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Bio Core I > Chapters 4-6? > Flashcards

Chapters 4-6? Flashcards

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1
Q

Fucntions of Proteins

A
  • Enzymes(-ase)
  • Signaling
  • Receptors
  • Structural
  • Transport
  • Storage(fats stored in vessicles)
  • Proteins make up a majority of stuff in bacterial cells(15%)
    • the shape of a protein determines its function
    • proteins are built from amino acids joined by peptide bonds
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2
Q

ATP Synthase

A
  • uses mechanical energy to make ATP
  • proteins span plasma membrane
    • are in phospholipid bilayer so must have some hdrophobic residue
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3
Q

Proteasomes

A
  • large protein “containers”(trash cans) where inside other proteins are degraded
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4
Q

Kinesin

A
  • motor protein
  • transports cellular cargo like organelles
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5
Q
A
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6
Q

Proteins can denature(unfold) and renature(refold)

A
  • When a purified proteins isolated from cells is exposed to a high conc. of urea it denatures
    • when we remove the urea it renatures
  • proteins can also be denatured by change in pH/heat
  • Noncovalent bonds break first
  • there are specific conditions for refolding
    • chaperones help proteins fold correctly
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7
Q

Misfolded proteins can cause disease

A
  • if you consume misfolded proteins your proteins begin misfolding
  • mad cow disease
    • bovine spongiform encephalopathy
    • infectious neurodegenerative disease
  • Alzheimer’s Disease
    • plaques in brain amyloid beta protein aggregation
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8
Q

Interactions stabilizing tertiary structure

A
  • The final shape is determined by a variety of bonding interactions between the “side chains” on the amino acids
  • Hydrogen bonds
  • Ionic Bonds
  • Disulphide Bridges
  • Hydrophobic Interactions and Van der Waals
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9
Q

Interactions stabilizing secondary structure

A
  • backbone of hydrogen bonds
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10
Q
A
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11
Q

Secondary structure alpha helix

A
  • Hydrogen bonds backbone
  • N-H to C=O, N+4 same chain
  • 1 turn = .54nm; 3.6 residues
  • side chains point out and towards N-terminus
  • Handedness(right or left)
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12
Q

Secondary structure beta sheet

A
  • Hydrogen bonds backbone
  • N-H to C=O, adjacent chains
  • 1 pleat=0.7nm(distance btwn two R-groups on 1 side
  • Side chains alternate on either side of sheet
  • Parallel or antiparaller
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13
Q

Amphipathic motifs

A
  • coiled-coil
    • EX: Keratin(wool, horns)
  • transmembrane helical proteins
    • opioid receptor(brain)
    • binds opiates(morphine heroin)
    • mediates responses
      • ex: altering the perception of pain
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14
Q

Proteins are often composed of multiple domains

A
  • protein domain: any segment of a polypeptide that can fold independently into a compact, stable structure
    • have distinct functions
    • 40-350 amino acids
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15
Q

Intrinsically disordered(unstructured) regions

A
  • have many functions
    • binding
    • tethering domains within a protein
    • tethering interacting proteins
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16
Q

protein assemblies

A
  • Ebola and Zika
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17
Q

Protein machines

A
  • chaperones, motor proteins, ribsomes
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18
Q
A
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19
Q
A
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20
Q

proteins show ligand binding specificity

A
  • Binding site compatibility:
    • size
    • shape
    • specific interactions
      • optimal binding by ligand satisfies ALL available bonds
21
Q

Enzymes bind to one of more ligands

A
  • these are called substrates
  • EX: lysozyme
    • hydrolase
    • natural antibiotic
    • substrate: polysaccharide chains
      • cleaves via hydrolysis
22
Q

enzymes catalyze reactions in many ways

A
  • enzymes catalyze rxns by:
    • orients two substrate molecules
    • rearrange charges in substrate
    • changes shape of substrate
      • lysozyme does so to stabilize transition state
23
Q

related enzymes share similar properties

A
  • enzyme family members
    • catalyze similar rxns(do similar chemistry)
      • EX: all kinases catalyze addition of phosphate groups
    • have similar active/binding sites
      • EX: many hydrolases(like lysozyme) have same amino acids in their active site
24
Q

5*Drugs are often protein ligands

A
  • ligand: any substance bound by a protein
    • EX: small molecules, other proteins, etc.
  • Drug = Ligand
  • Rational drug design
    • using knowledge of a bimolecular target(often the protein structure) to design a drug
    • EX: Gleevec and nilotinib treat Chronic mylogenous leukemia(CML)
      • CML is cause by chromosomal mutation
25
Q

5*targeting an enzyme to stop cancer

A
  • Qs to ask:
    • what is the enzyme’s function?
    • how does the enzyme complete its function?
    • does the enzyme have a ligand?
  • We must solve crystal structure of protein target with or without ligand
  • Can exploit differences in targeting
    • EX: an electrostatic interaction vs a hydrogen bond in one position
  • can also exploit similarities
26
Q

5*Targeting Abl: Kinases Bind and Hydrolyze ATP

A
  • Novartis first used all available kinase structures
    • designed library of potential kinase inhibitors
  • High-throughput screening for inhibition of Bcr-Abl
    • structurally characterized Abl kinase domain with hits
  • Hits from screen(Pyrimidine A) were a precursor to the optimized hit of imatinib(Gleevec; Glivec)
27
Q

5*Gleevec: the miracle cancer drug

A
  • Before Gleevec: 5 year survival rate-30%
  • With Gleevec-89%
  • Was fastest approved drug by FDA
  • BUT, discover some patients are immune to it’s effects! How?
    • random mutations in the BCR-Abl protein
28
Q

5*Nilotinib

A
  • Second generation CML Drug
    • developed using the structure of Gleevec bound to Abl kinase domain
29
Q

Feedback inhibition for regulation of enzymes is essential

A
  • BCR-Abl always “on”
    • leads to cancer b/c of unregulated cell proliferation
      • negative or positive
30
Q

Enzymes can be regulated Allosterically

A
  • Allosteric regulation: regulatory molecule binds to site other than enzyme active site, induces conformational change
    • non-competitive inhibition
    • can be negative or positive
31
Q

Proteins can be regulated via covalent modifications

A
  • hundreds!
  • EX:
    • phosphorylation
    • acetylation
    • ubiqutination
    • methylation
32
Q

DNA structure: the race

A
  • Linus Pauling- Caltech-1951 proposes correct model for protein structure. Working on DNA.
  • James Watson and Francis Crick-Working at Cavendish Labs on a model
  • Maurice Wilkins-At King’s working on DNA, X-ray crystallographer
  • Rosalind Franklin-biophysicist, X-ray crystallographer-comes to King’s College to work
33
Q

Franklin’s X-ray photo 51 solved structure of DNA

A
  • Tension btwn Franklin and Wilkins
  • Anti-female culture at King’s college
    • EX: Franklin not allowed to eat in some areas
  • Diffraction pattern, shown without her knowledge to Watson and Crick
  • Leaves DNA work, collaborates with Arthur Krug on viruses
    • Succumbed to ovarian cancer in 1958
34
Q

Watson’s Book: “The Double Helix”

A
  • Published after Nobel
  • Initially rejected by publishers
  • Wilkins, Crick also objects
  • Portrayal of Rosalind Franklin
    • asserts Franklin was not smart enough to interpret her own data
    • her notes indicate she had correctly interpreted data
35
Q
A
36
Q

DNA replication is semiconservative

A
  • occurs in nucleus, during interphase of cell cycle
37
Q

DNA synthesis begins at replication origins

A
  • Replication origins are:
    • 100 bp: simple organisms
    • variable length in humans
    • A-T rich
  • Bacteria: 1 replication origin
  • Humans:~10,000
38
Q

DNA Helicases and Single-stranded Binding proteins at origins

A
  • DNA helicase uses ATP hydrolysis to unwind helix
  • Single-stranded binding proteins(SSB) bind to unwound region
    • Essential to replication initiation
39
Q

Consequences for DNA replication process if each of the following were missing:

1) DNA polymerase
2) DNA ligase
3) Sliding clamp
4) Nuclease
5) DNA helicase

A

1) DNA polymerase: interrupt DNA synthesis
2) DNA ligase: Okazaki fragments would not bind back together
3) Sliding clamp: might begin replication, but DNA polymerase will come off so you will have short DNA breaks(see more in lagging than leading b/c lagging uses sliding clamp more often)
4) Nuclease: affects removal of RNA primer and integration of new nucleotides, wouldn’t have a repair process
5) DNA helicase: couldn’t unwind double helix and process wouldn’t start

40
Q
A
41
Q

DNA polymerase adds nucleotides to the 3’ end

A
  • DNA polymerase helper proteins:
    • sliding clamp keeps DNA polymerase on strand
    • clamp ladder helps sliding clamp assemble
  • has proofreading activity
42
Q

Replication forks are assymmetrical: leading and lagging strand

A
  • Leading strand
    • template is 3’-5’
    • continuously synthesized
  • Lagging strand
    • template is 5’-3’
    • synthesized in small Okazaki fragments
43
Q

RNA primers are needed for DNA synthesis

A
  • Primase:
    • RNA polymerase
    • short complementary RNA primers
  • needed to initiate replication
  • needed for Okazaki fragments
44
Q

Telomeres and Telomerase

A
  • Telomeres shorten over time
    • every cell division it shortens by ~30-200bp
    • “Molecular clock”
      • max cell divisions per cell: 50-70 times
  • Telomerase is not made in most cells
    • exception: egg and sperm cells
  • Cancer cells switch on telomerase production
45
Q

Spontaneous DNA damage

A
  • Spontaneous: naturally occurring mutations.
    • EX: depurination
      • Loss of entire purine base(A or G)
        • Sugar-Pu bond less stable than sugar-Py
      • result: may stall replication
    • deamination(loss of amine,NH3)
      • removal of amino group/amine from base
        • deamination of cytosine
46
Q

Induced DNA damage

A
  • Induced: exposure to physical or chemical agent(mutagens) that interact with DNA to cause a mutation
    • EX: radiation, chemical mutagens
    • EX: UV radiation
      • causes pyrimidine dimers
      • Result: DNA polymerase stalls
47
Q

Xeroderma Pigmentosum

A
  • Inability to fix UV damage
  • Recessive genetic disorder where DNA repair enzyme mutated
  • Cannot repair normal DNA UV damage (thymine dimers)
  • Multiple skin cancers
  • “Children of the Night”
    • can’t be exposed to UV rays from sun
48
Q

DNA repair

A
  • Mismatch Repair
    • repairs single-strand damage
      • nuclease helps remove incorrect nucleotide
      • DNA (repair) polymerase fills in space
      • DNA ligase seals space
49
Q

protein folding

A
  • hydrophobic forces:
    • polar aa side chains tend to be displayed on the outside of the folded protein, so they can interact with water
    • nonpolar aa side chains are buried on the inside to form a highly packed hydrophobic core of atoms that are hidden from water
  • weak noncovalent bonds: H bonds, electrostatic attractions, Van der Waals attractions
    • rly weak, so a large number of them is required
  • H bonds can form btwn water and polar side chains on outside
  • final folded structure = conformation
    • goal: minimized G(free energy)

Bio Core I (8 decks)

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