Biochemistry Ii: Exam 3 Part 2

Front 1

There are 3 sites on a ___S ribosome:

Back 1

70S

A P E

Front 2

__-site: binds the incoming aminoacyl-tRNA

Back 2

A-Site

Front 3

__-site: binds peptidyl-tRNA

Back 3

P-Site

Front 4

______-___ = tRNA + growing
peptide chain

Back 4

Peptidyl-tRNA

Front 5

__-site : transiently binds to outgoing deacylated tRNA

Back 5

E-Site

Front 6

______-___ = tRNA + amino acid

Back 6

Aminoacyl-tRNA

Front 7

There is a tunnel-like structure between the __ and __-sites where the growing polypeptide
leaves 70S ribosome.

Back 7

E + P

Front 8

Two subunits on eukaryotic ribosomes:

Back 8

40S + 60S

Front 9

Eukaryotic __S rRNA contains _______ ______ (peptide bond formation)

Back 9

28S

peptidyl transferase

Front 10

Protein synthesis proceeds from the __-terminus to the _-terminus.

Back 10

N to C

Front 11

mRNA is read in the __’ to
__’ direction.

Back 11

5' to 3'

Front 12

Codon-anticodon interaction is proofread by the ______

Back 12

Ribosome

Front 13

3 Initiation factors:

Back 13

IF-1
IF-2
IF-3

Front 14

Assists IF-3 in separating ribosome subunits by binding to 30S

Back 14

IF-1

Front 15

Bound to GTP, ____ binds fMet-tRNAfMet and then to P-site at start codon

Back 15

IF-2

Front 16

____ assists in separating ribosome subunits by binding to 30S

Back 16

IF-3

Front 17

Bound to GTP, _____ binds to aminoacyl tRNA (charged tRNA) and binds in A-site

Back 17

EF-Tu

Front 18

_____ Recharges EF-Tu with GTP

EF-Tu GDP -----> EF-Tu GTP

Back 18

EF-Ts

Front 19

Bound to GTP, _____ causes translocation of ribosome by one codon via the
energy from _____ hydrolysis to _____

Back 19

EF-G

GTP’s
GDP

Front 20

Bound to GTP, _____ assists in termination by binding to RRF at stop codon in
A-site and hydrolyzing its GTP to GDP to make everything dissociate from ribosome

Back 20

EF-G

Front 21

Binds to stop codon (UAA and UAG) in P-site and induces conformational change
causing peptidyl transferase to hydrolyze the peptide from tRNA in P-site

Back 21

RF-1

(release factor)

Front 22

RF-2 binds to stop codons (___ + ___) in P-site: same function as RF-1

Back 22

UAA
UGA

Front 23

Bound to GTP, ___ binds to RF-1 in A-site
● GTP hydrolysis to GDP causes RF-1 and ___*GDP to dissociate from A-site

Back 23

RF-3

Front 24

Binds in A-site to stop codon after RF-3*GDP leaves and is then bound by EF-G*GTP to end translation

Back 24

RRF

Front 25

3’ end of ____ rRNA (in the 30S subunit) binds to the Shine-Delgarno sequence to help position the P unit of the ribosome at the start
codon

Back 25

16S

Front 26

________________ = fMet

the amino acid required to
start translation in prokaryotes.

Back 26

N-Formylmethionine

Front 27

IF-2 GTP binds fMet-tRNAfMet, which is the only tRNA that binds to ____ ribosome

Back 27

30S

Front 28

Once IF-3 leaves, the ___ subunit rebinds forming the 70S initiation complex:
o Empty A-site
o fMet-tRNAfMet bound in P-site

Back 28

50S

Front 29

There are three main steps to elongation which occur many times per polypeptide:

Back 29

Decoding
Transpeptidaion
Translocation

Front 30

_________: Transfer of proper aminoacyl-tRNA from cytoplasm to A-site of ribosome

Back 30

Decoding

Front 31

Elongation:

__________: Covalent linkage of new amino acid to growing polypeptide chain.

Back 31

Transpeptidation

Front 32

_________: Movement of tRNA from A-site to P-site and simultaneous movement of
mRNA by 3 nucleotides (1 codon)

Back 32

Translocation

Front 33

Transpeptidation :nucleophilic attack from the __-_____ group of aminoacyl-tRNA in
the A-site to ____ _______ on peptidyl-tRNA in the P-site

Back 33

α-amino

carbonyl carbon

Front 34

Translocation involves what elongation factor?

Back 34

EF-G GTP

Front 35

Termination

After RF-1 or RF-2 bind to the stop codon and enter the __-site, peptidyl transferase (part of 23S rRNA) acts as a
_______ and hydrolyze the peptide

Back 35

A-site

hydrolase

Front 36

Termination:

When the peptide is hydrolyzed _______ binds to RF-1 (or RF-2) in the
A-site in order for RF-1 or 2 to leave.

Back 36

RF-3*GTP

Front 37

Termination:

RF-3*GDP leaves the A-site.
____ then binds the stop codon and ______ binds RRF, is hydrolyzed and releases everything.

Back 37

RRF

EF-G*GTP

Front 38

_____ toxin is a large molecule which acts catalytically, deactivating many ribosomes at once. It acts on eukaryotic ___ ribosomes.

Back 38

Ricin

80S

Front 39

antibiotics are small molecules which act specifically and _________ (1 molecule per 1 ribosome) on prokaryotic 70S ribosomes.

Back 39

stoichiometrically

Front 40

Puromycin resembles the 3’ end of ___________ tricking the bacteria into thinking it is a suitable aminoacyl tRNA for the A-site

Back 40

Tyrosyl-tRNA

Front 41

What type of bond is formed when puromycin enters the A-site, preventing translation.

Back 41

Amide

Front 42

Why is streptomycin injected rather than taken orally?

Back 42

It is a β-glycoside, cannot be broken down to be absorbed through GI.

Front 43

At low concentrations ___________ causes bacterial 70S ribosomes to misread pyrimidines in mRNA (C, U), which will result in the wrong amino acids being inserted into the protein.
This slows growth but does not cause cell death.

Back 43

Streptomycin

Front 44

At higher concentrations (i.e. the therapeutic dose), streptomycin inhibits ____________, resulting in cell death.

Back 44

initiation of translation

Front 45

________ is an antibiotic which binds to the 50S ribosomal subunit near the A-site and inhibits the peptidyl transferase activity of the ___ rRNA.

Back 45

Chloramphenicol

23S

Front 46

Why shouldn't puromycin and chloramphenicol be used simultaneously?

Back 46

They will both compete for the A-site

Front 47

Why is chloramphenicol only used in severe infections.

Back 47

It will destroy mitochondrial ribosomes as it recognizes them as bacterial ribosomes.

Front 48

_________ binds to the 30S ribosomal subunit and prevents aminoacyl-tRNA (charged tRNA) from binding to the A-site of the ribosome but still allows for the hydrolysis of EF-Tu*GTP to EF-Tu*GDP.

Back 48

Tetracycline

Front 49

What is the resulting protein called after treatment with tetracycline?

Back 49

Truncated non-functional protein

Front 50

______ is a toxic enzyme, specifically an N-glycosidase which cleaves N-glycosidic bonds. It was originally isolated from castor beans.

Back 50

Ricin

Front 51

Ricin binds to eukaryotic ___ ribosomes and removes a highly conserved ________ in 28S rRNA (the rRNA which contains peptidyl transferase).

Back 51

80S

adenine

Front 52

Removal of adenine from the highly conserved sequence in 28S rRNA prevents ________

Back 52

elongation

Front 53

_________ ___ allows the insertion of a selected gene (cut with endonucleases) to be inserted into a plasmid

Back 53

Recombinent DNA

Front 54

What is responsible for the overall number of genes in the human genome?

Back 54

Alternative Splicing

Front 55

True or False

There are no operons in eukaryotes.

Back 55

True

Front 56

Protein coding genes almost never exist in multiple copies with the exception of _________

Back 56

Histones

Front 57

A _____ _____ is a set of closely related genes that code for the same or similar proteins
and which are usually grouped together on the same chromosome.

Back 57

gene cluster

Front 58

____ ____ drugs are used in gene therapy to target a specific protein in an effort
to treat a genetic disorder caused by one specific protein.

Back 58

“Magic bullet”

Front 59

The changing of one nucleotide within a sequence of nucleotides in a group of similar genes is called a

Back 59

single nucleotide polymorphism (SNP = snip)

Front 60

______ drugs are used to target SNPs because they can be used to target a group of genes, making them more effective than the “magic bullet” drugs which can only target one specific
gene.

Back 60

"Dirty"

Front 61

_______ _____ _____ are highly repetitive sequences of DNA.

Back 61

Short tandem repeats (STRs

Front 62

True or False

Trinucleotide repeats are harmless

Back 62

False

Front 63

Explains why the severity of the disease increases with each
generation of passage =

Back 63

genetic anticipation

Front 64

There are two types of regulatory proteins:

Back 64

Repressors
Activators

Front 65

A negatively regulated gene is only transcribed in the absence of the _________.

Back 65

repressor

Front 66

A co-repressor is a ______ that binds to and activates repressors.

Back 66

ligand

Front 67

A ________ regulated gene is normally transcribed without the repressor bound to the
silencer site.

Back 67

negatively

Front 68

An ________ is a ligand that binds to the repressor to inactivate it

Back 68

inducer

Front 69

Gene is normally transcribed with an activator bound to the enhancer site.
_______ Regulated

Back 69

Positively

Front 70

_________ means that there is an operon which codes for more than one gene.

Back 70

polycistronic

Front 71

How does the lac repressor bind to the silencer sequence

Back 71

inserting its α-helix into the
major groove of DNA via a helix-turn-helix motif

Front 72

What is the name of the inducer that binds to the lac repressor for dissociation

Back 72

Allolactose

Front 73

An activator makes the recognition of the lac promoter region stronger in the absence of glucose:

Back 73

Catabolite Activator Protein
CAP / CRP

Front 74

In eukaryotes gene expression is mostly regulated through ___________ and_________, but some also use activators and repressors which are signaled via hormone levels

Back 74

phosphorylation

dephosphorylation

Front 75

By binding to a specific transmembrane receptor, hormones initiate ______ _____ _______ within the cell, which affect the activity of activators and repressors.

Back 75

signal transduction cascades

Front 76

A signal cascade is also known as

Back 76

amplification

Front 77

The degradative metabolism
involving the release of energy and
resulting in the breakdown of
complex materials

Back 77

Catabolic metabolism

Front 78

The constructive part of metabolism
concerned especially with
macromolecular synthesis

Back 78

Anabolic metabolsim

Front 79

A ______ is an enzyme which puts a phosphate group on an amino acid

Back 79

kinase

Front 80

There are two main types of receptors used in protein phosphorylation.

Back 80

Receptor is associated with tyrosine kinase.

Receptor is tyrosine kinase

Front 81

True or False

Cytokine receptors are
transmembrane

Back 81

True

Front 82

When the cytokine receptors dimerize, _____ ______ (JAK, a tyrosine kinase) is
activated and it phosphorylates tyrosine residues on itself and the cytokine receptors.

Back 82

Janus kinase

Front 83

Signal Transduction:

____ binds to the phosphorylated tyrosines through a ____ domain on its surface which specifically
recognizes and binds to
phosphorylated tyrosines.

Back 83

STAT protein

SH2

Front 84

Signal Transduction:

How is STAT protein activated?

Back 84

JAK phosphorylates STAT bound to SH2 receptor.
STAT dissociates and dimerizes with SH2.

Front 85

Signal Trandsduction:

Activated STAT will then activate the cytokine genes by binding to its _______ site on DNA within the cell’s nucleus.

Back 85

enhancer

Front 86

_____ is a tyrosine kinase inhibitor used to treat tumors associated with uncontrolled gene expression.

Back 86

Gleevec

Front 87

These antibiotics are ineffective after RNAP has left the promoter region:

Back 87

Rifamycin B + Rifampicin

Front 88

________ is found in the mushroom Amanita phalloides (the “death
cap”).

Back 88

α-amantin

Front 89

dyhyrdouridine is found in what part of tRNA
(ribosomal recognition)

Back 89

D-arm (loop)

Front 90

pseudouridine is found in the ______ arm of tRNA for ribosomal recognition.

Back 90

T-psi-C arm (loop)

Front 91

What part of tRNA carries the amino acid to attach to the new protein?

Back 91

Acceptor Stem

Front 92

The acceptor stem is the __' end of tRNA

Back 92

3'

Front 93

tRNA synthetase recognizes new amino acids based on: (3)

Back 93

size, charge,
hydrophobicity

Front 94

Ribsomes:

30S subunit
• __ proteins
• ___ rRNA (establishes the reading frame in prokaryotic translation)

Back 94

21

16S

Front 95

Ribosomes:

50S subunit
• __ proteins
• 5S rRNA
• ___ rRNA (catalyzes the formation
of the peptide bond)

Back 95

31

23S

Front 96

Example: 70S

The unit S means _______ ____, a measure of the rate of
sedimentation of a particle in a centrifuge, where the sedimentation
rate is associated with the size of the particle.

Back 96

Svedberg units

Front 97

40S subunit
o __ proteins
o ___ rRNA

Back 97

33

18S

Front 98

60S subunit
o __ proteins
o 5S rRNA
o 5.8S rRNA
o ___ rRNA contains peptidyl transferase
(catalyzes peptide bond formation)

Back 98

49

28S

Front 99

1 molecule per 1 ribosome =

Back 99

stoichiometrically

Front 100

Regulatory proteins are often _______ proteins modified by ligand binding.

Back 100

allosteric

Front 101

HMG proteins =

Back 101

high mobility group
(in gel electrophoresis)

Front 102

Epigenetics =

Back 102

Post modification of protein, changes the way DNA is packaged.

Front 103

If DNA is tightly bound to the histone octamer it is transcriptionally ________

Back 103

inactive

Front 104

_______ attaches to a lysine
residue on a membrane protein to mark it for endocytosis

Back 104

ubiquitin

Front 105

Most epigenetic modifications of histones occur at the ________ terminus on __ and __
.

Back 105

carboxyl

H3
H4

Front 106

Lys loses its positive charge when ________ which weakens histones bond to DNA.

Back 106

acetylated

Front 107

________ causes DNA to unbind
histone due to steric bulk hindering the histone-DNA binding.

Back 107

Trimethylation

Front 108

Phosphorylated serine on histone becomes ______ charged causing DNA-histone to weaken or break.

Back 108

negatively

Front 109

Transcriptionally active (uncondensed chromatin = _____)

Back 109

euchromatin

Front 110

Transcriptionally inactive (condensed chromatin = ______)

Back 110

heterochromatin

Front 111

________ _______(HAT) acetylates (puts on –COCH3) Lys residues on histone
proteins bound to DNA in a specific order.

Back 111

Histone Acetyltransferase

Front 112

HATs are usually part of a large oligomeric protein called ___________ _________

Back 112

transcriptional coactivators

Front 113

___________ _______ (HDACs) remove acetyl groups from Lys residues on histones.

condense chromatin
promotes transcriptional repression and gene silencing

Back 113

Histone Deacetylases

Front 114

________ _______(HMTs) methylate (add –CH3) to Lys and Arg residues on the carboxyl terminus of H3 and H4.
Strengthens DNA-histone bond ______ gene expression

Back 114

Histone Methyltransferases

silencing