Test 2 Flashcards
1
Q
What did Joseph Priestley call oxygen (1771)?
A
Dephlogisticated air
2
Q
Photosynthesis is the process by which…
A
Some cells can harvest energy from sunlight o produce energy rich organic compounds
3
Q
What are the 2 types of photosynthesis?
A
1) Oxygenic (produces oxygen)
2) Anoxygenic (No oxygen is produced)
4
Q
Oxygenic photosynthesis takes place in… (3)
A
1)algae
2)bacteria
3)plants
5
Q
Anoxygenic photosynthesis is found in four different bacterial groups… (name them)
A
1) Purple Sulphur Bacteria
2) Green Sulphur Bacteria
3) Green non-Sulphur bacteria
4) Heliobacteria
6
Q
Oxygenic photosynthesis is found in _____, _ groups of algae and essentially all ____ plants.
A
1) Cyanobacteria
2) 7
3) land
7
Q
Describe some characteristics of chloroplast (3)
A
1) Uses the energy from sunlight to create ATP and organic molecules (ex: sugar)
2) Contains their own circular DNA and ribosomes
3) Double plasma membrane
8
Q
What is the first step to Oxygenic photosynthesis?
A
Light-Dependent Step
Using light energy to split water and generate an H+ gradient for chemiosmosis (like ETC in aerobic respiration) to make NADPH and ATP.(occurs in thylakoid).
9
Q
What is step 2 for Oxygenic photosynthesis?
A
Light-Independent Step
Use that ATP to add H+’s to CO2 to make glucose in the Calvin Cycle (occurs in the stroma).
10
Q
What are pigments?
A
Molecules that absorb light energy in the visible range
-These are required for the successful completion of photosynthesis in the chloroplast.
11
Q
What are photons?
A
Particles of light that can act as discrete bundles of energy
-The energy of light is directly related to its wavelength (shorter wavelength photon have more energy)
12
Q
What is the absorption spectrum
(Of a molecule)?
A
The range and efficiency the photons absorb (which colour light is the pigment able to absorb)
-The absorption spectrums determine the colour of light that is absorbed. The colour we see is the colour that is reflected by the object (not absorbed)
13
Q
True or false?
Each pigment has its own absorption spectrum
A
True
14
Q
What does chlorophyll a do?
A
Converts light energy to chemical energy
15
Q
What does chlorophyll b do?
A
Carotenoids, etc. supplement chlorophyll a, and also protect plants from harmful radiation
16
Q
Why do indoor LED lights for plant production usually don’t have green lights?
A
This saves on electricity, since plants don’t need green lights to make photosynthesis
17
Q
What is the most important pigment found in the chloroplast and why?
A
Chlorophyll-a
-the only one that can directly convert light to chemical energy (b is an accessory pigment)
18
Q
How is chlorophyll structured?
A
-Contains a complex ring structure, called a porphyrin ring, with alternating single and double bonds with a magnesium atom at the center of the ring.
19
Q
How does chlorophyll carry out photosynthesis? (Transfer of energy)
A
The system of double bonds (resonant structures) is able to channel the energy absorbed by light for a few moments
The energy is then passed to a suitable molecule to carry out photosynthesis
20
Q
_________ and _______are pigments that help carry out photosynthesis
A
1) Carotenoids
2) Flavonoids
21
Q
How do carotenoids and flavonoids assist photosynthesis?
A
By capturing energy from wavelengths that are not efficiently absorbed by chlorophyll
22
Q
Are carotenoids and flavonoids always efficient in transferring energy?
A
No
23
Q
Carotenoids and flavonoids also act as antioxidants to…
A
Counter the production of free radicals generated during photosynthesis
24
Q
What is a free radical?
A
A molecule that contains an unpaired electron in an atomic orbital
25
Part of photosynthesis occurs in _______ present in the _______ membrane.
1) photosystems
2) thylakoid
26
What do photosystems contain?
Chlorophyll-a, associated pigments, and the accessory proteins required to carry out photosynthesis
27
What is a photosystems?
1) Antenna complex: pigments capture light energy and channels it to the reaction centre
2) Reaction centre: a chlorophyll molecule loses an electron (oxidized)
28
What do antenna complexes do?
Capture and transfer the energy from light to the reaction centre
-Proteins in the complex orient the pigments in an optimal direction for the absorption of light energy
-When light energy is captured, the pigments transfer the energy directly to other pigments until the energy (only energy) is transferred to the *reaction centre*
29
What happens after the transfer of energy in antenna complexes?
The excited electron in each molecule returns to the low energy level it had before the photon was absorbed
-Thus, it is energy, not the excited electrons themselves, that pass from one pigment molecule to the next
30
True or false? The antenna complex funnels the energy from one electron to the reaction centre?
False, the antenna complex funnels the energy from **many electrons** to the reaction centre
31
What does the reaction centre do (photosynthesis)?
A special pair of chlorophyll-a acts as a trap for photon energy, passing an excited electrons to an acceptor precisely positioned as its neighbour.
-Note that here in the rxn centre, the excited electron itself is transferred and not just the energy
32
Where does the transfer of excited electrons from the reaction centre go to?
The primary electron acceptor (plastoquinone)
33
How does chlorophyll get stored to its original condition (after rxn centre)?
A nearby weak electron donor (water in plants) passes a low-energy electron to the chlorophyll restoring it to its original condition
-Water splits to create O2 and H+
34
Summarize the light dependent step of photosynthesis
-The antenna complex of the photosystems captures the energy from sunlight and transfers it to the reaction centre
-*Magnesium* ions, present in the *special pair of chlorophyll-a* of the reaction centre will donate an electron the the acceptor, a plastoquinone (Pq).
-The magnesium with the help of the reaction centre proteins will then oxidize water (H2O) to regain the lost electron, producing O2.
-It requires the energy from **four photons** to complete the oxidation of two water molecules to produce molecular oxygen (O2).
35
Plants use _ photosystems to carry out light dependent reactions
2
-photosystems 2: 680nm and is called P680
-photosystems 1: 700nm and is called P700
Both systems are linked by the cytochrome complex (electron transport chain)
36
The plastoquinone (PQ) carries the electron in the first part of the electron transport chain of the ______ complex.
Cytochrome b6-f complex
37
The cytochrome b6-f complex acts as a _____ pump and will use the energy from the electrons to pump ____ into the ____ ______.
1) proton
2) protons
3) thylakoid lumen
38
The protein plastocyanin (PC) will transport the electrons to ….
Photosystems 1
39
What happens at photosystems 1 (PS1)?
-The antenna complex absorbs a photon’s energy which is transferred to the reaction centre.
-in the reaction centre, electrons are excited and donated to an electron accepting protein called **ferredoxin**.
-The incoming electrons from photosystems 2 replace the donated electrons (no water needed)
-Ferredoxin donates the electrons to NADP+, creating NADPH via the enzyme NADP reductase.
-NADP reductase is located on the stroma side of the thylakoid membrane
40
What is NADPH?
Coenzyme (high energy electron carrier)
Nicotinamine adenine dinucleotide phosphate (NADP+)
-It carries the electrons (2x) and proton (1x H)
-Carries the energy captured from light to the stroma where it will be used to generate high energy organic molecules (sugars).
41
How does ATP get created from the H+ gradient?
-The electron transport chain permits the pumping of H+ into the thylakoid lumen.
-Chemiosmosis carried out during photosynthesis is carried out in a similar manner than in the mitochondrion
-ATP is generated with the help of ATP synthase
42
What is produced during the light dependent step of photosynthesis?
NADPH (electrons and proton)
ATP (with the help ofATP synthase)
43
Where does the light-dependent and light-independent step of photosynthesis occur?
Light-dependent: thylakoid
Light-independent: stroma
44
What does the Calvin Cycle do?
Converts inorganic carbon into organic carbon in the form of carbohydrates
45
What are the 3 phases of the Calvin cycle?
1) Carbon fixation
2) Reduction
3) Regeneration of RuBP
46
What happens in Phase 1 of the Calvin Cycle?
CARBON FIXATION
-A carbon atom from **C**O2 is added to a five-carbon molecule (RuBP).
-This is done by *Rubisco*, a large **multienzyme compex** that catalyzes the fixation of CO2 and RuBP to PGA
The resulting 6 carbon molecule is unstable and immediately splits into 2x3 carbon molecules (PGA)
47
What happens in phase 2 of the Calvin cycle?
REDUCTION
-Energy from ATP add a phosphate to the 3-carbon molecule
-This phosphate is afterwards replaced by a hydrogen atom from NADPH (and electron)
-2 molecules of G3P will combine to make glucose *(this process is **NOT** part of the Calvin cycle)*
48
What is phase 3 of the Calvin cycle?
REGENERATION OF RuBP
-You need 6 **C**O2 to make one glucose (6**C**).
-So, 10 molecules of G3P will be used to regenerate RuBP.
-This is a multi step process that requires 6 ATP to transform 10 molecules of G3P (3C) into 6 molecules of RuBP (5C).
10 G3P X 3**C**= 6 RuBP x 5**C**
10 x 3 = 6 x 5
30**C**
49
How do cells build carbohydrates like glucose?
(Hint: light-independent process of photosynthesis)
-Use carbon from the CO2
-Energy from ATP produced by the light dependent step
-Reduction potential of the NADP**H**, produced by the light dependent step of photosystem I, provides a source of **H+** and electrons needed to bind them to carbon atoms.
50
What is the net equation of the Calvin cycle?:
_CO2+__ATP + __NADPH + Water —> _ G3P + __ Pi + __ADP + __ NADP+
1) 6
2) 18
3) 12
4) 2
5) 16
7) 18
8) 12
51
What’s the problem with ATP and NADPH ratio for the light dependent step of photosynthesis?
Ratio ATP/NADPH: ~1
We need a ratio of 1.5 for Calvin cycle
52
What is the solution for the ATP and NADPH ratio issue for the Calvin Cycle?
Light-dependent step: cyclic phosphorylation
-The chloroplast needs to make extra ATP
-It does this by ‘’short-circuiting’’ the non-cyclic phosphorylation, and reverting to cyclic phosphorylation to make up the missing ATP
53
True or false? Some bacteria use only cyclic photo phosphorylation
(Hint: solution for ATP and NADPH ratio section)
True
54
What is the light-dependent step (cyclic phosphorylation)?
hint: solution for ATP and NADPH ratio issue
-Light energy absorbed at PS I is used for ATP synthesis rather than NADPH synthesis
-High-energy electrons generated by photon absorption are transferred by the ferrodoxin (Fd) and plastoquinone (Pq) to the cytochrome bf complex rather than to NADP+.
-The cytochrome bf complex uses the electrons to pump H+ from the stoma to the thylakoid lumen
-The electrons are then returned to photosystem I by plastocyanin (PC)
-The H+ gradient between the lumen and stoma is used to create ATP by the ATP synthase
55
What is the problem with photorespiration?
-Rubisco that catalyzes the fixation of CO2 to RuBP (carboxylation) creating PGA.
-The carboxylation and oxidation of RuBP are catalyzed at the same active site on Rubisco, thus, CO2 and O2 compete with each other at this site.
56
Oxidation of RuBP occurs when….
Oxygen levels are relatively high, because O2 and CO2 compete for the same active site on RUBISCO
57
Fix carbon lost to photorespiration at 25 degrees is…
At 28 degrees is…
(For Rubisco photorespiration)
25 degrees: 20%
28 degrees: 50%
58
How do plants regulate water and gases?
Plants have little doors, called stomata, that can open and close to let water and gases go in or out of their leaves.
In hot temperature, plants will close their stomata to prevent water loss, limiting at the same time the entrance of CO2 inside the leaf and the exit of O2.
59
Under normal temperate conditions, stomata…
-Are open so CO2 can enter the leaf and O2 can exit it
-Water loss is not excessive, since temperature is not too high
-Therefore, photorespiration is not a major problem
60
Under high temperate conditions, stomata…
-Leaves lose water by evaporation
-Therefore, they close their stomata
-This will lead to an accumulation of O2 in the plant, and a decrease in CO2.
-Both these conditions will increase photorespiration
61
What are C3 plants?
Temperate plants are called C3 plants because the first fixed carbon molecule (PGA) is a 3-carbon molecule
62
How do C3 plants regulate photorespiration?
They **do not** possess any mechanism to regulate photorespiration
63
How do C4 plants avoid the problem of photorespiration?
Fixation of CO2 and the Calvin cycle occur in two different cells
(C4 plants include corn, sugar cane and grasses)
64
1) PEP carboxylase fix the carbon from CO2 to the ____ creating oxaloactetate
2) This is done in the ______ cell in the presence of 02.
3) PEP carboxylase has a higher ___ affinity and no affinity for __.
4) The C4 process requires ___ to function.
5) Oxaloactetate will transform to _____ and be transportated to the ________ cell.
6) Malate will be decarboxylated directly at the site of _____ allowing for a high concentration of ___ without the presence of __.
1) Phosphoenol pyruvate (PEP)
2) mesophyll
3) CO2, O2
4) ATP
5) malate, bundle-sheath
6) rubisco, CO2, O2
65
Each CO2 transported in the bundle-sheath cells cost the equivalent of __ ATP.
(FOR C4 PLANTS)
2
66
The production of 1 glucose requires 12 additional ___ compared to the Calvin cycle alone.
(FOR C4 PLANTS)
ATP
67
Why is maize not grown farther north than the saint-Lawrence?
Photorespiration is less of a problem in cooler temperatures
68
What are CAM plants and how do they avoid the problem of photorespiration?
-Tropical plants have found ways to avoid the problem of photorespiration
-Fixation of CO2 and the Calvin cycle occur in the same cells, but at different times (Night/day).
69
Fixation of CO2 into oxaloactetate (C4) (PEP carboxylase) happens at ____, while the stomata are ____, when the temperature is cooler.
Those oxaloactetate are transformed in other _____ molecules (organic acids) and accumulates at ____.
(FOR CAM PLANTS)
Night
Open
Organic
Night
70
Stomata are closed during the ___, the organic molecules are decarboxylated to ___ that enter the Calvin cycle.
(FOR CAM PLANTS)
1) day
2) CO2
71
True or false? CAM photosynthesis needs to invest ATP in the same way than C4 plants.
True
72
True or false? For CAM plants, light-independent steps produce the electrons and protons (NADPH) necessary to the Calvin cycle
False, **light dependent**
73
What are some nucleic acids’ functions?
-Storing genetic information (DNA)
-structural/catalytic function (r-RNA)
-directing the synthesis of proteins (m-RNA, t-RNA).
-Energy reaction molecules (ATP, NAD, FAD).
74
What are the 3 types of nucleic acids?
1) Deoxyribonucleic acid (DNA)
2) Ribonucleic acid (RNA)
3) Energy reaction
75
What are the types of RNA?
-Messenger ribonucleic acid (m-RNA)
-Transfer ribonucleic acid (t-RNA)
-Ribosomal ribonucleic acid (r-RNA)
76
What are the types of energy reactions? (Nucleic acids)
-Adenosite triphosphate (ATP)
-Nicotinamide adenine dinucleotide (NAD)
-Flavin adenine dinucleotide (FAD)
77
What are monomers and polymers of nucleic acids called?
1) Monomers: nucleotide
2) Polymer: nucleic acids
78
What is the structure of nucleic acids?
Phoshpte group
Pentose sugar:
-Ribose: OH in C-2 (RNA)
-Deoxyribose: H in C-2 (DNA)
Nitrogenous base
79
What is the back-bone in nucleic acids?
-Phosphate group + sugar
-Link together by phosphodiester bonds
-Links are made on C-5 and C-3 of the sugar giving the direction of the DNA 5’ to 3’.
80
Synthesis of DNA polymer (polynucleotide) is done by polymerase enzyme which adds nucleotide, one by one, only to the free _____ end of a growing DNA strand (5’ —> 3’)?
Hydroxyl (OH)
81
What are the purines and pyrimidines in nucleic acids?
Purines: Adenine (A) and Guanine (G)
Pyrimidines: Cytosine (C), Thymine (T) and Uracil (U) (only in RNA)
82
What is the double helix of DNA?
Two polynucleotide strands connected by hydrogen bonds
83
What are complementary base-pairing rules for DNA?
-Adenine (A) with Thymine (T) (2x H bonds)
-Guanine (G) with Cytosine (C) (3x H bonds)
84
How is the double helix formed for DNA?
The complementary strands of DNA are ‘’antiparallel’’
-The 5’ end of one strand is the 3’ end of the other
-In DNA, the paired chains of nucleotides twist together into a double helix
85
The double helix is considered DNA’s ____ structure
Secondary
86
What are characteristics of RNA?
1) Contain Ribose sugar instead of Deoxyribose
2) Includes the base uracil instead of thymine
3) Single polynucleotide strand
87
What are the several functions of RNA within the cell?
1) m-RNA:
Transfer information from DNA to the ribosome
2) r-RNA:
Structural part of the ribosome and has catalytic functions
3) t-RNA:
Carries amino acids to the ribosome
88
The subunits of the ribosome are composed of…
Proteins and rRNA
89
What do NAD and FAD do (nucleic acids)?
They are electron carriers for many cellular reactions
90
Who showed the heredity of traits (DNA)?
Gregor Mendel
91
Who discovered DNA?
Friedrich Miescher (german scientist)
92
In 1920, the study of DNA revealed that it is made up of….
A phosphate group, a pentose sugar and a nitrogenous base (A,T,G,C).
93
What did Frederick Griffith discover?
**Transformation**
-Traits (such as virulence) can be passed from the dead bacteria to the live non pathogenic strains
-It must be due to passing of molecules between dead and live cells
94
Who discovered the hereditary molecule? (3 ppl)
Colin Macleod
Oswald Avery
Maclyn McCarthy
95
What was the experiment to find the hereditary molecule?
(I.e: what did they **do** to find the molecule)
To determine which macromolecule is responsible for transmitting the information of virulence, they added specific enzymes that **degrade** *proteins*, *RNA*, and *DNA*
After the enzymes degraded their specific macromolecule, the researchers did the Frederick Griffith experiment and added a **non virulent R strain** to each tube.
96
What **is** the hereditary molecule?
DNA
97
What did Hershey and Chase do?
Used *bacteriophages* to prove that DNA is the hereditary molecule
98
What are phages?
-Viruses that infect bacteria
-Made up of proteins and DNA
-Reprogram bacteria to produce other phage viruses
99
What did Erwin Chargaff find?
The matching proportion of nucleotides
100
What are Chargaff’s rules (DNA)?
-The proportion of A = the proportion of T
-The proportion of C = the proportion of G
(This led to the AT and CG base pairing rules of today)
101
True or false? Erwin Chargaff figured out the structure of DNA
False, he discovered the nitrogenous base pairing
102
What did Rosalind Franklin do?
She was a researched in the Wilkins Lab and produced the first good DNA x-ray crystallography
-To work, X-Ray diffraction technique needs solids with regular, repeating units of atoms (crystal)
103
What is the diameter of…
Purine + Purine
Pyrimidine + Pyrimidine
Purine + Pyrimidine
Pur+Pur >2nm
Pyr+Pyr <2nm
Pur+Pyr = 2nm
104
What did Watson and Crick do?
Developed the first molecular model oDNA
-Solved the structure based on Franklin’s patterns and Chargaff’s rules.
105
What experiment did Watson and Crick do?
They never actually did any experiments
106
What did Watson and Crick propose?
(Hint: bonding)
The two strands (of DNA) were held together by formation of hydrogen bonds between bases on opposite strands
-Guanine (G) can form three hydrogen bonds with Cytosine (C)
-Adenine (A) can form two hydrogen bonds with Thymine (T)
107
What are the three models of *possible* DNA replication?
(Just the names)
1) Semiconservative model
2) Conservative model
3) Dispersive model
108
What is the semiconservative model?
(DNA replication)
-One strand of the parental duplex remains intact in daughter strands (*Semi*conserved)
-In the first replication, a new complementary strand is built from each parental strand, thus creating a DNA with new and old strands
-In the second replication, you will have an entire new DNA molecule and one DNA molecule with new and old strands
109
What is the conservative model?
(DNA replication)
-Both strands of the parental duplex would remain intact (conserved), and a new DNA copy would consist of all-new DNA strands
-In the first replication, both parental strands are being replicated, thus creating a new pair of DNA strands.
-In the second replication, you will have two new DNA duplexes and one new DNA duplex molecule and one old duplex.
110
What is the dispersive model?
(DNA replication)
-Copies of DNA would consist of mixtures of parental and newly synthesized strands.
-That is, the new DNA would be dispersed throughout each strand of both daughter molecules after replication
111
Which of the 3 models represents the reality of DNA replication?
Semiconservative model
112
What was the Meselson and Stahl experiment?
-First, the bacteria are grown in a medium containing a heavy isotope of nitrogen (15N)
-The bacteria will grow and divide, replicating their DNA and incorporating the heavy nitrogen (15N) into the DNA nitrogenous bases.
-They then extracted and purified some of the DNA and measured the density of the DNA using density gradient centrifugation
-This method uses centrifugation which separates molecules into **bands** according to their density
-DNA with heavy nitrogen (15N) will centrifuge lower in the tube due to its high density
-The bacteria will be transferred to a media containing light nitrogen isotope (14N)
-After one generation (one DNA replication) in light nitrogen isotope (14N), the nitrogen will be incorporated in the DNA
113
What are chromosomes?
Condensed DNA
114
What do identical twins result from?
The accidental split of the embryo during the first stage of cell division
115
What is the general concept of DNA replication?
-The parent molecule has two complementary strands of DNA linked with its specific partner (A-T and G-C)
-The first step in replication is separation of the two DNA strands
-Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand.
116
Where does DNA replication start for prokaryotes?
They have a singular circular molecule of DNA, so it starts at the origin of replication (only 1)
117
Which nitrogenous bases make up the origin of replication and why?
Adenine and Thymine because it is easier to separate (melt) because A-T have only 2 hydrogen bonds.
118
Which protein activates **initiation** of DNA replication at the origin of replication by separating the two DNA strands?
(For prokaryote)
DNAa
119
What does the DNAa protein permit (after the splitting of the two DNA strands)?
This permits the replisome (complex molecular machine which does the replication of DNA) to access the single DNA strand
120
DNA replication occurs in a … manner
(Prokaryote)
Bidirectional
121
DNA polymerase enzyme of the replisome adds nucleotides, one by one, only to the free _ end (OH) of a growing DNA strand (_ -> _), never to the _ end.
1) 3’
2) 5’->3’
3) 5’
122
What are the 3 things needed for DNA replication?
1) Template strand
2) Nucleoside triphosphate (nucleotide)
3) Replisome/DNA polymerase
123
What does helicase do (in DNA replication)?
And what does it require to work?
-It is an enzyme that untwists the double helix at the replication forks, separating the two parental strands and making them available as template strands
-This requires ATP
124
What does the single-strand binding protein (SSB) do?
(DNA replication)
Binds to the unpaired bases of the DNA strands, stabilizing them until they serve as templates for the synthesis of new complementary strands.
125
What does DNA gyrase do?
(DNA replication)
Is a topoisomerase enzyme that cuts and untwists ahead of the replication fork to relieve the strain caused by the helicase
126
What is a replisome?
(DNA replication)
The complex molecular machine that carries out replication of DNA (helicase, gyrase, SSB, primase DNA polymerase III, ligase, etc.)
127
What are primers and what are they synthesized by?
(DNA replication)
Small pieces of RNA (10-20bp) that is complementary to the DNA template strand
-They are synthesized by an RNA polymerase called **primase**
128
Primers have a free _’ end.
3
129
What doesDNA polymerase III have (DNA replication)
A beta-subunit that forms a clamp around the template stand
130
What direction is the strand getting replicated? (New strand, not template strand)
5’ -> 3’
131
Why are primers essential?
DNA polymerases cannot initiate the synthesis of a polynucleotide. They can only add nucleotides to the 3’ end of an already existing chain.
132
What does DNA polymerase I do? (DNA replication)
Replaces the RNA nucleotides of the primers with DNA versions (uracil to thymine), adding them one by one onto the 3’ end of the adjacent Okazaki fragment
133
What does DNA ligase do? (DNA replication)
Forms a **phosphodiester** bond between the two Okazaki fragments.
134
DNA Pol I and Pol III have 3’-5’ exonuclease activity which serves as….
A proofreading function because it allows the enzyme to ‘’back up’’ and remove a mis-paired base
135
True or false? Synthesis of DNA is done at different times on the leading and lagging strands?
False, they are done at the same time
136
True or false? The replisome contains all the enzymes necessary for DNA replication (multi enzyme complex)
True
137
1) DNA polymerase epsilon:
2) DNA polymerase delta:
3) PCNA SLIDING Clamp:
(Differences between prokaryotes and eukaryotes)
1) leading strand
2) lagging strand
3) clamp that attaches enzyme complex to the DNA
138
Why is eukaryotic replication complicated? (2 main factors)
1) Large amount of DNA organized into multiple chromosomes
2) Linear structure of the chromosomes
(This process requires new enzymatic activities only for dealing with the end of chromosomes; otherwise, the basic enzymology is the same)
139
Where does DNA replication start (eukaryotes)?
-Origin of replication is a stretch of DNA having a specific sequence and chromatin properties
-proteins that initiate DNA replication can recognize this sequence and teach to the DNA, separating the two strands and **opening a replication bubble.**
-Replication of DNA then proceeds in both directions until the entire molecule is copied
-Eukaryotic chromosomes may have hundreds or even thousands of replication origins, while prokaryotes have only one.
140
What is the problem with eukaryotes in terms of DNA replication?
The directionality of polymerase and their requirement for a primer creates a problem.
When the last primer is removed, there is no 3’ end to replicate the DNA using polymerase I.
141
True or false? Chromosomes get shorter at each DNA replication (eukaryote)
True
142
What is the solution to the problem eukaryotes have for DNA replication?
They use telomeres and telomerase
143
What is a telomere?
A Region of repetitive non coding nucleotide sequences at each end of a chromosome, which protects the coding portion of the new chromosome.
(Telomeres consist of hundreds or thousands of repeats)
144
What has telomere shortening been connected to?
The aging of cells
145
The progressive loss of telomeres may explain why cells can only…
Divide a certain number of times
146
What is telomerase?
Telomerase is an RNA-dependent DNA polymerase, meaning an enzyme that can make DNA using RNA as a template
147
How can telomere shortening be reversed?
Some cells can reverse telomere shortening using the telomerase enzyme that extends the telomeres of chromosomes.
148
What does telomerase do?
Adds nucleotides to the overhanging strand of the telomere
DNA replication machinery (RNA primer and DNA polymerase) produce double-stranded DNA
149
What type of cells is telomerase active in?
Germ cells (the cells that make sperm and eggs) and some adult stem cells
Note: telomerase is **not** usually active in most somatic cells (cells of the body)
150
Many cancer cells have […] active, which permits them to do cell division and DNA replication indefinitely
Telomerase
151
What is the basic unit of heredity?
Genes
152
What are genes composed of and what do they do?
A sequence of nucleotides in DNA that encodes the synthesis of RNA and generally induces the production of a polypeptide (protein).
153
Where is a gene present and what does it include?
Over a particular physical region (locus) of a double-stranded DNA molecule.
It includes the **transcription unit** or **RNA-coding region**, where transcription occurs from the DNA template strand so as to synthesize an RNA transcript in the 5’ to 3’ direction, running between the initiation and termination sites
154
What was Tatum and Beadle’s experiment?
-fungus is grown in minimal medium (minimal elements to support growth)
-Any cells that can grow on minimal medium must be able to synthesize all necessary biological molecules
-The fungus is exposed to x-ray to induce mutation of the DNA
-Then the fungus is grown in rich media
-If transferred to a minimal medium, some of the fungus cannot grow anymore but can grow if it’s supplemented with **arginine** (lost the genes coding from arginine pathway)
155
What were Tatum and Beadle able to do?
Genetically dissect the arginine biosynthetic pathway
156
What does the biosynthesis of arginine consist of?
A multi-enzyme pathway
157
How were Tatum and Bradley able to identify the specific enzymes that were mutated (inactive)?
By supplementing the minimal medium with intermediates molecules of the biochemical pathway
158
The 1st enzyme (E) transforms glutamate into […]
(Arginine multi enzyme pathway)
Ornithine
159
The 2nd enzyme (F) transforms ornithine into […]
(Arginine multi enzyme pathway)
Citruline
160
The 3rd enzyme (G) transforms Citruline into […]
(Arginine multi enzyme pathway)
Arginosuccinate
161
The 4th enzyme (H) transforms arginosuccinate into […]
(Arginine multi enzyme pathway)
Arginine
162
What did Tatum and Beadle conclude?
That a specific stretch of DNA, the gene, encodes for the structure of one enzyme protein
-They called this relation the one gene/one enzyme hypothesis
163
What is the central dogma?
Information passes in one direction, from the gene (DNA) it is transcribed to m-RNA, and translated to amino acids polypeptide (protein).
164
What are retroviruses?
RNA based viruses that use **reverse transcription** to insert their own code into the host genome during infection
165
What is the template strand?
The DNA that is transcribed to a single-strand m-RNA molecule
166
What is the coding strand?
The strand of DNA not used as a template
(Since it has the same sequence as m-RNA transcript (but T are U))
167
The m-RNA transcript’s sequence is ______ to the template strand
Complementary
168
The m-RNA transcript used to direct the synthesis of polypeptides (aka protein) is termed […].
Messenger RNA (m-RNA)
169
What does m-RNA do?
Carry the DNA message to the ribosome for processing
170
Why is the DNA to m-RNA step called transcription?
Because it produces a complementary copy of the DNA in m-RNA (T become U in m-RNA)
171
Why is the m-RNA to protein step called translation?
Because it requires translating from the nucleic acid to the amino acid ‘’languages’’
172
How many RNA polymerase do prokaryotes have?
1
173
What does transcription require? (5)
1) RNA polymerase
2) Promoter
3) Start site
4) Termination
5) Stop site
174
What are the steps to transcription?
1) Initiation
2) Elongation
3) Termination
175
RNA polymerase of prokaryotes exist in which forms? (2)
(Initiation step to prokaryotic transcription)
1) **Core polymerase**: composed of alpha and beta subunits. Can synthesize m-RNA from DNA, but cannot initiate transcription
2) **holoenzyme**: combination o the core polymerase with the sigma factor. This combo can accurately initiate synthesis.
176
Does transcription require a primer?
No
177
What are the steps to initiation?
(Prokaryotic transcription)
1) **sigma factor** joins the core polymerase to form the holoenzyme
2) **sigma factor** permits the recognition specific sequences of DNA called promoter at -35 and -10 base pairs from the start site.
3) The helix is open at -10 base pair regions and transcription begins at the start sites at +1 base pair from the *start site*.
4) The **sigma factor** dissociates from the core polymerase. However recent findings suggest that it’s rather weakly bound to the core during elongation
178
The initiation relies on […]
(Prokaryotic transcription)
Two sequences present in DNA called the promoter region
179
What is the promoter and what does it contain?
A region located upstream (before) the start signal (therefore it is not transcribed).
The promoter contains 2 binding sites for sigma factors of the RNA polymerase at -35 and -10 base pairs before the start sites.
180
When does the RNA polymerase start to unwind the DNA helix?
(Initiation of prokaryotic transcription)
At -10bp
181
What is promoter clearance (elongation for prokaryotic transcription)?
The hydrolysis of ATP or GTP provides the energy required for the polymerase to leave the promoter region and start transcription
182
What are the steps to *elongation* (prokaryotic transcription)?
-Promoter clearance: hydrolysis of ATP or GTP provides energy required for the polymerase to leave the promoter region and start transcription
-A transcription bubble is then formed as RNA is elongated
-The m-RNA grows in the 5’ to 3’ direction as ribonucleotides are added
-For each nucleotide in the template, RNA polymerase adds a matching RNA nucleotide to the 3’ end of the m-RNA strand.
-The RNA transcript is nearly identical to the coding strands of DNA (However, U instead of T and ribose sugar instead of deoxyribose)
-After the transcription bubble passes, the now-transcribed DNA is rewound as it leaves the bubble
183
What does the transcription bubble contain?
RNA polymerase, DNA template strand, and growing m-RNA transcript
184
What is termination in prokaryotic transcription (General)?
The end of a bacterial transcription unit is marked by terminator sequences that signal ‘’stop’’ to the polymerase
185
What are the 2 types of terminations (prokaryotic transcription)
1) Rho-dependent termination
2) Rho-independent termination
186
What is Rho-dependent termination (prokaryotic transcription)?
-The m-RNA that is produced contains a binding site for the Rho factor
-Rho factor binds to this sequence and starts ‘’climbing’’ up the transcript towards RNA polymerase
-When it catches up with the polymerase, Rho pulls the RNA transcript and the template DNA strand apart
-Another sequence found later in the DNA, called the transcription stop point, causes RNA polymerase to pause and thus helps Rho catch up.
187
What is Rho-independent termination in prokaryotic transcription?
-As the RNA polymerase approaches the end of the gene, it hits a region rich in C and G nucleotides
-The RNA transcribed from this region folds back on itself, and the complementary C and G nucleotides bind together
-The result is a stable hairpin that causes the polymerase to stall
-The hairpin is followed by a stretch of U nucleotides in the RNA, which match up with A nucleotides in the template DNA
188
True or false? The complementary U-A region of the RNA transcript forms a strong interaction with the template DNA?
(Prokaryotic transcription)
False, it is a weak interaction as there are only 2 H bonds between U-A
189
True or false?
Prokaryotes can do transcription and translation at the same time
(And why)
True!
Prokaryotes don’t have a nucleus, so they can directly do the transcription of DNA to m-RNA and translate it t polypeptide chains (aka protein)
190
What are the 3 RNA polymerases for Eukaryotes?
(And name their functions)
1) **RNA polymerase I**: transcribes ribosomal RNA (r-RNA)
2) **RNA polymerase II**: transcribes messenger RNA (m-RNA)
3) **RNA polymerase III**: Transcribes transfer RNA (t-RNA)
191
True or false? Each RNA polymerase recognizes its own promoter
True
192
What are the steps to initiation in eukaryotes?
-The initiation at RNA polymerase II promoters is analogous to prokaryotes, but eukaryotes use a host of *transcription factors* allowing *promoter recognition*
-*These factors first bind to the promoter* and then recruit **RNA polymerase II**
-The *transcription factors* interact with **RNA polymerase II** to form an *initiation complex* at the promoter.
193
What are the steps to elongation in eukaryotic transcription?
-When the transcript reaches about 20 nucleotides, it is modified by the addition of GTP to the 5’ PO4- group, forming what is known as the 5’ cap.
-This cap is joined to the transcript by its 5’ end, the only 5’ to 5’ bond found in nucleic acids
-The G in the GTP is also modified by the addition of a methyl group, so it often called a methyl-G cap.
(This structure is important for translation, RNA stability, and further processing)
194
What are the steps to termination in eukaryotic transcription?
A distinctive feature of eukaryotic transcription is that the 3’ end of transcription is not the real end of the m-RNA
-The transcript is cleaved downstream of a specific site (AAUAAA) while the polymerase is elongating and a series of 100 to 200 adenosine residues (A), called the 3’ poly-A tail, is added to the m-RNA
(The enzyme responsible for this is poly-A polymerase)
195
The G-cap and poly-A tail is added in which stages of eukaryotic transcription?
G-cap: elongation
Poly-A tail: termination
196
What is the function of the addition of a 5’cap and 3’ poly-A tail?
5’ cap:
-Protects the m-RNA from degradation; involved in translation initiation
3’ poly-A tail:
-Protection of the m-RNA from degradation
197
True or false?
Eukaryotes have a ‘’core promoter’’ like the prokaryote TATA sequence (-10 bp)
True, eukaryotes have a ‘’core promoter’’ that can be composed of a number of distinct elements, **including** the TATA box
198
What are exons and introns?
Exons: sequences that will be translated in protein
Introns: non-coding sequences (not translated into proteins)
199
True or false?
Both exons and introns are transcribed in the **Pre m-RNA**
True
200
What is eukaryotic pre-m-RNA splicing?
Before pre-mRNA can be translated into protein it must first get ready to leave the nucleus. It undergoes a maturing process
-A cutting complex forms called a spliceosome which snips out introns and links together the exons. This is called pre-mRNA splicing
201
How are spliceosomes formed?
(Eukaryotic pre-mRNA splicing)
The intron-exon junctions are recognized by small nuclear ribonucleoprotein particles called snRNPs
These snRNPs then cluster together with other associated proteins to form a larger complex called the spliceosome
202
True or false?
Introns all begin with the same 2-base sequence and end with another 2-base sequence that tags them for removal
(Eukaryotic pre-mRNA splicing)
True
203
What is eukaryotic pre-m-RNA alternative splicing?
The same gene doesn’t always produce the same protein
204
21,000 genes of the human genome can encode more than […] different proteins
100,000
205
~20,000 genes of the C. *elegans* genome can encode about […] different proteins (4% alternative splicing)
20,800
206
Exons compose only about […]% of the human genome
1%
207
Introns compose about […]% of the human genome
24%
208
Intergenic DNA represents […]% of the human genome and is composed of [….]
75%
Noncoding DNA
209
What does intergenic DNA do?
Occasionally acts to control nearby genes but most of it has no current known function
210
Remnants of ancient viruses compose about […]% of the human genome.
8%
Note: the viral DNA comes from retrovirus, which can copy their genome to the host genome during infection
211
What are the 4 main components for translating from m-RNA to a polypeptides protein
1) **Amino acids** (monomers of the polypeptide (protein))
2) **t-RNA** (brings the amino acids to the ribosome to make proteins)
3) **Ribosome** (the organelle that takes the information of the m-RNA and translate it into protein)
4) **m-RNA** (transcript of gene in RNA)
212
What are t-RNA characteristics?
-Different t-RNA molecules carry each 20 types of amino acids to the ribosome for incorporation into a polypeptide
-Accepter end binds to the amino acids
-Anticodon loop contains 3 nucleotides complementary to m-RNA codons
213
The aminoacyl-tRNA synthetases must be able to […]
Recognize specific t-RNA molecules as well as their corresponding amino acids
214
What is charged t-RNA?
When an enzymatic reaction joins an amino acid to a t-RNA.
(Note: an ATP molecule provides energy for this endergonic reaction)
215
What are the 2 functions of the ribosome?
-Decoding transcribed message (m-RNA)
-Forming peptide bonds
216
The formation of peptide bonds requires the enzyme….
Peptidyl transferase (ribozyme), which resides in the large subunit)
217
How to translate from m-RNA to a polypeptide?
-using codons or triplets of nucleotides in the m-RNA
-The ribosome reads the codons, producing a polypeptide
-Each codon codes for one amino acid but each amino acid can be coded for by more than one codon
218
Why is genetic code considered degenerate?
Each codon codes for one amino acid but each amino acid can be coded for by more than one codon
219
Translation always starts with the codon […] and stops with the codon […],[…], or […].
1) AUG (methionine)
2) UGA, UAG or UAA
220
What are the ribosome’s t-RNA binding sites?
(3)
1) A site - binds the t-RNA carrying the next amino acid
2) P site - binds the t-RNA attached to the growing peptide chain
3) E site - binds the discharged t-RNA so it can exit
221
What is the steps to initiation of translation for DNA to proteins?
(Hint: ribosome)
-The start t-RNA molecule with **methionine** fixes itself on the small ribosomal subunit
-The m-RNA is recruited by the small ribosomal subunit
-The t-RNA anticodon loop fixes itself to the corresponding m-RNA codon using **GTP**
-The large ribosomal subunit is positioned, so the **P site** is on top of the Met t-RNA
-The large ribosomal subunit is fixed to the small ribosomal subunit
222
What are the steps to elongation for DNA to proteins?
(Hint: ribosome)
Elongation adds amino acids
-2nd amino acid on the t-RNA in **site A** can bind and form a peptide bond with the amino acid in **site P**
223
How does the addition of successive amino acids occur (cycle)?
(Elongation during DNA to proteins)
1) Matching t-RNA anticodon with m-RNA codon
2) Peptide bond formation
3) Translocation of ribosome and ejection of the empty t-RNA (needs GTP)
224
What is termination for DNA to proteins?
(Hint: ribosome)
-Elongation continues until the ribosome encounters a stop codon
-Stop codons are recognized by *release factors* which release the polypeptide from the ribosome
225
What is wobble pairing?
-There are fewer t-RNAs than codons
-Pairing between the codon and the anticodon is less stringent than normal
-In some t-RNAs, the presence of modified bases with less accurate pairing of the anticodon enhances this flexibility
(Ex: G-U instead of G-C)
226
In eukaryotes, translation may occur in the […] or the […].
1) cytoplasm
2) Rough Endoplasmic reticulum (RER)
227
How does protein synthesis occur in the **rough Endoplasmic reticulum (RER)**?
-Signal at the beginning of the polypeptide sequence binds to the signal recognition particle (SRP).
-The signal sequence and SRP are recognized by RER receptor proteins
-Docking holds ribosome to RER and beginning of the protein-trafficking pathway
228
How does sickle cell anemia occur?
It is a mutation of only one base
-This single change from A to T, substitutes the polar charge Glutamic Acid to a non-polar Valine amino acid.
-This changes the 3D structure of the polypeptide and makes their quarternary structure into a sickle shape
229
What is point mutation?
Single base pair mutation in the DNA
230
What are types of point mutation (3)?
-Silent mutation (unchanged amino acid, ex: GGU or GGC gives gly regardless)
-Miss sense (ex: Gly becomes Ser)
-Nonsense (insertion of a stop codon too soon)
231
What are the types of frame shift mutation? (2)
Insertion
Deletion
(In both cases, you will have different codons and thus amino acids in the final protein)
232
What is chromosome mutation (large deletion)?
-Deletion of a larger region of a chromosome is usually fatal to the organism
- A large deletion from the short arm of chronometer 5 causes ‘’cri-du-chat’’ syndrome
-Usually results in early death, although many affected individuals show a normal lifespan
-respiratory problems
233
What happens if a region of a chromosome is duplicated?
(Chromosome mutation)
-The duplication of a region of a chromosome may or may not lead to phenotypic consequences
-Effects depend upon the location of the ‘’breakpoints’’ where the duplication occurred
-If the duplicated region does not lie within a gene, there may be no effect
234
What is an inversion (chromosome mutation)?
-An inversion results when a segment of a chromosome is broken in two places, reversed, and put back together
-An inversion may not have an effect on phenotype if the sites where the inversion occurs do not break within a gene
-In fact, although humans all have the ‘’same’’ genome, the order of genes in all individuals in a population is not precisely the same due to inversions that occur in different lineages
235
What is one of the most common chromosomal inversion variants?
Chromosome 9 inversion (with an estimated incidence of about 3.5%)
(note: not known if the rearrangements have clinical significance)
236
What is translocation (chromosome mutation)
-When a piece of one chromosome is broken off and joined to another chromosome
-Translocations can also move genes from one chromosomal region to another in a manner that changes the expression of genes in the region involved
-Two forms of leukemia have been shown to be associated with translocations that move oncogenes into regions of a chromosome where they are expressed inappropriately in blood cells
237
When/why do prokaryotes regulate gene expression?
Need to respond to their environment (constantly changing — need to adapt)
238
When/why do eukaryotes need to regulate gene expression?
In multicellular organisms, gene expression is critical for directing development and maintaining homeostasis
239
What are the 2 types of feedback mechanisms that metabolism control uses?
(Gene regulation)
1) Regulation enzymes:
competitive and non-competitive inhibition to turn on and off production
2) Regulation of gene expression:
Activating/deactivating genes using regulatory proteins that switch transcription on or off
240
Regulation of gene expression can be controlled at which levels? (3)
1) Transcription
2) Translation
3) Post-translation
241
Gene expression is often controlled by […] binding to specific DNA sequences
Regulatory proteins
242
What are characteristics of regulatory proteins?
(Gene regulation)
-Gene expression is often controlled by regulatory proteins binding to specific DNA sequences
-Regulatory proteins gain access to the bases of DNA at the major groove
-Within the major groove, nucleotides’ hydrogen bonds are unique for each base pair combination
243
What are DNA-binding motifs?
(Gene regulation)
-Regions of regulatory proteins which bind to DNA
-Helix structures form hydrogen bonds with nucleotides in the major groove, thus allowing each regulatory protein to bind to a specific DNA region
244
What is the helix-turn-helix motif in terms of gene regulation?
-Most DNA-regulatory sequences recognized by helix-turn-helix motifs occur in symmetrical pairs
-Such sequences are bound by proteins containing two helix-turn-helix motifs separated by 3.4 nm, the distance required for one turn of the DNA helix
-Having 2 protein-DNA-binding sites doubles the zone of contact between protein and DNA and greatly strengthens the affinity between them
245
What is the zinc finger motif?
-Zinc finger motif uses one or more zinc atoms to coordinate its binding to DNA
-Zinc finger motif exists in multiple forms, for example, a zinc atom links an alpha-helical segment to a beta-sheet segment so that the helical segment fits into the major groove of the DNA
-The effect is like a hand wrapped around the DNA with the fingers lying in the major groove
-The more zinc fingers in the cluster, the more the protein associates with DNA
246
What is the leucine zipper motif?
-Leucine zipper is created where a region on one subunit containing several hydrophobic amino acids (usually leucines) interact with a similar region on the other subunit
-This interaction holds the subunits together and creates a y-shaped structure where the two arms of the Y are helical regions that fit into the major groove of DNA, but on opposite sides of the helix, holding the DNA like a pair of tongs
247
Why regulate gene expression (bacteria example)?
Bacteria are frugal: they only express a gene if the protein is needed for the cell to survive
248
What are operons?
-Prokaryotic m-RNA may contain multiple genes and thus produce multiple proteins at once
-Prokaryotic genes are often organized such that genes encoding related functions are clustered together
-This grouping of functionally related genes is referred to as an operon
249
What do operons contain? (3)
1) A promoter: RNA polymerase building site
2) Operator: ‘’on-off’’ switch in the promoter region (if blocked, RNA polymerase cannot bind to make m-RNA)
3) Structural genes: code for gene products (ex: enzymes)
250
What are negative controls by repressors? (Prokaryote gene regulation)
-Repressors are proteins that bind to the operator to prevent or decrease the initiation of transcription
-They act as a kind of roadblock to prevent the polymerase from initiating effectively
251
What are positive controls by activators ( prokaryote gene regulation)?
The activators enhance the binding of RNA polymerase to the promoter to increase the frequency of transcription initiation
252
What is a regulatory gene?
A regulatory gene is located upstream of the operon and codes for the regulator protein (ex: repressor) which will affect the operator
253
What are the 2 types of operon?
1) inducible operon
2) repressible operon
254
What is an inducible operon?
Operon is off by default
(Ex: a bacterium will have their operon for lactase off by default and only produce the enzymes when it encounters lactose. It’s an inducible operon, since lactose induces the production of enzyme)
255
What are repressible operons?
Operon is on by default
(Ex: a bacterium will synthesize the amino acid tryptophan by default, their operon is on. However, when tryptophan is available in their food, it will stop producing this amino acid. It’s a repressible operon, since tryptophan represses the production of enzymes)
256
How do inducible operons work?
Regulator gene makes a functioning form a repressor protein
The repressor protein will bind to the operator and prevent the RNA polymerase from binding to the promoter site
257
How do repressible operons work?
Regulator gene makes a non-functioning form a repressor protein
RNA polymerase is able to bind to promoter and genes are transcribed
258
Multicellular organisms must activate or deactivate their genes according to… (3)
External stimuli
Internal stimuli
Regulate genes according to the type of cell (liver, skin, etc.)
259
Any human cell probably only expresses about […] of its genes at a time, and this proportion is […] in highly specialized cells (ex muscle cells, neurons, etc.)
1) 20%
2) even lower
260
The expression of eukaryotic genes can be regulated in which places? (5)
1) Chromatin modification (DNA and protein)
2) Transcription
3) RNA maturation
4) Translation
5) Degradation of proteins
261
What is chromatin?
-Chromatin is a complex of DNA and protein found in eukaryotic cells
-The primary function is to pack DNA into more compact structures
-The primary protein components of chromatin are histones, which bind to DNA wrapped around the histone
262
To be readable, DNA needs to be accessible to the […]
RNA Polymerase II
263
The […] of histones leads to the […] of the structure of the chromatin.
The […] structure of chromatin, permits access of the RNA polymerase to the […] and the initiation of transcription.
1) acetylation
2) loosening
3) loose
4) DNA
264
Histone methylation is the modification of certain amino acids in a histone protein by…
The addition of one, two, or three methyl groups
265
What is histone methylation associated with?
Transcriptional repression
(However, methylation of some **lysine** and **arginine** residues of histones results in transcriptional *activation*)
266
What is the correlation between histones and ATP?
-ATP-dependent chromatin remodelling factors
- Function as molecular motors that use energy from ATP hydrolysis to alter the relationships between histones and DNA
-Make DNA more accessible to regulatory proteins that in turn affect gene expression
267
What is epigenetic inheritance?
-It’s an alteration that must persist in the absence of the initiating stimulus, and be inherited through cell division
-The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
-DNA methylation and histone modification changes the way genes are expressed but not the DNA sequence
(For example, rice plants exposed to drought had offspring that increased tolerance to drought due to induced DNA methylation patterns)
268
What is the role of transcription factors?
-To initiate transcription, eukaryotic RNA polymerase II requires the help of proteins called transcription factors
269
What are the 2 types of transcription factors?
1) General transcription factors
2) Specific transcription factors
270
What do general transcription factors do?
(Eukaryotic gene regulation)
Necessary for the assembly of a transcription apparatus and recruitment of RNA polymerase II to a promoter to initiate transcription
271
What do specific transcription factors do?
Increase the level of transcription in certain cell types or in response to signals
272
What are general transcription factors?
Proteins that bind to the DNA promoter
-A host of general transcription factors are necessary to recruit RNA polymerase II to a promoter and assemble an initiation complex
-These factors are required for transcription to occur, but they do not increase the rate above this basal rate
273
High levels of transcription of particular genes depends on….
(GENE REGULATION)
The control elements interacting with specific transcription factors called an activator
274
What do activators do?
(Gene regulation)
Acts in specific tissue or in a time dependent manner to stimulate higher levels of transcription than the basal level
275
What are the 2 protein domains of activators?
(Eukaryotic gene regulation)
1) **DNA-binding domain**: recognizes a specific sequence of DNA of the control elements
2) **Activation domain**: interacts with the transcription apparatus (by binding to regulatory proteins such as coactivator and mediator proteins)
276
What do linked activators do?
(Eukaryotic gene regulation)
Facilitate a sequence of protein-protein interactions leading to the enhanced transcription of a given gene
277
Each enhancer is composed of…
(Gene regulation)
Approximately 10 control elements (each can only like 1 or 2 specific coacivators, mediator proteins and transcription factors)
278
A combination of control elements can only activate transcription when the appropriate […] are present.
(Gene regulation)
Activator proteins
279
The ultimate level of transcription depends on the presence of…
(Gene regulation)
-Activators
-Coactivators
-Mediator proteins
280
The nucleotide sequences that influence the lifespan of m-RNA in eukaryotes reside in the….
Untranslated region (UTR) at the 3’ end of the molecule
281
What leads to. The degradation of m-RNA by exonuclease?
(Hint: RNA maturation for **eukaryotic** gene regulation)
An enzyme recognizes a sequence in the UTR (untranslated region) and cuts the poly-A tail (leading to the degradation of m-RNA…)
282
What are microRNAs (mi-RNA)
-Small single stranded RNA molecules that are coded in the DNA but do to produce proteins
-Micro RNAs have specific bases that binds to m-RNA (complementary base pairs)
-Mi-RNA forms a complex with the protein that cleaves the m-RNA or blocks its translation by the ribosome
283
What is small interference RNA (si-RNA)
-Production of si-RNAs is similar to that of mi-RNAs, except that they arise from a long piece of double-stranded RNA (long loop)
-RNAs are processed by Dicer to yield multiple si-RNAs
-The si-RNA are then associated with proteins that will cleave the m-RNA when they will find a complementary the base pairs
-Most likely to evolve to protect against RNA virus by silencing them
284
How can the initiation of translation of selected m-RNAs be blocked?
-By regulatory proteins which bind to m-RNA sequences or structures (usually in the 5’ to 3’ UTR regions) and prevent the ribosome from binding
285
True or false?
The translation of all m-RNAs in a cell can be regulated simultaneously
True
286
How is the labeling of a protein for destruction carried out?
(Eukaryotic gene regulation)
By attaching a small *ubiquitin* protein to the targeted protein
287
What is a proteasome?
An organelle that degrades proteins marked with *ubiquitin*
288
What does the proteasome contain at its center and what is its function?
The protease enzyme (which cuts protein in small polypeptide fragments)
289
Why is proteasome important?
It isolates the protease enzyme from the rest of the cell and prevents the arbitrary destruction of other proteins
290
True or false?
The amino acids of the polypeptide fragments cannot be recycled to make new proteins
False!
They **CAN** be
