1-Proteins

Question 1

What are these drugs for? Gleevec, herceptin, Celebrex, Prempro, Velcade

Answer 1

Gleevec: CML Herception: breast cancer Ab against Her2 Celebrex: Cox2 inhibitor, anti-inflammatory Prempro: estrogen & progesterone Velcade: melanoma

Question 2

What is in blood serum other than RBCs and WBCs?

Answer 2

Fibrinogen, antibodies, spectrin, albumin, LDP, complement proteins,

Question 3

How many protein-encoding genes are there in the human genome?

Answer 3

22. 333

Question 4

What’s the transcriptome? proteome?

Answer 4

Trnascriptome: complete set of RNAs transcribed from a genome, in a particular cell type. Proteome: complete set of proteins encoded by a genome, in a particular cell type.

Question 5

What is proteomics?

Answer 5

The study of proteins at the proteome level.

Question 6

What is the function of clotting proteins?

Answer 6

Provide transient structure for wound healing

Question 7

Describe covalent and non-covalent bonds:

Answer 7

-Covalent bond: “permanent” sharing of electrons. Substantial energy to break; loss of structure. -Non-covalent bonds: partial electron-sharing, involve excision of water. Transient, reversible, breakable.

Question 8

What are hydrogen bonds?

Answer 8

A type of non-covalent bond that plays a major role in protein structure. Transient, no electron-sharing. Difference in partial charge attracts them to one another. Covalently bonded to donor but not with acceptor. Bonds with: F, O, N.

Question 9

What are the 4 levels of protein organization?

Answer 9

1ry: aa sequence formed by covalent bonds between the amino acids 2ry: substructures formed by H-bonding between 3ry: 3D structure formed by 1ry, 2ry structure, and additional elements (loops, disulfide bonds) 4ry: association of multiple polypeptide subunits

Question 10

What are the charges in amino acids at neutral pH?

Answer 10

-Amino group is +, and carboxyl group is - -Side chains charge varies among amino acids

Question 11

What are the hydrophobic amino acids?

Answer 11

Valine, Leucine, Isoleucine, Methionine

*Bulky, aliphatic, hydrophobic chains, greasy amino acids in the interior of proteins

Question 12

What are the aromatic amino acids?

Answer 12

Phenylalanine, Tyrosine, Tryptophan

Question 13

What are the basic amino acids?

Answer 13

Lysine, Arginine, histidine

*Depending on pH, side chains are basic or neutral

Question 14

What is an important characteristic of cysteine?

Answer 14

Contain a sulfhydryl (SH) at the end of side chain.

This allows for sulfide bridges formation betwene two cysteines.

Question 15

What are the polar amino acids?

Answer 15

Asparagine and Glutamine

*In the surface of proteins

Question 16

What is special about serine and threonine?

Answer 16

Serine and threonin side chains end in hydroxyl group (OH)

*This makes them substrates for protein kinases, which attach a phosphate group to the OH

Question 17

Which amino acids are acidic?

Answer 17

Aspartate and Glutamate

*Their side chains are carboxylic acis. At neutral pH, they have a negative charge,

Question 18

Draw a peptide bond:

Answer 18

Question 19

Why does the peptide have a planar character?

Answer 19

Because tresonance or delocalization of electrons across the peptide bond gives it partial double bond character.

This prevents free rotation of the bond from occurring

Question 20

What are the phi and psi angles?

Answer 20

They are protein rotation sites at the C-C bond and N-C bond

Question 21

What are the most common secondary structures of proteins?

Answer 21

1. Alpha helix
2. Beta sheet: parallel, andtiparallel
3. Beta turn (or beta band)

Question 22

How are alpha helices formed?

Answer 22

H-bonds within peptide backbone (C=O —— H-N), N is the H-donor, and O is the H-bond acceptor

Defined by phi/psi angles

The residues that form the bonds of the helix are 4 aa apart

Proteins that pass through the plasma membrane are alpha helical

Question 23

What is an alpha coil coil?

Answer 23

It is a protein made out of two alpha helical polypeptide chains coiled around each other. Chains are held together by non-covalent interactions. Ex. Keratin in hair and nails

Question 24

What are B-pleated sheets?

Answer 24

Extended peptide chain extended & stabilized by H-bonds.

R-groups alternate with regard to which side of chain they protrude from.

Antiparallel: one chain goes from amino to carbonyl terminal, and 2nd one from carbonyl to amino terminal

Mixed: parallel and antiparallel strands combined

Question 25

What is a Beta turn?

Answer 25

- It's a protein structural element that allows polypeptide chain to reverse direction - On surface of proteins - Often sites of glycosylation - Important sites of immunological recognition - Somewhat predictable from the amino acid sequence

Question 26

What are some characteristics of the tertiary structure of proteins?

Answer 26

- Stabilized mainly by weak bonding - Side chains play major roles - Not yet completely predictable

Question 27

What are the main protein folding principles?

Answer 27

- Most non-structural proteins are globular (or have globular domains) - Hydrophobic (nonpolar) aa's in the interior, and polar residues in the surface - Charge pairs (electrostatic bonds) are strong only in the absence of water - Pi stack interactions (between aromatic side chains) give stability - Key positions have stringent side c hain requirements - Only 1 energy minimum (native conformation) - Folding (and unfolding) intermediates

Question 28

What is the Afinsen experiment?

Answer 28

Experiment tested ribonuclease ability to gain back its original 3D structure after having been unfolded with BME (disulfide bonds) and urea (H-bonds). - \> Enzymatic activity was indeed restored once urea and BME were removed - \> Proved that 1ry sequence does determine the folding of proteins (but not completely)

Question 29

What is the function of chaperone proteins in protein structure?

Answer 29

Chaperone proteins help proteins fold, BUT do not direct the process. Ex. keep hydrophobic sections from sticking together

Question 30

What are some protein misfolding diseases? how do they arise?

Answer 30

- Spongiform encephalopathies (Mad cow, scrapie, Creuzfeldt-Jacob), Alzeheimer's disease - May arise due to mutations

Question 31

What are prions?

Answer 31

Proteinaceous infection particles. Something causes a normal protein to change its structure forming a prion protein. This one acts as template converting additional molecules into prions. These form aggregates (amyloid plaques), which disrupt normal cellular function and cause disease.

Question 32

What is a protein domain?

Answer 32

A unit of a proteins 3D structure that: - fold autonomously - formed from 2ry structural elements connected by loops - has its own hydrophobic core - independent functional or structural property

Question 33

What are the domains in Scr protein-tyrosine kinase?

Answer 33

- Kinase, linker, SH3, SH4, anchor, tail - Src protein catlayzes the phosphorylation of substrate proteins on tyrosine - Active and incative form of the protein (active when tyrosine binds tail)

Question 34

What are protein motifs?

Answer 34

- Fuctional/structural unit within domains - Short aa sequences involved in what the domain does - Ex. DFG in Src protein-tyr kinase: coordinates Mg that bind to the phosphates of ATP - Ex. GXGXphiG: part of loop that binds phosphates of ATP

Question 35

What are covalent protein crosslinks?

Answer 35

Bonds that help stabilize proteins. Common in proteins in extracellular harsh environments, (reducing environemtn inside the cell). The S-S bonds are the most common. S-H groups are often at active sites of enzymes. S-S is more inert, but it can take part in a function. ex. Insulin has 3 S-S bonds, interchain & intrachain

Question 36

How is X-ray chrystallography done?

Answer 36

- Must make crystals of our protein - Hit with X-rays - Obtain diffraction pattern -\> electron density map -\> atomic map

Question 37

What is NMR spectroscopy?

Answer 37

- Methoud used to determine protein structure - A magnetic field is applied to a protein in solution (atomic nuclei is magnetic) - Manetic ield aligns the spin states of the nuclei - As nuclei relaxes to original state, they emit radiation that provides structural information

Question 38

What is the main advantage and disadvanatage about using NMR?

Answer 38

Advantage: structure of proteins in their "natural" state, in solution Disadvantage: only good to about 100K MW (900 aa)

Question 39

How are quaternary structures stabilized?

Answer 39

Multiprotein assemblies are primarily stabilized by weak interactions (2ry and 3ry structures)