LS7A Wk 6

hydrophobic amino acids

"gav lim fwp"

roles of golgi apparatus

1) further modification protein and lips produced in ER 2) acts as sorting station as these proteins and lipids move to their final destinations 3) site of synthesis of most of the cell's carbohydrates

Assuming A-U and G-C pairing between the anticodon and the codon, what anticodon in tRNAMet would pair with the codon 5'-AUG-3'?

5'-CAU-3'

initiation codon

AUG- Met

Which of the following occurs in the E site of the ribosome during translation?

An uncharged tRNA is ejected from this site as the ribosome slides to the next codon.

Which of the following occurs in the P site of the ribosome during translation?

The tRNA carrying the growing polypeptide moves to this site as the ribosome slides to the next codon.

nuclear envelope

defines boundary of nucleus

primary structure

sequence of AA

How many aminoacyl-tRNA synthetase enzymes must be present in cells to properly synthesize proteins?

20, one for each amino acid

what part of the tRNA does the enzyme attach to AA

3' end of tRNA

tertiary structure

3-D shape of polypeptide

An mRNA molecule is synthesized that has a random sequence consisting of 25% A, 25% U, and 50% C. Among the amino acids in the polypeptide chains resulting from translation in a laboratory setting in which translation can be initiated anywhere along the mRNA molecule, what is the expected frequency of phenylalanine codons?

3/64

what is physiological pH

7.35-7.45

3 binding sites for molecule of tRNA

A (aminoacyl) site; P (peptidyl) site; E (exit) site

Enzymatic catalysis of the peptide bond between the growing polypeptide and the next incoming amino acid takes place in which binding site?

A site

Imagine that you and your colleagues are working in a lab to develop a protein synthesis system for a new type of synthetic cell. During your brainstorming sessions, you propose that polycistronic mRNA would be much more useful than mRNA that is only translated into one protein. This would allow for multiple proteins necessary for a particular function to be translated together. One of your colleagues says that is a good idea, but if you decide to go with polycistronic mRNA, you'd better make sure to use a prokaryotic translation system. Why might it be problematic to use a eukaryotic translation system with polycistronic mRNA?

Eukaryotic ribosomes initiate translation by binding to the 5′-cap, which is only at the end of the mRNA.

You are investigating an abnormal eukaryotic cell line that makes all of its mRNAs much longer than the mRNAs from normal cells. Intrigued, you examine the proteins in these abnormal cells and note that many of them are either much longer or much shorter than the normal proteins from nonmutant cells. Assuming there is just one mutant defect in these cells, which of the below possibilities is MOST likely?

The spliceosome is nonfunctional.

stop codons

UAA, UAG, UGA

charged tRNA

a tRNA that has an amino acid attached

Translation and elongation process in detail

a) initiation factors recruit the small ribosomal subunit and tRNA(met) and scan the mRNA for AUG codon b) when the complex reaches an AUG, the large ribosomal subunit joins, and the initiation factors are released ad a tRNA complementary to the next codon binds to the A site c) A reaction transfers the Met to the AA on the tRNA in the A site, forming a peptide bond d) the ribosome moved down one codon, which puts the AA carrying the polypeptide into the P site and the now uncharged tRNA into the E site,where it is ejected. A new tRNA complementary to the next codon binds to the A site e) The polypeptide transfers to the AA on the tRNA in the A site. The polypeptide is elongated by repeating steps in (d) and (e)

targeting of a transmembrane protein by means of a hydrophobic signal anchor sequence

a) proteins with signal-anchor sequences are threaded through a channel in the ER membrane until the signal-anchor sequence is encountered b) the ER channel releases protein into the membrane c) when translation is completed, the protein remains in the membrane

interaction of signal sequence and srp with arp receptor

a) the arp (signal recognition particle) binds to the signal sequence in the amino terminal end of the growing polypeptide and halts translation b) the srp bind to the srp receptor on the ER membrane c) the SRP receptor bring the ribosome to a transmembrane channel; the SRP dissociates; protein synthesis resumes; and the growing polypeptide chain is threaded through the channel d) the protein ends up in the lumen of the ER where it may remain, be transported to the lumen of another organelle or be secreted out of the cell

termination

addition of AA stops and the completed polypeptide chain is released from the ribosome

initiation in eukaryotes is where?

at the 5' can and the first AUG is the start codon

role of base pairing

base pairing determines the relationship b/t 3 base triplet in double stranded DNA to a codon in mRNA and b/t a codon in mRNA to an anticodon in tRNA

why is the antiparallel configuration of beta sheet more stable

because the carbonyl and amide groups are more favorably aligned for H bonding

what do chaperones bind to on proteins

bind with hydrophobic groups and non polar R groups to shield them

elongation factors

bound to GTP molecules and break their high energy bonds to provide energy for the elongation of the polypeptide

peptide bond

carboxyl group of one aa reacts with the amino group of the next aa in line

hydrophilic aa

cdesty hkr nq

general structure of AA

central carbon atom- alpha carbon connect to an amino group, carboxyl group, hydrogen atom, and R group

codon

coding for single AA in the polypeptide chain

aminoacyl tRNA synthetases

connect specific AA to specific tRNA molecules

How is the amino acid held on the charged tRNA?

covalent bond

what types of bonding can contribute to protein's tertiary structure

covalent, ionic, van der waal's, hydrogen bonding

Which of the following accurately describes the path traveled by a new protein as it is synthesized and released from the cell?

cytosol → ER → Golgi → vesicle → plasma membrane → external environment

nuclear localization signals

enable proteins to move through pores in the nuclear envelope

When physicians perform organ transplants, they make sure that there is a match between the donor (the person donating the organ) and the recipient (the person receiving the organ). What feature of the cell is being matched?

glycyoproteins in the plasma membrane

operon

group of functionally related genes located in tandem along the DNA and transcribed as a single unit from one promoter

When a charged tRNA is about to bind to the vacant A site of a ribosome, where is the growing polypeptide?

in the P site

Consider a protein that is targeted to be excreted to the outside of the plasma membrane. Where would this protein be located in the endoplasmic reticulum?

in the lumen (inside) of the ER

Consider a protein that is targeted to be excreted to the outside of the plasma membrane. Where would this protein be located in the Golgi?

in the lumen (inside) of the Golgi

Processes of translation

initiation, elongation, termination

initiation

initiator AUG codon is recognized and Met is established as the first AA in the new polypeptide chain

nucleus

innermost organelle of endomembrane system, store DNA

secondary structure

interaction of nearby AA

what is the tertiary structure of proteins determined by

interactions b/t AA side chains,

initiation in prokaryotes is where?

is at shine-dalgarno sequence, causing that mRNA can therefore be a polycistronic mRNA that codes for several polypeptides

why is glycine unique

its R group is hydrogen, increasing in flexibility of polypeptide backbone

nuclear pores

large protein complexes that allow molecules to move into and out of the nucleus

The ribosome ______BLANK subunit has _______BLANK binding sites for tRNA molecules.

large; three

endomembrane system

nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, plasma membrane, vesicles

what makes up the quaternary structures of protein

polypeptide subunits forming together

protein sorting

process by which proteins ends up where they need to be to perform their function

chaperones

proteins that help protect slow folding or denatured proteins until they can attain their proper 3D structure

folding domain

region of protein that folds in a similar way relatively independently of the rest of the protein

quaternary structure

results from interaction of polypeptide subunits

alpha helix and beta sheet

secondary structures that are stabilized by H bonding along polypeptide backbone

In a population of organisms, beneficial and harmful random mutations are retained or eliminated through the process of:

selection

translation

sequence of bases in RNA molecule known as mRNA is used to specify the order in which successive aa are added to newly synthesized polypeptide chain

vesicles

small membrane enclosed sacs that transport substances within a cell or from the interior to the exterior of the cell

lysosomes

specialized vesicles derived from the golgi apparatus that degrade damaged or unneeded macromolecules

elongation

successive aa are aded one by one to the growing chain

what is the ratio in eukaryotes of intracellular membranes to plasma membrane

tenfold greater

The fully folded structure of a functional protein composed of a single polypeptide chain is referred to as the _____ structure

tertiary

Binding sites for tRNA are located in:

the large ribosomal subunit.

proton pumps in regards to lysosomes

they keep the internal environment at acidic pH of 5

endocytosis

vesicle can bud off from the plasma membrane enclosing material from outside cell and bringing it into the cell interior

Most elements of the endomembrane system are connected by:

vesicular trafficking

release factor

when a stop codon is encountered this protein binds to the A site of the ribosome then causing the bond connecting the polypeptide to the tRNA to break and completing the chain

exocytosis

when a vesicle fuses with a membrane; empty its contents to extracellular space