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Cell biology III > New info for exam 1 > Flashcards

New info for exam 1 Flashcards

1
Q

Describe Transient vs epigenetic processes

A
  • mechanisms that alter chromatin structure may contribute to transient regulation of gene expression or epigenetic regulation
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2
Q

Examples of transient processes:

A
  • Gal regulon
  • regulation of PHO5
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3
Q

describe regulation of PHO5

A
  • high phosphate = repression of transcription of pho5
  • low phosphate = nucleosome ejection, swi/snf binding, transcription activation
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4
Q

PHO5

A
  • used by the cell to metabolize and import phosphate under phosphate starvation conditions
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5
Q

What is a recurring signal?

A
  • refers to the situation in which:
    chromatin structure contributes to gene expression
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6
Q

What are epigenetic mechanisms examples?

A
  • histone modification
  • DNA methylation
  • regulatory ncRNAs
  • RNA modifications in mRNA and lncRNA
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7
Q

What are epigenetic marks?

A
  • DNA methylation and histone modification
  • regulate gene expression (genes on or off)
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8
Q

What is the epigenome?

A
  • total of all epigenetic modifications
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9
Q

Epigenetic patterns?

A
  • patterns of epigenetic modifications can be passed to daughter cells through cell division
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10
Q

Methylome

A
  • sum of all DNA methylation changes in an individual’s genome
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11
Q

What are examples of stable epigenetic regulation?

A
  • automatic, no specific stimulus
  • X-inactivation, parental imprinting
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12
Q

What is epigenetic memory?

A
  • heritable change in gene expression or behavior that is induced by a previous stimulus
  • can either be developmental or environmental
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13
Q

Types of epigenetic memory:

A
  • cellular memory
  • transcriptional memory
  • transgenerational memory
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14
Q

What is cellular memory?

A
  • mitotically heritable transcriptional states established during development in response to developmental cues (through epigenetic marks)
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15
Q

What is transcriptional memory?

A
  • mitotically heritable changes in the responsiveness of organisms to environmental stimuli due to previous experiences
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16
Q

What is transgenerational memory?

A
  • meitotically heritable changes in the gene expression and physiology of organisms in response to experiences in the previous generations
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17
Q

Explain the role of epigenetics in development

A
  • produce patterns of gene expression in different cells as needed for growth and development of the organism
  • differences in gene expression are maintained by epigenetic mechanisms
  • dividing and differentiating cells remember what they are supposed to do through preserving epigenetic marks (cellular memory)
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18
Q

Explain the analogy of the epigenome

A
  • similar to a barcode. The barcode is the epigenome that scans for a specific organ… the bars on the barcode are histone mods and dna methylations
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19
Q

Describe propagation of epigenetic marks: DNA methylation

A
  • unmethylated –> methylated –> silenced –> hemi methylated –> restored methylation –> unmethylated
    (draw the circle)
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20
Q

Describe propagation of epigenetic marks: histone modification

A
  • nucleosomes are separated from original parental DNA during synthesis of daughter
  • partial disassembly + reassembly of nucleosomes during cell division = maintanance of chromatin states from one cell generation to the next
  • nucleosomes partially break.. new components added… new strand == old and new histones
  • original epigenetic state reestablished after replication based on epigenetic marks on the newly deposited nucleosomes
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21
Q

Can epigenetic marks be inherited?

A
  • yes
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22
Q

How are epigenetic marks inherited?

A
  • can be altered by environmental conditions (diet, stress)
  • if they are acquired due to the environment, they may be passed on to the next generation if present in the germ line
  • epigenetic modifications can be triggered by toxins, alcohol, addictive drugs, diet, exercise, trauma
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23
Q

describe the link between epigenetics and cancer

A
  • alteration of genes regulating epigenetic processes can be cancer drivers, caused by chamhes in DNA/RNA modifications, histone modifications, nucleosome remodeling
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24
Q

Describe the DNA modifications that take place in cancer

A
  • global DNA HYPOmethylation is common
  • HYPERmethylation is frequently detected in specific CpG-rich regions leads to the silencing expression of tumor suppressors (turning off tumor suppressor genes)
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25
Q

Why is studying epigenetic changes difficult when it comes to cancer?

A
  • high degree of genomic instability in cancer
  • difficulty distinguishing driver from passenger mutations
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26
Q

What is parental imprinting?

A
  • involves expression of only one of the inherited alleles of a gene, depending on the parent
  • expressed gene copy is always maternal in some imprinted genes and always paternal in others
  • recognized by different diseases caused by the same deleted region depending on whether the deletion was inherited form mother or father
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27
Q

Describe prader-willi syndrome

A
  • IGF2 (insulin growth factor 2) is expressed only on the paternally derived chromosome
  • deletion of part of the paternal copy of chromosome 15 that contains H19 and IGF2 results in prader-Willi syndrome
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28
Q

Describe Angelman syndrome

A
  • H19 gene is only expressed on the maternally derived chromosome
  • Same deletion results in Angelman syndrome
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29
Q

Describe X-inactivation

A
  • during early development (cleavage) one of the x chromosomes is inactivated in cells of a female which one is random
30
Q

Condensed and silenced X chromosome becomes a…

A
  • barr body
31
Q

Describe the role of Pol II pausing in transcribed genes

A
  • transcribed genes echibit transient pausing of pol II at promotor-proximal regions
  • release of Pol II into gene bodies is controlled by many regulatory factors
  • pause can affect: RNA splicing, type of protein produced
32
Q

Describe elongation rates

A
  • vary between and within genes, play a part in co-transcriptional processes such as splicing and transcription termination and maintenance of genome stability
  • many factors can modulate elongation rates, including histone marks and features of genes such as the number of axons
33
Q

What factors are responsible for differential mRNA processing?

A
  • 5’ capping and 3’ polyadenylation for mRNAs
  • alternative RNA splicing
  • RNA modification or RNA editing
34
Q

Describe alternative RNA slicing

A
  • results in generation of alternative mRNAs from a single gene
  • essential mechanism to increase complexity of gene expression
  • important role in cell differentiation
  • MAY be cell specific
35
Q

What is the term for the variants produced by alternative RNA splicing?

A
  • protein isoforms
36
Q

Describe RNA modification

A
  • cells make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase
37
Q

describe RNA nucleotide modifications

A
  • chemical modifications of the nucleotides in RNA molecules that occur post-transcriptionally (ex: addition of a methyl to adenosine)
38
Q

examples of post-transcriptional chemical modification of RNA?

A
  • deaminations
  • isomerizations
  • glycosylatins
  • thiolation
  • transglycosylations
  • methylation
39
Q

How does RNA nucleotide modification affect RNA?

A
  • affects folding, processing, localization, function, stability…
  • distinct local effects at the site of modification
  • globally to affect the structure of the particular RNA
40
Q

What type of RNA undergoes the most post-transcriptional modification?

A
  • tRNAs (transfer RNAs)
41
Q

What is the relationship between mRNA stability and RNA modification?

A
  • stability may be controlled by RNA modifications
42
Q

What determines the fate of a modified transcript?

A
  • writer proteins, RNA-binding proteins (recognize readers), and eraser proteins
43
Q

Describe the two major groups of tRNA modifications?

A

those that:
- affect overall structure of tRNA
- target function centers of tRNA (anticodon seq…), direct effect on decoding and protein synthesis

44
Q

describe RNA editing

A
  • alters RNA sequence
  • two distinct mechanisms
  • chemical/enzymatic modification
  • insertion/deletion editing
45
Q

describe chemical /enzymatic modification

A
  • targets and individual nucleotide
  • C-to-U:
    cytidine deaminases convert a C in RNA to a U
  • A-to-I:
    adenosine deaminases convert A to I (inosine), which ribosome translates as a G
46
Q

Describe insertion/deletion editing

A
  • insert or delete nucleotides in RNA
47
Q

How are the mechanisms of RNA editing mediated?

A
  • mediated by guide RNA molecules in editosomes
  • these RNA molecules base pair with RNA to be edited and serve as a template for the addition of nucleotides in the target
48
Q

What are the functions/consequences of RNA editing

A
  • alter amino acid seq (substitutions)
  • modulate RNA stability (down-regulation/degredation)
  • alter splice sites (alt splicing)
  • alter secondary structure generating a different protein-binding site
  • modification of regulatory RNAs
49
Q

How does RNA editing affect pre-mRNA splicing

A
  • RNA editing can create or eliminate splice sites and branch points
  • intron removal can determine availability of editing complementary sequences that are required to form dsRNA substrates for editing
50
Q

Describe selective mRNA translation?

A
  • mRNAs may be sequestered so that translation is delayed or inhibited
  • accomplished by
    small regulatory RNAs
    Inhibitory protein binding
51
Q

Describe control of mRNA degredation

A
  • mRNAs can be targeted for degredation by miRNAs
  • process is known as RNA interference (RNAi)
52
Q

Describe control of translation initiation

A
  • masking mRNA to delay/prevent translation
53
Q

Describe phosphorylation of eIF2 by stress-activated kinases?

A
  • when eIF2 is phosphorylated, translation is blocked
  • when eIF2 is not phosphorylated, translation occurs
54
Q

Describe codon usage bias

A
  • synonymous codons for the same amino acid are NOT used with equal frequencies in genome
    More tRNA = more likely for A site location
55
Q

Silent mutations

A
  • synonymous codon mutations that do not change protein sequences
56
Q

describe protein post-translational modification

A

(PTMs)
- increase the functional diversity of the proteome
1. covalent additional of functional groups or proteins
2. Proteolytic cleavage of regulatory subunits
3. degredation of entire proteins

57
Q

gene expression can be regulated post-translationally by:

A
  • proteolytic processing
  • chemical modification’
  • localization
  • degradation
58
Q

describe proteolytic processing

A
  • occurs when a protease cleaves one or more bonds in a target protein to modify activity
  • may lead to activation, inhibition or destruction of the proteins activity
    (cleavage is a molecular switch, a pivotal regulator)
59
Q

Phosphorylation main cellular function

A
  • intracellular signaling
  • cellcycle, growth, apoptosis
60
Q

Ubiquitination main cellular function

A
  • protein degradation
61
Q

acetylation and methylation main cellular function

A
  • chromatin regulation
  • transcriptional regulation
62
Q

glycosylation main cellular function

A
  • extracellular signaling
  • significant effects on protein folding, conformation, distribution, stability and activity
63
Q

SUMOylation main cellular function

A
  • intracellular transport
  • transcription regulation
  • apoptosis
  • protein stability
    -stress response
  • cell cycle regulation
64
Q

What causes an increase in proteome complexity

A
  • increase of complexity is caused by protein post-translational modification
65
Q

What is proteolysis?

A
  • degradation or breakdown of proteins into smaller polypeptides or amino acids
  • catalyzed by enzymes called proteases
66
Q

Purpose of intracellular degradation of entire protein:

A
  • removal of misfolded and damaged proteins
  • regulation of cellular processes, removal of enzymes and regulatory proteins
67
Q

two major proteolysis pathways:

A
  • ubiquitin-proteasome pathway
  • lysosomal proteolysis
68
Q

What is the ubiquitin-proteasome system

A
  • selective protein degradation
  • proteins tagged by covalent linkage to ubiquitin
69
Q

ubiquitylation

A
  • attachment of ubiquitin to a substrace protein
    1. ubiquitin activating enzyme (E1) activates ubiquitin (Ub)
    2. activated Ub is transferred to a ubiquitin- conjugating enzyme (E2)
    3. target protein recognized by ubiquitin ligase enzyme (E3), facilitates transfer of Ub from E2 to lysine residue in target protein
70
Q

Deubiquitinase (DUB)

A
  • cleaves ubiquitin from proteins including:
    ubiquitin tagged proteins
    ubiquitin units in a free polyubiquitin chain
71
Q

Draw the ubiquitin-proteasome system (simple)

A

-

72
Q

What is another role of ubiquitin other than degradation?

A
  • can serve as a tag for many processes depending on the lys residue

Cell biology III (18 decks)

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