Chapters 4-6? Flashcards
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
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
3
Q
Proteasomes
A
- large protein “containers”(trash cans) where inside other proteins are degraded
4
Q
Kinesin
A
- motor protein
- transports cellular cargo like organelles
5
Q
A
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
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
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
9
Q
Interactions stabilizing secondary structure
A
- backbone of hydrogen bonds
10
Q
A
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)
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
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
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
15
Q
Intrinsically disordered(unstructured) regions
A
- have many functions
- binding
- tethering domains within a protein
- tethering interacting proteins
16
Q
protein assemblies
A
- Ebola and Zika
17
Q
Protein machines
A
- chaperones, motor proteins, ribsomes
18
Q
A
19
Q
A
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
- catalyze similar rxns(do similar chemistry)
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
5\*targeting an enzyme to stop cancer
* 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
5\*Targeting Abl: Kinases Bind and Hydrolyze ATP
* 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
5\*Gleevec: the miracle cancer drug
* 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
5\*Nilotinib
* Second generation CML Drug
* developed using the structure of Gleevec bound to Abl kinase domain
29
Feedback inhibition for regulation of enzymes is essential
* BCR-Abl always "on"
* leads to cancer b/c of unregulated cell proliferation
* negative or positive
30
Enzymes can be regulated Allosterically
* Allosteric regulation: regulatory molecule binds to site other than enzyme active site, induces conformational change
* non-competitive inhibition
* can be negative or positive
31
Proteins can be regulated via covalent modifications
* hundreds!
* EX:
* phosphorylation
* acetylation
* ubiqutination
* methylation
32
DNA structure: the race
* 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
Franklin's X-ray photo 51 solved structure of DNA
* 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
Watson's Book: "The Double Helix"
* 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
36
DNA replication is semiconservative
* occurs in nucleus, during interphase of cell cycle
37
DNA synthesis begins at replication origins
* Replication origins are:
* 100 bp: simple organisms
* variable length in humans
* A-T rich
* Bacteria: 1 replication origin
* Humans:~10,000
38
DNA Helicases and Single-stranded Binding proteins at origins
* DNA helicase uses ATP hydrolysis to unwind helix
* Single-stranded binding proteins(SSB) bind to unwound region
* Essential to replication initiation
39
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
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
41
DNA polymerase adds nucleotides to the 3' end
* DNA polymerase helper proteins:
* sliding clamp keeps DNA polymerase on strand
* clamp ladder helps sliding clamp assemble
* has proofreading activity
42
Replication forks are assymmetrical: leading and lagging strand
* Leading strand
* template is 3'-5'
* continuously synthesized
* Lagging strand
* template is 5'-3'
* synthesized in small Okazaki fragments
43
RNA primers are needed for DNA synthesis
* Primase:
* RNA polymerase
* short complementary RNA primers
* needed to initiate replication
* needed for Okazaki fragments
44
Telomeres and Telomerase
* 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
Spontaneous DNA damage
* 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
Induced DNA damage
* 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
Xeroderma Pigmentosum
* 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
DNA repair
* Mismatch Repair
* repairs single-strand damage
* nuclease helps remove incorrect nucleotide
* DNA (repair) polymerase fills in space
* DNA ligase seals space
49
protein folding
* 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)
