De Levende Cel – Het boek
Samenvatting 2-1
Shape & structure
- The shape of a protein is specified by its amino acid sequence ( held together by covalent
peptide bonds, polypeptides)
- There’s a polypeptide backbone, consisting of a repeating of [N-C-C]
- Two different ends N terminus (NH3+, NH2, amino group)
C terminus (COOH, COO-, free carboxylgroup)
- Then there are side chains (these are not involved in the peptide bonds), they have unique
properties such as:
Nonpolar (hydrophobic) , polar can make hydrogen bonds with water that’s why it’s
hydrophilic.
Negatively or positively charged
Chemically reactive
Etc
- Long polypeptide chains are very flexible protein can fold in an enormous number of ways
- Noncovalent bonds help them maintain their shape:
Hydrogen bonds (H to N or H to O)
Electrostatic attractions (two opposite charges attract each other and thereby keep
the molecules close to each other)
Van der Waals attractions (small, local differences in charge can attract each other if
the two molecules fit into each other just right, surface is important)
Hydrophobic force (nonpolar side chains are forced together, this brings the polar
side chains on the outside where they can form hydrogen bonds with the water)
Final folded structure (conformation) Free energy G is minimized, this means that it’s energetically
favorable. There’s no energy in there that the cell could use.
A protein can be unfolded (= denatured) by disrupting the noncovalent bonds, this can be done by
adding solvents.
To get it back in shape (renaturation) just remove the solvents and it will fold again, aided by special
chaperone proteins.
Two common folding patterns:
1. Alfa helix
The N – H of every peptide bond is hydrogen bonded to the C = O of a neighboring peptide bonds 4
amino acids away.
,Side chains are not involved.
This pattern is very common. It forms when similar subunits bind to each other in a similar way.
2 or 3 alfa helices can wrap around each other (the hydrophobic sides inward), this way they
minimize the contact with the cytosol. Coiled coils
, 2. Beta sheets
Several strands of a polypeptide chain are held together by hydrogen bonding between peptide
bonds
Antiparallel and parallel. Core of many proteins. Give tensile strength. Very rigid.
Basis of amyloids structures: B sheets stacked together in long rows with amino acids side chains
interdigitated like a zipper.
A prion is a misfolded protein. They can sometimes form amyloid structures that can damage cells or
tissues.
A misfolded prion can convert properly folded proteins & form aggregates. “ infectious”
It can even spread to other individuals.
Levels of organization:
Primary structure Amino acid structure
Secondary structure Alfa helices & Beta sheets.
Tertiary structure Full three dimensional structure made by entire polypeptide chain.
Quaternary if the molecule exists as a complex of multiple chains, then it’s the interacting
polypetides.
Protein domain = segment of a polypeptide chain that can fold independently into a compact, stable
structure. Modular unit.
Different domains of a protein have different functions.
, An example:
A catabolite activator protein
Small domain – binds DNA
Large domain – binds cyclic AMP
Domains are connected by intrinsically disordered sequences.
There are 20 amino acids so there are 20^how many you use sequences. Not every sequence
however is useful. This depends on the structure. The right structures are found through evolution.
The folded proteins should not be able to engage in unwanted reactions with other proteins.
Protein families These are groups in which each member resembles the others in amino acid
sequence and three-dimensional structure.
Large protein molecules often contain more than one polypeptide chain. They bind noncovalently on
binding sites. Each chain is a subunit of the protein. Each subunit can have more than one domain.
2 subunits = a dimer
4 subunits = tetramer
Example: Hemoglobin (carries oxygen in red blood cells)
Two identical alfa globin subunits
Two identical beta globin subunits
Globular proteins Polypeptide chain folds up into a compact shape like a ball with an irregular
surface. (enzymes)
Fibrous proteins elongated structure, simple, collagen and elastin in the gel-like extracellular
matrix, keratin
Outside the cell are harsh conditions, proteins that are here are often stabilized by covalent cross-
linkages like disulfide bonds. S – S. These bonds are formed in the ER before secretion, they do not
change the final conformation but act as a stapler.
In one chain = intrachain. Between two chains is interchain.
How proteins work
- All proteins bind to other molecules (ligands)
- The protein has a binding site in the shape of the ligand. They bind with noncovalent bonds.
- Proteins usually bind to a specific ligand.
Antibodies: (immunoglobin proteins)
- Possible ligands are limitless.
Samenvatting 2-1
Shape & structure
- The shape of a protein is specified by its amino acid sequence ( held together by covalent
peptide bonds, polypeptides)
- There’s a polypeptide backbone, consisting of a repeating of [N-C-C]
- Two different ends N terminus (NH3+, NH2, amino group)
C terminus (COOH, COO-, free carboxylgroup)
- Then there are side chains (these are not involved in the peptide bonds), they have unique
properties such as:
Nonpolar (hydrophobic) , polar can make hydrogen bonds with water that’s why it’s
hydrophilic.
Negatively or positively charged
Chemically reactive
Etc
- Long polypeptide chains are very flexible protein can fold in an enormous number of ways
- Noncovalent bonds help them maintain their shape:
Hydrogen bonds (H to N or H to O)
Electrostatic attractions (two opposite charges attract each other and thereby keep
the molecules close to each other)
Van der Waals attractions (small, local differences in charge can attract each other if
the two molecules fit into each other just right, surface is important)
Hydrophobic force (nonpolar side chains are forced together, this brings the polar
side chains on the outside where they can form hydrogen bonds with the water)
Final folded structure (conformation) Free energy G is minimized, this means that it’s energetically
favorable. There’s no energy in there that the cell could use.
A protein can be unfolded (= denatured) by disrupting the noncovalent bonds, this can be done by
adding solvents.
To get it back in shape (renaturation) just remove the solvents and it will fold again, aided by special
chaperone proteins.
Two common folding patterns:
1. Alfa helix
The N – H of every peptide bond is hydrogen bonded to the C = O of a neighboring peptide bonds 4
amino acids away.
,Side chains are not involved.
This pattern is very common. It forms when similar subunits bind to each other in a similar way.
2 or 3 alfa helices can wrap around each other (the hydrophobic sides inward), this way they
minimize the contact with the cytosol. Coiled coils
, 2. Beta sheets
Several strands of a polypeptide chain are held together by hydrogen bonding between peptide
bonds
Antiparallel and parallel. Core of many proteins. Give tensile strength. Very rigid.
Basis of amyloids structures: B sheets stacked together in long rows with amino acids side chains
interdigitated like a zipper.
A prion is a misfolded protein. They can sometimes form amyloid structures that can damage cells or
tissues.
A misfolded prion can convert properly folded proteins & form aggregates. “ infectious”
It can even spread to other individuals.
Levels of organization:
Primary structure Amino acid structure
Secondary structure Alfa helices & Beta sheets.
Tertiary structure Full three dimensional structure made by entire polypeptide chain.
Quaternary if the molecule exists as a complex of multiple chains, then it’s the interacting
polypetides.
Protein domain = segment of a polypeptide chain that can fold independently into a compact, stable
structure. Modular unit.
Different domains of a protein have different functions.
, An example:
A catabolite activator protein
Small domain – binds DNA
Large domain – binds cyclic AMP
Domains are connected by intrinsically disordered sequences.
There are 20 amino acids so there are 20^how many you use sequences. Not every sequence
however is useful. This depends on the structure. The right structures are found through evolution.
The folded proteins should not be able to engage in unwanted reactions with other proteins.
Protein families These are groups in which each member resembles the others in amino acid
sequence and three-dimensional structure.
Large protein molecules often contain more than one polypeptide chain. They bind noncovalently on
binding sites. Each chain is a subunit of the protein. Each subunit can have more than one domain.
2 subunits = a dimer
4 subunits = tetramer
Example: Hemoglobin (carries oxygen in red blood cells)
Two identical alfa globin subunits
Two identical beta globin subunits
Globular proteins Polypeptide chain folds up into a compact shape like a ball with an irregular
surface. (enzymes)
Fibrous proteins elongated structure, simple, collagen and elastin in the gel-like extracellular
matrix, keratin
Outside the cell are harsh conditions, proteins that are here are often stabilized by covalent cross-
linkages like disulfide bonds. S – S. These bonds are formed in the ER before secretion, they do not
change the final conformation but act as a stapler.
In one chain = intrachain. Between two chains is interchain.
How proteins work
- All proteins bind to other molecules (ligands)
- The protein has a binding site in the shape of the ligand. They bind with noncovalent bonds.
- Proteins usually bind to a specific ligand.
Antibodies: (immunoglobin proteins)
- Possible ligands are limitless.
