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Cellular and Molecular Neuroscience > Slides 2 > Flashcards

Slides 2 Flashcards

1
Q

Localization and function of proteins is regulated by (3)

A
  • transcription
  • translation
  • post-translational modification
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2
Q

Transcription =

A

DNA information is copied into mRNA

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3
Q

Translation =

A

mRNA is used as a template to synthesize proteins

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4
Q

RNA splicing and editing in the nucleus change:

> Made of what?

A

Their sequence and the relative amount of resulting proteins
>exons

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5
Q

What are Non-coding RNA (ncRNA) that exert various regulator functions called?

A

Introns

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6
Q

What is pre-mRNA?

A

the mRNA that includes introns and exons

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7
Q

What is chromatin made of?

A

tightly packed DNA wound around proteins (histones) known as nucleosomes

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8
Q

Rosalind Franklin ans Raymond Gosling used X-ray diffraction to discover what?

A

That DNA exists in 2 forms:

  1. A the dry A form that holds less water
  2. The wet B form where water molecules cling to DNA, causing it to stretch out
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9
Q

How many layers are in every twist of DNA?

A

10

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10
Q

What bonds bind the 2 strands of DNA?

A

Hydrogen bonds

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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

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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

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13
Q

the highest energy yield from glucose comes from what?

A

NADH from glycolysis in mitochondria

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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
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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

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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)

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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

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18
Q

How much glucose is transported into the brain?

A

~3 times more than can be used

> good because none can be stored

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19
Q

What is the energy yield from glucose –> pyruvate?

A

2 ATP

2 NADH

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20
Q

Where is most of the energy of a cell produced?

A

In the mitochondria by oxidative phosphorylation

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21
Q

What are different energy substrates?

A
  • Carbohydrates (glucose after being converted into pyruvate)
  • Lactate
  • Ketone bodies
  • Fatty acids
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22
Q

What are the waste products of oxidative phosphorylation?

A

Carbon dioxide and water

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23
Q

ATP is synthesized via what enzyme?

A

ATP synthase

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24
Q

Methylation of DNA

A

Silencing
Closed chromatin
A form

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25
Q

Acetylation

A

Expressing
Open chromatin
B form

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26
Q

Promotor selection is determined by what?

A

The interaction of one or more transcriptional activators(s) with recognition sites (on DNA) near target genes

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27
Q

Activators recruit what?

A

Components of the transcription machinery

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28
Q

Activation of gene expression is induced by what?

A

A certain sequence of large proteins co-activator complexes

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29
Q

Activators also recruit APT-dependent nucleosome remodelling complexes, which do what?

A

Move or displace histones at the promoter

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30
Q

What epigenetic changes happen to the BDNF gene during stress?

A

Methylation –> reducing expression

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31
Q

How do anti-depressants work on the BDNF gene?

A

Reverses the suppression of BDNF through increased histone acetylation

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32
Q

What are the functions of chromatin?(3)

A
  • package DNA into chromosomes
  • control replication *
  • control expression **
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33
Q

Def of epigenetics:

A

Chromatin regulation outside the genetic code that can control gene expression

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34
Q

Unwound protein-chromosome complexes are called:

A

Chromatin

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35
Q

What is the basic unit of chromatin organization

A

147 base pairs

wrapped around a core of histone proteins

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36
Q

Packaging of chromatin affects:

A

gene expression

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37
Q

What is the difference between euchromatin and heterochromatin?

A 
Euchromatin = transcription can occur because it is open 
Heterochromatin = transcription cannot occur because it is closed
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38
Q

What are HAT and HMT and what do they do?

A

Histone (Acetyl or methyl) Transferases

> They moderate the amount of methylation or acetylation on chromatin

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39
Q

What do SWI/SNF do?

A

Opens up DNA to allow things to bind (transcription machinery, transcription factors and co-activators)

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40
Q

HDAC do what?

A

De-acetylate histones (make DNA more tightly packed)

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41
Q

What are 2 main benefits to the regulation of gene expression through epigenetics?

A
  1. It conserves energy - only have the proteins made when needed
  2. Having chromatin tightly packed saves space
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42
Q

What are the functions of methylation and acetylation

A

Methylation : makes brain regions stable

Acetylation : makes brain plastic

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43
Q

histones are made up of how many proteins?

A

8

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44
Q

First level of organization or packaging of DNA is:

A

Winding DNA strands around histones

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45
Q

Second level of organization of DNA:

A

Histones package together to form nucleosome complexes

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46
Q

Third level of organization of DNA:

A

Supercoiling (negative and positive charges attraction)

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47
Q

How many histones make up a nucleosome

A

4

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48
Q

Histone modification occurs at which amino acids?

A

Lysine amino acid

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49
Q

It is the level of acetylation of methylation that determines how tightly packed DNA is

A

Acetylation

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50
Q

Hyperacetylation

A

Chromatin is relaxed and accessible to the transcriptional proteins
> increased gene transcription

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51
Q

Hypoacetylation

A

Chromatin is condensed preventing access of transcriptional proteins
> gene silencing

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52
Q

What could be a function of inhibiting HDAC?

A

Inhibit the enzyme that breaks down acetylation

|&raquo_space; Increase acetylation

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53
Q

What does DNMT do?

A

Add methyl groups to DNA

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54
Q

What are MBD

A

Methyl binding domains - have repressor proteins (HDACs)

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55
Q

How does methylation directly silence a gene?

A

Doesn’t allow general or specific transcription factors to bind to gene

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56
Q

What are the transcriptional machinery?

A

RNA polymerases

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57
Q

How can hypomethylation be problematic (cancer)

A

Methylation exists to control cell division (reduce transcription), so a lack of methylation would result in unregulated growth (cancer)

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58
Q

How do drugs affect epigenetics?

A

They lead to the activation or inhibition of transcription factors and chromatin regulating proteins

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59
Q

How does alcohol withdrawal reduce BDNF levels and decreased dendritic density (anxiety behaviours)

A

HDAC activity increases and DNA becomes more tightly packed

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60
Q

Homodimer

A

protein complex with one subunit

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61
Q

Heterodimer

A

Protein with more than one subunit

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62
Q

What is the final step in assembling the Initiation Complex

A

The addition of a phosphate group to the CTD on RNA Polymerase II

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63
Q

What is Polymerase II able to do once it is phosphorylated?

A

Leave the PIC and begin synthesizing RNA

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64
Q

How is TFIIH like DNA helicase?

A

Can separate strands of DNA

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65
Q

What important thing happens after TFIIH separates the strands of DNA?

A

RNA Polymerase II can bind to the DNA and start RNA synthesis

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66
Q

What is elongation regulated by?

A

Developmental or cell signalling stimuli

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67
Q

What is the 5’ capping?

A

7-methylguanosine cap is added to the 5’ end of mRNA during elongation

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68
Q

What is the Poly (A) tail?

A

A series of As that are added to the 3’ end of the mRNA one elongation is complete

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69
Q

What is the purpose of the 5’ cap and poly (A) tail?

A

To protect the mRNA from degradation once it exits the nucleus, helps export DNA, binding to ribosome

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70
Q

Exons def

A

protein coding-sequences

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71
Q

introns def

A

intervening sequences that are removed from the pre-mRNA

|&raquo_space; Do not encode functional proteins

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72
Q

Why is it good to remove introns?

A

Because the extra non-coding mRNA would slow down transcription

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73
Q

If introns don’t code, why do that exist?

A

To increase the repertoire of the proteins that can be made from a single gene

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74
Q

How is pre-mRNA converted to mature mRNA?

A

By removing the introns from the pre-mRNA and ligation of exons by the spliceosomes

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75
Q

What are the splicosomes composed of?

A

5 subunits called snRNP (small nuclear ridonucleoparticles)

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76
Q

How do spiceosomes know how to identify introns?

A

snRNAs recognize motifs in DNA sequence that define the intron

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77
Q

How to splicosomes splice?

A

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

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78
Q

Are miRNA more often negative feedback-ing for excitation or inhibition

A

Inhibition

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79
Q

Is CREB and general or specific transcriptional factors?

A

Specific

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80
Q

What are characteristics of G-Protein linked signals?

A
  • slow neural response (ms to hours)
  • Modulates many things
  • signal is amplified
  • Allows for plasticity
81
Q

How does receptor binding enhance or inhibit expression of target gene?

A
  1. Direct interaction with ligand-activated GR with glucocorticoid response elements
  2. Interaction of the activated receptor with other transcription factors
82
Q

How does chronic stress inhibit neurogenesis

A

CORT- activated glucocorticoid receptors may inhibit CREB activity

83
Q

Transcription is the process that ensures the neuron maintains ____ and adequately responds to _____ _____

A

Homeostasis

Environmental Signals

84
Q

Gene expression is regulated by the presence of:

A
  1. Cis-regulatory sequences (where specific transcription factors bind)
  2. Protein complexes (transcription regulators)
85
Q

What are general transcription factors?

A

Proteins that help position Pol II on the promotor

> pull apart DNA and move Pol II into elongation mode

86
Q

Specific transcription factors

A

COntrol the expression of specific genes

87
Q

General vs Specific transcription factors

A 
General = Are basal and used for every gene 
Specific = express only certain genes
88
Q

How is CREB activation initiated?

A

By translocation of calcium sensor or by activating kinases

89
Q

Calcium sensors supports CREB phosphorylation through the activation of what?

A

CaMKIV

90
Q

What is the 5 step process of gene transcription regulated by second messengers?

A
  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
Q

How is CREB phosphorylated?

A
  1. CREB binds to cAMP response element (CRE)

2. Protein kinase A and CaMK2 stimulate phosphorylation

92
Q

CREM is part of the _____-zipper which means they do what

A

They can unwind DNA

93
Q

Leucine-zipper proteins bind to what DNA sequences

A

cAMP response element (CRE)

94
Q

What is the key enzyme that mediates transcription?

A

RNA Polymerase II

95
Q

What do polymerase 1 and 3 do?

A 
1 = transfer RNA 
3 = Ribosomal RNA
96
Q

RNA Polymerase II catalyzes transcription for what? (2)

A
  1. All protein coding genes

2. snRNAs

97
Q

What bond types does RNA polymerase II form?

A

Phosphodiester bonds

98
Q

What binds to the TATA box?

A

General transcription factors (TFIID) for Polymerase II

99
Q

Where is the TATA box located?

A

25 base pairs from the transcription start site

100
Q

Which part of the TFIID protein binds to the TATA box?

A

the TATA-Binding Protein (TBP)

101
Q

What does the TATA-Binding Protein do

A

It bends the DNA to alloe the transcription factors and RNA Polymerase to closer

102
Q

After TFIID have attached to the core promoter, how is the Pre-Initiation Complex formed?

A

By the attachment of the remaining general transcription factors

103
Q

What is the order the transcription factors bind in?

A
  1. TFIIA
  2. TFIIB
  3. TFIIF/RNA polymerase II
  4. TFIIE
  5. THIIH
104
Q

Summary of pre-initiation complex

A
  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
Q

Alternative Splicing

A

Increases the number of mRNA products any one gene can produce by skipping exons o adding introns

106
Q

Introns play a role in a wide range of gene expression regulatory functions such as (2)

A
  1. Nonsense mediated decay

2. mRNA export

107
Q

What are the 3 types of non-coding RNA?

A

Introns
tRNA
Ribosomes (rRNA)

108
Q

How can miRNA be used to treat obesity?

A

There are miRNA that inhibit the production of fat cells

109
Q

Gene expression is regulated by (4)

A
  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
Q

What does it mean to say that transcription factors are constitutively present?

A

They are present all the time, under basal conditions

111
Q

What does it mean to say that proteins are inducible?

A

They need to be transcribed, not present under basal conditions

112
Q

CREB activates which inducible transcription factor? Which is made up of what sub-units?

A

AP-1

Fos and Jun

113
Q

How long does AP-1 stay around after induction?

A

It is transcribed rapidly but then it goes away

114
Q

AP-1 is an ________ early gene

A

Immediate early gene

115
Q

AP-1 is a heterodimer made of what sub units?

A

C-Fos and C-Jun

116
Q

AP-1 is a _______ zipper

A

Leucine

117
Q

Are Fos and Jun present under basal conditions?

A

No, they must be transcribed

118
Q

What happens if C-Fos goes back into the nucleus by itself?

A

It is a negative feedback loop that will repress inducible transcription

119
Q

Intracellular signal transduction

A

A chain of reactions stimulated by a signal from the cell surface

120
Q

Which AP-1 dimer has leucine zipper properties?

A

C-Fos

121
Q

Long term drug use results on the increased expression of what transcription factor?

A

FosB/DeltaFosB

122
Q

Is Delta FosB transient or stable?

A

Stable, it is always present

123
Q

How is Delta FosB different from C-Fos?

A

It regulates the expression of different genes

124
Q

DeltaFosB increases transcription of ARC, which results in what?

A

Increases dendritic spine growth and makes lots of connections
>possible mechanism of addiction

125
Q

DeltaFosB sticks around even after you stop taking drugs, what repercussions does that have?

A

The drug seeking circuitry is still there so it will continue the drug seeking behaviours

126
Q

What are the 6 main functions of proteins?

A
  1. Metabolism
  2. Cell division
  3. Immune system defense
  4. Gene expression and regulation
  5. Physical structure
  6. DNA replication, transcription and translation
127
Q

The unique sequence of amino acids of a protein allow for what?

A

A unique 3D folded structure

128
Q

Alpha helix

A

A coil

129
Q

Beta pleat

A

A sheet

130
Q

What part of the amino acid determines the physical and chemical properties?

A

R-side chain (functional group)

131
Q

For a protein, shape determines _____

A

Function

132
Q

Polar amino acids have hydro____ R groups

A

hydrophilic

133
Q

Non-polar amino acids have hydro____ R groups

A

hydrophobic

134
Q

If proteins free float around in the cytosol, the amino acid side chains on the outside will be hydro____

A

hydrophilic

135
Q

2 characteristics of water soluble proteins

A
  • non-polar side chains on inside of molecule

- polar side chains on outside of molecule

136
Q

2 characteristics of membrane bound proteins

A
  • 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
Q

What type of amino acid lines the inside of protein channels?

A

Hydrophilic amino acids (because the hydrophobic ones are on the outside interacting with the membrane.

138
Q

The active sites of enzymes depend on the location and distribution of the polar and non-polar amino acids because:

A

Hydrophobic and hydrophilic interaction can play a role in substrate binding to the active site

139
Q

how many different amino acids are there?

A

20

140
Q

What can happen if there is a mutation that changes the charge of an amino acid?

A

the protein becomes less stable and it wobbles around.

> can bind with other unstable proteins

141
Q

What makes the Huntington’s gene diseased?

A

The repeat of the sequence CAG too many times (more than 37) causing it to misfold

142
Q

Fibrous proteins

A

Elongated proteins that are usually structural, sometimes functional

143
Q

Globular proteins

A

Compact and tightly coiled

144
Q

Native conformation of a protein

A

The tertiary structure that the protein naturally folds into

145
Q

Do proteins need help folding?

A

Most do not

146
Q

Primary structure

A

Sequence of amino acids

147
Q

Secondary structure

A

folding as a result of hydrogen bonding

|&raquo_space; alpha helix and beta pleated sheets

148
Q

Tertiary structure

A

Combination of the secondary folding into a 3D shape

149
Q

Quaternary structure `

A

The interaction between multiple protein subunits to make a large structure

150
Q

Are proteins fixed to one structure?

A

No, they can go back and forth

> usually between 3 and 4

151
Q

Some proteins require what type of assistance to fold properly?

A

Post translational modifications or molecular chaperone help

152
Q

What is the main post translational modification

A

Phosphorylation

153
Q

What happens if misfolded proteins start to accumulate?

A

Leads to the formation of protofibrils, fibrils, and inclusion bodies

154
Q

Which is the most common secondary structure?

A

Alpha helices

155
Q

Why are alpha helices more common than beta pleated sheets?

A

They have a thermodynamically stable conformation (less wobble, lower energy)

156
Q

Is high or low energy of a protein ideal at rest?

A

Low energy

157
Q

Which composition makes prions infectious?

A

When they are composed of mostly beta pleated sheets

158
Q

How do prions spread?

A

They can make natively formed proteins fold to have more beta pleated sheet (abnormal) conformation

159
Q

Most proteins are fibrous or globular?

A

Globular

160
Q

What do globular proteins typically look like?

A

Hydrophobic core and hydrophilic outer layer

161
Q

what type of bond binds the alpha helices and beta pleated sheets?

A

Disulfide bonds

162
Q

Attraction between negatively charged _____ groups and the positively changed _____ group stabilize the tertiary structure

A

Carboxyl group

Amino group

163
Q

What minor force can exist between non-polar side chains in proteins

A

Van der Wall forces

164
Q

What bonds stabilize quaternary structures?

A

Hydrogen bonding
Disulfide bridges
Salt bridges

165
Q

What are the 3 subunits of the g-protein called?

A

Alpha
Beta
Gamma

166
Q

what happens when a ligand binds to a g-protein?

A

it changes shape, causing the alpha subunit to break away

167
Q

What does the alpha subunit do once it breaks off?

A

Interacts with adenelal cyclase (AC) and converts ATP into cAMP, which activates PKA to phosphorylate CREB

168
Q

What does phosphorylation do? (4)

A

1) Regulate cell cycle
2) Growth
3) Apoptosis
4) signal transduction pathway

169
Q

What does glycosynation do (5)

A 
Effects on protein: 
Folding 
Conformation
Distribution 
Stability 
Activity
170
Q

What does ubiquitination do?

A

Catalyzes the degradation of the ubiquinated protein

171
Q

Why do proteins become uniquinated?

A

Because it is mis-folded

172
Q

Phosphorylation activates a protein when it is on _____ and inactivates it when it is on _____

A

Top

Bottom

173
Q

Is phosphorylation irreversible?

A

No

> By phosphytase

174
Q

What energy state is the protein at when phosphorylated?

A

Higher energy state

175
Q

Unfolded or misfolded are in a _____ energy state than the native conformation

A

Higher

176
Q

What can happen when there is an unfolded protein (3)

A
  1. Protein can refold
  2. Attract chaperones for disposal
  3. They can bind to other non folding proteins making aggregates
177
Q

Aggregations are at an even lower free energy state than the native form, what does this result in?

A

It makes it irreversible,

protein is no longer functional

178
Q

Oxygen goes directly where when it enters the cell?

A

Mitochondria

179
Q

Glycolysis is what process and it happens where?

A

When pyruvate is obtained from glucose

>In the cytoplasm

180
Q

Where is pyruvate made and then where does it go after it is created?

A

Cytoplasm

Mitochondria

181
Q

What elements are involved in oxidative phosphorylation?

A

Electron transport chain

182
Q

Kreb’s cycle is also known as:

A

TCA

183
Q

How much ATP does the Kreb cycle generate?

A

2 APT

184
Q

How much ATP is generated from the electron transport chain?

A

34

185
Q

How do ions enter the brain>

A

Ion channels

186
Q

What passes via membrane transport into the brain?

A

small lipophilic molecules, like oxygen

187
Q

Who are energy transport molecules like glucose transported into the brain?

A

Carrier mediated transport (solute carriers)

188
Q

Direct vs indirect pathway of a neuron getting energy

A

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
Q

Where does dimerization of AP-1 take place?

A

In the nucleus

190
Q

For this class, methylation happens on ____ and acetylation happens on ______

A 
Methylation = DNA 
Acetylation = Hystones
191
Q

HAT is recruited by what?

A

Sequence specific transcription factor (TF1)

192
Q

Acetylation is essential for _________-dependent nucleosome remodelling

A

SWI/SNF

193
Q

Drug-induced changes at the chromatin level are extremely _____ and define _____

A

Stable

Addiction

194
Q

What are 2 chromatin remodeler complexes?

A

SWI/SNF

195
Q

What percentage of the genome code for transcription regulating proteins?

A

5-10%

196
Q

What proteins can mediate cAMP mediated transcription?

A

CREB
CREM
ATF-1

197
Q

What are the 3 types of post-transcriptional modifications?

A
  1. Poly A tail
  2. 5’ cap
  3. Splicing
198
Q

What are the 3 names for the different forms of mRNA?

A

Transcript Variants
Splice variants
Isoforms

199
Q

The largest group of amino acids have what type of side chain?

A

Non-polar

Cellular and Molecular Neuroscience (4 decks)

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