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EOM 1 - Test 1 > Lecture 8: Proteins II > Flashcards

Lecture 8: Proteins II Flashcards

Proteins II

1
Q

What stabilizes α and β secondary structures of proteins?

A

Hydrogen Bonding

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2
Q

What is irregular arrangement of the polypeptide chain termed?

A

Random Coil

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3
Q

What three factors affect the α-helix? Where are the R-groups located?

A
  1. Hydrogen bonds between amide and carbonyl groups of amino acids 2. Proline causes disruptions 3. Bulky or Like Charged Amino Acids in proximity R-groups are located on the exterior of the helix
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4
Q

L-Amino Acids result in what type of α-helix?

A

Right Handed Helices

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5
Q

D-Amino Acids result in what type of α-helix?

A

Left Handed Helices

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6
Q

What types of amino acids are strong helix formers?

A

Small, hydrophobic R-groups, such as Alanine and Leucine

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7
Q

What two Amino Acids act as helix breakers?

A

Proline due to bond angles, and Glycine due to small size

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8
Q

What are the forms of β-Pleated Sheets? Which is stronger and why?

A

Parallel and Antiparallel Antiparallel is stronger due to linear hydrogen bonds

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9
Q

What is the orientation of hydrogen bonds in α-helices and β-pleated sheets?

A

α-helices: parallel to the backbone β-pleated sheets: perpendicular to the backbone

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10
Q

Which will be longer with same amount of AA residues–α-helices or β-pleated sheets? Why?

A

β-pleated sheets, almost fully extended, whereas α-helices are coiled

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11
Q

What two AA’s play a role in β-turns? What types of turns do these cause? (answer)

A

Proline (Type I), Glycine (Type II)

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12
Q

What configuration are most peptide bonds NOT involving Pro?

A

Trans (>99.9%)

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13
Q

What is required for Proline isomerization? Why are these clinically relevant?

A

proline-cis, trans-isomerases Cyclophilins participate in protein folding of viral invaders

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14
Q

What type of folding requires NAD+-dependent Dehydrogenases?

What binding domain does this include?

A

Rossman Fold

Nucleotide binding domain

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15
Q

What is the Φ angle around the α-carbon?

What is the Ψ angle around the α-carbon?

What are these in a fully extended polypeptide?

A

α-carbon - amide nitrogen bond

α-carbon - carbonyl carbon bond

180o

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16
Q

What type of diagram can predict protein secondary structure bond angles?

A

Ramachandran Diagram

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17
Q

What interactions stabilize protein tertiary and quartenary structure?

A

Hydrophobic/Hydrophilic (Van der Waals)

Ionic (salt bridges)

Hydrogen Bonds

Disulfide Bonds

18
Q

What are the two first important steps of X-Ray Crystallography?

What does the 2nd step lead to?

A
  1. Purify Protein (95-100%)
  2. Crystallize the Protein

Leads to static representation of the sample

19
Q

What are pros and cons of X-Ray Crystallography?

A

Pros: No size limits, well established

Cons: Difficult for membrane proteins, can’t see hydrogens

20
Q

What are the pros and cons of NMR for proteins?

A

Pros: No need to crystallize (visualize dynamic structure), can see hydrogens

Cons: Difficult for insoluble proteins, works best with small proteins

21
Q

What often regulates Quaternary protein structures?

A

oligomers

22
Q

What is difference between monomeric and dimeric proteins?

What is difference between homodimers and heterodimers?

A

Mono is single protein, dimeric is non-covalent forces holding two chains

Homodimers are same chain, hetero are different

23
Q

What structure do proteins emerge from and begin folding?

A

Ribosome

24
Q

What enzymes are involved in formation of β-turns upon initial folding?

A

Proline cis-trans isomerases

25
Q

What substances aid in the arrangement of secondary structural elements into domains?

A

Heat Shock Proteins (HSPs)

26
Q

What substance is responsible for segregating hydrophic region of proteins into the interior?

A

Chaperones

27
Q

In the final stage of protein folding, what stabilizes quaternary structures to mature conformations?

A

Protein disulfide isomerase

Hint: remember disulfide bridges

28
Q

What contributes to protein denaturation?

A

Temp Extremes

pH change

organic solvents

heavy metals

chaotropic agents

agitation/whipping

29
Q

What causes tau proteins to dissociate from microtubules within the axon?

A

Phosphorylation

30
Q

What are the major players in the main proteolytic pathway in eukaryotes?

A

Endosome-lysosome

Ubiquitin-proteasome

Mitochondrial enzymes

31
Q

Given a disorder which proteins are not degraded, what can one expect to be deficient (or not working properly)?

A

Proteolytic Pathway substrates

Endosome-lysosome

Ubiquitin-proteasome

Mitochondrial proteolythic pathway

32
Q

What is the relative sizes for the two main classes of proteins?

A

Fibrous, length to girth ratio > 10 (hotdogs)

Globular, length to girth ratio < 3 (chodes)

33
Q

What post translationally modified molecules are involved in intra-molecular cross-links?

What catalyzes this reaction?

What do these facilitate?

A

hydroxyPro

hydroxyLys

Catalyzed by metal containing enzymes

Intra-chain hydrogen bonding

34
Q

Where are fibrillar colanges synthesized?

A

Fibroblasts of loose connective tissue

Osteoblasts/Chondroblasts of bone/cartilage

35
Q

Given deficiency localizing in collagen dysfuntion, what would be possible source?

What is an example of this?

A

Deficiency in enzymes required to modify intra-linking molecules of collagen (hydroxyPro/hydroxyLys),

O2

Fe2++

Cu2+ (lysine)

Ascorbate (vitamin C) (water soluble)

36
Q

Consumption of sweet peas can result in what specific problem?

A

Lathyrism

Inhibity lysyl-oxidase, destabilizing collagen cross links, symptoms include skeletal and vascular problems

37
Q

Ehlers-Danlos Syndrome

A

Heterogeneous group of connective tissue disorders that result from defect in metabolism of fibrillar collagen molecules

Hint: Stretchy Skin photo

38
Q

What fibrillar protein is important for stretch and relaxation functions of various organs, ligaments, and connective tissue?

A

Elastin

Hint: Elastigirl

39
Q

What is the basic soluble unit of Elastin Cross Links?

A

Tropoelastin

40
Q

What is the role of α-1 Anti-trypsin?

What happens if this is degraded?

A

Inhibits elastase, which destroys elastin in alveolar walls of lungs

Protects from empysema and COPD

If degrades, elastase will continue to degrade elastin in organs

EOM 1 - Test 1 (16 decks)

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