Case 3: Lost in translation
Learning goals
- What is a protein?
Structure (3D)
Amino acids are tetrahedral structures. With a chiral C-atom
L-isomer amino acids, to which side the NH3+ is found on the left , are commonly
found, D amino acids are extremely rare.
Amino acids can bond by a peptide bond and form a dipeptide by combining the -
COO- group with the NH3+. So they could be linked as A-B, but also as B-A, which
makes different proteins. They could also form a tri- or tetrapeptide etc.
Peptides are short chains, polypeptides are long chains and proteins are even longer
chains. The amino acids are called residues.
The C-terminal amino acid or C-terminus is the residue with the free a-COO- group,
and the N-terminal amino acid or N-terminus is the residue with the free a-NH3+
group. We write the N-terminal residue on the left, proteins are thus synthesized
from N-terminus to C-terminus.
Chaperones help the chains to the structure to properly function, which are found in
the endoplasmic reticulum
- Primary structure: Describes the linear
sequence and determines the secondary
and tertiary structure. When the particular
R groups are in the proper positions, all of
the hydrogen bonds, salt bridges, disulfide
linkages and hydrophobic interactions that
stabilize the three-dimensional structure
of that molecule can form.
- Secondary structure: The pattern in which
proteins fold and align themselves
Alpha-helix: A secondary structure
where the protein folds into a coil
held together by hydrogen bonds
parallel to the axis of the coil
Beta-pleated sheet: A secondary
protein structure in which the
backbone of two protein chains in
the same or different molecules is
held together by hydrogen bonds
Random coil:
Extended helix:
- Tertiary structure: The three-dimensional arrangement of every atom in the
molecule
Covalent bonds: to stabilize by mostly disulfide
Hydrogen bonding: stabilizes between polar groups on side chains or
between side chains and the peptide backbone
, Salt bridge: electrostatic attractions, occur between two amino acids with
ionized side chains—that is, between an acidic amino acid (-COO2) and a
basic amino acid (-NH3+ or -NH2) side chain. The two are held together by
simple ion–ion attraction
Hydrophobic Interactions: In aqueous solution, globular proteins usually turn
their polar groups outward, toward the aqueous solvent, and their nonpolar
groups inward, away from the water molecules. The nonpolar groups prefer
to interact with each other, excluding water from these regions. The result is
a series of hydrophobic interactions
Metal Ion Coordination: Two side chains with the same charge linked via a
metal ion.
- Quaternary structure: The spatial relationship and interactions between subunits in
a protein that has more than one polypeptide chain
Hemoglobin: Hemoglobin in adult humans is made of four chains (called
globins): two identical a chains of 141 amino acid residues each and two
identical b chains of 146 residues each. Proteins that contain non-amino acid
portions are called conjugated proteins. The non-amino acid portion of a
conjugated protein is called a prosthetic group.
Collagen
Integral membrane proteins
What do they consist of
Proteins are made out of amino acids, they consist of an amino group, -NH2, and a
carboxyl group, -COOH. The common found amino acids are called: Alpha amino
acids, the amino group is linked to the carbon next to the -COOH carbon.
An important aspect to determine the structure and function is the polarity of the R
group. Nonpolar side chains are hydrophobic, repel water, and
polar/neutral/acidic /basic side chains are hydrophilic, attracted to water.
Mutations
A mutation is an error in the copying of a sequence of bases
Mutagens: Organic compounds which induce mutations by reacting with DNA.
Point mutation: May change the amino acid code if the mutations occurs in the right
place in the code.
Nonsense : The altered DNA sequence prematurely signals the cell to stop
building a protein
Missense: Change in base pair results in the substitution
of one amino acid
Silent : Change without a subsequent change in the
amino acid or the function of the overall protein
Frameshift mutation: Losing or gaining a single nucleotide base
Deletion: When a part of a chromosome is left out
Insertion: When part of a chromatid breaks off and
attaches to its sister chromatid
Chromosomal mutation:
Inversion: When part of a chromosome breaks off and
reattaches backwards.
Translocation: When part of one chromosome breaks
off and is added to a different chromosome
Transversion : When a purine is substituted for a
pyrimidine or a pyrimidine replaces a purine
Learning goals
- What is a protein?
Structure (3D)
Amino acids are tetrahedral structures. With a chiral C-atom
L-isomer amino acids, to which side the NH3+ is found on the left , are commonly
found, D amino acids are extremely rare.
Amino acids can bond by a peptide bond and form a dipeptide by combining the -
COO- group with the NH3+. So they could be linked as A-B, but also as B-A, which
makes different proteins. They could also form a tri- or tetrapeptide etc.
Peptides are short chains, polypeptides are long chains and proteins are even longer
chains. The amino acids are called residues.
The C-terminal amino acid or C-terminus is the residue with the free a-COO- group,
and the N-terminal amino acid or N-terminus is the residue with the free a-NH3+
group. We write the N-terminal residue on the left, proteins are thus synthesized
from N-terminus to C-terminus.
Chaperones help the chains to the structure to properly function, which are found in
the endoplasmic reticulum
- Primary structure: Describes the linear
sequence and determines the secondary
and tertiary structure. When the particular
R groups are in the proper positions, all of
the hydrogen bonds, salt bridges, disulfide
linkages and hydrophobic interactions that
stabilize the three-dimensional structure
of that molecule can form.
- Secondary structure: The pattern in which
proteins fold and align themselves
Alpha-helix: A secondary structure
where the protein folds into a coil
held together by hydrogen bonds
parallel to the axis of the coil
Beta-pleated sheet: A secondary
protein structure in which the
backbone of two protein chains in
the same or different molecules is
held together by hydrogen bonds
Random coil:
Extended helix:
- Tertiary structure: The three-dimensional arrangement of every atom in the
molecule
Covalent bonds: to stabilize by mostly disulfide
Hydrogen bonding: stabilizes between polar groups on side chains or
between side chains and the peptide backbone
, Salt bridge: electrostatic attractions, occur between two amino acids with
ionized side chains—that is, between an acidic amino acid (-COO2) and a
basic amino acid (-NH3+ or -NH2) side chain. The two are held together by
simple ion–ion attraction
Hydrophobic Interactions: In aqueous solution, globular proteins usually turn
their polar groups outward, toward the aqueous solvent, and their nonpolar
groups inward, away from the water molecules. The nonpolar groups prefer
to interact with each other, excluding water from these regions. The result is
a series of hydrophobic interactions
Metal Ion Coordination: Two side chains with the same charge linked via a
metal ion.
- Quaternary structure: The spatial relationship and interactions between subunits in
a protein that has more than one polypeptide chain
Hemoglobin: Hemoglobin in adult humans is made of four chains (called
globins): two identical a chains of 141 amino acid residues each and two
identical b chains of 146 residues each. Proteins that contain non-amino acid
portions are called conjugated proteins. The non-amino acid portion of a
conjugated protein is called a prosthetic group.
Collagen
Integral membrane proteins
What do they consist of
Proteins are made out of amino acids, they consist of an amino group, -NH2, and a
carboxyl group, -COOH. The common found amino acids are called: Alpha amino
acids, the amino group is linked to the carbon next to the -COOH carbon.
An important aspect to determine the structure and function is the polarity of the R
group. Nonpolar side chains are hydrophobic, repel water, and
polar/neutral/acidic /basic side chains are hydrophilic, attracted to water.
Mutations
A mutation is an error in the copying of a sequence of bases
Mutagens: Organic compounds which induce mutations by reacting with DNA.
Point mutation: May change the amino acid code if the mutations occurs in the right
place in the code.
Nonsense : The altered DNA sequence prematurely signals the cell to stop
building a protein
Missense: Change in base pair results in the substitution
of one amino acid
Silent : Change without a subsequent change in the
amino acid or the function of the overall protein
Frameshift mutation: Losing or gaining a single nucleotide base
Deletion: When a part of a chromosome is left out
Insertion: When part of a chromatid breaks off and
attaches to its sister chromatid
Chromosomal mutation:
Inversion: When part of a chromosome breaks off and
reattaches backwards.
Translocation: When part of one chromosome breaks
off and is added to a different chromosome
Transversion : When a purine is substituted for a
pyrimidine or a pyrimidine replaces a purine
