Chapter 9

Question 1

translation is???????? (1-5)

Answer 1

1. is the synthesis of proteins as directed by mRNA templates
2. is the only first step in the formation of a functional protein
3. polypeptides chains must fold in a appropriate conformations and often undergo various processing steps, sorting, and transport
4. gene expression is regulated at the level of translation in both prokaryotic and eukaryotic cells
5. there are also multiple controls on the amounts and activities of intracellular proteins, which ultimately regulate all aspects of cell behavior

Question 2

1. proteins are synthesized from mRNA templates by a process that has been highly conserved throughout evolution.

all mRNAs are read in the _____________. and polypeptide chains are sythesized from the amino to the carboxy terminus

Answer 2

5’ to 3’ direction

Question 3

2. ________ is specified by ____________ in the mRNA

Answer 3

each amino acid is specified by three bases (a codon) in the mRNA

Question 4

3. translation is carried out on_________, with tRNAs serving as adaptors

Answer 4

ribosomes

Question 5

4. protein synthesis involves interactions between 3 types of RNA (_______,_________,________), plus other proteins

Answer 5

mRNA, tRNA, rRNA

Question 6

______ align amino acids with corresponding _________. They are ____ nucleotide long and have characteristic cloverleaf structures resulting from base pairing between different regions

Answer 6

tRNAs

Codons on the mRNA template

they are 70-80 nucleotides long

Question 7

structure of RNAS

1. all tRNAs fold in compact ________ shapes, to fit onto ribosomes during translation

Answer 7

fold into L shapes

Question 8

structure of tRNAS

2. tRNAs have the sequence _______ at the _____ terminus, and amino acids are covalently attached to the ribosomes of the terminal adosine

Answer 8

2. sequence of CCA at the 3’ terminus
   sequence CCA
   at terminus 3’

Question 9

structure of tRNAs

3. The _________ binds to the appropriate codon by complementary base pairing

Answer 9

anticodon loop

Question 10

attachment of amino acids to specific tRNAs is mediated by enzymes called __________________

each of these 20 enzymes recognizes a single aminoale amino acid, as well as the correct tRNA to which it should attach

Answer 10

aminoacyl tRNA synthetases

Question 11

attachment of amino acids to tRNAs

this occurs in two steps

1. the amino acid is joined to AMP, forming __________
2. the amino acid is transferred to ____________ of the tRNA and AMP is released

Answer 11

1. the amino acid is joined to AMP, forming aminoacyl AMP

2. the amino acid is transferred to the 3’ CCA terminus of the tRNA and AMP is released

Question 12

translation of mRNA

1. the amino acid is then aligned on the mRNA template by complementary base paring
2. most amino acids are specified by more than one codon
3. Cells have about 40 different tRNAs for the 2- different amino acids
4. some tRNAs can reconize more than one mRNA codon, as a result of _________ at the _____ codon position

this allows G to pair with U, and inosine (I) to pair with U,C,or A

(guanosine is modified to inosine in the anticodons of some tRNAS)

Answer 12

4. as a resulting of NONSTANDARD BASE PARING (WOBBLE) at the 3rd CODON POSITION

Question 13

______________ are named according to their sedimentation rates in ultracentrifugation. ______ for bacteria and __________ for eukaryotics

Cells have many ribosomes, illustrating the importance of protein synthesis. E. coli has about 20,000; growing mammalian cells can have ten million

Answer 13

ribosomes
70s for bacteria
80s for eukaryotic

Question 14

all ribosomes have ______ subunits. Each subunit contains ____________ and characteristic proteins

the subunits of eukaryotic ribosomes are larger and have more proteins than prokaryotic ribosomes

Answer 14

TWO subunits

contains rRNA and characteristic proteins

Question 15

ribosome can be formed in vitro by ___________ from purified ribosomal proteins and rRNAs, which provides important experimental tool

Answer 15

self assembly

Question 16

rRNAs form characterisitic secondary structures by ____________.
Subsequent folding results in distinct 3D stuctures

Answer 16

complementary base pairing

Question 17

unambigous evidence for rRNA catalysis came from high-resolution structural analysis of ______ ribosomal subunit, in 2000

Answer 17

50s

Question 18

ribosomal proteins are absent from the site of the peptidyl transferase reaction showing that _____________________.

It is now thought that ribosomal proteins play a largely structural role, and the large ribosomal subunit functions as a ribozyme

this is evolutionary implications: RNAs are thorugh to have benn the first self-replicating macromolecules

Answer 18

rRNA is responsible for catalyzing peptide bond formation

Question 19

mRNAs have noncoding ________________ at the end.

most eukaryotic mRNAs are ____________, encoding in a single protien

prokaryotic mRNAs are often _________-, encoding multiple proteins, each of which is translated from an independent start site

Answer 19

untranslated regions (UTRs)

mono-cistronic

poly-cistronic

Question 20

in both prokaryotes and eukaryotes, translation always _________, usually encoded by ______

Answer 20

always starts with methionine

usually encoded by AUG

Question 21

the signals that identify initiation codons are different in prokaryotic and eukaryotic cells

1. initiation codons in bacterial mRNAs are preceded by ___________, that aligns the mRNA on the ribosomes

They can initiate translation at the 5’ end of an mRNA and at internal initiation sites of polycistronic mRNAS

2. eukaryotic mRNAs are recognized by the _____________ at the 5’ terminus.

the ribosomes then scan downstream of this cap until they encounter the initiation codon

Answer 21

1. SHINE-DALGARNO SEQUENCE

2. 7-METHYLGUANOSINE CAP

Question 22

translation occurs in 3 stages: _________,________, and ______.

a specific initatior _________ and the mRNA binds to the ______________________

Answer 22

initiation, elongation, termination

a specific initator METHIONYL tRNA and the mRNA bind to the SALL RIBOSOMAL SUBUNIT

the LARGE RIBOSOMAL unit then joins, forming a functional ribosome

Question 23

many nonribosomal protiens are also required for various stages of translation? (true/false)

Answer 23

true

Question 24

in _________________, initiation starts with a 30S ribosomal subunit bound to __________________- IF1 and IF3

then the mRNA, initator N-formylmethionyl (fMet) tRNA, and IF2 (bound to GTP) joint the complex

IF1 and IF3 are released, a 50S subunit binds to the complex and IF2 is released

Answer 24

in bacteria

initation factors

Question 25

______________- initiation is more ocmplex, and requires at least 12 proteins, designated elFs (eukaryotic initation factors) the initiator ______________ is bound to ____________ and the _____ is brought to the complex by __________-

Answer 25

in eukaryotes the initiator METHIONYL tRNA is BOUND TO eLF2, and the mRNA IS BROUGHT TO THE COMPLEX by eLF4E

Question 26

"Initation of translation in cells" - ribosome scan down the mRNA to identify ____________ - ATP hydrolysis - when AUG is identified, ______ triggers the hydrolysis of GTP bound to _____ - release of 2IF2 and other initation facotrs - initation factors are then released, and the 60S subunit joins the complex

Answer 26

identify AUG initiation codon when AUG is identified, eLF5 tiggers hydrolysis of GTP bound to elF2

Question 27

"elongation stage of translation" 1. the mechanism of elongation in prokaryotic and eukaryotic cells is similar 2. the ribosomes has three binding sites: _____,_________,________-" the initiator _____________ is bound at ________- the __________ binds to the _______

Answer 27

2. three binding sites: P (peptidyl) , A (aminoacyl), and E (exit)sites the initiator METHIONYL tRNA is bound at the P SITE the NEXT AMINOACYL tRNA bind to the A SITE

Question 28

"elongation stage of translation" hydrolysis of GTP bound to eEF1a and release of the ________ then the peptide bond is formed, catalyzed by the large ribosomal subunit and the now initator tRNA is at the P site

Answer 28

release of the elongation factor

Question 29

"translation of mRNA" The steps of ___________ 1. ribosome then moves three nucleotides laong the mRNA, positioning the ext codon in an empty A site 2. This step translocates the peptidyl tRNA from A to P, and the uncharged tRNA from P to E

Answer 29

translocation

Question 30

"translation of mRNA" translocation requires another _____________ (EF-G in prokaryotes and ________ in eukaryotes) and is coupled to _________

Answer 30

translation requires another ELONGATION FACTOR (EF-G in prokaryotes, eEF2 in eukaryotes) and is coupled to GTP HYDROLYSIS`

Question 31

"regeneration of eEF1 a GTP" as elongation continues, the __________ (or EF-Tu) released from the ribosome bound to GDP must be reconverted to its GTP form this requires another elongation factor, _____ (EF-T in prokaryotes). regulation of eEF1 alpha by GTP binding and hydrolysis is a common method of protein regulation

Answer 31

eEF1a eEF1b

Question 32

"termination of translation" elongation continues until a _________ ( UAA,UAG, UGA) is translocated into the ____________. _________ recognize the signals and terminate protein synthesis in prokaryotic cells RF1 recognizes UAA or UAG, RF2 recognizes UAA or UGA. in eukaryotic cells eRF1 recognizes all 3 stop codons

Answer 32

elongation continues until a STOP CODON is located into the A SITE RELEASE FACTORS recognize the sigals and terminate protein synthesis

Question 33

mRNAs can be translated simultaneously by several ribsomes. once a ribosome has moved away from the initiation site, another can bind to the mRNA and begin sythesis. a group of ribsomes bound to an mRNA molecule is called a polyribosome, or a __________

Answer 33

polysome`

Question 34

regulation of translation plays a key role in gene expression, include: 1. ___________________ 2. ___________________ Global translation activity is modulated in response to _____, _____________, ______________. Example: regulation of ferritin translation (a protein that stores iron) by repressor proteins: when iron is absent, ______________________________ binds to the iron response elements (IRE) in the 5' UTR, blocking translation

Answer 34

1. translation repressor proteins 2. noncoding microRNAs global translational activity is modulated in response to STRESS, NUTRIENT AVAILABILITY, and GROWTH FACTOR STIMULATION. when iron is absent, IRON REGULATORY PROTEIN (IRP)

Question 35

Some translational repressors bind to specific sequences in the 3' UTR some bind to initiation factor eLF4E, interfering with itis interaction with eLF4G and inhibiting initiation of translation

Answer 35

General

Question 36

______________________-mediated by short double-stranded RNAs, is used as an experimental tool to block gene expression at the level of translation

Answer 36

RNA interference (RNAi)

Question 37

in cells, it is an important mechanism of translational regulation. RNA interference is mediated by: two types of small RNAS mediated RNA interference small interfering RNAs (siRNAs)- produced from __________ by nuclease Dicer MicroRNAs (miRNAs)-transcribed by _________________, then cleaved by nucleases Drosha and Dicer

Answer 37

doulbe stranded RNAS RNA polymerase II

Question 38

one strand of miRNA or siRNA is incorporated into an RNA induced silencing complex (RISC) siRNAs generally pair with their targets and induce cleavage of the mRNA most miRNAs from ___________ that repress translation

Answer 38

mismatches

Question 39

as many as 1000 miRNAs are encoded in mammals; each can target up to 100 different mRNAs up to one-half of protein-coding genes may require regulatation by __________. they are important in embryonic development, and may play a role in cancer and other diseases

Answer 39

miRNA

Question 40

translation can also be regulated by modification of initiation factors. This results in a global effects on overall translational activity rather than translation of specific _____________

Answer 40

mRNAs

Question 41

__________________________ by regulatory ________________ blocks the exchange of bound GDP for GTP, inhibiting initiation of translation

Answer 41

phosphorylation of eLF2 and elF2B protein kinases

Question 42

feedback inhibition is an example of ___________________, in which a regulatory molecule binds to an enzyme site that is distinct from the catalytic site

Answer 42

allosteric regulation

Question 43

"phosphorylation and other modifications" phosphorylation is ________; can activate or inhibit proteins in response to environmental signals catalyzes by ______________, which transfer phosphate groups from ATP to the hydroxyl groups of side chains of serine, threonine, or tyrosine

Answer 43

phosphorylation is reversible catalyzed by PROTEIN KINASE

Question 44

phosphorylation is reversed by ______________ , which catalyze hydrolysis of phosphorylated amino acids protein kinases are often components of signal transduction pathways. Sequential action of a series of protein kinases can transmit a signal from the cell surface to target proteins in the cell, resulting in changes in cell behavior in response to environmental stimuli

Answer 44

protein phosphatases

Question 45

Example: in muscle cells epinphrine signals breakdown of glycogen to glucose-1-phosphate, providing energy for increased muscular acitivity this is catalyzed by _____________ phosphorylase, which is regulated by protein kinase the signalling pathway is initiated by allosteric regulation-epinephrine binds to cell surface receptor, and cAMP binds to cAMP-dependent kinsase the sinal is then transmitted to its target by the sequental action of protien kinase

Answer 45

catalyzed by glycogen phosphorylase

Question 46

other covalent modifications include:

Answer 46

acetylation of lysine methylation of lysine and arginine nitrosylation (addiiton of NO groups) to cysteine glycosylation of serine and threonine

Question 47

some proteins are regulated by covalent attachment of _________. addition of _____________ and other ubiquitin like proteins, such as __________, affect a variety of function

Answer 47

attachment of polypeptides addition of ubiquitin such as SUMO

Question 48

addition of ubiquitin (ubiquitylation) is a multistep process the specificity of ________________________ selectivity targets proteins for degration

Answer 48

E3 enzymes

Question 49

"protein- protein interactions" many proteins consist of multiple subunits; interactions between them can regulate protein activity Example: cAMP-dependent protein kinase has two _____________ and two __________ subunits in the inactive forms cAMP binds to the regulatory subunits, which induces conformational change and dissociation of the complex the free catalytic subunits are then enzymatically active protein kinases cAMP acts as an allosteric regulator by altering protein-protein interactions

Answer 49

cAMP-dependent protein kinase has two REGULATORY and two CATALYTIC subunits in active form

Question 50

protein levels in the cells are determined by rates of __________ and ________ half-lives of proteins vary greatly; differential rates of degradation are important in cell regulation many regulatory proteins have short half lives; this allows levels to change quickly in response to external stimuli faulty or damage protein are recognized and rapidly degraded

Answer 50

protein levels in cells are determined by RATES OF SYNTHESIS and RATES OF DEGRADATION

Question 51

the major pathway of protein degradation in eukaryotes is the __________________. ________ is highly conserved in all eukaryotes

Answer 51

ubiquitin-proteasome pathway ubiquitin

Question 52

ubiquitin is attached to the amino group of the side chain of a lysine residue, then more are added to form a chain. polyubiquinated proteins are recognized and degraded by a large protease complex the _________________--

Answer 52

the proteasome

Question 53

what are the four stages of mitosis?

Answer 53

phrophase metaphase anaphase telophase

Question 54

many proteins that control fundamental cellular processes are targets for regulated ___________ and ____________ example: cyclins that regulate progression through the divsion cycle of eukaryotic cells

Answer 54

ubiquitylation and proteolysis

Question 55

entry of cells into mitosis is controlled in part by ___________, a regulatory subunit of Cdk1 protein kinase the active cyclin B-Cdk1 complex induces entry into ____________ degradation of cyclin B by the proteasome then leads to inactivation of the Cdk1 kinase, allowing the cell to exit mitosis and return into interphase

Answer 55

cyclin B mitosis

Question 56

protein degradation can also take place in _________________- membrane-enclosed organelles that contain digestive enzymes, including proteases lysosomes digest extracellular proteins taken up by endocytosis, and take part in turnover of organelles and proteins containment of digestive enzymes in lysosomes prevents uncontrolled degradation of cell contents proteins move into lysosome by _________; vesicles (autophagosomes) enclose small areas of cytoplasm or organelles and then fuse with lysosomes

Answer 56

lysosomes autogphagy

Question 57

autophagy is activated in nutrient starvation, allowing cells to degrade ____________ and ________ and reutilize the components autophagy also plays a role in many developmental processes, such as insect metamorphosis, which involve extensive tissue remodeling

Answer 57

nonessential proteins organells