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Biochemistry > Proteins, Muscles, Antibodies > Flashcards

Proteins, Muscles, Antibodies Flashcards

1
Q

What value describes the conformation of a polypeptide backbone?

A

Torsion angles

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2
Q

What are the two torsion angles of a polypeptide backbone?

A

⍦ - C-C bond

∅ - C-N bond

-amide bond has little rotation because it is planar and has some double bond character

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3
Q

What is a Romachandran diagram?

A
  • indicates allowed conformations for a polypeptide (due to side chains only certain are allowed)
  • ⍦ vs ∅ plotted
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4
Q

What are the two exceptions to the romachandran diagram?

A

Proline and glycine

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5
Q

Describe proline’s torsion angles.

A
  • ∅ values are restricted to -60
  • restricted to one side of the plot, can only rotate on the side that has the H, not on the side with the R-group
  • more restrained motion
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6
Q

Describe glycine’s torsion angles.

A
  • less steric hinderance, allowed angles are greater
  • no R group, just 2 Hs
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7
Q

Describe the structure of a typical alpha helix.

(handed, residues, pitch, bonds, side chains)

A
  • right handed helix
  • 3.6 amino acids/residues per turn
  • pitch (distance covered per turn) = 5.4Ă
  • carbonyl (C=O) of Nth residue is hydrogen bonded to the N-H of the N+4th residues
  • side chains point outward and downward
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8
Q

How are beta sheets stabilized?

A
  • held together by H-bonds
  • H-bonds are between neighboring polypeptide chains
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9
Q

What are the two types of beta sheets?

A

parallel and antiparallel

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10
Q

Describe parallel beta sheets.

A
  • polypeptides run in the same direction (N-C) and (N-C)
  • H-bonds between the strands are angled
  • the crossover connection between strands is longer and goes out of the plane
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11
Q

Describe antiparallel beta sheets.

A
  • polypeptides run in opposite directions (N-C) and (C-N)
  • H-bonds between the strands are parallel
  • the crossover connection between strands is shorter and on the same plane
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12
Q

What are the two classes of proteins?

A
  • fibrous and globular
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13
Q

Describe fibrous proteins.

A
  • have repeating second degree structures
  • are structural proteins: hair, nails, muscle tendons
  • keratin and collagen are examples
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14
Q

What is the structure of Keratin?

A

coiled-coil

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15
Q

Describe a coiled-coil.

A
  • 2 alpha helices that wind around each other
  • 7-residue repeat a-b-c-d-e-f-g
  • a and d are non-polar and aggregate together due to the hydrophobic effect - minimize exposure to water
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16
Q

Describe the higher order structure of keratin.

A
  • coiled coil dimers
  • form protofilaments - which are connected by disulfide bonds (covalent linkages)
  • form protofibrils
  • form microfibrils (eg. hair)
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17
Q

How are disulfide bonds formed?

A

cysteine residues have thiol groups that form disulfide bonds under oxidizing conditions

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18
Q

How does the number of disulfide bonds impact keratin?

A
  • more disulfide bonds = harder keratin (nails)
  • fewer disulfide bonds = soft keratin (skin)
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19
Q

How can disulfide bonds in keratin be modified?

A

they can be reduced and reformed = allows for straightening/curing of hair

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20
Q

Describe the structure of collagen.

A
  • triple helix
  • 3 polypeptide chains wound around together
  • 30% Gly, 30% Pro or H-hydroxy Pro (Hyp)
  • repeating Gly - Pro - Hyp
  • Rope-like twist of 3 collagen peptides where each aa interacts
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21
Q

What is Hyp?

A
  • H-Hydroxy Proline
  • Addition of OH group catalyzed by prolyl hydroxylose
  • this enzyme requires a cofactor: ascorbic acid
  • vitamin c deficiency causes scurvy which is incorrectly formed/weak collagen
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22
Q

Why is Hyp important?

A

Hyp is a hydrogen bond donor that is necessary to maintain the strength of the triple helix interaction in collagen

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23
Q

Describe collagen crosslinking.

A
  • covalent crosslinking reaction between collagen strands
  1. Lysine is converted to allylysine (amine group converted to an aldehyde)
  2. Two allylysines form allylysine aldol
  3. Allylysine aldol + His forms 5-hydroxylysine
  4. Final product - 4 amino acids cross-linked together
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24
Q

Describe globular proteins.

A

have non-repetitive second degree structures

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25
Q

What is the tertiary structure of a protein?

A
  • the folding of second degree structural elements
  • positions of each atom in a protein, including side chains
  • Where is every atom located in 3D space?
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26
Q

What are two methods of determining tertiary structures?

A

x-ray crystallography and NMR

27
Q

What are the 3 steps in x-ray crystallography?

A
  1. Crystallize the protein
  2. Obtain diffraction pattern
  3. Map electron density

Different values of resolution, lower Ă allows for better mapping of protein

28
Q

What does NMR do?

A

identifies through space contacts of different functional groups

29
Q

What are the pros and cons of NMR vs X-ray crystallography?

A
  • NMR: smaller proteins only, dynamic (more information about movement)
  • X-ray: any size protein, static picture, contraining protein - minimizing movement, only one conformation displayed
30
Q

Describe the quaternary structure of proteins.

A
  • more than one polypeptide chain
  • eg. dimer, trimer
  • geometry of association of multiple polypeptides
  • non-covalent associations
31
Q

What controls protein stability?

A
  • hydrophobic effect - non-polar groups minimize contact with water and coalesce in the middle
  • electrostatic interactions - amino acids with + and - charges form salt bridges (non-covalent)
  • disulfide bonds - covalent bonds, 2-cysteines oxidize to form disulfide bonds
  • metal ions - eg. Zn finger - alpha helix celates to Zn metal to help hold structure together
32
Q

What is the hydropathy scale?

A
  • (-4.5) - (4.5)
  • number rating how hydrophobic each amino acid is
  • larger = more hydrophobic
33
Q

What conditions can be used to denature a protein?

A
  • heat - increased KE
  • pH changes - interfere with electrostatic interactions
  • detergent - nonpolar molecules break up hydrophobic interactions
  • chaotropic agents - disrupt hydrogen bonding interactions
34
Q

What are two examples of chaotropic agents?

A

urea, guanidinium

35
Q

What are intrinsically disordered proteins?

A
  • unfolded
  • fold when in contact with their binding partner
36
Q

When proteins fold, they go from _______ to _______

A
  • high energy, high entropy
  • low energy, low entropy
37
Q

Describe the process of protein folding.

A
  1. Secondary structural elements and local segments of second degree structure form (Rapid process)
  2. Tertiary structure forms, second degree elements collapse to form tertiary structure (Slow process)
38
Q

What chart illustrates protein folding?

A
  • folding funnel
  • energy x entropy
  • local energy minima are the dips
  • the lowest point is the most stable native structure
39
Q

What do chaperone proteins do?

A
  • assist with protein folding when stuck in minima
  • eg. heat shock proteins (Hsp70/90)
  • many of these are ATPases that catalyze the hydrolysis of a phosphate to allow a reaction that would not otherwise occur happen
40
Q

What proteins are essential to muscle contraction?

A

actin and myosin

41
Q

Describe the structure of muscles.

A
  • muscles are made up of bundles of muscle fibres
  • one bundle is made of a parallel array of myofibrils
  • one myofibril is made up of repeating sarcomere units
42
Q

Describe the structure of a sarcomere.

A
  • made of overlapping thick and thin filaments
  • repeating sarcomere units make myofibrils
43
Q

What changes as muscles contract?

A

the overlap between thick and thin filaments changes

44
Q

Describe the structure of a thick filament of a sarcomere.

A
  • made up of myosin - 1 thick filament has 100s of myosins
  • myosin has 6 polypeptide chains: 2x heavy, 4x light
  • N-term of heavy chain is a myosin head
  • C-term of heavy chain is a long coiled coil (a-d)
    • coiled coil regions stick together and myosin heads stick off
45
Q

Describe the structure of a thin filament of a sarcomere.

A
  • made up of actin
    • G-actin (globular/monomeric)
    • F-actin (fibrous/polymer)
  • polymer forms a double stranded helix
46
Q

How do thick and thin filaments of sarcomeres interact (general)?

A
  • each myosin head binds to one unit on the actin polymer
  • thick filament - myosin head
  • thin filament - actin
47
Q

What conversion occurs during the process of muscle contraction?

A

chemical energy (ATP hydrolysis) is converted to mechanical energy (movement of thick and thin filaments against each other)

48
Q

Describe the process of muscle contraction.

A
  • ATP binds myosin head
  • Myosin head is released from actin
  • Hydrolysis of ATP
  • Cocking of myosin head (changes angle)
  • Myosin head binds weakly to new actin
  • Releases Pi
  • Pi then allows stronger binding to actin
  • Power stroke - moves thin filament so myosin can be at correct angle
  • ADP released
49
Q

What are the two types of immune response?

A
  1. Cell mediated - T-cells
  2. Humoral - B-cells secrete antibodies
50
Q

What creates antibodies?

A

B-cells

51
Q

Describe the structure of antibodies.

A
  • antibodies have 4 subunits: 2x light chains, 2x heavy chains
  • they are glycosylated at CHO regions
  • light & heavy chains are linked with disulfide linkages, the two heavy chains are also linked with disulfides
52
Q

What makes up the “ends” of the antibody arms?

A
  • both light and heavy chains have variable and constant regions
  • the variable regions make up the ends of the antibody arms
53
Q

Describe the light chain of an antibody. What is it important for?

A
  • the variable domain of a light chain has hypervariable loops responsible for antigen binding
  • light chains also have a characteristic immunoglobulin fold - 3-4 antiparallel beta sheets linked by disulfides
54
Q

How does antigen binding occur?

A
  • antigen binds to hyper-variable loops through non-covalent interactions: hydrophobic, ionic, H-bonding
  • this binding can be super tight
55
Q

Describe the binding affinity of antibodies.

A
  • Kd (binding affinity) = 10-14 - 10-10 M
  • concentration of antigen for 50% occupancy
  • lower the value the tighter the binding
56
Q

How is antibody diversity created?

A
  • recombination of VDJC units
  • somatic mutations
57
Q

Describe our antibody system and how diversity is acquired.

A
  • immune system has a library of antibodies (>1018 )
  • each chain is encoded by multiple genes
    • light - VJC
    • heavy - VJDC
  • each individual B-cell combines different V,J,D,C to make a unique Ab
58
Q

What happens when a B-cell is exposed to an antigen?

A
  • upon exposure to an antigen B-cell proliferates
  • somatic mutation create diversity of antibodies
59
Q

What are the 3 types of monoclonal antibody therapies?

A
  1. antibodies directly block the function of our cell surface receptor
  2. antibodies recognize something specific to a cancer cell surface then recruits other immune cells like T-cells or macrophages to destroy the tumor cell
  3. antibody drug conjugate - antibody delivers toxic drug to tumor cell
60
Q

How do you generate monoclonal antibodies?

A
  1. Have antigen X expressed on tumor cells
  2. Inject mouse with antigen X
  3. Harvest lymphocytes - B-cells (can’t culture B-cells)
  4. Fuse these with mouse myeloma cells (they multiply indefinitely)
  5. Hybridomas formed (half myeloma, half-B cells) - purify for only hybridomas using selective media (in the media myeloma cells are not viable and only hybridomas survive)
  6. Clones that survive are screened for the antibody
61
Q

What are polyclonal antibodies?

A
  • a bunch of different antibodies that recognize the same antigen
  • produced by different B-cell clones, recognize many epitopes of the same antibody
62
Q

What are monoclonal antibodies?

A
  • single primary sequence of a light-chain heavy-chain combination
  • generated by identical B cells which are clones from a single parent cell - only recognize the same epitope of an antigen
63
Q

What is an epitope of an antigen?

A

a small site where an antibody binds

Biochemistry (12 decks)

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