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Biochem > 06 > Flashcards

06 Flashcards

1
Q

What is an advantage to gene regulation in eukaryotes
Why

A

cell specialization
- helps to conserve resources b/c transcription and translation take up a lot of energy

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2
Q

What are some possible causes to changes in gene expression

A

development
reproduction
response to energy
response to stress
disease (cancer)

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3
Q

how are prokaryotes a simpler model in gene expression

A
  1. no compatimentalization, no organelles
  2. transcript and translation combined
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4
Q

how is prokaryotic DNA organized for gene expression

A

all genes under the control of the same promoter (operon)
- all genes can be expressed or turned off at the same time

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5
Q

what is a polycistronic mRNA

A

genes in an operon transcribed in one mRNA

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6
Q

How are genes synthesized in prokaryotes

A

RNA polymerase binds to the promoter upstream of the coding regions

RNA polymerase starts transcribing the mRNA and transcribes all the genes into a single mRNA

Each protein product (structural gene) has its own start and stop codon that ribosomes will bind to synthesize the protein

the protein products may all be participants in the same biosynthetic pathway

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7
Q

how is prokaryotes gene expression controlled

A

at the level of transcription by the ability of the RNA polymerase to bind to the promoter

gene is turned on or off

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8
Q

What are repressors

A

regulatory proteins that prevent the polymerase from binding and initiating transcription
- negative control

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9
Q

What are inducers

A

small molecules that bind to the repressors and change conformation and make it unable to bind to the operator

inducers inactivates the repressor – RNA polymerase can bind to the DNA and transcription can proceed

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10
Q

How does the lac operon work
When is it used

A

inducer-repressor system in bacteria

used in E. coli to allow lactose to be used as a source of energy (when no glucose)

inducer: metabolite of lactose
- releases repressor and allows the genes to be transcribed
- all the genes transcribed are involved in the metabolism of lactose for energy

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11
Q

What happens when glucose is present on the lac operon

A

glucose is the preferred energy source – glucose present = genes turned off

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12
Q

What turns on the lac operon

A

lactate present
glucose low
repressor on

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13
Q

What regulates eukaryotic gene regulation

A

things that contribute to how much protein is present in the cell at any given time

accessibility of a gene (DNA too tightly packed)
ability of RNA polymerase to bind and start transcription
processing of RNA transcripts
mRNA stability and translation initiation
protein folding and stability

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14
Q

How do DNA associate with histone

A

histones are positively charged (with lots of lysine) and DNA is negatively charged

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15
Q

What causes histones to wrap less tightly

A

post-translational modifications on the histone protein to weaken the interaction
allows the DNA to open and become accessible

histone acetylation

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16
Q

What causes histones to wrap more tightly

A

methylaion of DNA and histones

transcription factors cannot bind and genes are not expressed

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17
Q

how do histone acetyltransferases weaken interactions with DNA

A

HATs transfer an acetyl group from acetyl-CoA to the lysine on a histone
- removes positive charge

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18
Q

How are acetyl group removed

A

histone deacetylases (HDACs) can remove the acetyl group and causes the histones and DNA to more tightly associate

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19
Q

What proteins help to stabalize RNA polymerase binding with DNA for transciption

A

TATA binding protein (TATA box) – stabalizing RNA polymerase
Trans-activators bind to nearby enhancer region in DNA
Hormone receptros can bind to other nearby regulatory elements

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20
Q

How does cortisol regulate transciption

A

cortisol binds to its receptor protein in the cytoplasm and releases its repressor from a repressor protein – reveals the nuclear-localization signal of the receptor and allows it to move to the nucleus and bind to DNA – receptor recruits more proteins from the transcription machinery to turn on gene expression

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21
Q

What are the different domains of receptor proteins

A

ligand binding domain
DNA binding domain
transactivation domain

22
Q

How do thyroid hormones control transcription

A

thyroid hormone receptors form a complex that is always on DNA and represses transcription of the downstream genes – keeps DNA wrapped around histones – when thyroid hormones bind, the repressor complex is replaced with an activator complex – complex allows release of DNA from histones and transcription can occur

23
Q

What happens when promotor regions of genes are methylated

A

gene expression is turned off

24
Q

how would you describe methylation patterns

A

inherited
- process is critical to cell differentiation and fetal development

25
Q

What are DNA binding motifs

A

transcription factors/proteins bind to specific sequences on DNA and have a conformation that fits into the grooves of DNA

fit into specific DNA sequences – “recognize” areas in the DNA

26
Q

how does alternative splice sites and stop codons control gene expression

A

different proteins may be made from the same gene in different tissues

27
Q

how does the poly (A) tail control gene expression

A

stabilize so that it exists for a longer period in the cytosol

28
Q

How does mRNA lifespan control gene expression

A

mRNA have their lifespan encoded into the DNA in the 3’ region, less protein is made from shorter-lived transcripts and this is encoded in the gene

29
Q

how many chromosomes do humans have

A

46

23 from each parent

30
Q

how many autosomal chromosomes do humans have

A

22

31
Q

how many sex chromosomes do humans have

A

1 pair

32
Q

what is a karyotype

A

complete set of chromosomes

33
Q

what is a genome

A

total of all DNA in the cell - contained in nucleus of eukaryotic cells

34
Q

what is a haploid cell (sperm or egg)

A

has 23 chromosomes, the egg and sperm combine into a diploid cell containing 46 chromomes

35
Q

what is a gene

A

sequence of DNA (plus its regulatory regions) that code for a protein or RNA molecule

36
Q

what is an allele

A

two versions of the same gene
- identical = homozygous
- different = heterozygous

37
Q

what is gene expression

A

control some of our haracteristics

38
Q

what is polymorphism

A

occurs when there is a difference in the DNA sequence between different individuals (stable if it exists in >1% of the population)

39
Q

what is a single nucleotide polymorphism (SNPs)

A

different individuals may have slightly different seuqnce of nucleotides

40
Q

How are mutations introduced

A

DNA replication when it is not repaired

41
Q

What are single base pair changeds

A

genetic differences due to a single base pair changed

42
Q

What are epigenetic studies

A

changes to the expression of genes that occur without any change in the underlying DNA sequence

43
Q

What are epigenetics

A

controls which genes are active (turned on) and inactive (turned off)

44
Q

How does epigenetics work

A

different chemical modifications or “tags” are added to the DNA to control if a gene is actively being expressed

tags on DNA can be added and taken off
- reversible
inheritable (mods can be accumulated during life that are passed on to the next generation)

45
Q

What are the different epigenetic tags

A

dna methylation
histone modifications
non-coding RNA – RNA that doesn’t code for a protein – but can control if an mRNA is translated

46
Q

How does DNA methylation work

A

occurs within DNA CpG islands (regions with a lot of Cs and Gs)

covlently attached to cytosine

silence genes – turn them off by blocking transcription machinery from binding

DNA methylatransferases add methyl groups onto DNA using a co-enzyme known as SAM (derived from the amino acid methionine)

47
Q

how are methy groups removed

A

demythylase

48
Q

how is methylation tags inherited

A

DNA replicates using semi-conservative replication

mthylation tags are copied on to the new strand of DNA – using parental strand as a template

can connect environment exposures to change in gene expression in later generations

49
Q

How do histone modifications work

A

help wrap DNA to keep it condensed

contains many positevely charged lysine aa residues

these residues can be modified by several post-translational modifications that can change how the histone proteins associate with DNA

50
Q

how are DNA wrappings loosened

A

modifications like methylation and acetylation remove the positive charge from lysine and weakens its interactions with DNA

loosens the DNA wrapped around the histone
- allows RNA polymerase to access teh DNA and start transcription

histone acetyltransferases add acetyl groups to histones using acetyl-CoA
histone deacetylases remove acetyle groups

Biochem (11 decks)

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