Molecular Biology Flashcards
1
Q
The human genome contains ___ chromosomes
A
24 (22 autosomes plus 2 sex chromosomes)
2
Q
The genome has multiple regions with high transcription rates, separated by long stretches of intergenic space.
What is intergenic space?
A
Intergenic space holds noncoding DNA regions that may direct the assembly of specific chromatin structure and can contribute to regulation of nearby genes though many have no known function.
3
Q
2 major components of intergenic space
A
Tandem repeats and transposons
4
Q
Gene
A
A DNA sequence that encodes a gene product
5
Q
A gene includes two regions. What are they?
A
The regulatory region: promoters and transcription stop sites
The (non)coding region: codes for protein or non-coding for RNA
6
Q
Single nucleotide polymorphisms
A
Single nucleotide changes once in every 1000 base pairs in the human genome
SNPs, pronounced “snips” are essentially mutations
7
Q
Code Number Variation
A
Structural variations in the genome that lead to different copies of DNA sections.
Large regions of the genome can be duplicated (inc. copying number) or deleted (dec copying number) via this process
8
Q
Repeated Sequences: Tandem Repeats
A
Short sequences of nucleotides are repeated one right after the other, from as little as three to over 100 times.
9
Q
Repeated Sequences: Transposons
A
Mobile genetic elements that can jump around the genome and cause mutations and chromosome changes such as inversions, deletions and rearrangements.
10
Q
DNA contains strands of nucleotides known as genes that serve as templates for the production of another nucleic acid known as:
A
RNA
11
Q
Transcription
A
The process of reading DNA and writing the information as RNA generating mRNA or non-coding RNA
12
Q
Messenger RNA (mRNA)
A
Read and used to construct proteins `
13
Q
Translation
A
Synthesis of proteins using RNA as a template
14
Q
Translation is accomplished by:
A
The ribosome
15
Q
What is a ribosome?
A
Massive enzyme composed of many proteins and pieces of ribosomal RNA (rRNA)
16
Q
Central Dogma
A
Inherited info is used to create objects via:
DNA –> RNA –> Protein
17
Q
Genetic Code & Its Alphabet
A
Language used by DNA and RNA to specify the building blocks of proteins
Its alphabet contains only 4 letters (A, T, G, C)
18
Q
Codon
A
3-letter nucleic word coding for a specific amino acid
19
Q
Start Codon(s)
A
AUG
20
Q
Stop Codon(s)
A
UAA: U Are Annoying
UGA: U Go Away
UAG: U Are Gone
Notifies ribosome that protein is complete and tells it to stop reading the mRNA
21
Q
Nonsense Codons
A
Another words for stop codons because they don’t code for an amino acid
22
Q
Often, all four of the codons with _________ encode the same amino acid.
A
Same first two nucleotides = same AA despite last nucleotide
23
Q
If CCU is changed to CCC will the amino acid change?
A
No
24
Q
Synonyms
A
2 or more codons encoding for the same amino acid
25
Degenerate
Genomic code is said to be degenerate because it has synonyms
26
An amino acid is specified by many codons, BUT
A codon only specifies a single amino acid
There is no code ambiguity
27
Mitosis produces two daughter cells with identical genomes, hence cell division requires:
DNA Replication
28
What phase does DNA replication occur during the cell cycle?
Replication occurs during the S phase (synthesis) in the interphase of the cell cycle.
29
Old DNA is called:
New DNA is called:
Prenatal DNA
Daughter DNA
30
Meselson & Stahl wanted to determine if DNA is semiconservative, conservative or dispersive.
Which was proven to be true?
What is semi-conservative replication?
What is conservative replication?
What is dispersive replication?
SC: After replication, one strand of the double helix is parental and one is newly synthesized daughter (old+new, old+new) (PROVEN TRUE)
CR: Parental DNA would remain as-is while an entirely new double stranded genome was created. (old+old, new+new)
DR: Both copies of the genomes were composed of scattered pieces of old and new DNA
31
DNA is semiconservative: this means
Individual strands of the double-stranded parent are pulled apart. A new daughter strand is synthesized using the prenatal DNA as a template to copy from. Each daughter chain is perfectly complementary to its parent.
32
DNA is usually tightly coiled. In the replication process:
The double helix is uncoiled and separated into two separate strands by an enzyme called Helicase.
33
Helicase
Uncoils and separates DNA for replication.
34
Origin of Replication (ORI)
Specific location (sequence of nucleotides) on the chromosome where the helices begins to unwind the DNA
35
When helicase unwinds the helix at the origin of replication, the helix gets wound more tightly above and below the ORI, like two ropes being unwound in the middle. How does the body prevent this from tearing the DNA?
Topoisomerases cut one or both of the strands and unwrap the helix, releasing the pressure from the helicase.
36
Topoisomerase:
Enzyme that cuts one or both strands of DNA to release excess pressure from the helicase unwinding the DNA in the center of the helix.
37
Single Stranded Binding Proteins (SSBP)
Protect DNA that has been unpackaged in preparation for replication and help keep the strands separated.
38
Another potential problem with replication of DNA is that the single strands are less stable than the double stranded DNA. How does the body account for this problem?
SSBPs (Single stranded binding proteins) protect the single strands and keep them separated.
39
Open complex
Separated single strands that allow replication to begin.
40
Primase
RNA polymerase that is the central component of primosome (RNA primer that synthesizes each template strand).
41
Primosome
RNA primer synthesizes each template strand
42
Why is primer synthesis important?
DNA polymerase cannot start a new DNA chain from scratch. It can only add nucleotides to an existing nucleotide chain. RNA primer is usually 8-12 nucleotides long and is replaced by DNA
43
Daughter DNA is created as a:
Growing polymer
44
DNA polymerase
Catalyzes the elongation of the daughter strand using the parental template. Elongates the primer by adding NTPs to its 3' end.
45
What direction is the template strand read in?
5'-3'
46
DNA polymerase is part of a large complex of proteins known as the:
Other proteins in this complex help DNA poly to:
Prokaryotic vs Eukaryotic replisome:
Replisome
Polymerize DNA quickly
P: 13 components & E: 27 proteins (more complexity in E needed because replication machinery must unwind DNA from histone proteins)
47
Since the two template strands are _____ , the two primers will elongate towards ______ of the chromosome.
antiparallel
opposite ends
48
Before each base pair is incorporated into the growing polymer,
DNA poly checks each nucleotide to make sure it forms the correct base pair
49
Thermodynamic driving force for the polymerization reaction is the:
Removal and hydrolysis of pyrophosphate (P2O7)^-4 from each double NTP added to the chain.
50
Polymerization occurs in the _____ direction, with or without exception?
5-3'
Lengthened by addition of a nucleotide to the 3' end of the chain. No exceptions
51
DNA polymerization requires a: t____
Template
Can't make DNA from scratch--must copy an old chain.
52
DNA polymerization requires a: p_____--
Primer
Cannot start a new nucleotide chain... RNA primer has to do so.
53
Both template strands are read from _____ while daughter strands are elongated _____
Read from 3'-5'
Elongated from 5'-3' **
54
Replication forks
Areas where the parental double helix continues to unwind
55
Leading strand
Replication is continuous into the widening of the fork
56
Lagging strand
Discontinuous... A lagging strand is dropped down behind the end of the leading strand as the fork widens this results in Okazaki fragments
57
Okazaki fragments
Fragments result of the lagging strand being dropped down behind the end of the leading strand
58
Eventually, all the RNA primers _____ and all the fragments are _______
are replaced by DNA
joined by an enzyme called DNA Ligase
59
DNA Ligase
Connects the Okazaki Fragments.
60
DNA polymerase is said to be processive. This means:
DNA poly is able to add thousands of nucleotides before falling off the template
61
Prokaryotes have ____ different DNA polymerases
5
62
DNA polymerase I (prokaryotes)
Starts adding nucleotides as the RNA primer.
5'-3' activity
Can only add about 15-20 nucleotides/second, so DNA poly III usually takes over about 400 pairs downstream of the ORI
Capable of 3'-5' exonuclease activity (proofreading) and removes primer via 5'-3' exonuclease activity while simultaneously leaving behind new DNA in 5-3' activity
DNA poly I is important in excision repair
63
DNA poly III (prokaryotes)
Super fast, super accurate elongation of the leading strand. 5-3 polymerase function and 3-5 exonuclease activity (enzyme moves backward to chop off nucleotide it just added if incorrect: proofreading function)
Replicative enzyme
64
Proofreading Function aka (_______) is:
Exonuclease activity
Enzyme moves backward to chop off nucleotides if it was added incorrect (3-5')
65
Theta replication and theta mechanism
Prokaryotes one circular chromosome has only one origin, as the replication proceeds the chromosome is duplicating and begins to look like the greek letter theta.
66
Eukaryotic Replication has ____ ORI's because:
Several ORIs because the chromosomes are so large that a single origin would be too slow.
"replication bubbles" along the DNA strand meet and the daughter strands are litigated together.
67
DNA replication machinery is unable to replicate sequences at the very end of the chromosomes because the DNA ligase cannot lay a primer on the end and then replace it with DNA because there is no DNA on the other side of the primer.
To compensate for this:
After each round of the cell cycle and DNA replication, the ends of chromosomes shorten.
Ends are known as telomeres
68
Telomeres
Disposable regions at the end of the chromosome
69
When telomeres become too short:
Critical length can be reached where the chromosome can no longer replicate and cells activate DNA repair pathways as a result while they go into a senescent state (not dividing just alive) or undergo apoptosis (pre-programmed death)
70
Hayflick limit
Number of times a normal human cell type can divide until telomere length stops cell division
71
Telomere shortening is linked to many:
Age related diseases
72
Telomerase: function?
Enzyme that adds repetitive nucleotide sequences to the ends of chromosomes and therefore lengthens telomeres
73
Telomerase is a _____ complex, containing ____ and ______
Transcriptase enzyme is:
RNA primer and reverse transcriptase enzyme (read DNA templates and generate DNA)
74
RNA template is:
3'-CCCAATCCC-5' allowing for chromosome extension
75
RNA template allows for chromosome extension one DNA repeat at a time. The DNA repeat codon is:
5'-GGGTTAGGG-3' (complement to template: CCCAATCCC)
76
The telomerase complex continuously polymerizes, then translocates, allowing:
Extension of six-nucleotide telomere repeats
77
In most organisms, telomerase is only present in the germ line, embryonic stem cells and some white blood cells. However, _____ can also express telomerase, which can help the cells ______
Telomere extension allows the cells to bypass _____ and ______ , and can therefore contribute to ________
Cancer cells
Immortalize
Senescence (existence without replication)
Apoptosis (Self-programmed death)
Transformation to a precancerous state
78
Genetic Mutation
Any alteration of the DNA sequence of the organisms genome
79
Germ-line mutations
Can be passed to the offspring, because they occur in the germ cells which give rise to gametes
80
Somatic mutations
Occur in somatic (non-gametic) cells and are not passed onto offspring
Only effect individual, not next generation
81
Point mutations
Single base substitutions (A in place of G)
82
Point mutations can be transitions or transversions.
Transitions are:
Transversions are:
Transitions: substitution of a pyramide for another pyramide or substitution of a purine for another purine)
Transversions: substitution of a pyramide for a purine, or vice versa
83
3 Types of Point Mutations
Missense, Nonsense, Silent
84
Missense Mutations
Causes one amino acid to be replaced with another amino acid... May not be serious if the AA are similar
85
Nonsense Mutations
A stop codon replaces a regular codon and prematurely shortens the protein
86
Silent Mutations
A codon is changed into a new codon for the same amino acid, there is no change in the proteins amino acid sequence
87
Insertion Mutation
Adding one or more extra nucleotides into the DNA sequence
88
Deletion Mutation
Deletion/removal of one or more nucleotides
89
Insertion and Deletion Mutations can cause
A shift in the reading frame
All AA in the gene will be changed and the whole gene will be read differently
90
Frameshift mutations
Cause a change in the reading frame of the gene
91
Frameshift can lead to:
Premature termination of translation (yielding an incomplete polypeptide) if an abnormal stop codon results
92
Insertions and deletions can also involve
Thousands of bases
93
Inversion Mutation
Segment of a chromosome is reversed end to end
94
For inversion to occur the chromosome undergoes:
Breakage and rearrangement within itself
95
Chromosome Amplification Mutation
Segment of a chromosome is duplicated
96
Translocation Mutation
Recombination occurs between non-homologous chromosomes creating a gene fusion where a new gene product is made from parts of two genes that were not previously connected.
Common in many cancer types
97
Translocation can be balanced or unbalanced meaning:
Balanced: no genetic information is lost
Unbalanced: genetic information is lost or gained
98
Tranposase
Cut and paste function that catalyzes mobility
Excision from donor and integration into a new genetic acceptor site (sometimes it is completely removed and then moved, other times it is duplicated and moved, while still maintained at the original location)
99
When transposons are mobilized they can insert in any part of the genome, and this can affect gene expression/mutation. They can jump into a protein-coding region and disrupt or mutate the sequence. They can also jump into:
Regulatory parts of the genome and ramp up gene expression at a nearby site
100
Loss of Heterozygosity Mutation
Diploid organism when one allele of a certain gene is lost, due to deletion or recombination
This makes the locus homozygous: there is only one gene copy in a diploid organism. If the remaining alley is mutated or defective, all normal expression oft he gene product is lost
101
Direct Reversal DNA Repair
Some types of mutation are reversible.
For ex, UV radiation can be reversed by normal light via photoreactivation (cal induce another type of mutation leading to myeloma)
102
Homology-Dependent Repair
Mutations on one strand can be repaired by the other undamaged strand.
103
Two types of homology dependent repair
Excision repair: divided into repair that happens before DNA replication
Post-replication repair: repair during and after NDA replication
104
Excision Repair
Removing defective bases or nucleotides and replacing them. If these bases aren't repaired, could induce mutations during replication since replication machinery cannot pair them properly.
105
Post-Replication Repair to subtypes:
How is the newly synthesized strand recognized?
Mismatch Repair and Genome Methlyation
Gene methylation or 3' terminus ID / DNA gaps
106
Mismatch Repair Pathway
Targets mismatched base pairs that were not repaired by DNA polymerase proofreading during replication
107
Genome Methylation
Help differentiate between the older and daughter DNA
Parental template strand will be labeled with methylated bases so bacterial machinery can read these methyl tags and known which base is the correct one (older stand) and which needs to be replaced (newer strand)
108
Double strand break repair:
Two types of pathways are Homologous recombination and Non-homologous end joining
The goal of both is to:
Reattach and fuse chromosomes that have come apart because of DSB
Can lead to deletions or translocations if done incorrectly
109
Homologous Recombination
Process where one sister chromatid can help repair a DSB in the other sister chromatid.
110
How does homologous recombination work?
1. DSB identified and trimmed to single stranded DNA by helicase and nuclease
2. Find complementary sister chromatid and form joint molecule (intertwined kinda)
3. DNA poly and ligase build new DNA
111
Non-homologous End Joining
Accomplish repair in cells not in the cell cycle because these cells do not have a sister chromatid to function as a complementary template
112
Non-homologous End Joining Process
1. Broken ends are stabilized and processed
2. DNA ligase connects the fragments
None of this requires specificity. The goal is just to reconnect broken chromosomes which can result in base pairs being lost or chromosomes being constructed in an abnormal way. This is all still better than DSB.
113
Gene expression
Process whereby the information contained in genes begins to have effects in the cell
114
RNA is distinct from DNA in three ways:
As a result of these differences, RNA is:
RNA is single stranded (except some viruses)
RNA contains uracil instead of thymine (U not T)
The pentose ring in RNA is ribose rather than 2' deoxyribose
Less Stable because can hydrolysis itself
115
Coding RNA
mRNA
Carries genetic information to the ribsomone for translation into protein
116
A strand of mRNA has several regions:
5' region (5'UTR)
Open Reading Frame (ORF)
5' region is not translated into protein (untranslated region) but is important to initiation and regulation
ORF is the region that codes for a protein; starts at start codon and ends at end codon.
117
Eukaryotic mRNA is usually monocistronic meaning
One gene, one protein principle meaning that each piece of mRNA encodes only one polypeptide (one ORF) hence there are as many mRNAs as there are proteins.
118
Because each mRNA can be read many times:
Each transcript can be used to make many copies of its polypeptide.
119
Prokaryotic mRNA is usually polyistronic meaning
mRNA codes for more than one polypeptide
120
mRNA is constantly produced and degraded based on the
Cells need for proteins encoded by each piece of mRNA
Allows cells to regulate amount of protein they synthesize
121
Heterogeneous nuclear RNA (hnRNA)
First RNA transcribed from DNA is an immature or precursor to mRNA in eukaryotes
Processing events are required for hnRNA to become mature mRNA
122
Since prokaryotes do not process their primary transcripts,
hnRNA is only found in eukaryotes
123
Non-coding RNA (ncRNA)
Functional RNA that is not translated into protein
124
Human genome codes for thousands of ncRNAs and there are several types... The two major types are:
Transfer RNA (tRNA) and ribosomal RNA (rRNA)
125
Transfer RNA (tRNA)
Responsible for translating the genetic code
Carries amino acids from the cytoplasm to the ribosome to be added to a growing protein
126
Ribosomal RNA (rRNA): how many types?
All serve as:
Human have four types of rRNA molecules
All serve as components of the ribosome and polypeptide chains
127
Although most enzymes are made from polypeptides, one rRNA has a catalytic function of the ribosome, this is called a:
Ribozyme
128
What is transcription and how does it relate to replication?
Process of making RNA from DNA as a template
Transcription is reading and writing, without changing the language... For this reason transcription is similar to replication in a lot of ways.
129
Both replication and transcription involve:
Template-driven Polymerization
130
Template-Driven Polymerization is:
RNA transcript is complementary to the DNA template just as the daughter strand is complementary to the parental strand
131
Driving force for replication and transcription:
Removal and subsequent hydrolysis of pyrophosphate from each nucleotide added to the chain, with the existing chain acting as a nucleophile.
132
Like replication, transcription only occurs in the:
5-3' direction
133
Unlike replication, transcription does or doesn't require a primer? Why?
Transcription does not require a primer because the primer in replication is a piece of mRNA made by the RNA polymerase
134
Another important difference between transcription and replication is the RNA polymerase lacks:
Exonuclease function, so it cannot correct its error/proofread
Therefore, replication is a higher fidelity process
135
Transcription, like replication, begins at:
A specific location on the chromosome called the start site (different name than the ORI for replication)
136
Sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription is called a:
Promoter
137
Point where RNA polymerization actually starts is called the:
Start Site
138
Template aka non-coding, transcribed, or antisense strand
Strand that is actually transcribed and complementary to the transcript (only one of the DNA strands encodes for a particular mRNA molecule)
139
Coding/Sense Strand
Same sequence as the transcript (except for a T in the place of U)
140
Transcription starts at a point and then proceeds ________ which is:
What does upstream mean?
Downstream: toward the 3' end of the coding strand) (referred to with positive numbers)
Toward the 5' end of the coding strand (referred to with negative numbers)
141
Start site
First nucleotide that is actually transcribed on the template strand
142
Which nucleotide is given the number +1?
The nucleotide on the coding site corresponding to the start site nucleotide on the template strand
143
In Prokaryotes, all types of RNA are made by the same:
RNA polymerase
Large enzyme complex with five subunits
144
What is the core enzyme in prokaryotes responsible for rapid elongation of the transcript?
RNA polymerase
145
The RNA polymerase is the core enzyme responsible for rapid elongation of the transcript, however this enzyme along cannot initiate transcript. An addition subunit termed: _____ is required to form what is called the ____, which is responsible for:
Sigma factor (sigma) is required to form the holoenzyme which is responsible for initiation
146
Three stages of transcription in prokaryotes
initiation, elongation, termination
147
Initiation of transcription in prokaryotes occurs when
RNA poly holoenzyme binds to a promoter
148
To initiation transcription, RNA poly holoenzyme binds to a promoter that contains two primary sequences called:
Pribnow box at -10
The -35 sequence
149
The holoenzyme scans across a chromosome like a train on a railroad until:
It finds a promoter and then it stops to form a closed complex
150
The RNA polymerase must ______ before it can synthesize RNA
Unwind the double helix DNA
151
A RNA polymerase bound at the promoter with a region of single stranded DNA is termed the ____
Once formed, it allows _____
Open complex
Transcription can now occur.
152
The sigma factor plats two roles in helping the polymerase find promoters:
1. Increase the ability of RNA poly to find promoters
| 2. Make holoenzyme more specific
153
The core enzyme elongates the RNA chain processively, meaning
One polymerase complex synthesizes an entire RNA molecule
154
As the core enzyme elongates the RNA, it moves down the DNA in a ____ direction in a _____, in which a region of the DNA double helix is unwound to allow the polymerase to access the complementary DNA template
Downstream direction
Transcription bubble
155
When a termination signal is detected, in some cases with the help of the protein called "rho", the:
Polymerase falls off of the DNA, releases the RNA and the transcription bubble closes
156
In eukaryotes, translation and transcription occur in the:
In prokaryotes, translation and transcription occur in the:
For eukaryotes, transcription occurs in the nucleus and then it is modified and transported across the cell membrane to be translated in the cytoplasm
Transcription and translation for prokaryotes occurs together in cytoplasm because the cell has no nucleus
157
Translation and transcription occur _____ in prokaryotes and _____ in eukaryotes
Simultaneously in P
| Non-simultaneously in E
158
Primary transcript in prokaryotes is:
Primary transcript in eukaryotes is:
mRNA (ready to be translated)
hnRNA (modified extensively before translation)
159
Splicing
Eukaryotic DNA has non-coding sequences intervening between segments that code for proteins
These intervening sequences contain enhancers or other regulatory sequences and can be quite long
160
Introns
Intervening sequences in the RNA
INtrons INtervene
161
Extrons
Protein coding regions of the RNA actually expressed
EXtrons are EXpressed
162
Before the RNA in eukaryotes can be translated:
The introns must be removed and the extrons connected via splicing
163
Spliceosome
Contains proteins and snRNA (small nuclear RNA)
Proteins bind to the snRNA forming snRNPs (small nucleic ribonucleic proteins)
164
The spliceosome assembles around each ____ that needs to be removed via a series of steps in which ________ as the reaction proceeds. This complex undergoes many _________
Introns
Different snRNPs are recruited and released
Conformational changes to attain catalytic activity
165
Two splicing reactions are catalyzed by the spliceosome
1. Intron forms a looped structure
| 2. Joins two externs and releases loop
166
Alternative splicing
For a given gene, there are different options for splicing patterns leading to different mRNAs (in length and sequence) being made from one DNA gene sequence
This increases the complexity in gene expression
167
hnRNA must be modified in two more ways (in addition to splicing) before translation can occur:
A tag is added to each end of the molecule (5' cap and a 3' poly-A tail)
168
Before translation, the hnRNA must be modified by adding a tag to each end of the molecule...
A 5' cap is:
A 3' poly-A tail is:
5' cap: methylated guanine nucleotides on the 5' side (made first)
3' poly-A tail: string of adenine nucleotides
169
The 5' cap is essential for _____ , while both the cap and the poly-A tail are important in:
Translation
Preventing digestion of the mRNA by the exonucleases that are free in the cell
170
In eukaryotes there are several types of RNA polymerases:
1.
2.
3.
RNA poly I, II and III
171
RNA poly I in eukaryotes:
Transcribes most rRNA
172
RNA poly II in eukaryotes:
Transcribed hnRNA (ultimately mRNA), snRNA and some miRNA
173
RNA poly III in eukaryotes:
Transcribes tRNA, siRNA, some miRNA and a subset of rRNA
174
Translation
Synthesis of polypeptides according to the amino acid sequence dictated by mRNA codons
175
During translation, the mRNA molecule attaches to a ribosome at a specific codon and the appropriate amino acid is delivered by a ___ molecule.
Then the: _____
The process is repeated until the _____, at which point the ribosome _____
tRNA
Ribosome binds the two amino acids together, creating a dipeptide
Polypeptide is complete at which point the ribosome drops the mRNA and the new polypeptide departs
176
Each tRNA is composed of a single transcript produced by
RNA poly III
177
The ____ structure of every tRNA molecule is ____
tertiary; similar
178
tRNA molecules have a ___ structure that is stabilized by ______
Stem-and-loop structure
H-bonding between bases on neighboring segments of the RNA chain
179
One end of tRNA is known as the anti-codon segment and is responsible for:
Anticodon:
Organizing the mRNA codon to be translated.
Three ribosome sequence that is complementary to the mRNA codon to be translated by the tRNA
180
A key step in translation is the:
It is this specificity that dictates:
Specific base pairing between the tRNA anticodon and the mRNA codon
Which amino acid will be added to a growing polypeptide chain by the ribosome
181
The other end of the tRNA molecule has the amino acid acceptor site which is responsible for:
Amino acid attachment to the tRNA (the same for all tRNA molecules)
182
The two ends of the tRNA molecule are:
Amino acid acceptor site and anticodon segment
183
Each tRNA molecule can be named based on the amino acid it is specific for... for example a tRNA molecule responsible for valine can be written as:
When the valine attaches it can be written as:
tRNAval
Val-tRNAval
184
The Wobble Hypothesis
First two codon-anticodon pairs obey normal base pairing rules, but the third position is more flexible
Explains that there are less tRNA molecules than AA codon combinations
185
There are 61 amino acid codons, so are there 61 tRNA molecule types?
No there are fewer than 45 so each tRNA must encode for more than one AA
186
I is especially wobbly in the third base pair and can bond to which different codon bases?
A U or C
187
5' Base in tRNA is:
- G
- U
- I
List the wobble 3' Base in Codons (mRNA)
G: U (wobble base)
U: G (wabble base)
I: A, U or C (all wobble bases)
188
tRNA loading (aka amino acid activation)
Reaction coupling of two-high energy phosphate bonds hydrolyzed to provide enough energy to overcome G>0 and high Ea to attach an AA to its tRNA molecule
189
Why is tRNA loading useful?
Because breaking the aminoacyl-tRNA bond will drive peptide bond formation forward
190
Amino acid activation/tRNA loading occurs in many steps...
1. An amino acid is attached to ____ to form ____ . In this reaction, the nucleophile is the acidic ____ of the amino acid and the leaving group is ___
2. The pyrophosphate leaving group is ____ to 2 orthophosphates. This reaction is ______
3. tRNA loading, an unfavorable reaction, is driven forward by the _______.
1. An amino acid is attached to AMP to form aminoacyl AMP . In this reaction, the nucleophile is the acidic oxygen of the amino acid and the leaving group is PPi
2. The pyrophosphate leaving group is hydrolyzed to 2 orthophosphates. This reaction is exothermic and spontaneous G<0
3. tRNA loading, an unfavorable reaction, is driven forward by the destruction of the high energy aminoacyl-AMP bond created in step one.
191
Overall, amino acid activation requires ______ because it uses two high energy bonds
An ATP equivalent is a single high-energy phosphate bond
You can get 2 ATP equivalent by:
2 ATP equivalents
Hydrolysizing 2 ATP to 2ADP + 2 Pi or by hydrolysizing 1 ATP to 1 AMP + 2 Pi
192
How is the attachment of the amino acid to each tRNA accomplished?
Aminoacyl-tRNA synthetase enzymes
193
Aminoacyl-tRNA synthetase enzymes are specific to:
Each AA. There is at least one aminoacyl-tRNA synthetase for every amino acid
194
The Aminoacyl-tRNA synthetase enzymes recognizes the tRNA and amino acids based on:
Their three-dimensional structures
195
Aminoacyl-tRNA synthetase enzymes function with ______ and ______
High specificity and low error rate
196
Amino acid activation serves two functions:
Specific and accurate amino acid delivery
Thermodynamic activation of the amino acid
197
Ribosomes are located in the ____
Cytoplasm
198
Each ribosome has a ___ and a ___
Small subunit and a large subunit
199
The unit of measurement used for ribosomes is the Svedberg (S). Svedbergs are a ______, meaning __________
Sedimentation rate
How quickly something will sink in a gradient during centrifugation--units aren't additive
200
The prokaryotic ribosome sediments in a gradient at a rate of 70S, so it is referred to as the ____
70S ribosome
201
Eukaryotes have an ______ ribosome
80S
202
In both E and P ribosomes, the complete ribosome has ____ special binding sites. Name them
3
A site, P site & E site
203
A site:
P site:
E site:
A: new tRNA delivers its amino acid
P: growing polypeptide chain still attached to the tRNA is located during translation
E: now-empty tRNA sits prior to its release from the ribosome
204
During translation, the next codon to be translated is exposed in the:
A site
205
tRNAs move through the sites from
A-P-E (Ape)
206
Basic pairing:
A with ___
G with ___
A with T
| G with C
207
On prokaryotes, as transcription is occurring, several ribosomes attach and start transcribing the DNA, so the transcription and translation occur in the ____
Same direction (5-3')
208
Because prokaryotes often have polycistronic mRNAs their ribosomes can also start translation in the middle of the chain. This means that
Termination and initiation sequences are found between each ORF
209
An upstream regulatory sequence is essential for initiation, just as in :
transcription
210
Shine-Dalgarno sequence
A ribosome binding site (Instead of a promoter)
211
Like transcription, translation has three distinct stages:
Many antibiotics function by:
Initiation, elongation and termination
Inhibiting a particular stage
212
Initiation of translation begins with the small ribosomal subunit binding to two initiation proteins called
IF1 & IF3
This complex then binds to the mRNA transcript
Next, the first aminoacyl-tRNA joins, along with a third initiation factor called IF2 which is also bound to one GTP molecule
Finally, the 50S subunit completes the complex. This process is powered by ____
The hydrolysis of one GTP molecule
213
The first aminoacyl-tRNA is also called the
Initiator tRNA aka fMet-tRNA(f-met)
214
The fMet stands for formylmethionine which is used as:
The first amino acid in all prokaryotic proteins
215
The P initiator tRNA sits in the __ site of the 70S ribosome , ____ bonded to the start codon
P site
| Hydrogen bonded to the start codon
216
Before P elongation, all the initiation factors
Dissociate from the complex
217
P Elongation, a three step cycle, begins once the initiation factors dissociate from the complex.
In the first step, the second amino-acyl tRNA enters the ___ and ___ bonds with the second codon
A site and hydrogen
218
In the first step of P elongation, the second amino-acyl tRNA enters the A site and hydrogen bonds with the second codon.
In the second step, the peptidyal transferase activity of the large ribosomal subunit (23S rRNA) catalyzes the formation of a peptide bond between fMet and the second amino acid.
The amino acid #2 acts as the nucleotide and the tRNA fMet acts as the LG . A new dipeptide is now attached to ____
tRNA #2
219
The third step of elongation during translation in prokaryotes is:
translocation
220
Translocation (3rd step of elongation in translocation of P) is:
tRNA #1 (empty) moves to the E site, tRNA #2 (holding growing peptide) moves to the P site and the next codon to be translated moves to the A site
221
Translocation process: tRNA #1 (empty) moves to the E site, tRNA #2 (holding growing peptide) moves to the P site and the next codon to be translated moves to the A site
Costs how much energy?
One GTP molecule
222
The new dipeptide is still attached to tRNA #2 and tRNA 3 is still H-bonded to codon #2. The presence of tRNA #1 is the E site is thought to:
Help maintain the reading frame of the mRNA (disruption of tRNA binding to the E site results in an increase in the number of frameshift mutations in the resulting protein)
223
Termination (3rd step of prokaryotes translation) occurs when the:
Stop codon occurs in the A site
224
During termination, (3rd step of prokaryotes translation) instead of tRNA,
A release factor enters the A site
225
During termination, (3rd step of prokaryotes translation) instead of tRNA, a release factor enters the A site. Instead of the tRNA, a release factor enters the A site.
This causes the peptidyl transferase to hydrolyze the bond between the last tRNA, and the completed polypeptide
Finally, the ribosome
Separates into its subunits and releases both the mRNA and the polypeptide
226
List the differences between eukaryotic and prokaryotic translation
1. Ribosome is larger in E and has different components
2. mRNA must be processed before translation in E
3. N-terminal amino acid is different in E (Met not fMet)
4. E mRNA must be spliced, capped, tailed and transported from the nucleus to the cytoplasm (can't proceed simultaneously)
227
Eukaryotes do not use the ____ sequence to initiation translation
Shine-Dalgarno
228
In E translation, there are 5' ___ sequences that start translation: a common one is called the _____, which is a consensus sequence typically located a few nucleotides before the start codon
UTR
Kozak Sequence
229
First, a 43S pre-initation complex forms, composed of the 40S small ribosomal subunit, the Met-tRNA(Met) and several proteins called eukaryotic initiation factors or eIFs.
Next, the assembled complex is recruited to the ____ of the transcript, by an initiation complex of ____
Additional proteins are recruited and the initiation complex stars ____ the mRNA from the 5' end, looking for a _____
Once the start codon is found, the ____ is recuited and ____
5' capped end
proteins (including other eIF proteins)
scanning
start codon
large ribosomal subunit
translation can begin
230
Cap-Dependent Translation
States that E translation starts at the 5' end of the mRNA and encodes for only one polypeptide chain
231
However, despite cap-dependent translation, E are also sometimes capable of:
Starting translating in the middle of an mRNA molecule
232
When a E starts translating in the middle of a mRNA molecule it is called
Cap-independent translation
233
To accomplish cap-independent translation, the transcript must:
Have an internal ribosome entry site (IRES) a specialized nucleotide sequence
234
Most IRES found in E:
Help the cell deal with stress or activate apoptosis
AKA help the cell make proteins under sub-optimal conditions
235
IRES help the cell make proteins under sub-optimal conditions why is this important?
Cell-independent translation allows the cell to make proteins when it is crucial for survival or pre-programmed death even though cell-dependent translation usually ceases during this time
236
Activation of translation using an IRES requires _____ than normal initiation
different proteins
237
Epigenetics
Focuses on changes in gene expression that are not due to changes in the DNA sequences, but. are either heritage or have long-term effect
238
Principle site of regulation of gene expression in both E and P
Transcription
More mRNA made, more protein
239
Both E and P DNA can be covalently modified by ______ .
In E: Bacteria methylation of new DNA occurs shortly after synthesis.
Why is there a delay?
Adding a methyl group
The delay is useful in mismatch repairs in E
240
In P: methylation can control gene expression by
Promoting or inhibiting transcription
241
In E: methylation turns off gene expression in two different ways
1. Methylation physically blocks the gene from transcriptional proteins
2. Certain proteins bind methylated CpG groups and recruit chromatin remolding proteins that change the winding of DNA around histones
242
One way to increase gene expression is to increase the copy number of a gene by ____
Increasing gene dose allows:
Similarly, ___ can cause a decrease in gene expression
Amplification
Cell to make large quantities of the corresponding protein
Gene deletion
243
Geonomic Imprinting is when:
Only one allele is of a gene is expressed
244
Gene imprinting is generational meaning
That a gene imprinted in an adult may be "unimprinted" and expressed in offspring
245
Silencing of a gene involves three things
GNA methylation, histone modification and binding of long non-coding RNAs
246
X chromosome inactivation
Females have two sex chromosomes, Xi (inactive) and Xa (active)
247
X chromosome inactivation implies that: every cell derived from each cell in the inner cell mass has _____, however, because each cell makes its own decision, ______
Same X chromosome inactivated
An adult can have different X chromosomes in different cells and tissues
248
Xi is very condensed and packaged _____, it also has _____
Heterochromatin
High levels of DNA methylation
249
What is the problem with transcription as the primary method of regulation for P?
That it is "pre-set" and cannot respond to changing conditions in the cell
250
The transcription of enzymes involved in biosynthesis should be inhibited by:
The transcription of enzymes involved in catabolic pathways should be inhibited by:
And activated by:
The product
The absence of the substrate
The presence of the substrate
251
Repressible enzymes
Anabolic enzymes whose transcription is inhibited in the presence of excessive product
252
Inducible enzymes
Catabolic enzymes whose transcriptions can be stimulated by the abundance of a substrate
253
Lac operon: kind of enzyme and codes for
Inducible enzyme
Codes for lactose catabolism
254
Trp operon: kind of enzyme and codes for
Repressible and codes for biosynthesis/anabolism
255
An operon has two components, a coding sequence for enzymes and ______ or _____
upstream regulatory sequences or control sites
256
Operons may also include genes for ___, but ___ .
These genes can be located elsewhere in the genome and typically have their own __
Regulatory proteins (repressors or activators) but don't have to
Promoters
257
The lac operon contains several components:
P region is
promoter site on DNA to which RNA polymerase binds to initiation transcription of Y, Z and A genes
258
The lac operon contains several components:
O region is
Operator site to which the Lac repressor binds
259
The lac operon contains several components:
Z gene is
Codes for enzyme beta-galactosidase, which cleaves lactose into glucose and galactose
260
The lac operon contains several components:
Y gene is
Codes for permeate, a protein which transports lactose into the cell
261
The lac operon contains several components:
A gene is
codes for transacetylase, an enzyme which transfers an acetyl group from acetyl-coA to beta-galactoside (not requires for lactose metabolism)
262
Genes with own promoter coding for proteins important in the regulation of the lac operon:
crp gebe
I gene
Crp gene: located at the distant site, this gene codes for a catabolite activator protein (CAP) and helps couple the lac operon to glucose levels in the cell
I gene located at a distant site, this gene codes for the Lac repressor protein
263
Protein products of crp and I
Control gene expression of Z,Y & Z
264
Bacterial cells preferentially uses ___ as an energy source
This means that in the presence of glucose:
In low glucose conditions, adenylyl cyclase is activated and cAMP levels are high. CAP binds cAMP and this complex binds the promoter of the lac operon to activate RNA poly at the operon and contributes to the operon being turned ______.
** Review **
Glucose
Lac operon will be off or expressed in low amounts
On when glucose is low
265
The I gene codes for a repressor protein which binds the operator of the lac operon. This:
Prevents RNA poly from binding the promoter and transcribing Z, Y and A genes
Blocks transcription when lactose is absent
Causes conformational change to make the operon fall off the DNA
266
I gene is allosteric meaning
Happens at a distant site from the operator binding
267
Therefore, high transcription of Z, Y and A genes occurs when ____ is absent and ____ is present
Glucose is absent and lactose is present
268
Low glucose results in an increased amount of _____, which binds to CAP and helps activate the ______ activity at the lac operon.
Lactose presence means the _____ is unable to bind the lac operator and negatively regulation transcription, thus the polycistornic mRNA is transcribed at ____
cAMP
RNA poly
Lac repressor protein
High levels
269
When lactose supply is scarce, there isn't enough to _____ and most of the repressor proteins return to their ______. They now ___ to the operator, ____ transcription levels
Bind to the repressots
Original Structure
Rebind to the operator, decreasing transcription
270
High Trp Operon Process
https://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&ved=2ahUKEwj23eW80unfAhWrVN8KHXJSC3oQjRx6BAgBEAU&url=https%3A%2F%2Fwww.khanacademy.org%2Fscience%2Fbiology%2Fgene-regulation%2Fgene-regulation-in-bacteria%2Fv%2Ftrp-operon&psig=AOvVaw0p8bpUUHAzJBNd_hwVOPEY&ust=1547430578454183
271
Low Trp: Operon
https://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&ved=2ahUKEwjs6fDT0unfAhWhd98KHbNKBVUQjRx6BAgBEAU&url=https%3A%2F%2Fwww.khanacademy.org%2Fscience%2Fbiology%2Fgene-regulation%2Fgene-regulation-in-bacteria%2Fv%2Ftrp-operon&psig=AOvVaw0p8bpUUHAzJBNd_hwVOPEY&ust=1547430578454183
272
Upstream control elements
Code promoter containing binding sites for the basal transcription complex and RNA poly II and TATA box
Binding of the TBP to the TATA box initiations transcription complex assembly at the promoter
273
Another kind of transcriptional regulation occurs when enhancer sequences are bound by
Activator protiens
274
Activator proteins can make effects when the enhance is located thousands of base pairs away from a promoter
This is accomplished by
DNA looping so the enhancer and activator proteins can get close to transcriptional machinery
275
Gene repressor proteins
Inhibit transcription
276
_______ have DNA binding domains and are crucial in transcription regulation
Transcription factors
277
RNA Translocation
mRNA transcripts aren't translated into proteins until they are localized properly in the cell
278
mRNA Survelliance
Cells closely monitor mRNA to ensure that only high-quality transcripts are read by the ribosome
Defective transcripts and stalled transcripts are degraded
279
Defective transcripts
Premature stop codons or no stop codons
280
Stalled transcripts
Ribosome is stalled in translation
281
RNA Interference
A way to silence gene expression after a transcript has been made
miRNA and siRNA mediated
siRNA bind to mRNA and degrades them
Amount of transcript decreases and gene expression is negatively regulated
282
Newly synthesized proteins from the ribosome cannot function--they need to be correctly folded, modified or processed and then transported to the right location
These modifications are called
Proteins can also be covalently modified
Post-translational modifications (occur after protein synthesis)
283
Chaperons
Proteins that fold new proteins (and other macromolecules) into the correct 3D structure
284
Zymogens (aka Proenzymes)
cleave proteins that may be dangerous
285
Signal to get ready
DNA Rep
DNA Transcription
DNA Translation
R: ORI
Transcription: promoter
Translation: sine-dolgarno (P) and kozak (E) found in 5' untranslated region
286
Signal to start
DNA Rep
DNA Transcription
DNA Translation
R: ORI
Transcription: start site
Translation: AUG codon
287
Key synthesis enzyme
DNA Rep
DNA Transcription
DNA Translation
R: DNA poly
T: RNA poly
T: Ribosome (rRNA and peptides)
288
Template molecule
DNA Rep
DNA Transcription
DNA Translation
DNA
DNA
mRNA
289
Read direction
DNA Rep
DNA Transcription
DNA Translation
3-5 on DNA template
3-5 on DNA template
5-3 on RNA template
290
Molecule synthesized
DNA Rep
DNA Transcription
DNA Translation
R: DNA
T: RNA (mRNA in P. hnRNA in E.)
T: Peptides
291
Prokaryotic location
DNA Rep
DNA Transcription
DNA Translation
Cytoplasm
Cytoplasm
Cytoplasm
292
Eukaryotic location
DNA Rep
DNA Transcription
DNA Translation
Nucleus
Nucleus
Cytoplasm
293
Signal to stop
DNA Rep
DNA Transcription
DNA Translation
R: Replication bubbles ligated together
T: Stop sequence or poly-A sequence
T: Stop codon (UAA, UGA, UAG)
