Cell Bio Exam 4 - pt.1 - Protein synthesis and sorting

What are the five major components involved in translating mRNAs into polypeptides?

Ribosomes, tRNA, aminoacyl-tRNA synthetases, mRNAs, protein factors

What do ribosomes do in translation?

carry out protein synthesis

What does tRNA do in translation?

align amino acids in the correct order along the mRNA template

What do aminoacyl-tRNA synthetases do in translation?

attach amino acids to their appropriate tRNA molecule

What do mRNAs do in translation?

encode the amino acid sequence information

What do protein factors do in translation?

facilitate several steps in the translation process

What is the structure of the ribosome?

two dissociable subunits called large and small subunits

What is the size of the large and small subunit in eukaryotes?

60S and 40S

What is the size of the large and small subunit in prokaryotes?

50S and 30S

What does each subunit contain?

variable amounts of proteins and rRNA molecules (differs between prokaryotes and eukaryotes)

What are ribosomes made of?

ribosomal RNA and proteins

Where do ribosomes reside?

in the cytoplasm of both prokaryotes and eukaryotes; also in mitochondria and chloroplasts for eukaryotes

How many binding sites are there on ribosomes?

4 binding sites (APEM)

What is the A binding site and what is it for?

Aminoacyl site; binds newly arriving tRNA with attached amino acid

What is the P binding site and what is it for?

Peptidyl site; the tRNA carrying the growing polypeptide chain resides

What is the E binding site and what is it for?

Exit site; site from which tRNAs leave the ribosome after they have discharged the amino acid

What is the M binding site and what is it for?

mRNA-binding site; binds a specific nucleotide sequence near the 5' end of mRNA and places the mRNA in proper position for translation of its codon

Where are the binding sites located?

at or near the interface between the large and small subunits

What does mRNA bring to the ribosome?

polypeptide-coding information

What is at the 5' and 3' ends of mRNAs?

5' and 3' untranslated regions

What is included in the 5'UTR and 3'UTR for eukaryotes?

5' cap and 3' poly A tail

What signals for where translation should start in prokaryotes and eukaryotes?

start codon: AUG

What signals for where translation should stop in prokaryotes and eukaryotes?

stop codons; UAG, UAA, UGA

What do prokaryotic mRNAs contain in their 5'UTR?

the shine-dalgarno sequence

What is the shine-dalgarno sequence?

ribosome binding site

What is the genetic code?

the set of rules by which information encoded in genetic material (DNA or RNA) is translated into proteins (amino acid sequences) by living cells

What is the triplet code?

a code in which three base pairs in double-stranded DNA are required to specify each amino acid in a polypeptide

What does it mean for the genetic code to be unambiguous?

one codon only codes for one amino acid, but multiple codons can specify for the same amino acid

What are two important features of the genetic code?

it is degenerate and nonoverlapping

What does it mean for the genetic code to be degenerate?

a given amino acid can be specified by more than one nucleotide triplet

What does it mean for the genetic code to be nonoverlapping?

each nucleotide is a part of one and only one triplet

How do amino acids attach to tRNA?

they form an ester bond at the 3' OH

What are the two kinds of specificity that tRNAs have?

each tRNA binds one specific amino acid, and each recognizes one or more mRNA codons that are specific to an amino acid

What is responsible for selection of the correct amino acid for each tRNA?

enzymes that catalyze formation of the ester bond

What is the enzyme responsible for linking amino acids covalently to the tRNA?

aminoacyl-tRNA synthetases

How many different aminoacyl-tRNA synthetases do cells have?

20 different ones for each of the 20 amino acids commonly used in proteins

What are tRNA called after they are bonded to an amino acid?

aminoacyl-tRNA

What part of tRNA binds to the mRNA?

anticodon of tRNA; located at opposite end of where amino acid attaches

What are the 3 stages of translation?

initiation, elongation, and termination

What direction is mRNA translated in?

5'-3' direction

What direction is the synthesis of the polypeptide in?

N-terminus to C-terminus

What three things does polypeptide chain elongation involve?

1. aminoacyl tRNA binding

2. peptide bond formation catalyzed by peptidyl transferase

3. translocation (A to P to E site)

What is the exception to translocation in chain elongation?

initiator tRNA binds P site directly

How is translation terminated?

when a stop codon arrives at the A site, it is recognized and bound by protein release factors

What is coupled with release of the completed polypeptide?

hydrolysis of GTP

What follows the release of the completed polypeptide?

dissociation of the tRNA, mRNA, ribosomal subunits, and release factors

What amino acid does the AUG start codon specify in eukaryotes?

methionine

What amino acid does the AUG start codon specify in bacteria?

N-formylmethionine

What are initiation factors?

eIFs, a dozen proteins used only by eukaryotes in translation

What is the Kozak sequence?

ACCAUGG; a common start sequence in eukaryotes

What is polypeptide folding facilitated by?

molecular chaperones

What is necessary for proteins to do before they can function?

folding into their correct three-dimensional shapes

How many molecular chaperones are required to facilitate protein folding?

several acting in sequence

When do molecular chaperones bind polypeptide chains?

during early stages of folding

What gives molecular chaperones the energy to bind to polypeptide?

ATP hydrolysis

How does the molecular chaperone detach?

it uses ATP hydrolysis to detach after polypeptide is properly folded

What is a missense mutation?

Point mutation in which a single nucleotide is changed, resulting in a codon that codes for a different amino acid.

What is a nonsense mutation?

point mutation that results in a regular codon turning into a stop codon

What is a silent mutation?

alters a base but does not change the amino acid

What is a frameshift mutation?

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

What is a duplication mutation?

When one or more bases are repeated

What is an inversion mutation?

A sequence of bases is reversed

What is a translocation mutation?

moves a segment from one chromosome to another, nonhomologous one

What must polypeptides undergo before they can perform their functions?

posttranslational modification

What is posttranslational modification for polypeptide chains in eukaryotes?

the methionine at the N-terminus is removed

Can whole blocks of amino acids be removed from polypeptides during posttranslational processing?

yes (insulin)

What are other processing events that involve chemical modification of amino acids?

methylation, phosphoylation, acetylation, and glycosylation

What is protein targeting or protein sorting?

the mechanism by which a cell transports proteins to the appropriate positions in the cell or outside fo it

What are the three categories of the compartments of eukaryotic cells?

1. the endomembrane system

2. the cytosol

3. mitochondria, chloroplasts, peroxisomes, and interior of nucleus

What is included in the endomembrane system?

ER, golgi apparatus, lysosomes, secretory vesicles, the nuclear envelope, and plasma membrane

Where does polypeptide synthesis begin?

cytosol

Where can polypeptides be transported to after they are about 30 amino acids long?

the endomembrane system, export from cell, staying in cytosol, or transferred to nucleus, mitochondria, chloroplasts, or peroxisomes

How are polypeptides transferred to endomembrane system or exported from the cell?

by cotranslational import

How are polypeptides transferred to nucleus, mitochondria, chloroplast, or peroxisomes?

by posttranslational import

What type of proteins is cotranslational import used for?

soluble proteins

What do polypeptides destined for the endomembrane system contain?

an ER signal sequence

What binds to the ER signal sequence and allows for the ER membrane to open up and allow the polypeptide to enter?

SRP: signal recognition particle

When does the polypeptide enter the ER?

as it is being synthesized (for soluble proteins)

What type of proteins is cotranslational insertion used for?

membrane proteins

What do membrane proteins destined for the endomembrane system contain?

a stop-transfer sequence or internal start-transfer sequence

When does cotranslational insertion of transmembrane proteins into the ER membrane occur?

it is inserted into the ER membrane as it is being synthesized

What does posttranslational import allow for?

some polypeptides to enter organelles after they have been synthesized

What do proteins contain that directs them to the target organelle?

a targeting signal

What two types of membrane receptors are used in posttranslational import of polypeptides into the mitochondrion?

TOM and TIM membrane receptoes

What do polypeptides contain that binds them to the TOM receptor to pass through the outer and inner mitochondrial membranes?

a transit sequence

Is the transit sequence cleaved after the polypeptide passes through the membrane?

yes by transit peptidase

What is TOM?

translocase of the outer mitochondrial membrane

What is TIM?

translocase of the inner mitochondrial membrane

What 3 things to chaperones do in posttranslational import of polypeptides into the mitochondrion?

1. keep the polypeptide partially unfolded after synthesis

2. drive the translocation itself

3. help the polypeptide fold into its final conformation