amino_acids-nonpolar.html: 14_1601-amino_acids-nonpolar.jpg
These amino acids have R groups composed only of carbon and hydrogen atoms,
making them nonpolar and hydrophobic.
Pro has a nitrogen atom and is sometimes classified as polar.
Met has a sulfur atom but remains hydrophobic
while phe and trp are sometimes classified as
aromatic, since they have a benzene-like ring.
amino_acids-polar.html: 13_F15_03-amino_acids-polar.jpg
These amino acids have oxygen, sulfur and/or nitrogen
in the R group, making them polar and hydrophilic.
They are electrically neutral molecules.
Gly is sometimes classified as nonpolar and
tyr is sometimes classified as aromatic.
amino_acids-polar_acidic.html: 13_F15_05-amino_acids-polar_acidic.jpg
These amino acids are carry a negative charge, making them acidic.
These very polar molecules are highly hydrophilic.
amino_acids-polar_basic.html: 13_F15_04-amino_acids-polar_basic.jpg
These amino acids are carry a positive charge, making them basic.
These very polar molecules are highly hydrophilic.
amino_acids.html: 13_F15_01-amino_acids.jpg
The R (radical) group confers specific chemical properties to each amino acid
and play a crucial role in determining the 3-dimensional conformation of the polypeptide.
The R groups can be divided into four main classes:
arginine_pathway.html: 13_F12-arginine_pathway.jpg
The metabolic pathway for synthesis of the amino acid arginine in Neurospora was established
by providing various mixes of supplements to seven different auxotrophic arginine mutants.
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Enzymes act as catalysts by lowering the energy of activation in cellular reactions,
thus speeding up the chemical reactions. As catalysts,
the enzymes are not part of the chemical reactions themselves, and can be re-used after the reaction.
colinearity.html: 14_15-colinearity.jpg
Colinearity
in the trpA gene that encodes the A subunit of the enzyme tryptophan synthetase in E. coli
is shown by comparing the gene maps of several mutants
and the altered amino acid positions in each mutant protein.
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The gene encoding a human cholesterol receptor contains 18 exons that encode 5 domains
in the protein.
Exons 2-6 comprise the domain for the binding site for cholesterol.
The next 8 exons comprise a domain homologous to the mouse hormone epidermal growth factor (EGF).
A similar domain is also found in many other polypeptides, including 3 blood-clotting proteins.
Other exons specify 3 domains that perform specific functions.
hemoglobin.html: 14_14-hemoglobin.jpg
The HbA and HbS hemoglobin molecules can be subjected to fingerprint analysis.
The protein is digested into peptide fragments by proteolytic enzymes.
The mixture is then subjected to paper electrophoresis
followed by paper chromatography at 90° to the electrophoresis.
The resulting two-dimensional "fingerprint"
reveals that HbS and HbA differ by a single peptide fragment.
Further analysis shows a single amino acid change:
valine is substituted for glutamic acid
at the 6th position of the beta chain.
hemoglobin_electrophoresis.html: 14_14-hemoglobin_electrophoresis.jpg
Pauling
(Nobel 1954) isolated normal (HbA) and sickle (HbS)
human hemoglobin molecules and separated them by electrophoresis.
Homozygous individuals (AA and SS) produced different hemoglobin migration bands,
while a heterozygote (AS) produced two bands, indicating the individual possesses both types of
proteins.
hemoglobins.html: 14_T02-hemoglobins.jpg
A variety of hemoglobin molecules are produced in humans at different stages of life.
All are tetramers consisting of seven
distinct polypeptide chains, each encoded by a separate gene.
Embryonic hemoglobin has
ζ (zeta) and
ε (epsilon) chains.
By eight weeks gestation, these are replaced by fetal hemoglobin with alpha chains and two types of
γ (gamma) chains.
98% of adult hemoglobin are HbA molecules consisting of
alpha and beta chains;
2% are HbA2, composed of alpha and
δ (delta) chains.
metabolic_blocks.html: 14_10-metabolic_blocks.jpg
Metabolism of the amino acids phenylalanine and tyrosine require several enzymes.
Various metabolic blocks due to mutations lead to defective enzymes and the disorders
phenylketonuria, tyrosinemia,
albinism,
and
alkaptonuria.
one-gene_one-enzymea.html: 14_11a-one-gene_one-enzyme.jpg
Beadle
and
Tatum
(Nobel 1958)
induced nutritional auxotrophic mutations in the bread mold
Neurospora
by exposing asexual conidia (spores) to radiation.
next
one-gene_one-enzymeb.html: 14_11b-one-gene_one-enzyme.jpg
By attempting to grow the mutants on minimal media supplemented with various organic compounds,
the nutritional mutation can be pinpointed.
next
one-gene_one-enzymec.html: 14_11c-one-gene_one-enzyme.jpg
Beadle and Tatum were able to determine that each genetic mutation is associated with a
loss of the enzymatic activity to synthesize a vitamin or an amino acid.
This led them to propose
the hypothesis that one gene specifies one enzyme.
(Now we know not all proteins are enzymes and some proteins have more than one polypeptide chain.)
peptide_bond.html: 14_17-peptide_bond.jpg
A peptide bond is formed when
the amino group of one amino acid reacts with the carboxyl group of another amino acid
by a dehydration (condensation) reaction, releasing a molecule of H2O.
video
polysomes.html: 14_09-polysomes.jpg
| Polysomes from rabbit reticulocytes (immature red blood cells) engaged in the translation of hemoglobin mRNA. video | Polysomes from salivary gland cells of the midgefly, Chironomus thummi; polypeptide chains can be seen emerging from the ribosomes. |
protein_structure-quaternary.html: 14_20-protein_structure-quaternary.jpg
Some proteins, especially enzymes, are oligomeric: composed of more than one polypeptide chain.
Hemoglobin is an oligomeric protein consisting of four protomer polypeptides:
two alpha and two beta chains that fit together with four heme groups in a
quaternary structure comprising the functional molecule.
Collagen is an example of a structural protein with a quaternary structure.
protein_structure-secondary-a.html: 14_18a-protein_structure-secondary-a.jpg
Hydrogen bonding in a regular, repeating pattern stabilizes sections of a polypeptide, forming an
alpha-helix secondary structure.
Alpha keratin
, the tough structural protein of hair, is rich in alpha helix.
continue
protein_structure-secondary-b.html: 14_18b-protein_structure-secondary-b.jpg
Hydrogen bonding may also form a beta-pleated-sheet secondary structure in a zigzagging plane.
Extensive beta-pleated-sheet regions provides strength and rigidity to structural proteins such as the
fibroin
found in silk.
video
protein_structure-tertiary.html: 14_19-protein_structure-tertiary.jpg
The secondary structure sections of a polypeptide may further be organized into a tertiary
structure by these interactions:
cysteine molecules.
ribosome-eukaryote.html: 14_01-ribosome-eukaryote.jpg
Eukaryote ribosomes are structurally similar to those of prokaryotes,
consisting of a large and a small subunit,
each composed of rRNA and ribosomal protein molecules.
Eukaryote versions are in general larger than prokaryote ones, and may be found either free-floating in the
cytoplasm or associated with the endoplasmic
reticulum.
ribosome-prokaryote.html: 14_01-ribosome-prokaryote.jpg
A prokaryote ribosome consists of a large and a small subunit.
Both subunits consist of one or more molecules of ribosomal RNA (rRNA) and several ribosomal proteins.
When the two subunits are associated with each other in a single ribosome, the structure is sometimes called a
monosome.
ribosome.html: 14_00-ribosome.jpg
X-ray diffraction model of a bacterial ribosome is made from
crystallized molecules extracted from Thermus thermophilus.
The model also shows three bound transfer RNAs, interacting with the rRNA of the two subunits.
sickle-cell_anemia.html: 14_13-sickle-cell_anemia.jpg
| Normal erythrocytes (red blood cells) have a biconcave disc shape. They contain hemoglobin molecules that appear red when oxygenated. | The recessive genetic disorder sickle-cell anemia results in abnormal hemoglobin molecules that cause erythrocytes to become elongated and curved under low oxygen levels. |
tRNA-3D.html: 14_04-tRNA-3D.jpg
tRNA-bases.html: 14_02-tRNA-bases.jpg
May tRNA nucleotides contain nitrogenous
bases
that are modified aftter transcription.
Due to wobble,
I (Inosine) and Im can base pair with U, C, or A.
tRNA-charging.html: 14_05-tRNA-charging.jpg
tRNA "charging" starts when an aminoacyl tRNA synthetase catalyzes the conversion of an
amino acid to aminoacyladenylic acid.
A hydrolyzed ATP
donates the phosphate to form the complex.
The amino acid is transferred to the appropriate tRNA at the 3' end.
There are 20 isoaccepting groups if tRNAs; each group is able to identify itself to its particular synthetase to carry a particular amino acid.
tRNA.html: 14_03-tRNA.jpg
A tRNA molecule contains many modified bases
and exhibits a secondary structure with a
series of paired stems and unpaired loops, folded into a specific 3-dimensional conformation.
The 3' end is the amino acid binding site, while the anticodon arm contains the anticodon
loop that recognizes a codon on the mRNA.
The anticodon (CGI) of this tRNAala molecule specifies the amino acid
alanine,
and can base pair with the triplets GCU, GCC, and GCA due to wobble.
translation_elongation1.html: 13_F07_01-translation_elongation.jpg
Step 1.
Second charged tRNA has entered A site, facilitated by EF-Tu.
Step 2.
translation_elongation2.html: 13_F07_02-translation_elongation.jpg
Step 2.
Peptidyl transferase catalyzes the formation of a peptide bond that links the two amino acids.
Uncharged tRNA moves to the E site (exit);
the mRNA is translocated three bases, resulting in the tRNA bearing the dipeptide
to shift into the P site.
Step 3.
translation_elongation3.html: 13_F07_03-translation_elongation.jpg
Step 3.
The first link is complete and the first uncharged tRNA is removed, facilitated by EF-G.
The third charged tRNA is ready to enter the A site.
Step 4.
translation_elongation4.html: 13_F07_04-translation_elongation.jpg
Step 4.
Third charged tRNA enters the A site, facilitated by EF-Tu.
Step 5.
translation_elongation5.html: 13_F07_05-translation_elongation.jpg
Step 5.
The second link is made, forming a tripeptide
which starts to emerge through a tunnel in the large subunit.
The second uncharged tRNA enters the E site, ready to be removed.
Step 6.
translation_elongation6.html: 13_F07_06-translation_elongation.jpg
Step 6.
The whole polypeptide chain is synthesized and released from ribosome.
video
translation_initiation-components.html: 13_F06_01-translation_initiation-components.jpg
Initiation of translation in E. coli involves the small ribosomal subunit,
an mRNA molecule,
the energy carrier GTP,
several initiation factors (
IFs
),
and a tRNA that carries the anticodon
UAC and is charged with the modified amino acid
N-formylmethionine (
f-met
).
video
translation_initiation-factors.html: 14_T01-translation_initiation-factors.jpg
translation_initiation.html: 13_F06_02-translation_initiation.jpg
Initiation
P (peptidyl or polymerization) site; IF3 is released.
GTP is hydrolyzed to provide energy for the reactions.
A (aminoacyl) site.
translation_termination.html: 13_F08-translation_termination.jpg
Termination
of protein synthesis is signaled by a stop codon in the A site: UAG, UAA, or UGA.
These codons do not bind a tRNA in the A site, so the A site is empty.
GTP-dependent release factors cleave the polypeptide chain from the terminal tRNA
in the P site, releasing it from the translation complex, which dissociates.
video