Exam 1 Steele Lecture 1

Question 1

What is a genome?

Answer 1

The complete set of DNA sequences making up the genetic component of an organism

Question 2

What is a transcriptome?

Answer 2

The complete set of RNAs transcribed from a genome, in a particular cell type, etc.

Question 3

What is a proteome?

Answer 3

the complete set of proteins encoded by a genome, in a particular cell type, etc.

Question 4

What is genomics?

Answer 4

The determination of genome sequences and the study of the sequences.

Question 5

What is proteomics?

Answer 5

The study of proteins at the proteome level (cf. to study of individual proteins).

Question 6

What is a covalent bond?

Answer 6

“Permanent” sharing of electron pairs. Rupture of such a bond requires substantial energy and results in a loss of protein structure.

Question 7

What is a non-covalent bond?

Answer 7

P.artial sharing of electrons or the exclusion of water. Transient, reversible, easily broken

Question 8

Describe a hydrogen bond.

Answer 8

The hydrogen bond, a type of non-covalent bond that plays a major role in protein structure.

Question 9

Describe primary protein structure.

Answer 9

the amino acid sequence of the protein; formed by covalent bonds between the amino acids

Question 10

Describe protein secondary structure.

Answer 10

substructures formed by hydrogen bonding between amino acids

Question 11

Describe the tertiary structure of a protein.

Answer 11

the three-dimensional structure of the protein; formed by the combination of primary structure, secondary structure, and additional elements (e.g. loops and disulfide bonds)

Question 12

Describe the quaternary structure of a protein.

Answer 12

structure formed due to association of multiple polypeptide subunits

Question 13

Describe the protein alpha helix.

Answer 13

• dependent on H-bonds from the peptide backbone, not from the R groups
• the helix is defined by phi & psy angles
• hydrogen bonds that form an alpha helix are between the CO group and the NH group
• N is always the H bond donor; O is always the H bond acceptor
• the residues that form the bonds of the helix are four amino acids apart
• R groups protrude from outer surface of the helix so well situated to interact with other parts of the helix
• parts of proteins which pass through the plasma membrane (e.g. the transmembrane segments of receptors and ion channels) are alpha helical

Question 14

What is an alpha coiled coil?

Answer 14

• two alpha helical polypeptide chains are coiled around each other
• the chains are held together by non-covalent interactions.

Question 15

Descrbe the beta pleated sheet.

Answer 15

• R groups alternate with regard to which side of the polypeptide chain they protrude from
• peptide chain extended rather than coiled
• parallel sheet: H bonds between N and C atoms on adjacent strands, one AA to one AA
• anti-parallel sheet: each amino acid is H-bonded to two different amino acids on adjacent strand

Question 16

Describe a beta turn.

Answer 16

• Turns chain 180°. Minimum of two amino acids involved in turn.
• A beta turn is a protein structural element that allows a polypeptide chain to reverse direction.
• On surfaces of proteins
• Often sites of glycosylation
• Important sites of immunological recognition
• Somewhat predictable from the amino acid sequence

Question 17

Describe tertiary structure.

Answer 17

• Stabilized mainly by weak bonding
• Side chains play major roles
• Not yet completely predictable
• The 3-D structure of a protein can be destroyed without destroying the primary structure (i.e. the protein can be unfolded)

Question 18

What are the 8 protein folding principles?

Answer 18

• Most non-structural proteins are globular (or at least their domains are)
• Folding is driven by burying hydrophobic amino acids in a non-aqueous (non-polar) interior
• Surface residues that interact with water are polar/charged
• Charge pairs (electrostatic bonds) are strong only in the absence of water
• Pi stack interactions (between aromatic side chains) can contribute to stability
• Key positions in the structure have stringent side chain requirements
• It is generally held that there is only one energy minimum (the native conformation)
• There are folding (and unfolding) intermediates

Question 19

Is Tertiary structure entirely dictated by primary structure?

Answer 19

No, Christian Anfinsen carried out an experiment in which he showed that a protein (ribonuclease) could be unfolded by breaking its disulfide bonds with a reducing agent (beta-mercaptoethanol) and disrupting hydrogen bonds with urea. The resulting unfolded protein had no enzymatic activity. We the reducing agent and urea were removed, the protein refolded and enzymatic activity was restored.

Question 20

What are prions?

Answer 20

Prions are a particularly interesting example of a protein misfolding disease. The are called prions because they are proteinaceous infection particles. The precursor to a prion is a normal cellular protein. Something causes the normal protein to change its structure, forming a prion protein. The prion protein is a template for converting additional molecules of the normal protein into prions. The prion versions of the protein also form aggregates, called amyloid. It is the amyloid aggregates which disrupt normal cellular function and cause disease.

Question 21

What is a protein domain?

Answer 21

• fold autonomously
• formed from secondary structural elements connected by loops
• has its own hydrophobic core
• has an independent funcitonal or structural property
• 3D structure of a protein can be sub-divided into united called domans

Question 22

What are protein motifs?

Answer 22

• Protein motifs are functional/structural units which occur within domains. Examples of motifs in the Src protein-tyrosine kinase are:
• GXGXphyG - part of the loop that binds the phosphates of ATP
• DFG - coordinates the magnesiums that bind to the phosphates of ATP

Question 23

Describe convalent protein crosslinks.

Answer 23

• More common in proteins in extracellular environments due to the reducing environment inside the cell (oxidation is a bad thing inside a cell) and harsher conditions outside the cell (where S-S bonds help stabilize the protein
• S-H groups often found at active sites of enzymes; S-S more inert although it can very occasionally take part in a function
• The disulfide bond (S-S) is the most common covalent cross-link in proteins

Question 24

Why are disulfide bonds important in antibodies?

Answer 24

• S-S also important in antibodies; link heavy to light chain and heavy to heavy chain

Question 25

What is X-Ray crystallography?

Answer 25

• Can determine 3D protein structure
• Must make a uniformly repeated lattice of molecules (i.e. crystals)
• Obtain a diffraction pattern
• Fourier transformation of this pattern reveals an electron density map, that can be converted to an atomic map.

Question 26

What is NMR?

Answer 26

• Determine 3D structure of protein
• Apply magnetic field to protein in solution - works because atomic nuclei are magnetic
• Magnetic field aligns the spin states of the nuclei.
• As the nuclei relax back to their original states, they emit radiation which provides structural information.
• Advantage – structure of proteins in solution
• Disadvantage – only good to about 100K MW (about 900 amino acids; x-ray crystallography has been used to determine the structures of whole viruses, which can consist of more than 100 proteins)

Question 27

Describe protein quaternary structure.

Answer 27

• Multiprotein assemblies - many (most?) intracellular proteins form such assemblies
• Primarily stabilized by weak interactions (like secondary and tertiary structures)
• Can be homomeric or heteromeric
• Proteomic studies have revealed a large number of interactions between proteins, some of which are stable enough to be considered quaternary structures