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M1W2 lectures > gene expression > Flashcards

gene expression Flashcards

1
Q

how do the DNA and RNA nucleotides differ?

A

the 5 carbon sugar
- DNA: deoxyribose (H at C2)
- RNA: ribose (OH group at C2)

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2
Q

list the different subtypes of RNA

A
  • mRNA
  • rRNA
  • tRNA
  • miRNA
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3
Q

what is mRNA?

A

messenger RNA, codes for proteins

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4
Q

what is rRNA?

A

ribosomal RNA, forms the basic structure of the ribosomes and catalyzes protein synthesis

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5
Q

what is tRNA?

A

transfer RNA, central to protein synthesis as adaptors between mRNA and amino acids

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6
Q

what is miRNA?

A

microRNA, regulatory function

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7
Q

what is the promoter region?

A

region of DNA that initiates transcription of a particular gene

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8
Q

what are exons?

A

coding regions of an RNA transcript

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9
Q

what are introns?

A

non-coding regions of an RNA transcript; they are largely structural but have some regulatory functions

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10
Q

what are transcription factors?

A

proteins responsible for initiating gene transcription (mRNA synthesis) by recruiting RNA polymerase

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11
Q

what is RNA polymerase?

A

enzyme that transcribes DNA to produce an mRNA copy

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12
Q

what is the function of RNA polymerase?

A

attaches at the promoter sequence of DNA and moves along the DNA, unzipping the strands
- mRNA is produced from 5’to 3’

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13
Q

what happens during RNA splicing

A

removes the noncoding intronic sequences from the mRNA
- leaving the finished transcription product containing only exons

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14
Q

what happens during mRNA translation?

A

mRNA is converted into a protein sequence

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15
Q

list the steps of mRNA translation

A
  • mRNA molecules move from the nucleus to the cytoplasm
  • mRNA binds to ribsomes (site of protein synthesis)
  • the ribosome moves along the mRNA molecule
  • translation starts at a start codon (AUG)
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16
Q

what is tRNA and its function?

A

a transport molecule that carries specific amino acids to a ribosome
- 20 different tRNAs exist
- each tRNA carries an amino acid
- it can recognize the correct codon on the mRNA molecule via its anticodon sequence

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17
Q

how does tRNA bring amino acids together?

A
  • the ribosome moves along the mRNA
  • tRNA brings in the correct amino acid
  • the amino acids are joined together by peptide bonds
  • the process ends when the stop codon is reached (UAA)
18
Q

list the steps of protein synthesis

A
  1. new protein synthesis starts on free ribosomes
  2. polypeptide chains enter the ER
  3. new protein accumulates in the ER lumen or embeds in the ER membrane
  4. golgi apparatus processes porteins and directs them to the plasma membrane or internal organelles
  5. proteins synthesized on the rough ER exit in transport vesicles
  6. vesicles fuse with the cis-gogli complex
  7. proteins migrate through the golgi cisternae to the trans-golgi
  8. proteins are then packaged in vesicles
19
Q
A
20
Q

what is the function of the golgi apparatus?

A

responsible for post translational modifications of proteins

21
Q

list the post translational modifications that occur in the golgi apparatus

A
  • formation of disulfide bonds
  • addition and processing of carbohydrates
  • specific proteolytic cleavages
  • assembly into multimeric proteins
  • proper folding of proteins
22
Q

what are the steps of the secretory pathway?

A
  • proteins for export are synthesized in the rough ER
  • proteins are then packaged into vesicles that bud off from the rough ER
  • the vesicles then fuse with the golgi and transfer proteins into the golgi lumen
  • secretory vesicles then bud off from the golgi and fuse with the plasma membrane for release of proteins (exocytosis)
23
Q

summarize the steps of RNA transcription and translation

A

come back

24
Q

define gene regulation

A

how a cell controls which genes are expressed
- this allows for different cell types to have different sets of genes active
- this results in different patterns of gene expression between cell typs (disease, development, etc.)

25
Q

what is gene regulation responsible for?

A
  • spatial expression
  • temporal expression
26
Q

define spatial expression

A

not every gene product is needed in every cell

27
Q

define temporal expression

A

different genes are expressed at different times in response to a wide range of factors (some genes only need to be active once they have been stimulated)
- e.g. hormones, growth factors, heat, etc.

28
Q

how is gene expression regulated?

A
  1. regulating the rate of transcription (via enhancers adn silencers)
  2. regulating the processing of RNA molecules
  3. regulating the stability of mRNA molecules
29
Q

how is the rate of transcription regulated and what is the purpose of this?

A
  • enhancers
  • silencers

these regions of DNA control the rate in which genes can be transcribed and translated into protein
- this is really important, particularly for spatial expression because different cells need different proteins at different times

30
Q

what is an enhancer and what is its function?

A

an enhancer is a short region of DNA that can bind to specific proteins (transcription factors) to significantly increase the likelihood of a nearby gene being transcribed
- activators (TFs) bind to enhancers

enhancers increase the rate of transcription
- often within the introns
- can also be distant and still influence its transcription

31
Q

what is a silencer and what is its function?

A

a silencer is a regulatory DNA element that reduces transcription from their target promoters
- counterpart to enhancer
- repressors (TFs) bind to silencers

silencers decrease the rate of transcription

32
Q

how is the processing of RNA molecules regulated?

A

alternative mRNA splicing is used to produce more than one protein product (with different functions and structures) from a single gene

33
Q

how is the stability of mRNA molecules regulated?

A

unstable mRNAs are degraded

34
Q

what is epigenetics?

A

the study of changes in organisms caused by the modification of gene expression rather than the alteration of the genetic code itself
- external modification of genes that turn genes ‘on’ or ‘off’
- does not change the DNA but affects how the cells read the DNA
- change in phenotype without a change in genotype

e.g. monozygotic twins or cloned animals with identical DNA sequences can have different phenotypes and susceptibilities to disease - this is due to epigenetics

35
Q

what are histone modifications?

A

reversible modifications to the chromatin structure which ultimately affects transcription by modulating access to chromatin by transcription factors

36
Q

list the histone modifications

A
  • methylation
  • acetylation
37
Q

what is acetylation and what is the result?

A

addition of an acetyl group (COCH3)
- results in loosely packed chromatin
- easier access for transcription factors

histone acetylation results in loose packing of nucleosomes
- transcription factors can bind the DNA and genes are expressed

37
Q

what is methylation and what is the result?

A

addition of a methyl group (CH3) to DNA

  • methyl groups are added to histones which changes the conformation of chromatin making it more compact, and transcriptionally inactive
  • results in gene silencing

methylation of DNA and histones causes nucleosomes to pack tightly together
- transcription factors cannot bind the DNA and genes are not expressed
- polymerases cannot get in, os the genes are silenced and inactive

38
Q

what is an epigenome?

A

the collection of chemical modifications of DNA and histones within a cell or organism that play a role in regulating gene expresison, regardless of the DNA sequence

39
Q

discuss epigenetics and disease, with examples

A
  • epigenome is dynamic and can repsond to the environment
  • e.g. diet, drugs, chemical exposure, stress, etc.
  • epigenetic modifications of DNA has been linked to numerous diseases, particularly cancer, and are transgenerational (passed down through generations without direct genetic inheritance)

some examples:
- diet has been shown to modify epigenetic patterns
- pollution may alter methyl marks and increase risk of neurodegenerative disease
- B vitamins may provide a level of protection against epigenetic effects of pollution

40
Q

discuss the example of nutrition influencing epigenetics during development in mice

A
  • individuals with an active agouti gene have a yellow coat and a propensity to become obese
  • the gene can be switched off by DNA methylation by dietary supplements which release methyl groups
  • the pups agouti genes then become methylated and thus inactive
  • the pups still carry the agouti gene but they lose the agouti phenotype
  • they have brown fur and no increased tendency towards obesity

M1W2 lectures (4 decks)

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