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BIOL 103 > (Lecture 5-6) Quiz 3 > Flashcards

(Lecture 5-6) Quiz 3 Flashcards

1
Q

What percent of our genome encodes proteins?

A

2%

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2
Q

Which parts of the central dogma are reversible?

A

DNA to RNA and RNA to protein (via transcriptional/translational regulation)

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3
Q

What are epigenetics?

A

Study of changes in gene expression or cellular phenotype that happens without changes in Watson-Crick base-pairing of DNA

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4
Q

What are the three regulatory RNAs (of significance for the lecture)?

A

siRNA, miRNA, IncRNA

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5
Q

What is DNA methylation?

A

An epigenetic change that occurs at CpG islands at promoters. It silences transcription. Bisulfite sequencing can detect the pattern of methylation. It is heritable after cell division, but also reversible (so the pattern can be altered)

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6
Q

How is DNA methylation conserved during replication?

A

During replication, a maintenance methylase catalyzes the formation int he new DNA strand

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7
Q

What happens if methylation cannot occur?

A

DNA methylation is essential for development. Those with methyltransferase mutations (preventing DNA methylation) have various anomalies and deficiencies.

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8
Q

What is a nucleosome?

A

The fundamental unit of chromatin. Contains 146 bp of DNA + 8 histone proteins.

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9
Q

What are the two states of chromatin?

A

Relaxed (DNA accessible) and condensed (DNA inaccessible)

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10
Q

What are heterochomatin?

A

Small, darkly staining, and irregular particles, often accumulated adjacent to the nuclear envelope (condensed)

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11
Q

What are euchromatin?

A

Dispersed and not easily stained, most abundant in cells with many genes in active transcription (relaxed)

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12
Q

What is position effect variegation (PEV)?

A

When a gene normally in euchromatin is juxtaposed with heterochromatin. AKA cells of the same type can express the same gene differently

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13
Q

Enhancers and suppressors of ________ include ______ _______

A

PEV; chromatin modifiers

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14
Q

What can affect readout of DNA (via chromatin modifications)?

A

Genetic mutations, environmental stressors

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15
Q

How are histone tails epigenetically modified?

A

They are heavily modified after translation. The covalent modifications are acetylation, phosphorylation, methylation, and ubiquitination

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16
Q

What is chromatin remodeling?

A

Allows for transcription. Transcription initiation requires nucleosomes to be less compact. Epigenetic chromatin remodeling changes DNA accessibility for transcription

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17
Q

How does histone lysine methylation affect gene expression?

A

Location and degree matter in affecting gene expression. So where this methylation occurs (enhancers, promoters, gene bodies) affects the type of regulation that occurs.

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18
Q

What are reader proteins?

A

They coordinate and integrate various modification signals, bring additional enzymatic machinery to specific chromatin loci, and determine substrate specificity of enzymes.

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19
Q

What is RNAi?

A

RNA interference. Gene silencing by double stranded RNA (dsRNA)

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20
Q

What does the presence of dsRNA do (in the case of RNAi)?

A

Presence of dsRNA leads cells to specifically degrade any other RNAs with the same sequence, using small interference RNAs

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21
Q

What is often generated from viral replication?

A

dsRNA, which can also be formed by aberrant transcription from genetic elements in the host genome?

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22
Q

What are the theorized origins of RNAi?

A

May have evolved as an RNA immune system and/or mechanism to silence certain genomic regions / genes.

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23
Q

How are miRNAs produced and how do they act?

A

They are produced from precursors and act by regulation of target genes

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24
Q

What is the difference between siRNA and miRNA?

A

siRNA is exogenous, double stranded (taken up by cells, eg. viral infection)
miRNA is endogenous, single stranded (made by cells themseleves

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25
Q

What is the role of miRNAs

A

They control other genes (target genes)

26
Q

How do microRNAs function

A

They degrade target gene mRNA or disrupt its translation.

27
Q

What are transposons?

A

Genes that can “jump” (transposable elements). Are specific sequences of DNA, found in many animals, makes up almost half of our genome, and structurally and functionally diverse.

28
Q

What are the two types of transposable elements?

A

Non-autonomous elements (need presence of another transposable element encoding a transposase) and autonomous elements (transpose by themselves) .

29
Q

What are the three types of transposition?

A

Cut and paste transposition: Element is cut out of one site on a chromosome and placed elsewhere.
Replicative transposition: Element is replicated, and one copy inserted at new site; one copy remains at original site.
Retrotransposition: An element’s RNA is used as template to synthesize DNA molecules, which are inserted into new chromosomal site.

30
Q

What element of transposons causes differences in genome size?

A

Different numbers of transposons

31
Q

Transposable elements can ______ the _____ landscape

A

disrupt; epigenetic

32
Q

How do transposons (theoretically) play a role in neuronal diversity?

A

20% of the human genome is made up of transposons (autonomous retrotransposons). They are active during neuronal differentiation (cut and paste).

33
Q

What are the two distinct cell layers generated by the ICM in the mammalian blastocyst?

A

Epiblast (primitive ectoderm) and hypoblast (primitive endoderm)

34
Q

During gastrulation, what generates all three primary germ layers?

A

The epiblast

35
Q

What does the blastodisc consist of?

A

An upper epiblast and a lower hypoblast (joined at the margins).

36
Q

What is the blastocoel?

A

The fluid filled space between the epiblast and hypoblast

37
Q

What are the three parts of amphibian gastrulation?

A

Involution: inward movement through the dorsal lip
(endodermal and mesodermal cells)
Convergent extension: cells elongate in the direction of movement and intercalate
Epiboly: ectodermal cells flatten and move toward the site of involution

38
Q

Why is embryonic development four dimensional?

A

Because somitogenesis is temporally regulated

39
Q

Where do muscles and bones derive from?

A

Somites (blocks of paraxial mesoderm)

40
Q

Which axis do somites form along?

A

The anterior-posterior axis

41
Q

How is somitogenesis temporally regulated?

A

It helps to specify different parts of a somite (to form specific tissues) and to specify the identity of each somite along A-P axis

42
Q

What is the sclerotome?

A

Cartilages and bones of vertebral column and ribs

43
Q

What is dermomyotome?

A

Dermis and skeletal muscles of the body and limbs

44
Q

Does one somite equal one vertebra?

A

No. Each vertebra is formed by the posterior half of one somite and the anterior half of the next somite.

45
Q

Which genes are essential for somite specification of spinal column segments

A

Hox genes (overlapping function of a combination of hox genes specifies segment identity)

46
Q

Which regions do hox genes affect (in drosophila)?

A

Epidermis, CNS, visceral mesoderm

47
Q

What is the different between orthologs and paralogs?

A

Orthologs are same/similar genes in different species. Paralogs are multiple copies of the same gene

48
Q

What are the homeotic genes in plants (similar to hox)?

A

MADS box genes

49
Q

What do mutations in homeotic genes cause?

A

Transformation of one organ type into another (homeosis or homeotic transformation)

50
Q

In the ABC model of flower development, which two parts negatively regulate each other?

A

A and C

51
Q

What are the four stages of limb/wing development?

A

Initiation, outgrowth, patterning and, chondrogenesis/ossification

52
Q

What axis does outgrowth happen on?

A

Proximal-distal

53
Q

What axis does patterning occur on?

A

A-P and D-V

54
Q

Is FGF signaling necessary or sufficient for limb development initiation?

A

Both

55
Q

What is the apical ectodermal ridge (AER)?

A

A signaling center essential for limb outgrowth

56
Q

Why are snakes limbless?

A

Pythons have no forelimbs and severely reduced hindlimbs. Expansion of thoracic identity in the axial skeleton and failure in forelimb initiation (the signaling center for limb outgrowth is not activated) cause limblessness.

57
Q

What is the ZPA and why is it immportant?

A

The zone of polarizing activity. It is a signaling center essential for limb patterning along A-P axis.

58
Q

What is chondrogenesis and ossifiation?

A

Formation of cartilages and bones, including:
condensing of cartilage, segmentation, joint formation, and regression of interdigital tissue

59
Q

What mediates regression of interdigital tissue?

A

Apoptosis (death by suicide or a form of programmed cell death)

60
Q

What is apoptosis?

A

Programmed cell death. It is a precisely regulated process, and as needed for development as mitosis is (formation of fingers and toes, menstruation, elimination of surplus neurons)

BIOL 103 (6 decks)

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