Biochem #7 Flashcards
1
Q
what leads to the diverse array of cells in the body?
A
Different cells express different genes which leads to the diverse array of cells in the body. This is despite the fact that all DNA has the possibility to express all genes.
2
Q
central dogma of molecular biology
A
major steps in the transfer of information from DNA to proteins.
o DNA replication occurs in the 5-3 direction, as does mRNA synthesis and ribosomal translation. Protein is produced in the N (amino) to C (carboxy) direction
3
Q
from ribosomes, protein is produce in the ____ direction
A
N to C
4
Q
gene
A
unit of DNA that encodes a specific protein or RNA molecule, and through transcription and translation the gene can be expressed.
5
Q
DNA coding strand
A
identical to the mRNA (except T for U)
6
Q
DNA template strand
A
complementary and antiparallel to the mRNA.
7
Q
messenger RNA
A
carries the information specifying the amino acid sequence of the protein to the ribosome.
Transcribed via RNA polymerase enzymes.
• Done in the nucleus
Undergoes post transcriptional modifications before it leaves the nucleus sometimes.
Codons: 3 nucleotide segments on the mRNA that are read by the ribosome.
Monocistronic: each mRNA molecule translates to only one protein product (eukaryotes)
Polycistronic: starting translation at different locates in the mRNA can result in different proteins.
8
Q
monocistronic and polycistronic
A
Monocistronic: each mRNA molecule translates to only one protein product (eukaryotes)
Polycistronic: starting translation at different locations in the mRNA can result in different proteins.
bacterial RNA is generally polycistronic
9
Q
transfer RNA
A
responsible for converting the language of nucleic acids to the language of amino acids and peptides.
Contains a folded strand of mRNA with an anticodon that pairs with the proper codon on the mRNA in the ribosome
Charged or activated with a specific amino acid that pertains to the anticodon/codon pair.
• Attached to the 3’ OH end of the tRNA, CCA nucleotide sequence here.
Aminoacyl-tRNA synthetase: activates the tRNA with the correct amino acid. Specific for the specific amino acid.
• Uses two high energy ATP bonds, which are used to supply the energy to create the peptide bond during translation.
10
Q
charged or activated tRNA
A
activated with a specific amino acid that pertains to the anticodon/codon pair.
• Attached to the 3’ OH end of the tRNA, CCA nucleotide sequence here.
11
Q
Aminoacyl-tRNA synthetase
A
activates the tRNA with the correct amino acid. Specific synthetase for the specific amino acid.
• Uses two high energy ATP bonds to add the tRNA to the amino acid. This high energy bond is then used to supply the energy needed for the peptide bond formed during translation.
12
Q
ribosomal RNA
A
synthesized in the nucleolus and function as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm.
Many rRNA molecules function as ribozymes: enzymes made of RNA molecules instead of peptides.
• Helps in the formation of peptide bonds and also splicing out its own introns in the nucleus.
13
Q
How many codons are there?
A
64
14
Q
what are the stop codons
A
UAA, UAG, UGA
15
Q
what are the start codons
A
AUG
16
Q
what does the start codon code for?
A
met
17
Q
degeneracy
A
more than one codon can specify a single amino acid
18
Q
wobble position
A
the variable 3rd base in a codon.
• Evolutionary advantage to protect against mutations because mutations in the wobble position tend to be silent or degenerate.
19
Q
point mutation
A
mutation occurs and it affects one of the nucleotides in a codon.
20
Q
expressed mutations
A
if the mutation is in a certain point, then it can affect the primary amino acid sequence of a protein
21
Q
missense mutations
A
a mutation where one amino acid substitutes for another
22
Q
nonsense mutation
A
a mutation where the codon now encodes for a premature stop codon (truncation mutation)
23
Q
reading frame
A
the three nucleotides of a codon and the order they are read
24
Q
frameshift mutation
A
occurs when some number of nucleotides are added to or deleted from the mRNA sequence.
• Can be very detrimental, resulting in changes to the amino acid sequence or premature truncation of the protein.
25
are mutations in introns a big deal?
no not if they are cleaved out
26
introns vs exons
exons are expressed while introns are cleaved out
27
transcription
the creation of mRNA from DNA template is transcription.
28
transcription
the creation of mRNA from DNA template is transcription.
29
describe initiation of transcription
Helicase and topoisomerase are involved in unwinding the dsDNA and preventing formation of supercoils.
30
template strand
antisense strand
| the strand that the mRNA is synthesized from.
31
RNA is synthesized by a DNA-dependent RNA polymerase. Scans the DNA looking for _____
promoter region
32
another name for the promoter region in eukaryotes is _____
TATA box (usually falls around -25)
33
transcription factors
help the RNA polymerase locate and bind to this promoter region.
o Does not require a primer to start
34
whart are the roles of RNA pol I, II, and III in eukaryotes?
RNA pol I: located in the nucleolus and synthesizes rRNA
RNA pol II: located in the nucleus and synthesizes hnRNA (pre-processed RNA) and small nuclear RNA (snRNA)
RNA pol III: located in the nucleus and synthesizes tRNA and some rRNA.
35
RNA pol travels in the ____ which allows transcribed mRNA in the ____
3 to 5 direction
| 5 to 3 direction
36
Does RNA pol proofread its work?
No
37
coding strand
sense strand
| DNA that is not used as a template during transcription, same as mRNA except mRNA has U’s for T’s.
38
what do the numbers mean on the gene with regard to transcription?
+1: the first base transcribed
Negative numbers: to the left of the start of transcription where the promoter is.
Positive numbers: downstream of the gene
0: does not exist
39
what does the number 0 on the gene for transcription mean?
it does not exist
40
hnRNA to mRNA from ____
post-transcriptional modifications
41
after transcription, in the nucleus, ____ are spliced, and ____ are ligated
introns
| exons
42
lariat
introns that are released after being spliced
43
alternative splicing
when the primary transcript of hnRNA is spliced together in different ways to produce multiple variants of proteins encoded by the same original gene.
44
discuss the 5' cap
Is added during transcription and is recognized by the ribosome as the binding site. It also protects the mRNA from degradation in the cytoplasm.
45
3' poly A tail
* Added to the 3’ end of the mRNA transcript and protects the message against rapid degradation.
* Assists with export of the mature mRNA from the nucleus.
46
nuclear pores
used by the mRNA to exit the nucleus.
47
translation
converting the mRNA transcript into a functional protein
48
what is the ribosome composed of
proteins and rRNA
49
the small and large subunits of the ribosome only come together during ____
protein synthesis
50
what is the difference between eukaryotic and prokaryotic translation initiation?
For eukaryotes, mRNA has to be transferred to the cytoplasm before translation begins but in prokaryotes it begins before the mRNA is even complete yet.
51
what are the factors involved in the 3 steps of translation?
initiation factors (IF), elongation factors (EF), and termination release factors (RF)
52
describe translation initiation
Prokaryotes: small subunit binds to the Shine Dalgarno sequence in the 5’ untranslated region, Initial amino acid is fMet
Eukaryotes: small subunit binds to the 5’ cap structure, Initial amino acid is methionine
The charged initiator tRNA binds to the AUG start codon in the P site of the ribosome.
53
describe translation elongation
handing down the peptide chain from each tRNA to the next (only the amino acid on top is being handed down while the uncharge tRNA is eventually kicked)
3 step cycle that is repeated for every AA after the initial methionine is added
1. A site: holds the incoming aminoacyl tRNA complex. Next to be added, determined by mRNA codon in A site
2. P site: holds the tRNA that carries the growing polypeptide chain
• Peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site, which requires peptidyl transferase (part of the large subunit). GTP is used for energy during the formation of this bond.
3. E site: the uncharged tRNA pauses here before exiting the ribosome. Unbinds from mRNA and is now ready to be charged again.
Elongation Factors: recruit charged tRNA and GTP.
Signal sequences can also be present on the proteins that help them get sent to a certain place.
54
describe translation termination
Reach stop codon in the A site, release factor binds to the stop codon, termination factors help to hydrolyze the completed polypeptide chain from the final tRNA and the polypeptide chain is released from the tRNA in the P site.
55
order of APE in ribosome describe
EPA pretty much and mRNA is read 5 to 3
56
chaperones
posttranslational
| assist the protein in its folding process
57
what are two different things that must happen for some proteins to become active following translation?
o Some proteins must be cleaved to become active while others must come together to form their quaternary structure before they are active.
58
phosphorylation
addition of phosphate group by kinases.
59
carboxylation
addition of carboxylic acid groups, usually act as calcium binding sites.
60
glycosylation
addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination.
61
prenylation
addition of lipid groups to certain membrane-bound enzymes.
62
operon
a cluster of genes transcribed as a single mRNA; all relate to each other.
o Very common in prokaryotic cells
o Ex: trp operon in E. coli (negative repressible system)
Turned off when there is too much tryptophan in the system.
63
inducible operon systems
the system is normally off but can be induced to be on
The repressor is bonded tightly to the operator system and acts as a roadblock.
Negative control mechanism.
Allows genes to only be produced when they are needed.
Inducer binds to the repressor and allows the RNA polymerase to function.
Ex: lac operon (negative inducible system)
• Induced by the presence of lactose
• It is also activated by catabolite activator protein (CAP) which acts through a positive control mechanism
64
describe the lac operon
negative inducible system
| normally off but can be induced to turn on in the presence of lactose.
65
describe the trp operon
negative repressible system
| normally on but can be bound to to turn off
66
describe the order along the genome of regulator, structural, operator, promoter
regulator, promoter, operator, structural
67
repressible systems
the system is usually on but can be made to turn off
Allow constant production of protein product. The repressor made by the regulator gene is inactive until it binds to a corepressor then binds to the operator site to stop future transcription.
Sometimes negative feedback of the protein product that shuts it off.
68
jacob-monod model
prokaryotes
used to describe the structure and function of operons.
o In this model, operons contain structural genes, an operator site, a promoter site, and a regulator gene.
o Structural gene: codes for the protein of interest.
o Operator site: a nontranscribable region of DNA that is capable of binding a repressor protein
o Promoter site: similar in function to promoters in eukaryotes
o Regulator gene: codes for a repressor protein
69
transcription factors
transcription-activating proteins that search the DNA looking for specific DNA-binding motifs. Two domains:
o DNA-binding domain: binds to a specific nucleotide sequence in the promoter region or to a DNA response element (a sequence of DNA that binds only to specific transcription factors) to help in the recruitment of transcriptional machinery.
o Activation domain: allows for the binding of several transcription factors and other important regulatory proteins, such as RNA polymerase and histone acetylases, which function in the remodeling of chromatin structure.
70
gene amplification
: amplification of transcription of a particular gene due to signals
o Enhancers: consists of response elements that allow for the control of one gene’s expression by multiple signals. many txn factors can bind to one enhancer.
Might be distance between the promoter and the enhancer so the DNA must bend to bring them together.
By using enhancer regions, genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels.
71
enhancers
consists of response elements that allow for the control of one gene’s expression by multiple signals. many txn factors can bind to one enhancer.
Might be distance between the promoter and the enhancer so the DNA must bend to bring them together.
By using enhancer regions, genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels.
72
gene duplication
allows for more copies of the gene in the genome. Mass transcription of the gene product.
73
histone acetylation
Transcription factors that bind to the DNA can recruit other coactivators such as histone acetylases.
Acetylation of histone proteins decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA, opening the chromatin structure.
74
histone deacetylase
proteins that function to remove acetyl groups from histones, which closes the chromatin conformation and decreases gene expression levels in the cell.
75
DNA Methylation: DNA methylases
add methyl groups to cytosine and adenine nucleotides, which silences genes.
Methylation occurs during development to silence genes that no longer need to be expressed.
76
mRNA is produced in what direction?
mRNA is produced in the 5' to 3' direction, adding onto the 3' end.
77
which end of the tRNA is the amino acid added to?
the 3' end after a CCA sequence
78
are all aminoacyl tRNA synthetases the same?
No, each type of amino acid is activated by a different one
79
how many ATPs does it cost to charge a tRNA molecule?
2
80
what type of RNA is synthesized in the nucleolus?
rRNA
81
each codon specifies _____ amino acids but many codons can specify ____
only
| the same amino acid
82
what is the name of the enzyme used to charge tRNA with their correct amino acid?
aminoacyl-tRNA synthetase
83
are there tRNA molecules that recognize the stop codons?
no, when these codons come up it just leads to the release of the protein from the ribosome.
84
what are the benefits of the wobble position in the genetic code?
it allows for mutations to occur and not have an effect on the protein product.
85
what are mutations in the wobble position called?
degenerate or silent
86
missense vs. nonsense mutation
missense: one amino acid subtitutes for another
nonsense: the codon produced by the point mutation now encodes for a premature stop codon
87
what is another word for a nonsense mutation?
truncation mutation
88
where does a silent mutation occur?
occurs in a wobble position, introns, or noncoding DNA.
89
what are the roles of helicase and topisomerase during transcription?
they play the same roles as in replication
topoisomerase: prevents supercoiling
helicase: unwinds the DNA
90
what is another name for the DNA template strand?
the antisense strand
91
what is the difference between RNA polymerase and DNA polymerase in terms of starting?
RNA polymerase does not need a primer to begin
92
Does RNA polymerase proofread its work?
no
93
what is mRNA called before posttranscriptional modifications?
heterogenous nuclear RNA (hRNA)
94
in the genetic code chart, the codons represent the ______ strand
coding (same except for U for A)
95
what is the name of the complex that accomplishes splicing of hnRNA and what is in it?
spliceosome
small nuclear RNA (snRNA)
small nuclear ribonucleoproteins (snRNPs)
96
do introns or exons get spliced?
introns
97
what are the formal names of the 5' cap and polyA tail?
5' cap: 7-methylguanylate triphosphate cap
| 3' tail: polyadenosyl tail
98
what is an example of a mutation in noncoding DNA that can effect the final protein?
mutation in the splice sites
99
explain the process of splicing
removal of introns, joining of exons, uses snRNA and snRNPs in the spliceosome to create a lariat, which is then degraded; exons are ligated together
100
what are the formal names of of the binding sites in the ribosome?
A: aminoacyl
P: peptidyl
E: exit
101
what is the difference between eukaryotes ribosome and prokaryotic?
eukaryotic: 40S + 60S == 80S
prokaryotic: 30S + 50S == 70S
102
what is the rRNA not transcribed in the nucleolus?
5S
103
compare where the small ribosomal subunit binds: eukaryotes vs. prokaryotes
eukaryotes: 5' cap
prokaryotes: shine-dalgarno sequence in the 5' untranslated region
104
where does the Met tRNA initially bind to the start codon in the ribosome?
P site
105
what is the name of the enzyme that creates the peptide bond in the ribosome?
peptidyltransferase
106
is there energy required to form each peptide bond in the ribosome?
yes, energy from GTP.
107
Are tRNA reused?
yes, once they leave the E site of the ribosome then they can be recharged.
108
what do initiation factors do?
help the large subunit bind to the smaller subunit
109
what do elongation factors do?
recruit aminoacyl-tRNA along with GTP
110
signal sequences on the N-terminal end of the protein do what?
dictate that the ribosome move to the rough ER so that the protein can be directly translated into the lumen of the ER (for proteins being excreted or going to the nucleus, cell membrane, or lysosomes.
111
what is the role of release factor?
it binds to the stop codon on the mRNA sequence in the A site and recruits a water molecule to be used to hydrolyze the completed polypeptide chain from the P site.
112
what are some examples of posttranslational modifications?
correct folding
cleavage events (to form active peptides or cleaving the signal sequence)
subunits come together to form quaternary structure
adding other biomolecules: phosphorylation, carboxylation, glycosylation, prenylation
113
what does a regulator gene code for?
repressor
114
where is the promoter site with respect to the operator site and the regulator site
promoter - operator - gene that makes protein
115
is the operator site transcribed in prokaryotes?
no
116
negative control mechanisms
the binding of a protein reduces transcriptional activity
117
positive control mechanisms
the binding of a molecule increases transcription of a gene
118
explain the role of the CAP protein in lac operon
CAP: catabolite activator protein
activated by cAMP in the presence of lactose (when glucose levels are low). Binds to promoter region of lac operon to increase transcription.
119
what is the role of the corepressor
binds to the repressor and activates it in a repressible operon system.
120
what are the two recognizable domains of transcription factors?
DNA binding domain
| Activation domain
121
where can transcription factors bind?
promoter or DNA response element (a sequence of DNA that binds only to specific transcription factors)
122
response element
a sequence of DNA that binds only to specific transcription factors
123
cis regulators vs. trans regulators
cis: promoter, right next to the gene
trans: transcription factors, they are proteins that must be translated in the cytoplasm and transported back to the nucleus for action.
124
because of the location of enhancers, DNA oftentimes must ____ to bring the enhancer elements closer to the promoter
bend
125
are heterochromatin or euchromatin more methylated?
heterochromatin are, which plays a factor in heterochromatin DNA being more silenced.
126
____ acetylation and ___ methylation in transcriptional control
histone
| DNA
127
2 roles of elongation factors
bring in incoming tRNA and move growing strand from A to P site while moving ribosome down the mRNA
128
which stages of protein synthesis require energy?
all 3 parts, initiation, elongation, and termination.
129
do enhancers bind to multiple promoters?
no. specific transcription factors bind to specific DNA sequences (ex: enhancer) and to specific RNA polymerase at a single promoter sequence.
