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Biology 202 > Proteins > Flashcards

Proteins Flashcards

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1
Q

What 6 elements are key structural components of cells?

A

C N O H (these make up 99% of cell)

P, S, Cl, K, Ca, Na, Mg (0.9%)

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2
Q

What are the 4 main classes of macromolecules of cells (monomer and polymer)? Name their different structural types if they have any.

A

sugar… polysaccharide… can be linear or branched

amino acids… proteins… 1 stucture

Nucleotide… nucleic acids… 2 structural types

Lipid.. NO POLYMER… many structural types

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3
Q

How many amino acids in an oligopeptide? What are some examples and what is their general function? Are these considered proteins?

A

2-20 AA

NOT A PROTEIN

neuropeptides (opiate peptides, substance P, vasopressin)

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4
Q

How many amino acids in a polypeptide? Are these considered proteins?

A

greater than or equal to 30, usually several hundred though

Considered proteins

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5
Q

Are proteins folded or unfolded when they are newly synthesized?

A

unfolded

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6
Q

In order to be funcitonal, proteins must be?

A

Folded PROPERLY

if misfolded they may not function or have abnormal function

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7
Q

What are the three traits that all proteins share?

A
  1. all have a stable 3D shape, known as a conformation.
  2. all proteins bind to at least one molecular target
  3. all proteins perform at least one cellular function
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8
Q

Describe the general structure of an amino acid, there are 4 things.

A
  1. Amino terminus
  2. Core alpha carbon
  3. Carboxy terminus
  4. side group (Confers properties of amino acids)
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9
Q

Where do the peptide bonds form between two amino acids?

A

Between the carboxy group of one and the amino group of another.

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10
Q

What are the elements of a protein backbone? What does this leave out?

A

H, N, C, O

This leaves out the diverse side groups

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11
Q

What chemical reaction forms a peptide bond? Briefly describe it.

A

Dehydration

By taking 1 O from the carboxy group and 2 H from the amino group the two amino acids form a peptide bond and H2O is a byproduct.

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12
Q

What are the 5 different classes of amino acids? Describe them.

A
  1. Aliphatic: nonpolar carbon chain
  2. Aromatic: Carbon RINGS
  3. Polar side groups: not chaged
  4. Positively charged
  5. Negatively charged
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13
Q

How many amino acids do humans use?

A

20

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14
Q

How many levels of protein structure are there? Very briefly describe these.

A

PRIMARY - the sequence of amino acids linked by peptide bonds

SECONDARY - H-bonds between either amino acids in same backbone (alpha helix), align amino acid chains (pleated sheet), and 3rd type is a random coil

TERTIARY - Side group interactions, described as either local or global.

QUANTERNARY - Proteins made up of more than 1 polypeptide chain.

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15
Q

In regards to the TERTIARY STRUCTURE, what is meany by local (3A) vs global (3B: overall) structure? What is a motif? What is a domain? What are the 4 we cover?

A

Local: This is the combination of multiple individual secondary structures into “motifs”. A domain is made up of a larger arrangement of these motifs in sections of the protein.

Overall: This is the shape of the entire protein, can be shown in ribbon form (shows secondary structure as well as tertiary motifs) or in space-filling form which just shows the overall shape.

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16
Q

What are amyloid fibers created from? Where and with what disease have these fibers been found in humans?

A

These are when proteins misfold in a way where many beta sheets are stacked on each other.

These have been found in the brains of people with alzheimers and other neurodegenerative diseases.

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17
Q

What are the two types of 3B structures we cover in class?

A
  1. globular - not necessarily a sphere, but roughly that shape
  2. fibrous - long and rod-shaped. Made from parallel cross-linked polypeptide chains
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18
Q

Describe the QUATERNARY protein structure. What is an example?

A
  • present in multimeric proteins, or proteins with multiple polypeptide subunits.
  • about the spatial arrangement of each subunit in the protein.
  • Interactions between the polypeptide subunits are the same interactions involved in the secondary and tertiary structures. There are covalent (disulfide) and weaker noncovalent bonding present.
  • antibodies are an example of a protein with a quaternary structure. They have 2 light chain and 2 heavy chain polypeptides. On the ends of each chain they have a variable regions to form the antigen binding site.
19
Q

Describe the 5 different large protein assemblies that can form in the quaternary structure,

A
  1. Dimer - two polypeptide subunits linked together.
  2. helix - coil shaped
  3. ring
  4. Spherical shell
  5. hollow tube
20
Q

What is the only covalent bond that occurs in protein folding?

A

DISULFIDE

21
Q

What are the 4 noncovalent bonds involved in protein folding?

A
  1. H-bond
  2. electrostatic interactions (ionic bonds) - when they occur on interior they neutralize and charged residues to keep interior hydrophobic.
  3. Hydrophobic interactions on interior that leave polar residue at surface to interact with water
  4. Van der waals at very short distances.
22
Q

How does a protein switch conformation?

A

Through reorganization of a few of its non-cavalent bonds.

23
Q

Describe the Anfinsen experiment for protein folding. What does the result of this experiment tell us?

A
  1. Ribonuclease A contains strong disulfide bonds between their cysteine AA.
  2. Harsh chemical added (2-mercaptoethanol and urea) the disulfide bonds are broken and the protein unfolds.
  3. Remove the chemical and expose protein to air, observed the protein return to its native conformation including restoration of disulfide bonds.

This tells us that all necessary information for proper protein folding is contained in its primary level structure.

24
Q

What are some caveats to the invitro denatured protein experiment? Why do proteins renature?

A
  1. Most proteins cant refold to their active conformation.
  2. If they can, it is a much slower process than what happens in the cell.
    - they renature due to that conformation being their lowest energy state.
25
Q

What must a protein be able to do in order to be functional? How is this possible?

A

They must be able to be activated and inactivated, this is possible by it having multiple conformations.

26
Q

What are the 4 mechanisms we cover for controlling protein activity?

A
  1. Chemical modification of amino acids (switch states)
  2. Binding of small molecules to allosteric sites (switch states)
  3. Binding of regulatory proteins to protein (switch states)
  4. Protein degradation (controls amount, therefore control activity)
27
Q

Are chemical modifications of amino acids reversible?

A

YES

28
Q

What are the 7 types of covalent modification of proteins? (Mechanism #1)

A

Disulfide bonds

glycosylation (adding sugars)

Adding lipids into membrane (farnesyl)

phosphate groups (activate/repress)

methyl groups (activate/repress)

acetyl groups (activate/repress)

ubiquitin (activate/repress)

29
Q

Is allosteric regulation a short quick or slow long process?

A

short and quick

30
Q

What proteins are primarily controlled allosterically?

A

enzymes

31
Q

Is allosteric control an efficient mechanism?

A

NO, it costs a lot of energy.

32
Q

What are some examples of small molecules that bind to allosteric sites?

A

ATP, GTP, Ca2+, cAMP, GDP

33
Q

What are the two examples of binding of regulatory proteins to proteins to regulate their activity (mechanism #3)?

A
  1. Adenylate cyclase - activated when alpha s binds to it and is inhibited when alpha i attaches to it

Protein kinase A - can be allosterically regulated by cAMP or can be regulated by a protein.

34
Q

Are the changes in structures by mechanisms 1-3 causing a large change in structure or are they pretty small?

A

They are small changes that have LARGE effects. But they are reversible.

35
Q

What are 3 degradation mechanisms of proteins? Where are they located in the cell? (mechanism #4)

A
  1. proteasomes - in the cytosol and nucleus
  2. Lysosomes - in the plasma membrane and golgi
  3. Soluble proteases - in the ECM
36
Q

Is protein degradation reversible?

A

NO, but expression can be increased to bring more proteins back.

37
Q

What role does ubiquitin play in the proteasome?

A

A POLY-ubiquitin tab is the signal for degradation to occur by the proteasome

38
Q

What are the 5 types of proteins discussed in class?

A

Enzymes - catalyst for chemical reaction

motor - generate force to move cells

response - detect signals inside or outside cells, transduce signals and activate cellular changes

structural - provide scaffolds for cell or structures within scaffold

transport - move materials in and out of the cell

39
Q

Do many proteins tend to work in complexes?

A

YES YEAS YE

40
Q

describe xray crystallography

A
  1. purify single protein
  2. crystallize protein
  3. use xrays to obtain diffraction pattern to find structure by looking at the angle and intensity of the diffracted beams
41
Q

Describe gel electrophoresis.

A

Any proteins with subunits are broken using mercaptoethanol and ran through to gel, it is all based ont heir molecular weight. heavier moves slower.

42
Q

Describe the western blot test.

A

This is when an antigen is separated from other molecules via electrophoresis. Then using antibodies that are labeled to attach to the antigen it is identified.

43
Q

Can you label antibodies to specific proteins and allow them to tag the protein to loaclize them via microscope?

A

YES, pectin in plants is an example of this in plants.

Biology 202 (3 decks)

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