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Biology 2B03 > Week 2 + Module 1 > Flashcards

Week 2 + Module 1 Flashcards

(53 cards)

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1
Q

Protein functions

A

1) Cell structure
2) Sensors for environmental changes
3) Enzymes/catalysts
4) Gene regulation
5) Signaling between cells
6) Cell transport

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2
Q

Immunoglobin proteins

A

recognize viruses/antigens and removes them

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3
Q

Adenylate kinase

A

Defines substrate binding domain vs activity domain

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4
Q

Primary protein structures

A
  • linear array of amino acids (residues)
  • joined by peptide bonds

N-terminus = amino end

C-terminus = Carboxyl end
- next aminos added to carboxyl end

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5
Q

Condensation/hydrolysis

joining/breaking amino acids

A
  • proteins are dehydrated polymers made of amino acids bound by peptide bonds

Condensation
- polymerize amino acids and release water

Hydrolysis
- breaks polymers by adding water

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6
Q

What part of protein structure affects function

A

Properties of side chains (r groups) affect structure and function

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7
Q

How are amino acids classified

A

Solubility (in water) or polarity

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8
Q

Protein solubility

means a protein can…

A

Physical property of a molecule that can transiently bond with water through hydrogen bonding

Is thermodynamically favourable

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9
Q

Soluble proteins

A
  • polar
  • hydrophilic
  • exterior of proteins
  • soluble in aq
  • hydrogen bond with water
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10
Q

Insoluble proteins

A
  • nonpolar
  • hydrophobic
  • core of proteins
  • doesn’t h-bond with water so water will bond with itself
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11
Q

Hydrophobic amino acids

A

Aromatic (aromatic rings)
1. Phenylalanine
2. Tyrosine*
3. Tryptophan

Aliphatic (hydrocarbon chains)
1. Alanine
2. Valine
3. Isoleucine
4. Leucine
5. Methionine

*tyrosine both phobe/phile bc of OH- on aromatic ring

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12
Q

Hydrophilic amino acids - charged

A

Basic / (+) charge
1) Lysine
2) Arginine
NH3+

Acidic / (-) charge
1) Aspartic acid
2) Glutamic acid
COO-

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13
Q

Hydrophilic amino acids - uncharged

A

Polar / uncharged
1) Serine
2) Threonine
-OH

3) Asparagine
4) Glutamine
-NH2

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14
Q

Special amino acids

A

Cysteine
- disulphide bridges

Glycine
- small and allows for chain bends

Proline
- forces kink in chain

Histidine
- pH dependent charge

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15
Q

Peptide bonds

A
  • hold amino acids together
  • formed in condensation reaction
  • between N of amino and O of COO-
  • occurs in the ribosome
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16
Q

Primary structure

A
  • linear arrangement of amino acids
  • sequence is determined by nucleotide sequence of encoding gene

20^n possible sequences

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17
Q

Chemical interactions in amino acids

A
  • statistical coil when stable interactions

Ionic bonds
- btwn +/- ions
- ex. Coo- and NH3+

Hydrogen bonds
- btwn partially + charged atom and unpaired electrons from another atom

Hydrophobic effects
- aggregation of nonpolar molecules in aq to reduce interactions with water
- form a micelle
- higher entropy

Van der Waals
- aka LDFs
- transient dipole between noncovalent atoms induces in another
- strong in Tokay gecko feet where there are many

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18
Q

Secondary protein structure

A
  • local chemical interactions forming motifs
  • distinct, conserved, and geometric
  • associated with particular functions
  • spiral alpha helices
  • planar beta folded sheets
  • turns/loops
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19
Q

Alpha helices

A
  • carbonyl oxygen h-bonds to H of amide

C=O—H-N

  • independent of specific R groups
  • cylinder with side chains pointing out
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20
Q

Beta pleated sheets

A
  • laterally packed strands
  • H bonds between amide and carboxyl OR amino groups
  • strand length varies
  • parallel or antiparallel
  • independent of specific R groups
  • side chains point up and down
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21
Q

Hinges, turns, loops

A

B turn
- aminos 1 and 4 connected through hydrogen bond

  • proline pos 2
  • glycine pos 3
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22
Q

Coiled-coil

Study These Flashcards
A
  • 2 alpha helices
  • amphipathic
  • leu in position 4
23
Q

Zinc finger

Study These Flashcards
A
  • 3 variants (C2H2, C4, C6) c=cystine, h=histidine
  • 1 alpha helix and 2 beta strands held by zinc atom
24
Q

Beta barrel

Study These Flashcards
A
  • last and first beta strands form a hydrogen bond
  • forms channel across a hydrophobic membrane
25
Helix-loop-helix motif
- 2 alpha helices joined by a loop - loop can bind ca2+ using carboxyl of asp or glu
26
Tertiary structure
- monomeric protein that's folded - can fold independently
27
2 types of protein domains
1. Functional domains - regions that perform a certain activity 2. Structural domains - recognizable shape or characteristic
28
Describe the Src protein tertiary structure
2 functional - small kinase domain -> ATP binding - large kinase domain -> alpha helix rich 2 structural - SH2 - SH3
29
Quaternary structure
- subunits in a multimeric protein - composing of more than one amino acid chain (polypeptides) dimer = 2 polypeps / 2 subunits trimer = 3 polypep homodimer = 2 identical polypep heterodimer = 2 different polypep
30
Describe the haemaglutinin protein quaternary structure
3 subunits = 1 protein
31
Intrinsically unstructured proteins
- lack structure as tertiary "structures" - need to interact with a substrate to form a stable conformation ex. zinc finger
32
Post-translational modifications - what are they?
- modification of amino side chains after synthesis - happens to pretty much every protein in a cell
33
Post-translational modifications - acetylation
- add acetyl - protects against intracellular protease (protein) degradation - regulates gene expression by altering protein/DNA interaction REVERSIBLE
34
Post-translational modifications - methylation
- add methyl - regulates gene expression by weakening histone/DNA association REVERSIBLE
35
Post-translational modifications - phosphorylation
- transfer phosphate group from ATP to -OH using kinases -OH of serine, tyrosine, threonine - removal of phosphate group by phosphatase - activate or deactivate proteins by changing shape or ability to bind
36
Post-translational modifications - hydroxylation or carboxylation
hydroxylation - add OH - needed for functional collagen - catalysis enzyme needs vit C, none = scurvy = collagen issues carboxylation - add COO-
37
Post-translational modifications - glycosylation and lipidation
glycosylation - addition of carbs - sugars added to OH groups of serine and threonine in golgi lipidation - addition of lipid molecules - anchors protein to hydrophobic membranes
38
Chaperones - function
- assist folding
39
Native conformation experiment
- most thermodynamically stable conformation - spontaneous, reversible, and unique - not technically static, just in stable conformation most of the time - random folding till it gets to stable state In-vitro - denatured ribonuclease A and broke H bonds and disulphide bridges - added dialysis to remove denaturants - automatically / spontaneously refolded
40
Villin protein folding
- 3 alpha helix (36 residue) headpiece stabilized by interactions in the cytosol - hydrophobic core made of 3 phenylalanines
41
Diseases related to misfolding
Hereditary - Cystic fibrosis - Emphysema - Alzheimer's - Tay Sachs Prion-based - Creutzfeld-Jacob - Mad Cow - Fatal familial insomnia
42
Sickle cell anemia
Normal hemoglobin - 2 alpha subunits - 2 beta subunits = tetramer Sickle cell anemia - B-globin glutamate to valine - Glu6Val - aggregate and build up - block capillaries - cant carry O2 to all organs
43
Genetic amyloid-related disease
- single changes in nucleotides change amino acid sequence and lead to fibril formation Fibrils are aggregations of misfolded protein
44
Unfolded protein response
- unfolded proteins accumulate in the ER lumen - get bound by GRP78 - activate stress sensors ATF6/PERK/IRE1 -> induce UPR !!! - stop translation - activate transcription factors for genes promoting ER homeostasis & cell survival -> if prolonged, transcribe apoptosis (death) genes
45
What is a prion (2 words), what is another name for them
infectious protein - term coined by stanley prusiner spongiform encephalopathies
46
What are prions? How are they acquired?
- fatal transmissible neurodegenerative diseases acquisition - spontaneous - heritable - infectious - lengthy incubation period with non-conventional immune response
47
Prion disease features
- rapidly progressive dementia - ataxia and incoordination - movement disorders - visual problems - akinetic mutism
48
Prion example - PrP(Sc) vs. PrR(c)
PrR(c) -> normal protein - Alpha helices - Soluble - PK/protease sensitive - No aggregation PrP(Sc) -> prion - Beta sheets - Insoluble - PK resistant - Aggregation - membrane anchored glycoprotein - not transmembrane so they can go infect other cells - elevated levels in neuronal synaptic membranes
49
Prion mode of infecting others
1. nucleation of healthy unfolded proteins 2. formation of amyloid fibrils 3. break into more seeds
50
Human prion protein gene (PRNP)
- located on short / p arm of chromosome 20 - mutations in this gene for people with inherited prion disease - leads to conformational change in protein to become prionic
51
PrP(Sc) to PrR(c) conversion
- PrR(c) synthesized, folded, glycosylated in ER - GPI anchor is a glycolipid that is attached to the c-terminus - done post-translationally - 2 fatty acids anchor it into membrane - PrP(Sc) accumulates near PrR(c) with potential for conversion can occur in endosomes or lysosomes as well
52
Prion effect on the cell
- cell surface signals of PrR(c) are decreased in prion infected cells - most PrP(Sc) in recycling endosomes (by edge) - impairs Golgi trafficking
53
Are prions always bad - yeast
- yeast cells evolved epigenetic prion conversion for fast on-demand adaptations to stressful situations - Mod5 prion lets them be fungicide resistant

Biology 2B03 (12 decks)

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