino acid side chains?

Hydrophobic, polar, positively charged, and negatively charged.

Which amino acids are hydrophobic/nonpolar?

Gly, Ala, Pro, Val, Leu, Ile, Met, Phe, and Trp.

What are the properties of hydrophobic amino acid side chains?

They are nonpolar, vary in shape and size, do not interact well with water, and pack together to form compact structures.

What is the bulkiest hydrophobic amino acid?

Tryptophan; contains a indole in its side chain

What potential does tryptophan have?

Potential for hydrogen bonding.

Which amino acids are polar?

Ser, Thr, Tyr, Asn, Gln, Cys, and His.

Why are polar amino acids hydrophilic and more reactive than hydrophobic amino acids?

Their side chains make them hydrophilic and more reactive.

What functional group does cysteine contain?

A sulfhydryl (thiol, –SH) group.

What can pairs of cysteine –SH groups form?

Disulfide bonds.

Where is histidine often found?

In enzyme active sites.

Why is histidine important in enzyme active sites?

Its pKₐ is near 6, close to physiological pH, allowing it to accept or donate protons in a pH range starting at 6.

What does “positively charged” mean for amino acids?

They are likely to have a positive charge at physiological pH.

How do positively charged amino acids interact with water?

They are highly hydrophilic.

Which group does arginine contain?

A guanidinium group.

Which amino acids are positively charged at physiological pH?

Lysine and arginine.

What does “negatively charged” mean for amino acids?

They are likely to have a negative charge at physiological pH.

What functional group do negatively charged amino acids have?

A carboxylate functional group.

When are aspartic acid and glutamic acid protonated?

Only at a highly acidic pH.

Which amino acids are negatively charged at physiological pH?

Aspartate and glutamate.

How is a peptide bond (amide bond) formed?

By linking the α-carboxyl group of one amino acid to the α-amino group of another amino acid.

What is a residue in a polypeptide?

Each amino acid unit in a polypeptide.

What gives a polypeptide chain directionality?

It has an α-amino group at the N-terminal and an α-carboxyl group at the C-terminal.

What is the N-terminus

Has the free amino group; is always first

What is the C-terminus?

Has the free carboxyl group; is always last

What does a polypeptide consist of?

A main chain (backbone) and distinctive amino acid side chains (R-groups).

What hydrogen-bonding potential does the polypeptide backbone have?

It contains carbonyl (C=O) groups and NH groups.

What role do carbonyl (C=O) groups have in hydrogen bonding?

They are hydrogen-bond acceptors.

What role do NH groups have in hydrogen bonding?

They are hydrogen-bond donors.

What is the shape of a peptide bond?

It is essentially planar; a lot of flexibility

What are two linked cysteines called?

Cystine.

What type of bonds are disulfide bonds?

Cross-links.

How are disulfide bonds formed?

By oxidation of a pair of cysteine residues.

Why was the amino acid sequence of insulin a landmark in biochemistry?

It showed that a protein has a precisely defined amino acid sequence linked by peptide bonds.

What is secondary structure?

A three-dimensional structure formed by hydrogen bonds between main-chain N–H and C=O groups of nearby amino acids in the linear sequence.

What are examples of secondary structure?

α helices, β pleated sheets, and turns.

What is the structure of an α helix?

A tightly coiled, rodlike structure, with R groups extending outwards in a helical array

Which backbone groups form hydrogen bonds in an α helix?

All backbone CO and NH groups, except those near the ends of the α helix.

What is a β strand?

A common form of secondary structure.

How is a β pleated sheet formed?

By adjacent β strands.

What links β strands to form a β sheet?

Hydrogen bonds link two or more β strands to form a β sheet

How can adjacent strands run in a β sheet?

In the same direction (parallel), opposite directions (antiparallel), or a combination of directions (mixed).

How are amino acids hydrogen bonded in an antiparallel β sheet?

The NH group and CO group of each amino acid are hydrogen bonded to the CO group and NH group, respectively, of a partner on the adjacent chain.

How can polypeptide chains reverse direction?

By making reverse turns (β turns or hairpin turns) or loops.

What is the role of the β-sheet in the protein core?

It holds the protein together.

What can flexible loops at the top and bottom of a protein do?

Interact with other proteins and substrates.

What is tertiary structure?

The overall fold of a polypeptide chain.

What type of protein is myoglobin?

A highly compacted, globular, α-helical protein with a heme prosthetic group.

What amino acids are found almost exclusively in the interior of myoglobin?

Hydrophobic amino acids, except for two critical histidine residues.

What is a prosthetic group in a protein?

Added to the protein after the proton has been synthesized.

What type of residues are found in the protein interior?

Mostly nonpolar residues tightly packed together.

Where are hydrophobic amino acids found in membrane-embedded proteins?

In contact with the hydrophobic membrane.

Where are polar and charged amino acids found in membrane-embedded proteins?

Surrounding a water-filled channel

What are the multiple polypeptide chains in a protein called?

Subunits.

What is quaternary structure?

The spatial arrangement of subunits and the nature of their interactions.

How simple can quaternary structure be?

Two identical polypeptide chains, called a homodimer.

How complex can quaternary structure be?

Dozens of different polypeptide chains.

What are fibrous proteins?

Proteins that form long, extended structures with repeated sequences.

What are examples of fibrous proteins?

α-Keratin and collagen.

Where is collagen the main fibrous component?

Skin, bone, tendon, cartilage, and teeth.

How often does glycine appear in collagen?

At every third residue.

What sequence recurs frequently in collagen?

Glycine–proline–hydroxyproline.

What is hydroxyproline?

Proline that has been post-translationally modified.

What is the structure of collagen?

Three intertwined helical polypeptide strands that form a superhelical cable.

What stabilizes the collagen structure?

Hydrogen bonds between strands.

Which amino acid can fit into collagen’s crowded interior?

Glycine.

How many amino acid residues does ribonuclease contain?

124 amino acid residues.

How many disulfide bonds cross-link ribonuclease?

Four disulfide bonds.

What does BME do to ribonuclease?

It reduces disulfide bonds.

What does urea disrupt?

Hydrogen bonds and electrostatic interactions.

What determines a protein’s 3D structure?

Its amino acid sequence.

What steps reestablish correct disulfide pairing?

A trace of β-mercaptoethanol, followed by reoxidation.

What is meant by a cooperative transition during protein folding or unfolding?

Much of the protein transitions between folded and unfolded states in a coordinated manner

What neurological disorders are associated with protein misfolding and aggregation?

Alzheimer disease, Parkinson disease, and Huntington disease.

What are amyloidoses?

Normally soluble proteins are converted into insoluble fibrils rich in β sheets.

What are amyloid fibrils prone to do?

Aggregate, or cluster together.

How do abnormally folded protein aggregates promote further misfolding?

They serve as a nucleus that recruits more proteins to abnormally fold.

What follows abnormal protein folding and aggregation?

Neuronal cell death.

What are examples of prion diseases?

Creutzfeldt-Jakob disease, kuru, mad cow disease, and scrapie

What is the transmission agent in prion diseases?

A protein.

What happens to normal prion protein (PrP) in prion disease

It is converted to an altered conformation that aggregates.

What does PrPˢᶜ do?

It catalyzes the conversion of normal PrP into PrPˢᶜ, the disease-state protein.

What do abnormal β-sheets cause?

Conversion of more PrP into PrPˢᶜ.

What are posttranslational modifications?

Alterations in a protein’s structure after it is synthesized in the cell.

What does protein phosphorylation regulate?

Enzyme activity.

Which amino acid is important for disulfide bonds?

Cysteine.

Which amino acid is an imino acid?

Proline.

Which amino acid structure should you know?

Glycine.

Which amino acids are planar aromatic?

Phenylalanine, tryptophan, tyrosine, and histidine