BIO 151 exam 4 content Beate Wone

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Prokaryotic DNA shape:

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1

Prokaryotic DNA shape:

Circular, double stranded, supercoiled

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2

where is DNA found in a prokaryotic cell?

in the nucleoid

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3

Folding of DNA is facilitated by what proteins in a prokaryotic cell?

nucleoid-associated proteins (bind to and fold DNA)

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4

Folding of DNA is facilitated by what proteins in a eukaryotic cell?

histone proteins (bind to and fold DNA)

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5

Eukaryotic DNA shape:

Linear, double stranded, supercoiled

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6

Where is DNA found in eukaryotic cells?

in the nucleus

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7

All the cells in a eukaryotic organism (except __________) have the same DNA.

gametes

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8

What makes cells and tissues different from eachother?

which sets of genes are expressed

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9

What does the genes that are expressed determine?

types of proteins and functional RNAs produced, and phenotype and function of cell

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10

What is the reason that fertilized eggs become complex multi-cellular organisms?

Gene expression

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11

_______ _________ is the process of controlling which genes in a cell's DNA are expressed.

gene regulation

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12

What is the default state for most genes?

"OFF"

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13

Muscle cells differ from nerve cells mainly because they:

express different genes

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14

What are the main 3 steps that gene regulation occurs at?

transcription, translation, and post-translation

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15

What are additional levels of control for gene regulation?

chromatin remodeling, RNA processing, mRNA stability

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16

In Chromatin remodeling, cells detect chemical signals for 2 reasons:

short term cellular responses and gene activity regulation

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17

Short term cellular responses in chromatin remodeling include:

changes in membrane permeability and activation/deactivation of enzymes/proteins

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18

reasons for gene activity regulation in chromatin remodeling include:

producing specific proteins and to trigger transcription

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19

Why is chromatin remodeling necessary?

DNA is packed tightly in the nucleus and RNA polymerase cannot access it, so the chromatin around the gene must be remodeled

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20

Chromatin consists of:

DNA complexed with histones and other proteins

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21

Histones are

the most abundant DNA associated proteins

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22

Nucleosome is

about 200 bases of negatively charged DNA wrapped around a core of 8 positively charged histone proteins, repeating beadlike structures spaced with linker DNA

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23

nucleosomes form 30 nm fibers that are attached to scaffold proteins to:

hold entire chromosome in place

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24

When chromosomes condense before cell division, they are:

more tightly packed

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25

Chromatin's elaborate structure is important because...(2 reasons)

it allows the DNA to fit in the nucleus and it plays a key role in regulating gene expression

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26

What is the product of chromatin remodeling?

a chromosome(sister chromatids) in its condensed form

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27

Eukaryotic DNA has _________ where RNA polymerase binds to initiate transcription.

promoters

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28

chromatin must be ___________ to expose promoter for RNA polymerase to bind.

decondensed

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29

What are the 2 ways to remodel chromatin?

DNA methylation and histone modification

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30

Is methyl polar or nonpolar?

nonpolar

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31

Methylated DNA is __________ DNA.

condensed

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32

unmethylated DNA is ___________ DNA

Decondensed

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33

What causes DNA to become decondensed/unmethylated?

acetylation

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34

DNA condensation is triggered by

the addition of methyl groups (-CH3) to cytosine (CpG islands) in the promoter of genes

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35

The addition of methyl groups to trigger DNA condensation is called

methylation

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36

What enzyme recognizes CpG islands?

DNA methyl transferase

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37

Reversal of methylation is done by which enzyme?

demethylase

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38

Why do actively transcribed genes usually have few methylated CpG sequences near the promoter?

because they don't want to be condensed, condensation prevents replication process

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39

Methylation when you should have demethylated and vise versa can cause what?

cancer (depends on what the DNA is coding for)

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40

Enzymes can add a variety of chemical groups to histones with different effects. What are these chemical groups?

Methyl groups, acetyl groups, phosphate groups and short polypeptide chains

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41

Histone modifications can promote either __________ or ___________.

condensation, decondensation

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42

More acetyls and fewer histones means that DNA is likely ______.

decondensed/open

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43

True or false: histone methylation does not necessarily condense DNA.

True

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44

Histone acetylation ___________ DNA.

decondenses

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45

Removal of acetyl and addition of methyl functional groups to histone tails __________ DNA.

condenses

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46

More methyl = (more/less) likely that DNA condenses.

more

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47

True or false: DNA and histone methylation condense DNA and make a gene inaccessible to RNA polymerase.

False

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48

True or false: In those sections of DNA where histones are resistant to acetylation, gene transcription will be decreased.

true

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49

What does variation of chromatin modification patterns between cells allow for?

differential gene expression in different tissues and cells

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50

When a cell divides what is passed on to the daughter cells?

patterns of methylation and acetylation

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51

Epigenetic inheritance

any inheritance mechanism that is not due to differences in DNA sequences

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52

____________ _____________ can record life events that influence phenotypes of offspring.

epigenetic mechanisms

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53

Examples of lifestyle factors with epigenetic effects

nutrition, physical activity, smoking, alcohol use, pollutants, emotions/stress, working nights

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54

How many general transcription factors are there and what determines where they bind?

6 and the promoter sequence

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55

What sequence is unique to each gene?

promoter-proximal elements

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56

proximal =

closer

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57

distal =

further

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58

Binding of ___________ ____________ ________ promote or inhibit transcription.

regulatory transcription factors

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59

What provides a mechanism for eukaryotic cells to express certain genes but not others?

promoter proximal elements

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60

General transcription factors is used in eukaryotes instead of ________ in prokaryotes.

sigma

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61

____________ _____________ elements are specific to certain areas/parts of the body.

promoter proximal

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62

What is a distal control element? Where are they located?

Regulatory sequences, can be hundreds of thousands of bases upstream OR downstream from the promoter

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63

Which regulatory sequences increase the rate of transcription?

enhancers

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64

How many regulatory sequences are there?

2, enhancers and silencers

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65

what is the effect of binding the repressor TF?

Decreasing rate of transcription, silencer

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66

What transcription factor is needed to start transcription in all cells?

General (Basal) transcription factor

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67

What transcription factor binds to DNA region called enhancers, silencers or promoter proximal elements?

Regulatory transcription factors

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68

What transcription factor binds to core promoter?

General (Basal) transcription factor

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69

Which transcription factor can increase or decrease levels of transcription?

regulatory transcription factors

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70

Basal TFs together with RNA polymerase form ______ _________ _________ that assembles near the start site on the promoter.

Basal transcription apparatus

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71

Which transcription factor is responsible for expression of particular genes?

regulatory transcription factors

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72

What is sufficient to initiate minimal levels of transcription?

basal transcription apparatus (RNA polymerase + Basal TFs)

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73

TF stands for...

transcription factors

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74

What are the 3 regulatory mechanisms that must occur before the final product appears?

  1. different ways of splicing the same primary transcript

  2. altering availability of mRNAs (translate or destroy)

  3. altering protein activity after translation has occurred

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75

These proteins bind to genes at sites known as enhancers and speed the rate of transcription.

activators

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76

these proteins bind to selected sets of genes at sites known as silencers and thus slow transcription.

repressors

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77

These adaptor molecules integrate signals from activators and perhaps repressors.

coactivators

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78

in response to injunctions from activators, these factors position RNA polymerase at the start of the coding region.

basal transcription factors

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79

post translational regulation allows cells to respond to:

new conditions rapidly

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80

Cells keep an _________ protein waiting.

inactive

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81

inactive proteins can quickly activate in response to:

altered conditions

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82

In eukaryotic gene expression, the step that most prokaryotes do not use is:

RNA processing

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83

A mutation occurs that reduces the effect of an enhancer for a set of genes. What would be reduced?

the amount of protein produced by the set of genes

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84

Alternative splicing during gene expression occurs only inside the nucleus in:

eukaryotes

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85

Rats that are the offspring of parents that were raised with poor nutrition have a greater chance of developing disorders similar to type 2 diabetes, regardless of the alleles they inherit. This shows that __________ ____ ______ ___________ may be inherited.

patterns of gene expression

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86

Which of the following types of gene expression regulation occurs in eukaryotes but is rare or non-existent in prokaryotes?

a.coordinating transcription by organizing genes into operons

b. alternative splicing of primary transcripts

c. phosphorylating proteins to activate them

d. using proteins to help RNA polymerase bind and start transcription

alternative splicing of primary transcripts

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87

Evolution explains how life __________, not how life __________.

changes, started

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88

Theory of evolution states that:

all species are related and gradually change over time confirmed through observations and experiments

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89

Macroevolution:

major changes among living organisms over long periods of time

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90

microevolution

changes in population of a species over a shorter time period

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91

Charles Darwin described evolution as:

descent with modification

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92

Who created the theory of evolution?

Charles Darwin

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93

The branching evolution history of species or other major groups of organisms is called ___________.

phylogeny

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94

A ____________ ________ is a simplified diagram of the branching evolution history of species or other major groups of organisms.

phylogeny tree

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95

What is a species?

classification of organisms

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96

___________ is the scientific method of classifying and naming organisms by grouping them by shared traits or characteristics.

taxonomy

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97

taxonomic unit in the biological system of classification

taxon

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98

examples of taxons:

species or genus

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99

Categories of taxonomic hierarchy in order from largest to smallest:

Domain Kingdom Phylum Class Order Family Genus Species

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100

Human Domain

Eukarya

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