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Biology 1113 > Chapter 18 - The Genetics Of Bacteria And Viruses > Flashcards

Chapter 18 - The Genetics Of Bacteria And Viruses Flashcards

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1
Q

What are the two ways that bacteria regulate enzymes?

A

Feedback inhibition

Operon model

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2
Q

What’s feedback inhibition

A

Adjusting the ACTIVITY of the enzymes (fast response)
Typical of anabolic pathways

activity of the first enzyme in the pathway is inhibited by the pathways end product –> if tryptophan accumulates in a cell, it shuts down the synthesis of more tryptophan by inhibiting enzyme activity

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3
Q

What’s the operon model?

A

Regulation of enzyme PRODUCTION (slower)
Catabolic systems

regulate the expression of the genes encoding the enzymes by not transcribing the genes in the first place –> genes encode for the subunits of the enzymes

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4
Q

What are coordinately controlled genes?

A

5 genes code for the subunits of the enzymes that make tryptophan –> the five genes are clustered together on the bacterial chromosome and a single promotor serves all the genes

The advantage of grouping genes of related function into one transcription unit is that single on/off switch can control the function of all of them

All the enzymes for the metabolic pathway of that amino acid are all synthesized at one time

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5
Q

What is an operator

A

A segment of DNA that’s the on/off switch for coordinately controlled genes that’s positioned within the promoter or sometimes between the promoter and the enzyme coding genes

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6
Q

What’s a repressor

A

The trp operon is turned on by itself but the operon can be switched off by the trp repressor which binds to the operator and blocks attachment if RNA polymerase to the promoter to prevent transcription

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7
Q

Since regulatory genes like depressors are always expressed, why isn’t the trp operon switched off permanently

A

The trp is an also steric protein with two forms

Inky when a tryptophan molecule bunds to the repressor alert an allosteric site does the repressor protein change its shape to the active form which can attach to the operator and turn the operon off

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8
Q

What’s a corepressor?

A

A small molecule that cooperates with a repressor protein to switch an operon off (tryptophan)

When trp accumulates more trp molecules are associated with the repressor which are then active and bind to operators to shut down pathway enzymes = regulation!

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9
Q

How do bacteria usually respond to environmental change?

A

Regulate transcription

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10
Q

what are repressible operons?

A

its transcription is usually on but can be inhibited when a specific small molecule binds allosterically to a regulatory protein

ex. trp operon (need activated repressor to block pathway)

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11
Q

whats an inducible operon?

A

usually off but can be stimulated when a specific small molecule interacts with a regulatory protein

ex. lac operon:
- regulatory gene, lacI, codes for an allosteric repressor protein that can switch off the lac operon by binding to operator
- the lac repressor is active by itself!
- a special small molecule called an inducer, inactivates the repressor (allolactose)

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12
Q

what are inducible enzyme?

A

the enzymes of the lactose pathway are inducible enzymes because their synthesis is induced by a chemical signal, allolactose

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13
Q

what is negative control?

A

regulation of trp and lac operons involves NEGATIVE control of genes because the operons are switched OFF by the ACTIVE form of the repressor

so even though the operon is being turned on in the lac pathway, that’s by the nonactive form of the repressor - the active form of the repressor turns both pathways off

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14
Q

whats an activator?

A

a protein that binds to DNA and stimulates transcription of gene (CAP) - regulatory protein

cAMP accumulates when glucose is SCARCE and relays to CAP the glucose levels

presence of CAP determines rate of transcription as long as the operon is repressor free

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15
Q

what is positive regulation?

A

when cAMP binds to the regulatory protein CAP, it assumes its active shape and can attach upstream of lac promoter which increases affinity of RNA polymerase for the promoter

by increasing rate of transcription, the attachment of CAP to the promoter directly stimulates gene expression and is positive regulation!

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16
Q

what is CAP?

A

an activator of gene expression

glucose low = cAMP –> cAMP + CAP = lac operon ON
glucose high = no cAMP = inactive CAP = lac operon OFF

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17
Q

regulation of chromatin structure

A

histone acetylation promotes transcription by opening up the chromatin structure!

histone methylation can lead to condensation of chromatin and reduce transcription –> adding a phosphate can help loosen it again

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18
Q

DNA methylation

A

can methylate certain bases in DNA, usually cytosine

long stretches of inactive DNA are generally more methylated than regions of actively transcribed DNA

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19
Q

what’s genomic imprinting?

A

methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development

removal of extra methyl groups can turn on some of these genes → once methylated, genes usually stay that way in successive cell divisions

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20
Q

what’s epigenetic inheritance?

A

inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself

Chromatin modifications don’t entail a change in the DNA sequence

A good reversible mechanism for X-inactivation of regions of genes on one or the other of the two X-chromosomes in human females is enzymatic methylation of histones and/or DNA

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21
Q

what are control elements?

A

segments of noncoding DNA that are binding sites for proteins called transcription factors

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22
Q

what are transcription factors?

A

regulate transcription by binding to DNA sites associated w/ controlling activity of a promoter

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23
Q

what are general transcription factors?

A

some transcription factors are essential for the transcription of all protein-coding genes

a few bind to a DNA sequence like the TATA box within the promoter but most bind to protein like other transcription factors and RNA pol II

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24
Q

what leads to high levels of transcription?

A

interaction of control elements with another set of proteins called specific transcription factors

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25
Q

what’s an enhancer?

A

the more distant distal control elements, groupings of which are called enhancers

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26
Q

what are specific transcription factors?

A

activators or repressors

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27
Q

what strongly effects that rate of gene expression?

A

The rate of gene expression can be strongly increased or decreased by the binding of either activators or repressors (specific transcription factors) to the control elements of enhancers

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28
Q

DNA bending

A

Protein-mediated bending of the DNA is thought to bring the bound activators into contact with a group of mediator proteins (they come in separately) which in turn interact with proteins at the promoter

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29
Q

transcription factors that are repressors

A

can inhibit gene expression by binding directly to control element DNA which blocks activator binding – others interfere with the activator itself so it can’t bind the DNA

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30
Q

what is silencing?

A

when repressors recruit proteins that remove acetyl groups which decreases gene expression

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31
Q

what’s important in regulating transcription?

A

each enhancer is composed of 10 control elements, each of which can bind only one or two specific transcription factors – it’s the combination of control elements in an enhancer associated with a gene that is important in regulating transcription of a gene

liver vs. lens cell have different groups of activator proteins

32
Q

operons and coordinately expressed genes in eukaryotes vs bacteria

A

co-expressed eukaryotic genes, such as genes coding for the enzymes of a metabolic pathway, are typically scattered over different chromosomes → here, coordinate gene expression depends on the association of a specific combination of control elements with every gene of a dispersed group → activator proteins that recognize the control elements bind to them and promote simultaneous transcription of the genes, no matter where they are in the genome (all have the same colors of control elements which are recognized by a certain activator no matter where they are in the DNA)

different than bacteria where coordinately controlled genes were clustered into an operon which is regulated by a single promoter and transcribed into a single mRNA molecule

33
Q

what are transcription factories?

A

Chromosomes in the interphase nucleus aren’t completely isolated

Different loops from the same chromosome or from other chromosomes may congregate in such sites, some of which are rich in RNA polymerases and other transcription associated proteins = transcription factories

34
Q

how can initiation of translation be blocked?

A

the initiation of translation can be blocked by regulatory proteins that bind to specific sequences or structure within the untranslated region at the 5’ or 3’ end, preventing the attachment of ribosomes

35
Q

what is global control?

A

translation of all the mRNAs in a cell can be regulated simultaneously

usually involves activation or inactivation of one or more of the protein factors required to initiate translation

36
Q

why can bacteria change their patterns of protein synthesis so quickly?

A

Bacterial mRNA molecules typically are degraded by enzymes within a few minutes of their synthesis → short life span is why bacteria can change their patterns of protein synthesis so quickly in response to environmental changes

Eukaryote mRNA typically survive for hours, days, weeks

Nucleotide sequences that affect how long an mRNA remains intact are often found in the untranslated region at the 3’ end

37
Q

how are regulatory proteins activated/inactivated?

A

by reversible addition of phosphate groups

38
Q

what is selective degradation?

A

The length of time each protein functions in a cell is regulated by means of selective degradation → to mark a certain protein for destruction, the cell attaches molecules of a small protein called ubiquitin to the protein → proteasomes recognize ubiquitin-tagged proteins and degrade them

39
Q

what happens to untranscribed DNA even though 75% of the human genome is expressed at some point?

A

People used to think the rest of the DNA was untranscribed since it didn’t specify proteins or RNA so therefore it didn’t contain meaningful genetic information → (introns account for only a fraction of this transcribed nontranslated RNA) → this suggests that a lot of the genome may be transcribed into “non-protein-coding RNAs (ncRNA)”

40
Q

what are two types of small ncRNA?

A

microRNA (miRNA)

small interfering RNA (siRNA)

41
Q

what is miRNA? what does it do to mRNA?

A

Small single stranded RNA molecules capable of binding to complementary sequences in mRNA molecules

miRNA forms a complex with protein and then the miRNA allows the complex to bind to any mRNA molecule with at least 7/8 nucleotides of complementary sequence → miRNA-protein complex then either degrades the target mRNA or blocks its translation

42
Q

what is siRNA? what does it do to mRNA?

A

associates with the same proteins as miRNA, producing similar results

the distinction between miRNA and siRNA is based on subtle differences in the structure of their precursors which are both RNA molecules that are mostly double stranded

43
Q

what is RNA interference?

A

Blocking of gene expression by siRNA is called RNA interference (RNAi) and it’s used as a means of disabling specific genes

44
Q

chromatin remodeling by ncRNA

A

ncRNA can remodel chromatin structure: ex. Formation of heterochromatin at the centromere

45
Q

what are piwi-interacting RNAa?

A

they induce formation of heterochromatin, blocking expression of some parasitic DNA elements in the genome known as transposons

also reestablish appropriate methylation patterns in the genome during gamete formation

46
Q

evolution of RNA types?

A

siRNA –> miRNA –> piRNA

47
Q

what are the stages of zygote development?

A

1) cell division
2) cell differentiation
3) morphogenesis

48
Q

what is cell differentiation?

A

the process by which cells become specialized in structure and function

49
Q

what is morphogenesis?

A

the physical processes that given an organism its shape constitute morphogenesis: the development of the form of an organism and its structures

50
Q

What generates the first differences among cells in an embryo?

A

The specific genes expressed in any particular cell of a developing organism

51
Q

what two sources of information “tell” a cell which genes to express at a given time during development?

A

1) egg’s cytoplasm

2) the environment

52
Q

what does the egg’s cytoplasm do to tell a cell which genes to express? what are cytoplasmic determinants?

A

cytoplasm of an unfertilized egg is not homogenous → mRNA, proteins and organelles are distributed unevenly in the unfertilized egg

maternal substances in the egg that influence the course of early development are called “cytoplasmic determinants”

after fertilization, early mitotic divisions distribute the zygote’s cytoplasm into separate cells and the nuclei of these cells can thus be exposed to different cytoplasmic determinants since substances are spread unevenly

53
Q

what does the environment do to tell a cell which genes to express? what’s induction?

A

becomes increasingly important as the number of embryonic cells increases

the most influential are the signals impinging on an embryonic cell from other embryonic cells in the vicinity, including contact with cell-surface molecules on neighboring cells and the binding of growth factors secreted by neighboring cells – such signals cause changes in the target cells, a process called induction – the molecules conveying these signals within target cell are cell-surface receptors and other signaling pathway proteins

signaling molecules send a cell down a specific developmental path by causing changes in its gene expression that eventually result in observable cellular changes

54
Q

what is determination?

A

a term that refers to the point at which an embryonic cell is irreversibly committed to becoming a particular cell type – once it undergoes determination, it can be placed in another location in the embryo and still differentiate into the cell type that is its normal fate

55
Q

what are determined muscle cells called?

A

myoblasts

56
Q

what is a master regulatory gene?

A

Researches identified several “master regulatory genes” whose protein products commit the cells to becoming skeletal muscle → the molecular basis of determination is thus the expression of one or more of these master regulatory genes

57
Q

how does determination work?

A

signals from other cells lead to activation of master regulatory gene, myoD, –> cell then transcribes mRNA and makes myoD protein (a transcription factor that acts as activator)

the cell is now a myoblast and is committed to being muscle cell

58
Q

how does differentiation work?

A

myoD protein stimulates myoD gene further to make more myoD –> myoD then activates other genes that are necessary to make the cell a muscle cell

also turns on genes that stop cell cycle division of nondividing myoblasts fuse to become mature muscle cells/fibers

59
Q

what is pattern formation?

A

Cytoplasmic determinants and inductive signals both contribute to the development of a spatial organization in which the tissues and organs of an organism are all in their characteristic places

60
Q

what is positional information?

A

o The molecular cues that control pattern formation are collectively called positional information and are provided by cytoplasmic determinants and inductive signals

These cues tell a cell its location relative to the body axes and to neighboring cells

61
Q

what’s modular construction?

A

an ordered series of segments – the segments make up the body’s three major parts:

  • head
  • thorax
  • abdomen

fruit flies and anthropoids have this

62
Q

what are homeotic genes?

A

control pattern formation in the late embryo, larva, and adult

63
Q

what are embryonic lethals?

A

mutations with phenotypes causing death at the embryonic or larval stage → since these organisms never reproduce, they can’t be bred for study

Mutations affecting a process as fundamental as segmentations would surely be embryonic lethals

64
Q

what play a role in axis formation in drosophila?

A

cytoplasmic determinants –> they would also have to look at DNA of mom to identify all the genes that affect segment formation

65
Q

how did researchers determine which genes effected segment formation?

A

mated mutagenized flies then scanned their descendants for dead embryos or larvae with abnormal segmentation/defects

ex. To find genes that might set up the anterior-posterior axis they look for embryos/larvae with abnormal ends like two heads/tails and predict that such abnormalities would arise from mutations in maternal genes required for correctly setting up the offspring head

66
Q

what are maternal effect genes?

A

Cytoplasmic determinants establish axes of Drosophila body → these substances are encoded by genes of the mother called maternal effect genes: a gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardless of the offspring’s own genotype!

also called egg-polarity genes

67
Q

what is bicoid? whats the morphogen gradient hypothesis?

A

a morphogen that determines head structures –> mom that has two mutant bicoid alleles lacks the front half of its body

example of the morphogen gradient hypothesis where gradients of substances called morphogens establish am embryo’s axes and other features of its form

68
Q

what are oncogenes?

A

cancer-causing genes which are carried in certain types of viruses (counterparts were found in animals)

oncogenes arise from genetic change that leads to an increase either in the amount of the proto-oncogene’s protein product or in the intrinsic activity of each protein molecule

69
Q

what are photo-oncogenes?

A

normal version of the cellular genes that code for proteins that stimulate normal cell growth and division

70
Q

what are the three changes that convert photo-oncogenes to oncogenes?

A

1) movement of DNA within genome - if it ends up near active promoter transcription may increase
2) amplification of proto-oncogenes: increases # of copies of gene through gene duplication
3) point mutations in a control element which causes increase in gene expression or produce a more active protein

71
Q

what are tumor suppressing genes?

A

genes whose products inhibit cell division because the proteins they encode help prevent uncontrolled cell growth

repair damaged DNA which prevents the cell from accumulating cancer-causing mutations, control adhesion of cells to each other, other proteins are components of cell-signaling pathways that inhibit the cell cycle

72
Q

ras gene? mutations?

A

ras gene is a porto-oncogene that relays signals from growth factors to a cascade of protein kinases and the response is stimulation of cell cycle

pathway won’t operate unless triggered by appropriate growth factor but certain mutations in as gene can lead to production of hyperactive as protein that triggers kinase cascade even in absence of the growth factor being bound to the receptor

73
Q

p53? mutations?

A

sometimes when there’s damaged DNA, an intracellular signal leads to synthesis of a protein that suppresses the cell cycle

the genes for the components of these pathways act as tumor-suppressor genes (p53) - it encodes a specific transcription factor that promotes synthesis of protein that inhibits cell cycle

so…a mutation that knocks out the p53 gene can lead to excessive cell growth and cancer

74
Q

what mutations are common in individuals with colorectal cancer?

A

Inherited mutations in the tumor-suppressor gene adenomatous polyposis coli are common in individuals with colorectal cancer

75
Q

what is heterogeneity?

A

tumors differ in significant ways! that’s what makes curing cancer so hard

Biology 1113 (12 decks)

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