Protein Synthesis and Protein Function Flashcards
what do ribosomes contain?
multimeric structure constituting of >50 proteins and one copy of each of 4 rRNAs (18S, 5.8S, 28S, 5S)
ribosomes are assembled in the
nucleus within the nucleolus
unlike other organelles, the nucleolus is not a
membrane bound structure
Small nucleolar RNAs (snoRNAs) serve as
guide
RNAs to direct specific modifications of the rRNAs
these modifications include (2)
about 100 methylations of the 2-OH
position on the nucleotide ribose sugar and 100
isomerizations of uridine nucleotides to pseudouridine.
Free ribosomes
move anywhere in the cytosol, but not found in the nucleus and
other organelles
membrane bound ribosomes
if the protein being made contains an Endoplasmic
Reticulum (ER) targeting sequence, then the ribosome is associated
with the rough ER. These types of proteins are transported to their
destination through a secretory pathway and are usually associated
with the plasma membrane or secreted out of the cell.
mRNA is “read” by the ribosomal machine as a
triplet of sequential nucleotides (called a codon)
Translation starts at the — end of the mRNA
5’
tRNAs are “charged” by the addition of
a specific amino acid that corresponds to that codon
his aminoacyl-tRNA is
created by the action of enzymes called
aminoacyl-tRNA
synthetases
Protein translation uses base pairing between the mRNA
codon and a triplet complementary sequence in the tRNA
called the
anticodon
steps of translation (4)
activation
initiation
elongation
termination
activation
formation of aminoacyl-tRNAs
initiation
binding of small ribosome to 5’-end
of mRNA and subsequent binding of initiator
Met-tRNA
elongation
synthesis of peptide chain
termination
synthesis stops and peptide
(protein) is released from the ribosome
The third base in the anticodon triplet (3’ base of the codon)
is the least important for base pairing and some “—” is
tolerated, which means that
wobble
if the third base is a U it can pair with A, G or I (Inosine) and if it is a C it can pair with a G or I
Translation starts with an — codon in the mRNA, which in
about 90% of the mRNAs is the first — in the mRNA.
AUG
AUG
codes for
Methionine
Translation stops when
stop codons are encountered in the
mRNA (generally two consecutive stop codons)
translation summary
- A small ribosomal subunit attaches to the 5’
end of the mRNA due to recognition of the
5’cap structure. - This subunit then moves along the mRNA
until it encounters the first Methionine
codon (AUG) where the Met-tRNA and the
large ribosomal subunit bind. Aminoacyl-
tRNAs bind in the A site (aminoacyl-site) of
the ribosome. - The ribosome moves 5’to 3’ along the
mRNA. As the ribosome moves the Met-
tRNA is simultaneously shifts to the P site
(peptide site). The A site is now open for
the next aminoacyl-tRNA corresponding to
the next codon to bind. - A peptide bond is formed between the Met-tRNA and the new aminoacyl-tRNA in the A site leaving the dipeptide in the A site and an “empty” tRNA in the P site. The ribosome then moves simultaneously discharging the empty tRNA and shifting the peptide into the P site. This process is repeated over and over until a Stop codon is encountered.
- Termination of the polypeptide chain involves hydrolysis of the ester bond which releases the protein.
Rifamycin
Prevents RNA synthesis
Tetracycline
Blocks binding of the aminoacyl-tRNA to the A-site (also binds to
newly forming mineralizing surfaces such as bone and teeth)
Streptomycin
Prevents the switch from translation initiation to elongation and
also can cause protein miscoding
Chloramphenicol
Blocks the peptidyl transferase reaction so elongation is prevented
Erythromycin
Blocks the ribosome exit channel in the ribosome so elongation is
inhibition
how are proteins classified? (2)
protein structure
protein function
protein structure (4)
– Amino acids and sequences
– Secondary structure
– Tertiary structure
– Quaternary structure
protein function (2)
– Motifs
– Domains
primary structure
amino acid
sequence
Secondary structure refers to stretches of the
polypeptide chain that form
α helices or β sheets
how can beta sheets be arranged (2)
anti-parallel beta sheet
parallel beta sheet
Changes in Amino Acid Sequence can have a Profound
Effect on
Protein Structure and Function
Tertiary structure refers to the
full 3D
structure of the protein
Quaternary structure is a designation used for
proteins that have multiple polypeptide chains
(subunits) and
refers to the complete
structure of all subunits
Protein motifs are shared sequences of amino
acids that can be used to identify
potential
members of a protein family
Shared motifs
generally equate to
similar functions
Protein domains are structural entities that
function essentially independently within a
protein and can be built from a specific motif or
set of motifs
A single protein can have multiple (2)
motifs and
domains
examples of protein sequence motifs (5)
• Proteolytic enzyme cleavage sites • Phosphorylation sites • Binding motifs (e.g. RGD sequence, heparin binding site, etc) • Transmembrane spanning sequences • Protein secretion leader sequences
Many proteins have a “—”
structure, which also appears in other proteins
supersecondary
These structural motifs are formed
by the 3D arrangement of amino acids and do
not necessarily
predict a biological function
in addition there are also sequence motifs
that can be found in both (2)
proteins and DNA
These sequence motifs generally have
biological significance
Helix-loop-helix
common in transcription
factors and consists of α helices bound by a
looping stretch of amino acids
Helix-turn-helix
DNA binding motif consisting
of two α helices joined by a short stretch of
amino acids
Zinc finger
DNA binding motif consisting of
two β strands
DNA sequence motifs (2)
DNA promoter and TF binding sites
DNA sequence repeat elements
100s of programs and dozens of databases
currently that catalog all of the known (2)
promoter
and transcription factor binding sequences in DNA
Amelogenin
stabilizes the amorphous Ca-P phase, control of apatite crystal
morphology and organization, control of enamel thickness.
Amelogenins have the ability to self-assemble into nanosperes and
thereby guide HAP crystal formation/growth.
Ameloblastin
Cell adhesion protein, controls cell differentiation, maintains rod
integrity
Enamelin
Cooperates with amelogenin to control mineral nucleation and
elongated growth
Kallikrin 4
Digests enamel proteins during maturation stage facilitating their
removal and hardening the final layer of enamel
Mmp-20
Cleaves amelogenin, ameloblastin and enamelin at the secretory stage
to produce stable intermediates with defined functions.
enamel is formed by
ameloblasts
what is enamel composed of?
90% amelogenin and 10% enamelin
as apatite crystals grow — is removed
amelogenin
Amelogenin is high in (4), but contains no (2)
proline, leucine, histidine and glutamine
hydroxyproline or cystine
Two genes for amelogenin, one on the X (AMELX) and the other on the Y (AMELY) chromosome, which results in minor differences in the — between males and females
enamel
dentin formation occurs before
formation of enamel (Reciprocal Induction)
— differentiate from cells in the dental papilla
Odontoblasts
odontoblasts secrete their organic matrix around the area that is directly
adjacent to the
inner enamel epithelium
Odontoblasts move towards center of tooth forming the
— —
odontoblast process
Odontoblast process secretes hydroxyapatite crystals and
mineralizes matrix forming the — —
mantle dentin
(2) dentin form through different process
Primary and secondary
major component of dentin
type 1 collagen (`90%)
Dentin Sialophosphoproteins (DSPP)
Immediately cleaved after secretion into DSP,
DGP and DPP
Dentin Matrix Protein 1 (DMP1)
Produced by odontoblasts and early-stage
osteocytes
Bone Sialoprotein
Role in biomineralization
Osteopontin
HA binding and contains an RGD motif,
mineralization inhibitor
MEPE
Matrix Extracellular Phosphogylcoprotein,
contains an RDG motif and in bone appears to be
an inhibitor of mineralization
cementoblasts (2)
acellular cementum
cellular cementum
Cellular cementum
cementoblasts arising from
adjacent area of bone
Acellular cementum
arising from dental follicle
Acellular cementum
arising from dental follicle
— cementum forms first
Acellular
Acellular cementum
arising from dental follicle
cementum contains (3)
cementoblasts
collagen
osteopontin, osteocalcin, osetonectin (SPARC), BSP, BAG75, others
what is the PDL formed from?
fibroblast cells from the central follicle
cells secrete collagen, which interacts with
fibers on the surface of adjacent bone and cementum
