Slides 2 Flashcards
(199 cards)
1
Q
Localization and function of proteins is regulated by (3)
A
- transcription
- translation
- post-translational modification
2
Q
Transcription =
A
DNA information is copied into mRNA
3
Q
Translation =
A
mRNA is used as a template to synthesize proteins
4
Q
RNA splicing and editing in the nucleus change:
> Made of what?
A
Their sequence and the relative amount of resulting proteins
>exons
5
Q
What are Non-coding RNA (ncRNA) that exert various regulator functions called?
A
Introns
6
Q
What is pre-mRNA?
A
the mRNA that includes introns and exons
7
Q
What is chromatin made of?
A
tightly packed DNA wound around proteins (histones) known as nucleosomes
8
Q
Rosalind Franklin ans Raymond Gosling used X-ray diffraction to discover what?
A
That DNA exists in 2 forms:
- A the dry A form that holds less water
- The wet B form where water molecules cling to DNA, causing it to stretch out
9
Q
How many layers are in every twist of DNA?
A
10
10
Q
What bonds bind the 2 strands of DNA?
A
Hydrogen bonds
11
Q
What does it mean to say that DNA is anti-parallel?
A
5’ end of one strand is paired with the 3’ end of its complimentary strand
12
Q
What is the most important energy source in the brain?
A
Oxygen –> brain used 50% of oxygen that goes through it
> only 10% of glucose
13
Q
the highest energy yield from glucose comes from what?
A
NADH from glycolysis in mitochondria
14
Q
Pathways linked to the tricarboxylic acid (TCA) pathway and oxidative metabolism are essential for: (6)
A
- NT turnover
- synthesis of excitatory and inhibitory NT
- mRNA, protein, lipids, and organelle turn over
- Axonal transport
- Ion pumping to maintain and restore ionic gradients
- Synthesis of amino acids
15
Q
The brain is not able to store any oxygen, what does that mean for the supply?
A
It needs to be continuous to meet the energy needs
16
Q
Do oxygen and glucose require energy to pass through the BBB?
A
Oxygen passes right through, no energy needed
Glucose passes through channels (indirectly need energy to make channels)
17
Q
What are the functions of the glucose channels Glut 1, Glut 3, and Glut 5?
A
Glut 1 = astrocyte taking glucose from blood
Glut 3 = astrocyte transferring glucose into neuron
Glut 5 = microglia
18
Q
How much glucose is transported into the brain?
A
~3 times more than can be used
> good because none can be stored
19
Q
What is the energy yield from glucose –> pyruvate?
A
2 ATP
2 NADH
20
Q
Where is most of the energy of a cell produced?
A
In the mitochondria by oxidative phosphorylation
21
Q
What are different energy substrates?
A
- Carbohydrates (glucose after being converted into pyruvate)
- Lactate
- Ketone bodies
- Fatty acids
22
Q
What are the waste products of oxidative phosphorylation?
A
Carbon dioxide and water
23
Q
ATP is synthesized via what enzyme?
A
ATP synthase
24
Q
Methylation of DNA
A
Silencing
Closed chromatin
A form
25
Acetylation
Expressing
Open chromatin
B form
26
Promotor selection is determined by what?
The interaction of one or more transcriptional activators(s) with recognition sites (on DNA) near target genes
27
Activators recruit what?
Components of the transcription machinery
28
Activation of gene expression is induced by what?
A certain sequence of large proteins co-activator complexes
29
Activators also recruit APT-dependent nucleosome remodelling complexes, which do what?
Move or displace histones at the promoter
30
What epigenetic changes happen to the BDNF gene during stress?
Methylation --> reducing expression
31
How do anti-depressants work on the BDNF gene?
Reverses the suppression of BDNF through increased histone acetylation
32
What are the functions of chromatin?(3)
- package DNA into chromosomes
- control replication *
- control expression ****
33
Def of epigenetics:
Chromatin regulation outside the genetic code that can control gene expression
34
Unwound protein-chromosome complexes are called:
Chromatin
35
What is the basic unit of chromatin organization
147 base pairs
| wrapped around a core of histone proteins
36
Packaging of chromatin affects:
gene expression
37
What is the difference between euchromatin and heterochromatin?
```
Euchromatin = transcription can occur because it is open
Heterochromatin = transcription cannot occur because it is closed
```
38
What are HAT and HMT and what do they do?
Histone (Acetyl or methyl) Transferases
| > They moderate the amount of methylation or acetylation on chromatin
39
What do SWI/SNF do?
Opens up DNA to allow things to bind (transcription machinery, transcription factors and co-activators)
40
HDAC do what?
De-acetylate histones (make DNA more tightly packed)
41
What are 2 main benefits to the regulation of gene expression through epigenetics?
1. It conserves energy - only have the proteins made when needed
2. Having chromatin tightly packed saves space
42
What are the functions of methylation and acetylation
Methylation : makes brain regions stable
| Acetylation : makes brain plastic
43
histones are made up of how many proteins?
8
44
First level of organization or packaging of DNA is:
Winding DNA strands around histones
45
Second level of organization of DNA:
Histones package together to form nucleosome complexes
46
Third level of organization of DNA:
Supercoiling (negative and positive charges attraction)
47
How many histones make up a nucleosome
4
48
Histone modification occurs at which amino acids?
Lysine amino acid
49
It is the level of acetylation of methylation that determines how tightly packed DNA is
Acetylation
50
Hyperacetylation
Chromatin is relaxed and accessible to the transcriptional proteins
> increased gene transcription
51
Hypoacetylation
Chromatin is condensed preventing access of transcriptional proteins
> gene silencing
52
What could be a function of inhibiting HDAC?
Inhibit the enzyme that breaks down acetylation
| >> Increase acetylation
53
What does DNMT do?
Add methyl groups to DNA
54
What are MBD
Methyl binding domains - have repressor proteins (HDACs)
55
How does methylation directly silence a gene?
Doesn't allow general or specific transcription factors to bind to gene
56
What are the transcriptional machinery?
RNA polymerases
57
How can hypomethylation be problematic (cancer)
Methylation exists to control cell division (reduce transcription), so a lack of methylation would result in unregulated growth (cancer)
58
How do drugs affect epigenetics?
They lead to the activation or inhibition of transcription factors and chromatin regulating proteins
59
How does alcohol withdrawal reduce BDNF levels and decreased dendritic density (anxiety behaviours)
HDAC activity increases and DNA becomes more tightly packed
60
Homodimer
protein complex with one subunit
61
Heterodimer
Protein with more than one subunit
62
What is the final step in assembling the Initiation Complex
The addition of a phosphate group to the CTD on RNA Polymerase II
63
What is Polymerase II able to do once it is phosphorylated?
Leave the PIC and begin synthesizing RNA
64
How is TFIIH like DNA helicase?
Can separate strands of DNA
65
What important thing happens after TFIIH separates the strands of DNA?
RNA Polymerase II can bind to the DNA and start RNA synthesis
66
What is elongation regulated by?
Developmental or cell signalling stimuli
67
What is the 5' capping?
7-methylguanosine cap is added to the 5' end of mRNA during elongation
68
What is the Poly (A) tail?
A series of As that are added to the 3' end of the mRNA one elongation is complete
69
What is the purpose of the 5' cap and poly (A) tail?
To protect the mRNA from degradation once it exits the nucleus, helps export DNA, binding to ribosome
70
Exons def
protein coding-sequences
71
introns def
intervening sequences that are removed from the pre-mRNA
| >> Do not encode functional proteins
72
Why is it good to remove introns?
Because the extra non-coding mRNA would slow down transcription
73
If introns don't code, why do that exist?
To increase the repertoire of the proteins that can be made from a single gene
74
How is pre-mRNA converted to mature mRNA?
By removing the introns from the pre-mRNA and ligation of exons by the spliceosomes
75
What are the splicosomes composed of?
5 subunits called snRNP (small nuclear ridonucleoparticles)
76
How do spiceosomes know how to identify introns?
snRNAs recognize motifs in DNA sequence that define the intron
77
How to splicosomes splice?
They cleave the sugar phosphate backbone at the G at the start of the exon and then "glues" it to the A at the start of the other exon
78
Are miRNA more often negative feedback-ing for excitation or inhibition
Inhibition
79
Is CREB and general or specific transcriptional factors?
Specific
80
What are characteristics of G-Protein linked signals?
- slow neural response (ms to hours)
- Modulates many things
- signal is amplified
- Allows for plasticity
81
How does receptor binding enhance or inhibit expression of target gene?
1. Direct interaction with ligand-activated GR with glucocorticoid response elements
2. Interaction of the activated receptor with other transcription factors
82
How does chronic stress inhibit neurogenesis
CORT- activated glucocorticoid receptors may inhibit CREB activity
83
Transcription is the process that ensures the neuron maintains ____ and adequately responds to _____ _____
Homeostasis
| Environmental Signals
84
Gene expression is regulated by the presence of:
1. Cis-regulatory sequences (where specific transcription factors bind)
2. Protein complexes (transcription regulators)
85
What are general transcription factors?
Proteins that help position Pol II on the promotor
| > pull apart DNA and move Pol II into elongation mode
86
Specific transcription factors
COntrol the expression of specific genes
87
General vs Specific transcription factors
```
General = Are basal and used for every gene
Specific = express only certain genes
```
88
How is CREB activation initiated?
By translocation of calcium sensor or by activating kinases
89
Calcium sensors supports CREB phosphorylation through the activation of what?
CaMKIV
90
What is the 5 step process of gene transcription regulated by second messengers?
1. Ligand binds to G-protein
2. Activates adenylyl cyclase which increases levels of cAMP
3. Increase in cAMP activated PKA in cytosol
4. Released subunits travel into nucleus
5. Subunits phosphorylate CREB
6. pCREB recruits co-activator CBP which stimulates gene transcription
91
How is CREB phosphorylated?
1. CREB binds to cAMP response element (CRE)
| 2. Protein kinase A and CaMK2 stimulate phosphorylation
92
CREM is part of the _____-zipper which means they do what
They can unwind DNA
93
Leucine-zipper proteins bind to what DNA sequences
cAMP response element (CRE)
94
What is the key enzyme that mediates transcription?
RNA Polymerase II
95
What do polymerase 1 and 3 do?
```
1 = transfer RNA
3 = Ribosomal RNA
```
96
RNA Polymerase II catalyzes transcription for what? (2)
1. All protein coding genes
| 2. snRNAs
97
What bond types does RNA polymerase II form?
Phosphodiester bonds
98
What binds to the TATA box?
General transcription factors (TFIID) for Polymerase II
99
Where is the TATA box located?
25 base pairs from the transcription start site
100
Which part of the TFIID protein binds to the TATA box?
the TATA-Binding Protein (TBP)
101
What does the TATA-Binding Protein do
It bends the DNA to alloe the transcription factors and RNA Polymerase to closer
102
After TFIID have attached to the core promoter, how is the Pre-Initiation Complex formed?
By the attachment of the remaining general transcription factors
103
What is the order the transcription factors bind in?
1. TFIIA
2. TFIIB
3. TFIIF/RNA polymerase II
4. TFIIE
5. THIIH
104
Summary of pre-initiation complex
1. TBP attaches and bends DNA as TATA box
2. Bend gets TFIIB to put RNA Polymerase II at transcription start site
3. TFIIH opens promoter complex
105
Alternative Splicing
Increases the number of mRNA products any one gene can produce by skipping exons o adding introns
106
Introns play a role in a wide range of gene expression regulatory functions such as (2)
1. Nonsense mediated decay
| 2. mRNA export
107
What are the 3 types of non-coding RNA?
Introns
tRNA
Ribosomes (rRNA)
108
How can miRNA be used to treat obesity?
There are miRNA that inhibit the production of fat cells
109
Gene expression is regulated by (4)
1. Control of transcription rate
2. Control of splicing and processing of mRNA
3. Control of transport and localization of mRNA
4. Control rate of degradation of transcripts
110
What does it mean to say that transcription factors are constitutively present?
They are present all the time, under basal conditions
111
What does it mean to say that proteins are inducible?
They need to be transcribed, not present under basal conditions
112
CREB activates which inducible transcription factor? Which is made up of what sub-units?
AP-1
| Fos and Jun
113
How long does AP-1 stay around after induction?
It is transcribed rapidly but then it goes away
114
AP-1 is an ________ early gene
Immediate early gene
115
AP-1 is a heterodimer made of what sub units?
C-Fos and C-Jun
116
AP-1 is a _______ zipper
Leucine
117
Are Fos and Jun present under basal conditions?
No, they must be transcribed
118
What happens if C-Fos goes back into the nucleus by itself?
It is a negative feedback loop that will repress inducible transcription
119
Intracellular signal transduction
A chain of reactions stimulated by a signal from the cell surface
120
Which AP-1 dimer has leucine zipper properties?
C-Fos
121
Long term drug use results on the increased expression of what transcription factor?
FosB/DeltaFosB
122
Is Delta FosB transient or stable?
Stable, it is always present
123
How is Delta FosB different from C-Fos?
It regulates the expression of different genes
124
DeltaFosB increases transcription of ARC, which results in what?
Increases dendritic spine growth and makes lots of connections
>possible mechanism of addiction
125
DeltaFosB sticks around even after you stop taking drugs, what repercussions does that have?
The drug seeking circuitry is still there so it will continue the drug seeking behaviours
126
What are the 6 main functions of proteins?
1. Metabolism
2. Cell division
3. Immune system defense
4. Gene expression and regulation
5. Physical structure
6. DNA replication, transcription and translation
127
The unique sequence of amino acids of a protein allow for what?
A unique 3D folded structure
128
Alpha helix
A coil
129
Beta pleat
A sheet
130
What part of the amino acid determines the physical and chemical properties?
R-side chain (functional group)
131
For a protein, shape determines _____
Function
132
Polar amino acids have hydro____ R groups
hydrophilic
133
Non-polar amino acids have hydro____ R groups
hydrophobic
134
If proteins free float around in the cytosol, the amino acid side chains on the outside will be hydro____
hydrophilic
135
2 characteristics of water soluble proteins
- non-polar side chains on inside of molecule
| - polar side chains on outside of molecule
136
2 characteristics of membrane bound proteins
- non-polar side chains are on the surface to come into contact with membrane
- polar amino acids will line the interior of the pores
137
What type of amino acid lines the inside of protein channels?
Hydrophilic amino acids (because the hydrophobic ones are on the outside interacting with the membrane.
138
The active sites of enzymes depend on the location and distribution of the polar and non-polar amino acids because:
Hydrophobic and hydrophilic interaction can play a role in substrate binding to the active site
139
how many different amino acids are there?
20
140
What can happen if there is a mutation that changes the charge of an amino acid?
the protein becomes less stable and it wobbles around.
| > can bind with other unstable proteins
141
What makes the Huntington's gene diseased?
The repeat of the sequence CAG too many times (more than 37) causing it to misfold
142
Fibrous proteins
Elongated proteins that are usually structural, sometimes functional
143
Globular proteins
Compact and tightly coiled
144
Native conformation of a protein
The tertiary structure that the protein naturally folds into
145
Do proteins need help folding?
Most do not
146
Primary structure
Sequence of amino acids
147
Secondary structure
folding as a result of hydrogen bonding
| >> alpha helix and beta pleated sheets
148
Tertiary structure
Combination of the secondary folding into a 3D shape
149
Quaternary structure `
The interaction between multiple protein subunits to make a large structure
150
Are proteins fixed to one structure?
No, they can go back and forth
| > usually between 3 and 4
151
Some proteins require what type of assistance to fold properly?
Post translational modifications or molecular chaperone help
152
What is the main post translational modification
Phosphorylation
153
What happens if misfolded proteins start to accumulate?
Leads to the formation of protofibrils, fibrils, and inclusion bodies
154
Which is the most common secondary structure?
Alpha helices
155
Why are alpha helices more common than beta pleated sheets?
They have a thermodynamically stable conformation (less wobble, lower energy)
156
Is high or low energy of a protein ideal at rest?
Low energy
157
Which composition makes prions infectious?
When they are composed of mostly beta pleated sheets
158
How do prions spread?
They can make natively formed proteins fold to have more beta pleated sheet (abnormal) conformation
159
Most proteins are fibrous or globular?
Globular
160
What do globular proteins typically look like?
Hydrophobic core and hydrophilic outer layer
161
what type of bond binds the alpha helices and beta pleated sheets?
Disulfide bonds
162
Attraction between negatively charged _____ groups and the positively changed _____ group stabilize the tertiary structure
Carboxyl group
| Amino group
163
What minor force can exist between non-polar side chains in proteins
Van der Wall forces
164
What bonds stabilize quaternary structures?
Hydrogen bonding
Disulfide bridges
Salt bridges
165
What are the 3 subunits of the g-protein called?
Alpha
Beta
Gamma
166
what happens when a ligand binds to a g-protein?
it changes shape, causing the alpha subunit to break away
167
What does the alpha subunit do once it breaks off?
Interacts with adenelal cyclase (AC) and converts ATP into cAMP, which activates PKA to phosphorylate CREB
168
What does phosphorylation do? (4)
1) Regulate cell cycle
2) Growth
3) Apoptosis
4) signal transduction pathway
169
What does glycosynation do (5)
```
Effects on protein:
Folding
Conformation
Distribution
Stability
Activity
```
170
What does ubiquitination do?
Catalyzes the degradation of the ubiquinated protein
171
Why do proteins become uniquinated?
Because it is mis-folded
172
Phosphorylation activates a protein when it is on _____ and inactivates it when it is on _____
Top
| Bottom
173
Is phosphorylation irreversible?
No
| > By phosphytase
174
What energy state is the protein at when phosphorylated?
Higher energy state
175
Unfolded or misfolded are in a _____ energy state than the native conformation
Higher
176
What can happen when there is an unfolded protein (3)
1. Protein can refold
2. Attract chaperones for disposal
3. They can bind to other non folding proteins making aggregates
177
Aggregations are at an even lower free energy state than the native form, what does this result in?
It makes it irreversible,
| protein is no longer functional
178
Oxygen goes directly where when it enters the cell?
Mitochondria
179
Glycolysis is what process and it happens where?
When pyruvate is obtained from glucose
| >In the cytoplasm
180
Where is pyruvate made and then where does it go after it is created?
Cytoplasm
| Mitochondria
181
What elements are involved in oxidative phosphorylation?
Electron transport chain
182
Kreb's cycle is also known as:
TCA
183
How much ATP does the Kreb cycle generate?
2 APT
184
How much ATP is generated from the electron transport chain?
34
185
How do ions enter the brain>
Ion channels
186
What passes via membrane transport into the brain?
small lipophilic molecules, like oxygen
187
Who are energy transport molecules like glucose transported into the brain?
Carrier mediated transport (solute carriers)
188
Direct vs indirect pathway of a neuron getting energy
Direct: glucose goes into the neuron and ATP is generated there
Indirect: glucose goes into astrocyte and generates ATP and gives it to neuron
189
Where does dimerization of AP-1 take place?
In the nucleus
190
For this class, methylation happens on ____ and acetylation happens on ______
```
Methylation = DNA
Acetylation = Hystones
```
191
HAT is recruited by what?
Sequence specific transcription factor (TF1)
192
Acetylation is essential for _________-dependent nucleosome remodelling
SWI/SNF
193
Drug-induced changes at the chromatin level are extremely _____ and define _____
Stable
| Addiction
194
What are 2 chromatin remodeler complexes?
SWI/SNF
195
What percentage of the genome code for transcription regulating proteins?
5-10%
196
What proteins can mediate cAMP mediated transcription?
CREB
CREM
ATF-1
197
What are the 3 types of post-transcriptional modifications?
1. Poly A tail
2. 5' cap
3. Splicing
198
What are the 3 names for the different forms of mRNA?
Transcript Variants
Splice variants
Isoforms
199
The largest group of amino acids have what type of side chain?
Non-polar
