1
Q
Main Functions in the cell
A
Enzymes , Structural , Transport, Storage, Signaling, Receptors, Gene regulation , Special Functions
2
Q
Rarely the sequence of amino acids is NOT sufficient for determine the function of the protein.
Some proteins require a non-protein molecule to enhence their performance.
What are the four examples of non-protein molecule?
A
- Cofactors
- Coenzymes
- Prosthetic Groups
- Other modifications
*These groups may be covalently or non-covalently connected with the structure of the protein.
3
Q
What are the prosthetic groups?
A
Compound of non-amino acidic nature linked to protein.
ex) Heme group
4
Q
What is the general term of cofactor indicating?
A
A functional non-amino acidic component that render(표현하다) possible the enzymatic activity
ex) usually a metal ion or little molecules
5
Q
What are the coenzymes?
A
Coenzyme are a class of cofactors, organic molecules with a complex structure required by an enzyme.
- They content vitamins of nucleotide (NAD+, NADP+, FAD, Coenzyme A)
6
Q
How are the proteins made?
A
Proteins are made by 20 amino acids linked by peptide bonds.
7
Q
What is the polypeptide backbone?
A
Polypeptide backbone is the repeating sequence of the N-C-C- N-C-C … in the peptide bond.
8
Q
What is the two things which is not part of the backbone or the peptide bond?
A
- Side chain
2. R-Group
9
Q
What are the 10 polar amino acids which is hydrophilic?
A
@Side Chain - Negative 1. Aspartic Acid ( Asp) 2. Glutamic acid (Glu) @Side Chain - Positive 3. Arginine (Arg) 4. Lysine (Lys) 5. Histidine (His) @Side Chain - Uncharged Polar 6. Asparagine (Asn) 7. Glutamine (Gln) 8. Serine (Ser) 9. Theonine (Thr) 10. Tyrosine (Tyr)
10
Q
What are the 10 nonpolar amino acids which is hydrophobic?
A
@Side Chain - Nonpolar
- Alanine
- Glycine
- Valanine
- Leusine
- Isoleucine
- Proline
- Phenylalanine
- Methionine
- Tryptophan
- Cysteine
11
Q
How the Polypeptide backbone made?
A
- The carboxylic group of one AA(amino acid) can condense with the amino group of another AA.
- Removing water and forming a Covalent C-N Bond.
12
Q
What are the two thing that the dipeptide has?
A
- An amine group at one end (the N-terminus)
2. A carboxylic group at the other (the C-terminus)
13
Q
Is the C=O bond (Peptide bond, in the carbonyl of the peptide group) actually a double bond?
A
No, actually the electrons forming this double bond are shared (in resonance structure).
Thanks to the resonance, the peptide bond is very similar to a double bond.
- It is shorter than the C-N single bond in a normal amine, but it is longer with respect a double bond.
14
Q
Is there free rotation around the peptide bond?
A
No, there is no free rotation around the peptide bond placing C,O,N and H between them in one plane.
15
Q
Are the polipeptide chain is linear?
A
No, not linear and rigid.
16
Q
How the final protein shape is determined?
A
The Amino acid sequence.
- Conformation : Spatial arrangement of atoms depending on bonds and bond rotations, and it is particularly stable and has the lowest level of free energy.
17
Q
What is the four weak interactions that the native protein is folded through?
A
- Hydrophobic interactions
- Hydrogen bonds
- Ionic bonds
- Van der Waals forces
18
Q
Which makes the protein to loose this conformation?
A
Particular conditions (Heat, pH, Chemical treatments) by a process of UNFOLDING (Denaturation).
19
Q
What is the example of primary structure?
A
Amino acid residues
20
Q
What is the example of the secondary structure?
A
Alpha Helix, Beta Sheet
21
Q
What is the example of the third structure?
A
Polypeptide chain
22
Q
What is the example of the quaternary structure?
A
Assembled subunits
23
Q
What is the primary structure of a protein refers?
A
It refers to its amino acid sequence.
24
Q
How amino acids in peptides and proteins are joined together?
A
By the peptide bonds.
25
How the protein sequences are written?
From left to right.
From the protein's N-terminus to C-terminus.
26
What is the secondary structure?
It is the local spatial arrangement of polypeptide's backbone atoms without regard to the conformations of its side chains.
27
What makes the alpha helix being more stabilizing?
Hydrogen bonds between the backbond carbonyl oxygen and amide nitrogen atoms.
28
Hydrogen bonds occur with position in residues?
H-bonds occur between residues located in the (n) and (n+4) positions relative to one another
29
What are the 5 different type of restrictions able to modify the helix stability?
1. The electrostatic repulsion and/or actraction between amino acids
2. The dimension of R groups
3. Interactions between side chains
4. Proline residues
5. Glycine R-group is too small and destabilizes the helix
30
What is the tendency of Beta-strands?
Beta-strands tend to occur in pairs or multiple copies in Beta-strands that interact with one another via H-bonds directed perpendicular to the axis of each strand.
31
How long is Beta-stands in proteins?
Most Beta-stands in proteins are 5-8 aas long.
32
How many amino acids are consist of Beta-turn?
Beta-turns consist of 3-4 amino acids that form tight bends, where are present Glycine and Proline.
33
What are the longer connecting segments between Beta-strands called?
Loops
34
Beta strands can be oriented in anti-parallel or parallel organization.
Describe about anti-parallel and parallel in Beta-sheets.
1. Anti-parallel : The polypeptide chain runs organizing different stretchs in opposite direction with respect to the next.
2. Parallel : The stretchs are organized in the same direction with long looping sections between them.
35
While the primary structure is intuitive, it is more complicated to understand how to get the secondary structure.
What determines the secondary structure?
Torsion angles
1. alpha-Carbon with N = Phi
2. alpha-Carbon with C = Psi
36
Describe about the value of angles (Phi) and (Psi).
The angles (Phi) and (Psi) can assume values corresponding to a plane angle, with positive and negative values corresponding to the rotation of peptide plane in the CLOCKWISE (Phi) or COUNTER-CLOCKWISE (Psi) direction.
The values of angles (Phi) and (Psi) of every amino acid describe the polypeptide chain conformation.
37
In Ramachandran Plot, the areas in dark blue represent what?
It represent the conformations sterically allowed (no sterical overlapping).
38
In Ramachandran Plot, the areas in blue represent what?
It represent the conformations are always possible, but they are at maximum extent of the stability in the context of not good contacts between atoms.
39
In Ramachandran Plot, the areas in light blue represent what?
It represent they are permitted only those structures just due to the presence of little bulky residues.
40
What does the Ramachandran plot provides?
1. The Ramachandran plot provides and easy way to view the distribution of torsion angles in a protein structure.
2. It also provides an overview of excluded regions showing which rotations of the polypeptide are not allowed due to steric hindrance (collisions between atoms).
3. The Ramachandran plot of a particular protein may also serve as an important indicator of the quality of its three-dimensional structures.
4. In the regions with the most stable structures, is then possible to predict the type of secondary structure always considering the combination of the torsion angles.
41
What does the tertiary structure refers?
It refers to the folded 3D structure of a protein.
It is also known as the NATIVE STRUCTURE or ACTIVE CONFORMATION.
42
What is the tertiary structure stabilized by?
It is stabilized by NONCOVALENT INTERCATIONS between secondary structure elements and other internal sequence regions (between the R groups exposed inside and outside the protein).
Keep in mind that most proteins are somewhat flexible and undergo subtle conformational changes while carrying out their functions.
43
What does the quaternary structure refers?
It refers to the number of subunits, their relative positions and contacts between the individual monomers in a multimeric protein.
Multi-subunit (multimeric) proteins have another level of structural organization known as QUATERNARY STRUCTURE.
44
Describe about four features about protein.
1. Each protein has a specific chemical and structural function.
2. The structure of a protein is determined by its amino acidic sequence (Primary Structure).
3. The function of a protein, directly depends on its structure.
4. Each protein has a specific and unique tridimensional structure that is stabilized by not covalent interactions.
45
Why the secondary structure motifs have a consensus sequence?
Because the amino acids sequence ultimately determines structure.
46
How the Beta barrel is composed of?
A beta barrel is a beta-sheet composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond).
Beta-strands in many beta-barrels are arranged in an antiparallel fashion.
47
What are there other different types of secondary structure?
1. Hairpin loops (alpha reverse turns) - often between anti-parallel beta strands.
2. Omega loops - beginning and end close (6-16 residues)
3. Extended loops - more than 16 residues
48
What can be proteins classified in?
1. Fibrous proteins : With a secondary bi-dimensional structure (even if it is a tridimensional organization)
2. Globular proteins : Mostly characterized by TERTIARY and QUATERNARY STRUCTURE.
A compact shape like a sphere with irregular surface.
In many cases, multimeric proteins achieve extremely large sizes, e.g. 10s-100s of subunits.
* Such complexes exhibit the highest level of structural organization known as SUPRAMOLECULAR STRUCTURE.
49
What are three important Fibrous Proteins?
1. Keratin - Component of hairs, horns and nails.
2. Collagen - The most important component of the extracellular matrix (ECM).
3. Elastin - Unstructured fibers that gives elasticity to some tissues.
These last proteins are basic structural elements and have special mechanical properties.
*They are found ad components of skin, connective tissues, blood vessels, sclera and cornea of eye.
50
How the KERATIN is composed of?
It is a molecule formed by 2 right-handed helices coiled together (coiled-coil) shape and organized in PROTOFILAMENTS and PROTOFIBRILS.
* 2 KERATIN polypeptides form DIMERIC COILED COIL.
* PROTOFILAMENTS are formed from 2 staggered rows of associated coiled coils.
* PROTOFILAMENTS dimerize to form a PROTOFIBRIL, 4 of which form a MICROFIBRIL.
51
What is the four features of COLLAGEN?
1. It is the most abundant protein in the body.
2. It is long, rigid structure and it is the major component of the connective tissues such as bone, cartilage, teeth, tendon and the fibrous matrices of skin and blood vessels.
3. Vertebrates have 46 genetically distinct polypeptide chains that are assembled into 28 collagen varieties found in different tissues in the same individual.
4. Type 1 has 285kDA m.w., length of 3000 amstrong, width of 14 amstrong.
52
How the COLLAGEN is composed?
It is composed by three alpha-HELICES wrapped around one another in a rope like fashion.
This structure of triple helix is also called SUPER alpha-HELIX.
53
What are the 4 characteristics of COLLAGEN composition?
1. Collagen is a glycoprotein containing GALACTOSE and GLUCOSE as the carbohydrate content.
2. Collagene has a particular primary structure in each of the three helices, due to the presence of GLYCINE, that is found in every third position of the polipeptide chain.
3. It fits into the restricted spaces where the 3 chains of the helix, come together.
4. It is also present PROLINE; it facilitates the formation of the alpha-helix, because its ring structure causes curve in the peptide chain, and consequently the super helix formation.
54
How the primary structure is formed?
It is formed by a repeating sequence, and Glycine residues are part of it : GLY-X-Y
* GLY : GLYCINE
* X = Frequently(80%) PROLINE
* Y = It is often HYDROXYPROLINE (Hyp), but can be HYDROXYLYSINE (Hyl).
55
When the HYDROXYLATION of PROLINE and LYSINE RESIDUES occurs?
It occurs after their incorporation into the polypeptide chains (POST-TRANSLATIONAL modification) with a reaction catalyzed by PROLYL (or LYSIL) HYDROXYLASE.
* The hydroxylation of proline generates 4-Hydroxyproline (4-Hyp) or 3-Hydroxyproline (3-Hyp).
* The hydroxylation of lysine generates 5-Hydroxylysine
56
When does the hydroxylation occurs and what are the requirements for the reaction?
Hydroxylation occurs in the ER(Endoplasmic Reticulum) Cisternae and the reaction requires specific COFACTORS.
* Specific COFACTORS are O2, Fe and ascorbic acid (Vitamin C).
* In a second midification, the hydroxyl group of HYDROXYLYSINES residues are ENZYMATICALLY GLYCOSYLATED by adding GALACTOSE and GLUCOSE as the carbohydrate content.
57
What give stability and strength to hydroxyproline and hydroxylysine?
Hydroxyproline and hydroxylysine give stability and strength by H-bonding and by glycosilation.
58
What makes the bond formation between the exposed R-groups of neighboring collagen monomers?
In collagen, amino acid side chains need to be exposed in a radial pattern on the surface of the superhelix.
This allows bond formation between the exposed R-groups of neighboring collagen monomers.
And this leads to aggregation into fibrils.
59
What is the requirement for the hydroxylation enzymes to exert their function?
Without the specific cofactors (O2, Fe and ascorbic acid), the hydroxylation enzymes cannot exert their function.
60
what is the main disease resulting from the deficiency of VITAMIN C?
SCURVY.
* This disease often presents itself initially as symptoms of illness and lethargy, followed by formation of spots on the skin, spongy gums and bleeding from the mucous membranes.
* Additionally, collagen fibrils cannot be cross-linked, greatly decreasing the tensile strength of the assembled fiber.
61
What is the components of Tertiary Structure?
1. FOLD : Corresponds to a well-defined and recognizable structure, that is to the 3 dimensional structural organization.
2. DOMAIN : Represents a STRUCTURAL AND FUNCTIONAL PROTEIN.
62
What can DOMAINS be? ( in two way)
It may occur that DOMAINS are also :
1. different functional and structural PORTIONS of one protein.
2. different functional and structural UNITS of one protein, if the protein is formed by different monomers.
* Different domains can impart different functions to proteins.
* Proteins can have one or many domains depending on the protein size.
63
The biological function of some molecules is determined by what?
By multiple polypeptide chains, the multimeric proteins.
* Chains can be
1) Homeodimer : IDENTICAL
2) Heterodimer : DIFFERENT
*The interactions stabilizing multimers are the same as that found in tertiary and secondary structures.
64
What types of bonds are there in proteins which is non-covalent bonds?
1. Ionic bond
2. Hydrogen bond
3. Van der wals attractions
65
What is the disulfide bond which is resulting from an oxidative process?
It is a sulfur-sulfur chemical resulting from an oxidative process that links nonadjacent -SH of cyteines present in a protein.
66
What is the type of disulfide bonds?
It is cystein-cystein linkage which is a stable part of their final folded structure and those in which pairs of cysteines alternate between the reduced and oxidized states.
67
What is the denaturation?
Denaturation is the loss of the three-dimensional structure.
68
How can you do the reversible process?
By the removal of the denaturant agent so that allows to resume spontaneously the native structure.
*IRREVERSIBLE process : The protein doesn't return to the original condition.
69
What the prof for the amino acid sequence contains enough information to specify tertiary structure?
The prof is that the proteins can spontaneously fold from an UNFOLDED STATE to their FOLDED NATIVE STATE.
*Bonds within the peptide backbone seek out different possible conformations until to the obtaining of the final tertiary structure.
70
What is the protein folding?
Protein folding = Spontaneous acquisition of native conformation under physiological conditions.
71
What is the protein folding problem consists of two parts?
1. Creating a stable, well-defined structure with the LOWEST FREE ENERGY CONTENT and that is significantly MORE STABLE than all other possible structures.
2. Finding a way to get to that structure.
72
Why the protein collapses?
Due to hydrophobic effect.
73
In the protein collapses, hydrophobic environment drives what?
It drives formation of sencondary structure to form molten globule.
74
Repacking of molten globule leads what?
It leads to native structure.
75
Packing of secondary structure elements leads what?
It leads to molten globule.
76
How long does it takes to fold and to reach their native conformation?
Proteins follows specific path to fold and to reach native conformation in less than few seconds.
77
What is the beginning step of protein folding?
The folding begins with the formation of local segments of secondary structure (5 milliseconds).
78
Which point of view is that the native structure is the most stable?
By the thermodynamically point of view.
79
A protein during its folding process, which state must be proceed?
From a State of HIGH ENERGY AND ENTROPY LEVELS to another state characterized by LOW ENERGY AND ENTROPY LEVELS.
80
Which represents a free energy surface for the folding process?
The FUNNEL represents a free energy surface for the folding process.
* The protein folding process is highly cooperative.
* Recesses and gorges represent the conformations temporarily acquired.
* Substantial exclusion of water occurs very early in the folding process.
81
(REFOLDING AFTER DENATURATION PROCESS)
| Duringthe spontaneous refolding process, the polypeptide chain is subjected to what?
1. The formation of secondary structure shape (alpha helices and/or beta sheets).
2. The formation of the three-dimensional structure (if it is not a fibrous protein).
* For many years, it was assumed that all the denatured proteins in vitro, have the ability to fold correctly, after the removing of the denaturant agent.
* It was demonstrated that just the SMALLER PROTEINS, having simple structures, possess this ability.
82
What are the two factors that seem to prevent and hinder the correct folding of LARGER PROTEINS?
1. The tendency to form insoluble aggregates.
| 2. The propensity to undertake different pathways leading to an incorrect folding.
83
What is the misfolded proteins?
1. Unstable and not functional.
| 2. Stable but working with a not correct function.
84
What is molecular chaperones?
It is small proteins able to help the folding and can help a new, or a denaturated protein to adopt the correct native conformation.
*Their primary function is to find and rescue misfolded proteins.
85
What is the folding agents which makes proteins being kinetically slow and assists in vivo?
The Chaperones.
*These proteins are found in all organisms and even in different organelles of eukaryotic cells.
86
What is the three part that chaperones assist in?
1. Folding of nascent polypeptides made by translation.
2. Re-folding of proteins denatured by environmental demage, such as heat shock.
3. Molecular chaperones bind to unfolded nascent polypeptide chains as they emerge from the ribosome, and prevent aggregation, misfolding, and degradation.
87
What is the word which is describe the chaperone?
It is HEAT SHOCK PROTEINS.
* For example, in drosophila cells, is normally synthesized a protein of PM70.000 whose concentration increases significantly by exposure of the cell to temperatures of 36'C ~ 37'C.
It is possible to observe a decrease of synthesis of other proteins of the cell and the devices deputies to work at high protein synthesis schemes for the synthesis of the protein of PM70.000 .
* THIS PROTEIN HAS BEEN IDENTIFIED WITH THE CODE : HSP70 (HSP = Heat Shock Protein).
88
What is the result of thermal shock to HSP70?
In fact, protein synthesis capacity was almost completely devoted to synthesize HSP70, able to restore the three dimensional structure of proteins denaturated as result of thermal shock.
* After, it was clarify that HSP70 belong to a subclass of CHAPERONINS that are part of a broader class of proteins produced by the cell also in response to a variety of different stimuli such as :
1) Heat shock, heavy metals, chemotherapeutic molecules, toxic agents.
2) Pathological situation : Viral infections, fever, inflammation, tumors.
89
What is the eukaryotic CHAPERONIN?
Eukaryotic CHAPERONINS are large multimeric complexes related to the bacterial GroEL and GroES proteins.
90
How the GroES is constituted by?
GroES is constituted by 7 subunits joined together to form a sort of single disc that caps GroEL at one end.
91
How the GroEL is consists of?
GroEL consists of 14 subunits organized in two groups, each of 7 subunits.
* These two groups are overlapped and form two different zone.
1) One upper : CIS Conformation
2) One lower : Trans Conformation
92
What is ATPase DOMAIN?
It recognizes and binds the ATP as the energy source, in order to perform their auxiliary action in the proper folding of misfolded or denatured proteins.
* It is upper part of Cis Conformation. (In GroEL)
93
What is SUBSTRATE (PROTEIN) RECOGNITION DOMAIN?
It is deputated to recognize and bind misfolded proteins to attend in folding process.
* It is lower part of CIS Conformation. (In GroEL)
94
Describe about the mechanism of action of the GroEL/GroES complex.
The mechanism of action of the GroEL/GroES complex is comparable to that of a CAGE, that blocks inside the unfolded protein and releases it just when properly folded.
* This process occurs thanks to hydrolysis of 7ATP molecules, that induces a conformational change in the GroEL-GroES complex.
95
Describe the process of folding process.
Once the polypeptide enters the upper cavity, 7ATP molecules bind the ATPase domain of each of the seven subunits forming the upper domain(CIS).
The hydrolysis of the 7 ATP molecules, induces a CONFORMATIONAL CHANGE, and provokes the shift of GroES on the apex of GroEL, where it acts as a sort of cap closing the unfolded protein inside the channel, until the end of folding process.
96
Why is so important the role of chaperons?
Most of proteins in the body maintain their correct native conformation, but if they lost this structure, and if not intervene chaperones, they are proteolytically degraded.
In case it is performed neither of the two mechanisms of repair/removal of a bad protein product, this can precipitate forming insoluble aggregates known as AMYLOID FIBERS.
97
What are the disease result from protein misfolding or caused by amyloid formation?
1. Alzheimer's disease
2. Cystic Fibrosis
3. Mad Cow disease (prions)
4. Transmissible spongiform Encephalophaties
5. Inherited form of Emphysema and even many cancers
98
What is the name of the agent which causes Alzheimer's disease or stuff like that?
It's called PRIONS, structures made from PrP protein normally present in the brain with unknown function.
* Prions are aggregated forms of the PrP protein(PrPSC).
* The normal PrP protein contains large areas folded as alpha-helix; in PrPSC protein, in some regions, the helices are converted into beta structures that are associated to form AGGREGATES OR AMYLOID FIBRILS.
* One of the great discoveries in medicine and was that certain infections associated with neurological diseases were transmitted by agents similar to viruses but CONSISTING ONLY PROTEINS.
99
Where is the AMYLOID PRECURSOR PROTEIN cleaved?
In Alzheimer's disease, it is cleaved into a peptide product (Beta-amyloid) that aggregates and precipittes in AMYLOID FILAMENTS.
100
The misfolding of Beta-amyloid, leads what?
Beta-amyloid, which involves a transition from alpha-helical to beta-sheet conformation, leads to filament formation.
* In MAD COW DISEASE( Transmissible Spongiform Encephalopathy), prion proteins precipitate causing lesion.
Protein
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