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Biochem K > Proteins > Flashcards

Proteins Flashcards

1
Q

difference between conformation and configuration?

A

-conformation: Refers to the spatial relationships between the atoms in the molecule. No broken or new bond formed.

-Configuration: Refers to the geometric relationship between atoms/functional groups.
change in configuration = braking bonds and forming new ones. eg. D- L- configurations of AA’s.

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2
Q

Fibrous proteins?

A

Structural proteins. eg collagen ect.

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3
Q

Globular proteins?

A

Mostly enzymes + hemoglobin/myoglobin

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4
Q

Lipoproteins?

A

contain covalently bound lipid(s).

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5
Q

Glycoproteins?

A

contain covalently bound carbohydrates.

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6
Q

Metalloproteins?

A

contain tightly associated metal ions.

eg. myo- and hemoglobin and cytochromes.

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7
Q

how many distinct conformations can a polypeptide potentially adopt?

A

10’50

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8
Q

What interactions is the protein folding driven by?

A
  • H-bonding
  • Ionic interactions
  • Van Der Waal’s
  • Hydrophobic packing.
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9
Q

what allows transition between alternative structures of a protein?

A

They can undergo reversible changes in performing biological functions => change there configurations and back.

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10
Q

What is the primary structure?

A

Refers to the linear sequence of the amino acids within the polypeptide chain /backbone.
Basically its the different ways the 20 AA’s can arrange themselves.

  • The primary structure is determined by the gene corresponding to the specific protein synthesized and the polypeptide bonds holding them together.
  • contains N-terminus and C-terminus.
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11
Q

Explain what makes up the secondary structure.

A

Its the folding of short (3-30 residues) continous segments of the polypeptide into geometrically ordered units.

  • Its the interactions between adjacent or near amino acids in the polypeptide backbone.
  • There are two main orders of secondary structures:
  • Alpha helix
  • Beta pleted sheet.
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12
Q

What is an Alpha helix and how is it formed?

A

It’s a secondary structure, a spiral structure consisting of a tightly packed, coiled backbone around an imaginary longitudinal axis.
-its the simplest secondary structure.

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13
Q

Which configuration of the AA’s does the alpha helix contain?

A

Only L-configuration thats why a right handed is a far more stable helix, thus all proteins found in alpha helices are right handed.

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14
Q

Where does the stability of the alpha helix arise from?

A

Hydrogen bonding between the oxygen of the polypeptide bond carbonyl group and the hydrogen of the amino group 4 residues down the polypeptide chain.

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15
Q

What provides the thermodynamic driving force for the formation of alpha helices?

A

The ability to form a maximum amount of hydrogen bonds and supplemented by van der waals interactions in the core of the helix

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16
Q

Why is proline not able to participate in alpha helix formation, and what is the result of its inability to do so?

A

The peptide bond nitrogen of proline lacks a hydrogen thus it is not able to form h-bond in the backbone.
Therefore proline can only be stable when withing the first turn of the alpha helix (where it participates with oxygen and not hydrogen), if found elsewhere it will disrupt the conformation of the helix and produce a bend.

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17
Q

Explain amphipathic helices.

A

The hydrophobic R-groups project out of the helix at one side and the hydrophilic project out on the opposite side..

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18
Q

Why do the r-group project outwards in a helix?

A

To avoid steric interactions.

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19
Q

What are keratins?

A

A family of closely related proteins that are almost entirely alpha helical.

  • Found in mammals and have evolved for strength. (hair, nails, claws, horns etc.)
  • belongs to a larger family known as IF (intermediate filament proteins)
  • Keratins have right handed alpha helix mainly
  • Consists of two alpha helices twisted around each other, forming super helices, (resulting in super twisted coiled coils). => this type of structure gives it its strength.
  • contain crosslinks (disulfide bonds) which stabilizes the structure and permits close packing.
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20
Q

Where are other IF proteins found in mammals?

A

In the cytoskeleton.

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21
Q

How can certain AA residues disrupt the alpha helix and which are those residues?

A

Acidic Glutamate (Glu) and asp and Basic His, Lys and Arg can disrupt the helix by forming hydrogen bonds or by electrostatically repelling each other.

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22
Q

How can the Amphipathic helices create channels and pores in the membrane?

A

They are well adapted to the formation of interphases between hydrophobic residues and hydrophilic residues which allows small polar molecules to pass.

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23
Q

What are beta pleted sheets?

A

The second most common secondary structure of polypeptides.

  • All components are involved in hydrogen bonding of the peptidebonds carbonyl oxygen and amino groups hydrogen.
  • They’re composed of two or more beta strands which are almost fully extended but form a zig zag pattern.
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24
Q

Which is the main stabilizing factor of the beta sheet?

A

H- bonding, although theyre a lot more loosely packed than what are the alpha helices.

  • The hydrogen bonds are perpendicular to the backbone, holding together either antiparallel strands or parallel strand.
  • either of the two conformations allow a maximum amount of h-bonds between the segments.

(however the dude mentioned that the ani- parallel conformation may be more stable due to the orientation of the h bonds that are formed)

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25
How does the aniparallel differer from the parallel in beta sheets?
-Anti.. : N-terminus found with C-terminus (Opposite charge may be stabilizing?look up) adjacent chains in popposite direction. -Parallel: adjacent chains in same direction. N-terminus found with N- terminus and C- with C etc. the direction is usually indicated by arrows.
26
What is the "orientation"/structure of the beta sheets? | Are they completely flat?
They're not always completely flat. most of them tend to have a slight right handed twist. Clusters of these twisted strands are sometimes referred to as Beta- barrels.
27
What are beta barrels?
They are interchain hydrogen bonds which sometimes are formed between the peptide bonds of the backbone of separate polypeptide chains or within the same backbone when folded back on itself. (then the hydrogen bonds are intrachain bonds) -The beta barrels form the cores of many Globular proteins.
28
In which order or orientation does the R-groups of the polypeptide components project out of the beta sheet?
In opposite direction to their adjacent residues. | -Every second to one side, and every second to the other.
29
What stabilizes the alpha helix?
Primarily the H-bonding of the backbone. =>alone the H-bonds are quite week, but collectively they're strong. - locating the negatively charged amino acid residues at the positively charged Amino-terminus to stabilize the dipole nature. - Disulfide bridges (crosslinks) (- C-terminus is thought ti be stabilizing (And N-terminus destabilizing))
30
What factors DESTABILIZE the Alpha helix? | or decreases its stability?
1) -Electrostatic repulsion or attraction of adjacent positively or negatively charged side chains. eg. A long block of Glutamate or aspartate residues within a polypeptide chain will not be able to form helical structure since the residues will repel each other. Same thing for the positively charged AA's like arg and lys. 2) -Bulkiness of adjacent AA's (?) 3) -if there are positively charged AA's at the C-terminus and negatively chared AA's at the N-terminus. (???) 4) -Ionic interactions between AA's side chains spaces 3-4 residues apart. 5) the presence of proline due to its inability to form H-bonds. => it inserts a kink.
31
Name other secondary structures
Beta turns, loops and bends.
32
What secondary structures does the typical Globular proteins usually have?
-About half of them resides in alpha helces and betea turns and half in Loops, bends and turns.
33
What are turns and bends regarding the secondary structure of proteins?
Turns and bends refer to short segment of amino acids that join two units of secondary structures, such as two adjacent strands of an antiparallel beta sheet.
34
What are loops regarding the secondary structure of proteins?
Loops are formed in regions that contain residues BEYOND the minimum number necessary to connect adjacent regions of secondary structure. -For many enzymes loops are the "bridge domains" responsible for binding substrate and contain amino acetyl residues that can participate in catalysis.
35
What are Helix-loop-Helix motifs?
The are supersecondary structures which provide the oligonucleotide- binding portion of many binding proteins, such as repressors and transcription factors.
36
Define Superseconday structures.
They're structural motifs that are intermediate in the scale between secondary and tertiary structures. eg. Helix-loop-Helix motifs and E-F hands of calmodulin.
37
What are Epitopes?
Loops and bends that reside on the surface of proteins and are accessible sites for recognition and binding of antibodies.
38
How are loops stabilized since they lack apparent structural regularities.
-They adopts a specific conformation which is stabilized by H-bonding, Salt bridge formation and hydrophobic interactions with other portions of the proteins.
39
Which portions or the protein are the disordered regions and how do they assume an ordered conformation?
The C- and N-terminals since they have a hight conformational flexibility. -They assume ordered conformation by binding a ligand. This allows them to act as ligand-controlled switches of function and activity of the protein.
40
Define Tertiary structure of proteins.
Refers to the 3D structure of a polypeptide. How secondary structures such as alpha helices, beta sheets, turns and loops are assembled to form Domains, and how these domains are spatially related to one another.
41
What are domains?
A domain is a section of protein structure (assembled secondary structures) which can perform a specific chemical or physical task such as binding substrate or ligand.
42
Which Which proteins consist of a single domain?
``` Simple proteins, particularly those which interact with a single substrate. eg. -Myoglobin -Lysozyme -Triose phosphate isomerase ```
43
Which proteins consists of two domains?
Lactate dehydrogenase | has a domain for NAD+ on its N-terminus and one for Pyruvate on its C-terminus
44
Which family does Lactate dehydrogenase belong to?
Oxireductases => Dehydrogenases.
45
What is Rossmans fold?
Its a N-terminal NAD(P)+ binding domain which is common for all the members of the oxireductase family.
46
How has a large family of Oxireductases evolved to utilize NAD(P)+/NAD(P)H for the oxidation and reduction of a wide range of metabolites? Give examples of the enzymes which have this function.
By fusion of segments coding for Rossmans fold and that coding for a variety of C-terminal Domains to achieve this function. Exapmples are: - Alcohol dehydrogenase - Glyceraldehyde-3phosphate dehydrogenase - Malate dehydrogense - Quinone oxireductase - 6-phospogluconate dehydrogenase - D-glycerate dehydrogenase - Formate dehydrogenase etc. ...
47
What is the function of hydrophobic membare domains?
They anchor proteins to membranes and enable them to span them
48
What is the role of Localization sequences?
They target proteins to specific subcellular or extracellular locations.
49
What does regulatory domains do?
They trigger changes in the protein function in response to the binding of allosteric effectors or coalent modifications.
50
What more, asides from domain formation is part of the tertiary structure?
Migration of hydrophobic domains, or sidechans to the interior etc. and overall binding (ionic or polar) between R-groups. -hydrogen binding between serine (OH) and threonine with electron rich atoms of adjacent R-groups.
51
Define; - Monomeric proteins - Dimeric proteins - Homodimers - Heterodimers
- Monomeric proteins; consist of a single polypeptide chain. - Dimeric proteins; consists of two peptide chains. - Homodimers; contain two copies of the same polypeptide chain - Heterodimers ; contain two different polypeptide chains joined together in a quatrinary structure.
52
What is renaturation?
Its the process in which the Proteins, whose conformation has been disrupted refold.
53
Why does Denatured proteins still have regions of native structure intact, even when denatured?
Because the Native structure is thermodynamically , thus energetically favored. thats why they dont just fold into random coils even when denatured.
54
Which are the steps of protein folding?
i will write this eventually, cant be bothered atm.
55
What are molten globules?
when the hydrophobic... migrate to the interior and It is a partially folded protein in which the modules of the secondary structures rearrange until a mature conformation has been formed.
56
is protein folding a rigid process?
No, it possesses flexibility, can be rearranged.
57
How does Oligomeric proteins fold?
in oligomeric proteins , individual protomers tend to fold first, before they associate with other subunits.
58
What is the role of Auxiliary proteins?
They assist folding by speeding up the process of folding and guiding it toward a productive conclusion.
59
When are Aggregates formed?
When proteins fail to spontaneously refold in vitro and instead they form these insoluble aggregates which are disordered complexes or partially folded polypeptides held together predominantly by hydrophobic interactions.
60
What is the role of chaperones? | What are they?
They are proteins which participate in protein folding in over half of all proteins of mammals. -The chaperones prevent aggregation and provides an opportunity for the protein itself to form appropriate secondary units and the migration of hydrophobic portions without forming aggregates by providing a shielding environment until the molten globule has been formed.
61
Which are the two mentioned Chaperones and what are their functions in the folding process?
- Hsp70 : are a heat chock proteins (and chaperones) which bind to short sequences of hydrophobic AA's that emerge while a new polypeptide is being synthesized, shielding them from the solvent. - Hsp 60 : often called Chaparonins, act later in the folding process, but also together with hsp 70 chaperones. They're donut shaped and have a cavity they provide sheltered environment in which p.p can fold until the hydrophobic side chains are buried inside as well.
62
Which enzyme initiates the sulfide bridge formation between the polypeptide chains to stabilize the tertiary structure? and how?
Protein-suflhydryl oxidase. by catalyzing the oxidation of cystein residues.
63
What is the result of a dietary lack of Riboflavin, and why?
It is associated with an increase of improper protein folding of disulfide containing proteins. -Because many eukaryotic Sulfhydryl oxidases are flavin-dependent.
64
What is the role of Disulfide Isomerase?
It catalyzes the disulfide exchange by: - catalyzing the rupture of S-S bonds - then catalyzing reformation of another (more appropriate) "partner".
65
Which enzymes catalyze the transformation of proline from trans to cis?
Proline-cis-trans isomerase, a family of proteins also known as: Cyclophilins.
66
What are the functions of cyclophilins?
1) Isomerization of Proline from cis to trans | 2) Folding of proteins expressed by viral invaders.
67
In which conformation are all the X-Pro peptide bonds synthesized? (X= any AA)
Trans
68
How many percent of x-prolin peptide bonds are in trans configuration of a mature protein?
94% | The remaining 6% have been isomerized into Cis configuration by cyclophilins.
69
Explain how proteins are conformationally dynamic molecules.
they can fold and unfold 100's or thousands of times. | more on p.47
70
What is the important function of Glutathionine?
-It can reduce inappropriate disulfide bonds that may be formed due to exposure oxidizing agents such as O2, hydrogen peroxide or superoxide. (lecture- reduces peroxides)
71
Prion disease
p46
72
Alzheimers disease
p46
73
Beta-Thalassemias disease
p46.

Biochem K (10 decks)

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