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Lecture 4 & 5 Flashcards

1
Q

Who was Gerhardus Johannes Mulder?

A

-calculated molecular formula of egg and serum albumin
-proposed that proteins were made of smaller building blocks (called grundstoff)
-used acid hydrolysis to try to determine what grundstoff (discovered aa)
-first to use the word “protein”

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2
Q

Who was one of the fathers of biochemistry and what did he do?

A

Anselme Payen

discovered the first enzyme (diastase) in 1833 -extracted from malt solution

DID NOT KNOW AMYLASE WAS A PROTEIN

isolated and named cellulose

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3
Q

In what order are amino acid sequences written?

A

written from the N terminus (+NH3) to the C terminus (COO-)

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4
Q

What is the primary structure of proteins?

A

the amino acid sequence

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5
Q

What did Sanger’s work do?

A

implied there was a template in the cell that contained this information (the terminus and how they should be read)

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6
Q

What is the amino acid sequence?

A

Asp-Phe-Ile-Asn

or

DFIN

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7
Q

Why did Frederick Sanger win the Nobel Prize in 1958? What else did he do?

A

For sequencing insulin

-proved proteins had a defined primary structure
-second Nobel prize for sequencing DNA

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8
Q

What did Sanger use for his work?

A

Edman’s protein sequencing

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9
Q

What does cyanogen bromide (CNBr) cleave and what are the results?

A

cleaves the polypeptide at the C-terminal side of methionine

-produces a peptide homoserine lactone
-generates a new N-terminus

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10
Q

What is cleaved and what is blocked in protein sequencing?

A

cleaving disulfides
blocking cysteines

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11
Q

What is the order of the central dogma?

A

DNA makes RNA which makes Protein

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12
Q

Most polypeptides contain how many amino acids?

A

between 50 and 2000 amino acids

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13
Q

What is the average molecular weight of an amino acid?

A

110 daltons

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14
Q

What is the average molecular weight of proteins?

A

from 5500 to 220,000 daltons

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15
Q

Intracellular proteins

A

often lack disulfides

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16
Q

Extracellular proteins

A

often have disulfides

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17
Q

How can you get an estimate of a protein’s molecular weight?

A

by multiplying the number of protein amino acids by 110

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18
Q

Who received the Nobel prize for hemoglobin?

A

Max Perutz

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19
Q

Proteins are made by:

A

amino acid condensation

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20
Q

If we mix 2 amino acids in solution will we get a dipeptide?

A

no

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21
Q

Phylogenetic trees based on protein homology are consistent with _______ ____ sequences or morphology.

A

Phylogenetic trees based on protein homology are consistent with RIBOSOMAL RNA sequences or morphology.

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22
Q

What kind of proteins have a common ancestral protein?

A

homologous proteins

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23
Q

Conserved residues generally have a purpose related to:

A

structure
function

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24
Q

Proteins with similar ____ normally have similar _____.

A

Proteins with similar FUNCTION normally have similar STRUCTURE.

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25
What is more conserved than sequence?
structure
26
Can proteins be modified?
yes
27
Insulin maturation involves what?
involves the formation of three disulfide bonds and three proteolytic cleavages of the peptide bond, resulting in two disulfide-linked polypeptides
28
For protein folding, what must there be with amino acids?
a. the stereochemistry of each amino acid must be maintained -atomic connectivity -bond lengths -bond angles -ring planarity -dihedral angles b. covalent bonds can NOT be broken or formed
29
What does the peptide plane restrict?
restricts torsions
30
In protein folding, what is Levinthal's Paradox?
given a polypeptide of 101 residues with each residue having 3 possible conformations -it would take YEARS to try all possible conformations...much longer than the universe has existed
31
What is a paradox?
folding for most small proteins is very fast
32
Anfinsen's Dogma
for small globular proteins: -native structure determined ONLY by the protein's sequence or -native structure is a UNIQUE, STABLE, and KINETICALLY ACCESSIBLE minimum of the free energy for a given environment (temp., solvent concentration etc.)
33
Why was Christian B. Anfinsen awarded the Nobel prize?
Ribonuclease A folding
34
In the statement- "native structure is a UNIQUE, STABLE, and KINETICALLY ACCESSIBLE minimum of the free energy for a given environment (temp., solvent concentration etc.)" explain unique, stable, and kinetically assessable.
UNIQUE: only one conformation having this free energy STABLE: conformation resists change (energy surface that looks like a funnel) KINETICALLY ASSESSABLE: smooth energy path between the two states
35
Primary structure determines tertiary structure.
Afinsen's Dogma
36
Disulfide bonds form AFTER the protein folds.
Protein Disulfide Isomerase (PDI)
37
How many possible S-S combinations are there?
105
38
What is denaturation?
the disruption of native conformation of a protein, with loss of biological activity (use heat or chemicals) -proteins fold cooperatively
39
During the folding process, what happens to the polypeptide?
the polypeptide collapses into an intermediate "molten globule" due to the hydrophobic effect, then backbone is rearranged to achieve a stable native conformation
40
What is the driving force of protein folding?
-the large increase in entropy as water is released to bulk solvent -hydrophobic collapse and secondary structure forms at same time
41
What are the four hypothetical protein-folding pathways, and which is which according to the picture?
1) extended structure 2) partial secondary structure 3) approximate tertiary structure 4) native structure
42
What do proteins fold by rather than by random?
Proteins fold by the progressive stabilization of intermediates rather than by random search
43
Chaperonin-assisted protein folding
needs energy -hydrolysis of several ATP molecules is required
44
E. coli Chaperonin (HSP60 or GroE)
prevents incorrect protein aggregation -protein folding takes place inside the central cavity
45
What are the four principles of the protein folding problem?
1) bury hydrophobic groups 2) expose charged groups or neutralize with salt-bridges 3) expose polar groups or satisfy h-bonding 3) obey stereochemical restraints
46
Hydrophobic collapse
results in the disordered peptide condensing around a weakly ordered folding nucleus, usually a small turn or short stretch of local secondary structure
47
Some folding features are cooperative, what is an example of this?
the amphipathic helix
48
What does an amphipathic helix need?
needs other structure to shield its hydrophobic surface needs another HYDROPHOBIC structure to shield its HYDROPHOBIC surface
49
What is the problem of main chain h-bonding?
how to bury hydrophobic side-chains in the core of a protein and still satisfy the strong dipole and h-bonding needs of the peptide backbone
50
What did Linus Pauling the "Super Scientist" earn his two Nobel prize's for?
1st: Helices and Strands 2nd: Peace Prize
51
The alpha-Helix
carbonyl (C=O) of reside 1 accepts a proton from the amide hydrogen (N-H) of residue (n +4) 3.6 residues per turn H-bond between atoms 1 and 13
52
What does 3.6 residues imply?
For every turn (3.6 residues) of the alpha-Helix, there are between 3 and 4 H-bonds
53
Where are amphipathic helix's typically found?
often found on the protein's surface or at protein-protein interfaces
54
Is there such thing as a single amphipathic helix in solution?
NO
55
What do you do at the generate wheel? Helical Wheel
its where residues are spaced 100 degrees apart -place AA at each position -shows that the helix has one hydrophilic side and one hydrophobic side
56
What two ways can sheets and strands be? What is a, and what is b?
Parallel and anti parallel a) anti parallel b) parallel
57
With peptide bond torsion angles, how is native conformation achieved?
by rotating the main and side chain torsion angles
58
There are cis and trans isomers. There is a strong preference for ___ due to steric clash.
trans
59
Proline is a special case when it comes to cis and trans isomers. Why?
it permits both cis AND trans conformers
60
What two amino acids often appear in turns, and why?
GLY and PRO GLY- small side chain PRO - cis configuration is amenable to tight turns
61
For both type 1 and type 2 beta turns:
- the 1st and 4th amino acids are H-bonded - the 2nd and 3rd are usually H-bonded to H20
62
Why is proline known as a helix killer?
it does not have an N-H group needed for continuing the H-bonding scheme its unique cyclic structure prevents it from forming the necessary H-bonds to maintain a stable alpha helix causing kink or disruption breaking the helix structure
63
The pI of the protein depends on what?
its sequence
64
What is the pKa of the: N-terminal C-terminal Ionizable side chains
N-terminal (NH3): ~ 10 C-terminal (COO-): ~ 2 Ionizable side chains: varies by a.a.
65
Proteins are charged. The charge depends on what?
the pH as you change the pH of the buffer, the charge of the protein will also change as charged groups are titrated
66
The pH where the protein has no net charge is what?
is the pI of the protein
67
What are prions? Mis-folding
same sequence different fold
68
What do prions lead to?
leads to aggregation (plaque formation)
69
Building the proteins tertiary structure:
Motifs -> Folds -> Domains -> Structure
70
In: Motifs -> Folds -> Domains -> Structure What are Motifs?
recognizable combination of secondary structures (helices, stands, and turns) that appear in different proteins and are usually associated with a function
71
In: Motifs -> Folds -> Domains -> Structure What is a Fold?
the order and topology of secondary structure elements in a domain can contain one or more motifs
72
In: Motifs -> Folds -> Domains -> Structure What are Domains?
a section of a polypeptide that folds independently of the rest
73
In: Motifs -> Folds -> Domains -> Structure What is Structure (tertiary)?
the three dimensional conformation of a natively folded polypeptide made up of one or more domains
74
What are common motifs?
helix-loop-helix coiled coil helix bundle beta alpha beta unit hairpin beta meander greek key beta sandwich
75
Common domain folds:
parallel twisted sheet beta barrel alpha/beta barrel beta helix
76
Quaternary structure
the association of two or more natively folded polypeptide chains (subunits) into an oligomeric complex polypeptides can be different but complex has defined stoichiometry
77
Each molecule has the same ___ fold but overall ___ is different.
Each molecule has the same GLOBIN fold but overall FUNCTION is different.
78
Globular proteins
usually water soluble, compact roughly spherical hydrophobic interior hydrophilic surface
79
Fibrous proteins
mechanical support collagen tendons skin hair
80
Membrane proteins
transport signaling
81
What is collagen?
a structural protein that is a component of skin, bone, tendons, cartilage, and teeth.
82
What does collagen consist of?
three intertwined helical polypeptide chains that form a superhelical cable NOT ALPHA HELICES HELIX IS NOT AN ALPHA HELIX
83
What do different proteins in the cell do?
they interact with one another

BCMB (6 decks)

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