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Biochemistry > 4.3 - 4.4 > Flashcards

4.3 - 4.4 Flashcards

1
Q

Tertiary proteins

A

The overall 3D arrangement of all atoms

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2
Q

Quaternary structure

A

Arrangement of protein subunits in 3D

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3
Q

What are the two major groups of proteins?

A
  1. Fibrous
  2. Globular
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4
Q

Fibrous proteins

A

Have polypeptide chains arranged in long strands

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5
Q

Globular proteins

A

Have polypeptides chains folded into a spherical or globular shape

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6
Q

______________ usually consist of a single type of secondary structure & their 3 structure is simple

A

Fibrous proteins

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7
Q

_________ are the most enzymes & regulaotry proteins (soluble in the cytoplasm)

A

Globular proteins

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8
Q

Fibrous proteins are adapted for ________ function

A

structural

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9
Q

Alpha keratin are made for __________ & favored only in mammals & found in hair, nails, wools, etc

A

Strength

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10
Q

Alpha keratin are part of the ________________

A

Intermediate filament (IF) proteins (All IFproteins have a structural function & share the structural features by the alpha keratin)

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11
Q

The alpha keratin helix a ________ helix

A

Right hand

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12
Q

The alpha helices of alpha keratins are arranged as a _____________ where two strads of alpha keratin are overlapped parallel & are wrapped together to form a supertwisted coiled coil (which makes it stronger)

A

Coiled coil

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13
Q

The supertwist of keratin forms a ________ helix & its surfaces is made up of hydrophobic amino acid residues (keratin is rich in hydrophobic residues such as Ala, Leu, Ile, Met,, & Phe)

A

Left hand

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14
Q

Protein function depends on its ____ structure

A

3D

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15
Q

Protein strucuture is determined by its ________ sequence

A

Primary

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16
Q

ALpha keratin has a ____ residue pseudo repeat of : abcdefg where a & d position are nonpolar & mostly on one side

A

7

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17
Q

Hair keratin has pairs of alpha helices to form a two - chain coiled coil where they then combine with other two chain coiled coil to make ____________ then protofibrils

A

Protofilamanets

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18
Q

Collagen is also made to provide _______ where its found in connective tissue like tendons, cartilage, bone, the eye, etc

A

Strength

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19
Q

Collagen helix is ______ & has 3 aa residues per turn

A

Left handed

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20
Q

The 4 structure of alpha keratin is made up of the________ wrapping around each other

A

supertwist

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21
Q

Collagen is also coiled coil but has 3 separate polypeptides called ____ chains that supertwist together to make its 3 & 4 structure

A

Alpha chains

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22
Q

The helical twisiting is ______ handed in collagen

A

right handed

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23
Q

The amino acid sequence in collagen is ________ where X is pro , Y is 4-hdp mostly made up of gly & the pro & 4-hyp provide thee sharp twisting of the collagen helix ).

A

Gly-X-Y

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24
Q

Collagen has a left hand helical twist but its supertwist forms a _____

A

right hand

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25
Q

Basic structure of collagen is a triple helix & is 3 left hand helices twist together to form a _________ supertwist

A

Right hand

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26
Q

________ provide strength, support, resiliency, & resistance (in tendons it has a rope like fiber & the skin has loosly woven fibers)

A

Fibers

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27
Q

________ create a rigid structure unable to adapt to alpha helix angles

A

Pro & 4-hyp

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28
Q

____ is located along central axis of a triple helix where other residues can’t fit

A

Gly

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29
Q

The __________ form between Gly N-H & Pro C-O in an adjacent chain in the triple helix twist

A

interchain H-bonds

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30
Q

_____________ (collagen fibrils) are made up of multiple triple helical collagen molecules

A

Tropocollagen

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31
Q

A single ____________ has a large effect on collagen function bc they disrupt the Gly - X-Y repeat that gives collagen its helical structure (Gly-X-Y can’t be replaced by another amino acid residue without having harmful effects on the collagen structure)

A

residue subsitituon

32
Q

Silk fibrioin is produced by moths & spiders & its polypeptide chains are predominatly in the ____ conformation

A

beta conformation

33
Q

Silk fibroin are also rich in ____ & ______ residues & its structure is stabilized by hydrogen bonding & London dispersion forces between sheets

A

Ala & Gly

34
Q

_________ is an oxygen-binding protein of muscle cells & functions to store oxygen & to facilitate oxygen diffusion in contracting muscle tissue

A

Myoglobin

35
Q

__________ is abundant in muscle of diving animals like whales, seals, etc bc storage & distribution of oxygen by muscle myoglobin permits the dinning mammals to remain submerge for a long time

A

Myoglobin

36
Q

______ & globular protein structure is stabilized by hydrophobic effect

A

Myoglobin

37
Q

The ______ group in myoglobin & hemoglobin is in a tight pocket were the accessibilty of the heme group is restricited since free heme group in an oxygenated solution oxidizes from Fe 2+(binds to O2) to Fe3+ (doesn’t bind to O2)

A

Heme group

38
Q

Motif (fold)

A

Is a recognizable folding pattern involving two or more elements of 2 structure & the connections between them (like two 2 structure folded against each other) (can be alpha helix or beta sheets or both, ex. coilied coil of alpha keratin)

39
Q

What are the two terms for describing structure pattern?

A
  1. Motif
  2. Domain
40
Q

Domain

A

Is a part of a polypeptide chain that is independently stable or could undergo movement as a single entity to the entire protein

41
Q

Usually large proteins with a few hundred aa residues fold into two or more _______ & a domain can still remain its native 3D structure even when separated from the polypeptide chain of the protein ( each domain may have its own function)

A

Domain

42
Q

Small proteins usually have _____ domain where the domain itself is the whole protein

A

one

43
Q

What are the constraints of folding for polypeptides?

A
  1. The hydrophobic effect makes a large contribution to the stability of protein structure
  2. When alpha helix & beta sheets are both in a protein they found at different structural layers bc the backbone of a polypeptide segment in the beta conformation can’t easily H Bond to an alpha helix that is adjacent to it
  3. Segments adjacent to each other in the amino acid sequence are usually stacked adjacent to each other in the folded structure
  4. The beta conformation is most stable in the right hand orientation
44
Q

Intrinsically disordered proteins

A

Have properties different from classical structures where they lack a hydrophobic core & have charged amino acids such as Lys, Arg, & Glu (Also contain Pro residue which disrupt ordered structure )

45
Q

Since __________ proteins lack an ordered structure they can facilitate a kind of protein interaction

A

intrinsically disordered

46
Q

Protein family

A

Proteins with similar primary strucuture and/or similar 3 structure & function (ex. globin family & myoglobin)

47
Q

Superfamilies

A

Two or more families that have little similarities in amino acid sequence but mostly the same structure

48
Q

Most proteins are multisubunit (have mulitple subunits) where a multisubunit protein is called _________

A

A multimer

49
Q

Oligomer

A

A multimer with just a few subunits

50
Q

Protomer

A

The repeating structural unit in multieric proteins

51
Q

_________ is the organization of proteins with multiple subunits (oligomer, dimer, tetramer, etc)

A

4 structure

52
Q

______ subunits can be identical (like in protomers) or different & its structure is stabilized by weak noncovalent interaction

A

4 structure

53
Q

___________ is a tetramer or a dimer of alpha beta protomer

A

Hemoglobin

54
Q

Loss of protein structure results in loss of _______

A

Function

55
Q

Denaturation

A

A loss of 3D structure which results in a loss of function (proteins denature when the environment they are in changes such as small increase in heat energy (or cold), pH changes (which alters ionization state of side chains & other groups & addition of chaotropic agents or detergents that disrupt the hydrophobic effect such asguanidiinium ions or Urea)

56
Q

A protein denaturing curve is _______ shape which indicates cooperactivity

A

Sigmoid

57
Q

Protein denaturation is ___________ due to the weak stabilizing forces which lead to the denaturation curve which lead to the sigmoid shape

A

Cooperative

58
Q

Melting temp at _____ denaturated is the Tm (which depends on pH & ionic strength)

A

50%

59
Q

Protein renature (reform) after denaturant is removed since only the _________ is needed to do so

A

Primary sequence

60
Q

Globular single subunit is ______ in the cytoplasm (ex.myoglobin)

A

soluble

61
Q

Globular subunits can have the same or _______ subunit (ex. hemopglobin)

A

Different

62
Q

Unfolding of protein is a _________ process where loss of structure in one part of the protein destabilizes other parts

A

Cooperative

63
Q

_________ sequence determines 4 structure ( the 3 structure of a globular protein is denatured by its amino acid sequence) (determines the native conformation)

A

Amino acid

64
Q

Renaturations

A

When denatured protein returns to their native conformation

65
Q

Describe the Anfinsen experiment

A
  1. Ribonuclease A in its native state is catalytically active but when urea & mercaptoethanol is added it unfolds
  2. In its unfolded state its inactive & disulfide cross-link are reduced to yield cys residues
  3. When urea & mercapoethamol is removed the protein (nonuclease) spontaneously returns to its native state where its catalytically active & disulfide cross- linked reforms
66
Q

Polypeptides fold _______ by stepwise process

A

Rapidly

67
Q

What are the other stabilizing forces?

A
  1. H-bonds (minor contribution, contributes to cooperative folding & 2 structure, 2-8kj/mol)
  2. Electrostatic interaction & ion pairs or salt bridge (small contribution)
  3. Vna der waals forces in the packed protein interior
  4. Disulfide bonds (form within or between polypeptide) chains between cysteines)
  5. Metal coordination (Metal coordination bu side chains)
68
Q

________ interactions are the main stabilizers

A

Hydrophobic

69
Q

Folding for many proteins requires ________ which are proteins that interact with partially folded or improperly folded polypeptides to make the correct folding occur

A

Chaperones

70
Q

What are the two major types of chaperones?

A
  1. Hsp 70 family
  2. Chaperones
71
Q

The _______ family is usually found in cells that are stressed by elevated temps & bind to regions of unfolded polypeptides that are rich in hydrophobic residues (bind & release peptide hydrophobic regions)

A

Hsp 70

72
Q

The _______ protect proteins that are denatured by heat

A

Hsp 70

73
Q

_________ are required for the folding of proteins that don’t spontaneously fold (its system is called Hsp 60)

A

Chaperones

74
Q

Defects in protein folding provide the molecular basis for a wide range of human _________ disorders

A

Genetic

75
Q

Many conditions such as ________ diabetes, Alzheimer disease & Parkinson disease are caused/ associated with a misfolding mechanism

A

Type 2

Biochemistry (26 decks)

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