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BIOCHEMISTRY 1 > 1-Proteins > Flashcards

1-Proteins Flashcards

1
Q

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

A

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

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2
Q

What is in blood serum other than RBCs and WBCs?

A

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

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3
Q

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

A
  1. 333
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4
Q

What’s the transcriptome? proteome?

A

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.

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5
Q

What is proteomics?

A

The study of proteins at the proteome level.

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6
Q

What is the function of clotting proteins?

A

Provide transient structure for wound healing

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7
Q

Describe covalent and non-covalent bonds:

A

-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.

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8
Q

What are hydrogen bonds?

A

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.

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9
Q

What are the 4 levels of protein organization?

A

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

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10
Q

What are the charges in amino acids at neutral pH?

A

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

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11
Q

What are the hydrophobic amino acids?

A

Valine, Leucine, Isoleucine, Methionine

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

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12
Q

What are the aromatic amino acids?

A

Phenylalanine, Tyrosine, Tryptophan

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13
Q

What are the basic amino acids?

A

Lysine, Arginine, histidine

*Depending on pH, side chains are basic or neutral

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14
Q

What is an important characteristic of cysteine?

A

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

This allows for sulfide bridges formation betwene two cysteines.

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15
Q

What are the polar amino acids?

A

Asparagine and Glutamine

*In the surface of proteins

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16
Q

What is special about serine and threonine?

A

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

17
Q

Which amino acids are acidic?

A

Aspartate and Glutamate

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

18
Q

Draw a peptide bond:

A

19
Q

Why does the peptide have a planar character?

A

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

20
Q

What are the phi and psi angles?

A

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

21
Q

What are the most common secondary structures of proteins?

A
  1. Alpha helix
  2. Beta sheet: parallel, andtiparallel
  3. Beta turn (or beta band)
22
Q

How are alpha helices formed?

A

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

23
Q

What is an alpha coil coil?

A

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

24
Q

What are B-pleated sheets?

A

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

25
Q

What is a Beta turn?

A
  • 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
26
Q

What are some characteristics of the tertiary structure of proteins?

A
  • Stabilized mainly by weak bonding
  • Side chains play major roles
  • Not yet completely predictable
27
Q

What are the main protein folding principles?

A
  • 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
28
Q

What is the Afinsen experiment?

A

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)
29
Q

What is the function of chaperone proteins in protein structure?

A

Chaperone proteins help proteins fold, BUT do not direct the process.

Ex. keep hydrophobic sections from sticking together

30
Q

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

A
  • Spongiform encephalopathies (Mad cow, scrapie, Creuzfeldt-Jacob), Alzeheimer’s disease
  • May arise due to mutations
31
Q

What are prions?

A

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.

32
Q

What is a protein domain?

A

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
33
Q

What are the domains in Scr protein-tyrosine kinase?

A
  • 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)
34
Q

What are protein motifs?

A
  • 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
35
Q

What are covalent protein crosslinks?

A

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

36
Q

How is X-ray chrystallography done?

A
  • Must make crystals of our protein
  • Hit with X-rays
  • Obtain diffraction pattern -> electron density map -> atomic map
37
Q

What is NMR spectroscopy?

A
  • 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
38
Q

What is the main advantage and disadvanatage about using NMR?

A

Advantage: structure of proteins in their “natural” state, in solution

Disadvantage: only good to about 100K MW (900 aa)

39
Q

How are quaternary structures stabilized?

A

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

BIOCHEMISTRY 1 (7 decks)

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