Block 1 proteins

Question 1

Regulatory proteins (relation to folding)

Answer 1

EARLY Chaperones (heat shock) : help protein form its native state

• stopping protein aggregation during formation
• letting misfolded proteins refold
• carrying protein precursors

LATE Chaperonins (Hb60) : also help

• provide a good environment to fold and prevent aggregation

Question 2

Heat shock proteins (e.g., Hsp70, Hsp60, Hsp90) help protein folding

Answer 2

• Express anti-denaturing or misfolding proteins
• They’re expressed more under heat, hypoxic, and chemical stress conditions
  (I.e when protein needs protecting

Question 3

Protein’s native state

Answer 3

A thermodynamically favourable state where proteins can carry out their functions

Question 4

Amino Acid charge depends on pH

Answer 4

low ph –> +1NH, 0 COOH =+1
high ph –> 0NH, -1COOH = -1
physiological pH —> +1NH, -1COOH =0

Question 5

Non-polar (hydrophobic) AA’s “Pimps Know, Good Ass Lures In Very Wet Money From People”

Answer 5

Glycine, Alanine, Leucine, Isoleucine, Valine, Tryptophan, Methionine, Phenylalanine, Proline

Question 6

Polar (hydrophilic) AA’s “ Too Sad Cops Question Your Name”

Answer 6

Threonine, Serine, Cysteine, Glutamine, Tyrosine, Lysine

Question 7

Neutral AA’s “Sometimes Neutrality Causes Quagsire’s Yawn”

Answer 7

Serine, Lysine, Cysteine, Glutamine, Tyrosine

Question 8

Essential AA’s “PVT TIM HALL)

Answer 8

Proline, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine (5yrs and under) asparagine, Leucine, Lysine

Question 9

Proteins are made of

Answer 9

L AA’s

Question 10

Resonance in AA’s

Answer 10

lets amino residues share electrons and have partial double bonds to increase the binding strength

Question 11

primary protein structure traits

Answer 11

has covalent/peptide bonds that are rigid and planar

Question 12

Secondary protein structure traits

Answer 12

Can be either alpha helixes or beta sheets which have H-bonds
the first NH and last COOH have no H-bonds

Question 13

Alpha helix traits

Answer 13

intra-chain that’s parallel to the helix, has small/uncharged molecules, forms covalent bond cross linking, and has right handed helical chains
Proline and Glycine disrupt it

Question 14

Beta pleated sheet traits

Answer 14

Inter-chain that’s perpendicular, has serine, proline, alanine, and glycine

Question 15

Globular vs Fibrous proteins

Answer 15

Both are made from secondary protein structures

Globular proteins are made from a mix of alpha helix and beta sheets

Fibrous proteins only have one of the two (Only alpha or only beta)

Question 16

Thyrotropin-Releasing Hormone

Answer 16

Stimulates the anterior pituitary to release TSH

Question 17

Glutathione

Answer 17

1st defense against oxidative stress

Question 18

Enkephalins

Answer 18

opioid-like pain relief

Question 19

Oxytocin

Answer 19

Uterine contractions

Question 20

Bradykinin

Answer 20

inhibits inflammatory response

Question 21

Vasopressin

Answer 21

increase water reuptake in the kidneys

Question 22

Little gastrin

Answer 22

stimulates P cells to secrete more acid

Question 23

Substance P

Answer 23

Neurotransmitter

Question 24

Gramicidin

Answer 24

Antibiotic

Question 25

Simple proteins

Answer 25

only have aa units/residues (ribonuclease A, Albumin etc)

Question 26

Conjugated/complex proteins

Answer 26

have polypeptide chains + chemical components (lipoproteins, glycoproteins, flavorproteins)

Question 27

Tertiary protein structure traits

Answer 27

3-D Its hydrophobic chains are inward, and the hydrophilic are outward Usually spherical or globular and stabilized by its R-group interactions (salt-bridges) Has many and large protein domains (where it can do a function)

Question 28

Quaternary structure

Answer 28

it's an oligomeric protein i.e 2+ polypeptide chains involved (if the chains are the same = homooligomer, if different = heterooligomer) Its an arrangement of subunits into a complex (held by non-covalent forces, H-bond, salt-bridges, van der wals) Its subunits have their our tertiary structures

Question 29

Elements of protein folding (4)

Answer 29

- need a correct sequence of AA's - good cell environment - balance between folding states - protect quality control system (i.e chaperones and proteases are working)

Question 30

Unfolded protein response (to changes in the ER)

Answer 30

- Translation will be inhibited to reduce the amount of new protein synthesized - ER chaperone transcription will be increased - More proteins to degrade misfolds will be synthesized

Question 31

Endoplasmic Reticulum Associated Degeneration (ERAD)

Answer 31

It degrades misfolded proteins (in cystic fibrosis the ERAD is fucked and the ER accumulated misfolds)

Question 32

Ubiquitin Pathway & its dysregulation

Answer 32

ubiquitin "tags" misfolds to signal to proteases to come cleave it Dsyregulation of proteosome can lead to cancers, myeloproliferative diseases, and neurodegenerative diseases in cases where the PQC (protein quality control) gets overwhelmed aggregation is favored

Question 33

Conditions that can arise when aggregation is favored

Answer 33

Amyloidosis type conditions, because misfolds (amyloids with B-stranded shape) accumulate and become toxic, you can see it with a congo red stain and polarized lights (looks green)

Question 34

Protein misfolding diseases loss of function vs gain of function

Answer 34

Loss-of-function pathogenesis (protein deficiencies): when proteins are degraded too early by the PQC mechanisms Gain-of-function pathogenesis (disease/toxicity): misfolded protein accumulates too much

Question 35

Failed protein folding can lead to which conditions (3)

Answer 35

cystic fibrosis Marfans Amyotonic lateral sclerosis

Question 36

Unstable protein folding can lead to which condition(1)

Answer 36

cancer

Question 37

non-trafficked proteins can lead to which conditions (2)

Answer 37

Familial hypercholesteremia alphac1-antitrypsin deficiency

Question 38

Insoluble aggregates that are deposited toxically can lead to which conditions (~4)

Answer 38

Neurodegenerative diseases Alzheimers Prion Parkinsons etc

Question 39

Alzheimer's

Answer 39

defective tau and beta amyloid protein mild symptoms = short-term memory loss moderate symptoms = can't learn/re-learn new info, long-term memory loss, mood/personality changes severe = inconctinence and gait ataxia risks: amyloid precursor protein mutations & down syndrome common in 65yrs +