1. A small ribosomal subunit attaches to the 5’ end of the mRNA due to recognition of the 5’cap structure. 2. 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. 3. 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. 4. 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. 5. Termination of the polypeptide chain involves hydrolysis of the ester bond which releases the protein.

Protein Synthesis and Protein Function Flashcards by sophie rosen

what do ribosomes contain?

multimeric structure constituting of >50 proteins and one copy of each of 4 rRNAs (18S, 5.8S, 28S, 5S)

How well did you know this?

Not at all

Perfectly

ribosomes are assembled in the

nucleus within the nucleolus

How well did you know this?

Not at all

Perfectly

unlike other organelles, the nucleolus is not a

membrane bound structure

How well did you know this?

Not at all

Perfectly

Small nucleolar RNAs (snoRNAs) serve as

guide

RNAs to direct specific modifications of the rRNAs

How well did you know this?

Not at all

Perfectly

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.

How well did you know this?

Not at all

Perfectly

Free ribosomes

move anywhere in the cytosol, but not found in the nucleus and
other organelles

How well did you know this?

Not at all

Perfectly

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.

How well did you know this?

Not at all

Perfectly

mRNA is “read” by the ribosomal machine as a

triplet of sequential nucleotides (called a codon)

How well did you know this?

Not at all

Perfectly

Translation starts at the — end of the mRNA

5’

How well did you know this?

Not at all

Perfectly

tRNAs are “charged” by the addition of

a specific amino acid that corresponds to that codon

How well did you know this?

Not at all

Perfectly

his aminoacyl-tRNA is

created by the action of enzymes called

aminoacyl-tRNA

synthetases

How well did you know this?

Not at all

Perfectly

Protein translation uses base pairing between the mRNA
codon and a triplet complementary sequence in the tRNA
called the

anticodon

How well did you know this?

Not at all

Perfectly

steps of translation (4)

activation
initiation
elongation
termination

How well did you know this?

Not at all

Perfectly

activation

formation of aminoacyl-tRNAs

How well did you know this?

Not at all

Perfectly

initiation

binding of small ribosome to 5’-end
of mRNA and subsequent binding of initiator
Met-tRNA

How well did you know this?

Not at all

Perfectly

elongation

synthesis of peptide chain

How well did you know this?

Not at all

Perfectly

termination

synthesis stops and peptide

(protein) is released from the ribosome

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

Translation starts with an — codon in the mRNA, which in

about 90% of the mRNAs is the first — in the mRNA.

AUG

How well did you know this?

Not at all

Perfectly

AUG

codes for

Methionine

How well did you know this?

Not at all

Perfectly

Translation stops when

stop codons are encountered in the

mRNA (generally two consecutive stop codons)

How well did you know this?

Not at all

Perfectly

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.

How well did you know this?

Not at all

Perfectly

Rifamycin

Prevents RNA synthesis

How well did you know this?

Not at all

Perfectly

Tetracycline

Blocks binding of the aminoacyl-tRNA to the A-site (also binds to
newly forming mineralizing surfaces such as bone and teeth)

How well did you know this?

Not at all

Perfectly

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

Protein Synthesis and Protein Function Flashcards

(81 cards)