Comprehensive Study Guide for BIOL 5330 Final Exam

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1
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EXAM 1: Which of the following is the correct order of parts of a gene?

a) Promoter - Start Codon - Exon - Intron - Stop Codon

b) Promoter - Start Codon - Intron - Exon - Stop Codon

c) Start Codon - Promoter - Intron - Exon - Stop Codon

d) Promoter - Intron - Exon

a) Promoter - Start Codon - Exon - Intron - Stop Codon

2
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EXAM 1: An alternative form of a given gene at a single locus, which differs in DNA sequence and often results in altered protein expression is known as ______.

allele

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EXAM 1: The observable properties of a trait is known as ________; while the genetic properties that produce a trait is known as its ________.

1. Phenotype

2. Genotype

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EXAM 1: Which of the following is NOT a functional domain/motif found in proteins?

a) DNA binding domain

b) cellular targeting sequence

c) transmembrane domain

d) ligand domain

e) all of the above

d) ligand domain

5
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EXAM 1: True or False? Heritable changes in gene expression that are NOT due to changes in DNA sequence could be due to epigenetic effects.

True

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EXAM 1: Which of these are common epigenetic mechanisms we discussed in lecture?

a) regular non-coding RNAs (RNAi)

b) methylation

c) histone modifications

d) all of the above

d) all of the above

7
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EXAM 1: True or False? A "loss of function" mutation has reduced a complete lack of normal gene function in control to a "gain of function" mutation that has gained or added a novel gene function.

True

8
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EXAM 1: True or False? Mutagens produce different types of mutations in DNA

True

9
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EXAM 1: True or False? One key point in the regulations of many transcription factors is localization to the mitochondria.

False

10
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EXAM 1: True or False? Dimerization commonly plays a part of signal transduction pathways

True

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EXAM 1: True or False? Inhibition and Activation can occur as part of the same signaling pathway

True

12
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EXAM 1: True or False? Some signaling pathways act over long distances

True

13
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EXAM 1: True or False? Experimental methods examining RNA expression levels do not directly examine protein levels

True

14
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EXAM 1: Which of the following are advantageous reasons for having phosphorylation in a signal transduction pathway?

a) new proteins do not need to be synthesized

b) it is easily reversible

c) it can occur quickly

d) all of the above

d) all of the above

15
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EXAM 1: A primary use of mutants by scientists in genetic studies is to help determine what?

The function of a gene

16
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EXAM 1: Match the following alternations of the wild-type DNA sequence ATTGCAGCT with the type of mutation:

ATAGCT

deletion

17
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EXAM 1: Match the following alternations of the wild-type DNA sequence ATTGCAGCT with the type of mutation:

ATTCAGCT

deletion

18
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EXAM 1: Match the following alternations of the wild-type DNA sequence ATTGCAGCT with the type of mutation:

ATGTCAGCT

transposition

19
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EXAM 1: Match the following alternations of the wild-type DNA sequence ATTGCAGCT with the type of mutation:

ATTGCTCAAGCT

insertion

20
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EXAM 1: Match the following alternations of the wild-type DNA sequence ATTGCAGCT with the type of mutation:

AGTGCAGCT

substitution

21
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EXAM 1: Which of these listed below is NOT a general type of mutation?

a) frameshift

b) adaptive

c) reversion

d) conditional

e) lever

e) lever mutation

22
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*** EXAM 1: Effects of this mutation type can be stronger than a null mutation with complete loss of gene function

Dominant Negative

23
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EXAM 1: Match the name with the described function: Reporter/Marker

Ability to track expression of a gene

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EXAM 1: Match the name with the described function: Overexpression

Determine effects of too much ...

25
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EXAM 1: Match the name with the described function: RNAi or Antisense

determine effects of reducing gene expression

26
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EXAM 1: Match the name with the described function: TAG

ability to track expression of a protein

27
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EXAM 1: When conducting a mutagenesis screen-- looking for a defect in a specific phenotype regardless of the particular gene involved is know as a ___________

Forward genetic screen

28
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EXAM 1: Why use Homologous recombination or CRISPR instead of other methodologies to generate transgenic organisms?

Selectable Gene Targeting

29
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EXAM 1: Which of the following might be a reason that you would decide to make a condition or inducible version of a transgenic organism?

a. all of these are good answers

b. you could control the gene expression in a specific spatial pattern

c. you could control the gene expression in a specific manner

d. you could control the gene expression in a specific temporal manner

a. all of these are good answers

30
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EXAM 1: Enhancer elements can function by ___________

act on gene transcriptions from a distance of over 10,000 base pairs away

31
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EXAM 1: This is NOT a feature of cis-regulatory elements?

Often composed of 5-25 amino acids

32
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EXAM 1: Which of these is a major transcription factor class or family we discussed?

a. lecine finger

b. beta scaffolding

c. zinc finger

d. helix-binding

b. beta scaffolding

33
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EXAM 1: Which of these is NOT a major signaling pathway involved in development?

a) alpha kinase

b) hedgehog

c) g-protein

d) beta-kinase

e) all of the above

f) alpha & beta kinase

f) alpha & beta kinase

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EXAM 1: The Receptor Tyrosine Kinase (RTK) signaling pathway repeatedly makes use of which of the following processes in its signaling?

Phosphorylation

35
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EXAM 1: what is a standard outcome at the end of a general transcription factor signaling pathway?

gene expression is activated

36
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EXAM 1: what is a feature of the Notch signaling pathway that makes it different from the other signaling pathways that we discussed?

both the receptor becomes part of the signal pathways and the ligand a membrane spanning proteins

37
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EXAM 1: Which of the following is NOT a mechanism for eliminating a signal in a signal transduction pathway once that signal has been initiated?

a) paracrine/autocrine loop

b) destruction of the receptor

c) negative signal of feedback loop

d) sequestration of the receptor

a) paracrine/autocrine loop

38
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EXAM 1: This mechanism for maintaining a signal from a signal transduction pathway involves the activation of a signal from one cell, which then activates its neighboring cell, which then activates a signal in the original cell.

Paracrine loop

39
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EXAM 1: Name and order the FOUR major parts of a general transcription factor signaling pathway

1. ligand

2. receptor

3. signaling cascade

4. transcription factors

40
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EXAM 1. Which of the parts of signal transduction pathway is most likely to be the most complex?

3. signaling cascade

41
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EXAM 1: match the characteristic or feature with whether it is likely to be found in a Model System or a Non-Model system.

A unique organism characteristic

Non-Model System

42
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EXAM 1: match the characteristic or feature with whether it is likely to be found in a Model System or a Non-Model system.

Sequenced and well annotated genome

Model System

43
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EXAM 1: match the characteristic or feature with whether it is likely to be found in a Model System or a Non-Model system.

Large Physical Size

Non-Model System

44
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EXAM 1: match the characteristic or feature with whether it is likely to be found in a Model System or a Non-Model system.

Large Number of Progeny

Model System

45
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EXAM 1: match the characteristic or feature with whether it is likely to be found in a Model System or a Non-Model system.

Abnormal Genetics

Non-Model System

46
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EXAM 1: Match the characteristic to whether it would be General or Specific.

Ease of Use

General

47
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EXAM 1: Match the characteristic to whether it would be General or Specific.

Rapid Generation Time

Specific

48
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EXAM 1: Match the characteristic to whether it would be General or Specific.

Readily Available

General

49
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EXAM 1: Match the characteristic to whether it would be General or Specific.

Ease of Data Generation

General

50
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EXAM 1: Match the characteristic to whether it would be General or Specific.

Large Numbers of Progeny Produced

Specific

51
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EXAM 1: Match the characteristic to whether it would be General or Specific.

Genome Sequenced and Annotated

Specific

52
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EXAM 1: Indicate the Model System where each characteristic is a positive.

Short life cycle

Caenorhabditis elegans

53
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EXAM 1: Indicate the Model System where each characteristic is a negative.

Short life cycle

Mus musculus - mouse

54
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EXAM 1: Indicate the Model System where each characteristic is a negative.

Easy to care for

Mus musculus

55
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EXAM 1: Indicate the Model System where each characteristic is a positive.

Easy to care for

Drosphila melanogaster

56
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EXAM 1: Indicate the Model System where each characteristic is a positive.

Ability to see internal organs

Caenorhabditis elegans

57
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EXAM 1: Indicate the Model System where each characteristic is a negative.

Ability to see internal organs

Drosphila melanogaster

58
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EXAM 1: Which of the following is NOT an important factor to consider when designing a mutagenesis screen as we discussed?

a) mutation rate

b) organism

c) type of gene or phenotype

d) mechanisms of mutant screening

e) all of the above

e) all of the above

59
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EXAM 1: This is a common feature used in the generation of transgenic organisms to help determine if it was successfully made transgenic?

A marker that can easily be selected

60
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*** EXAM 2: Name the different tissue layers that are responsible for forming each of the following tissues/organ.

Digestive System or Gut

endoderm

61
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*** EXAM 2: Name the different tissue layers that are responsible for forming each of the following tissues/organ.

Circulatory System & Muscles

Mesoderm

62
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*** EXAM 2: Name the different tissue layers that are responsible for forming each of the following tissues/organ.

Nervous system & Skin

Ectoderm

63
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EXAM 2: Why is it important for an organism to override an initial establishment of axis determination in a developing embryo?

In order to properly orient the developing organism to the enviornment

64
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EXAM 2: Gastrulation involves the migration of cells which can occur in different patterns, yet during this process there is always the formation of a set of common layers known as?

Germ Layers

65
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EXAM 2: Which of the following becomes the cue for default axis determination if all environmental cues are eliminated from a developing embryo?

Site or Sperm Entry in the Egg

66
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*** EXAM 2: True or False? Transcription factors, such a B-catenin in Sea Urchin, often play an important role during early embryo development

True

67
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EXAM 2: True or False? The first organ produced during organogenesis is an ANIMAL in the GUT

False

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EXAM 2: True or False? Fertilization, as a developmental stage consists of MORE than one step/stage.

True

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EXAM 2: True or False? Three basic tissue systems are established in the development both of plants and animals

True

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EXAM 2: The neural tube formed during neurulation originates from what germ layer?

Ectoderm

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EXAM 2: Name two different types of cell movements we discussed that occur during gastrulation

1. Delamination

2. Epiboly

72
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EXAM 2: Which of the following best describes a meristem?

a. a group of stem cells

b. a region of the embryo that produces the epidermis

c. any plant cell with nucleus

d. a region of the plant containing stem cells where nearly all tissues & organs are derived.

e. all of the above

d. a region of the plant containing stem cells where nearly all tissues & organs are derived.

73
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EXAM 2: Which of the following is NOT true about fate maps?

a. can only be made over the entire development of an organism

b. easier to generate in embryos

c. provide a lineage of cells from an early to later stage of development

d. construction require detailed understanding of the organism

a. can only be made over the entire development of an organism

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EXAM 2: Which of the following is NOT a method or tool that has been used to construct fate maps?

a. realtime PCR

b. genetic markers

c. fluorescence dyes

d. physical alteration of cells

a. realtime PCR

75
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*** EXAM 2: General mechanisms involved in regulating morphogen gradients that we discussed in lecture.

Possible Final Question: Morphogen gradients are regulated by a number of different mechanisms. List 3.

1. Cross Repression

2. Positive Feedback

3. Feed Forward Loop

76
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EXAM 2: Which of the following is required to differentiate cells with a single morphogen?

a. presence of a morphogen gradient

b. morphogen response genes with different thresholds

c. all of these answers are essential

d. morphogen gradient responsive genes

e. presence of a morphogen

c. all of these answers are essential

77
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EXAM 2: Which of the following is NOT one of the 4 maternal gene systems involved in coordinating control of embryo polarity in Drosphila?

a. dorsal-ventral system

b. anterior/posterior system

c) terminal system

d) segment system

d) segment system

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EXAM 2: True or False? Multiple segment formation that divides a Drosphila embryo during developmental is a process that requires a single morphogen gradient.

False; requires MORE than one.

79
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EXAM 2: True or False? Homeotic genes are key factors in evolutionary development because they can change identities of entire body parts of segments.

True

80
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EXAM 2: Molecular parsimony is a process where duplicated genes can diverge in different ways. Name One outcomes:

1. gene loss

others:

2. degeneration

3. neofunctionalization

4. subfunctionalization

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*** EXAM 2: Homologs are genes related to each other evolutionary. _______ are genes in different species that have evolved from a common ancestral gene through speciation, while ______ are genes within a genome that have occurred by gene duplication.

1. Orthologs

2. Paralogs

82
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*** EXAM 2: There are 5 different general pathways we discussed by which environmental factors can alter phenotypes through differential gene expression, name 3:

1. Indirect Activation

2. Direct Activation

3. Modification of Genes

Others:

4. Methylation

5. Direct Activation or Signaling Pathways

83
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*** EXAM 2: Macroevolutionary patterns of changes occur through changes in gene function or changes in gene expression.

Name 3 different types of changes in gene expression that lead to standard evolutionary developmental patterns of change

1. Heterotopy

2. Heterochromy

3. Heterotypy

Others: Heterometry

84
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EXAM 2: Match all 6 points of the three major animal body axes.

1. Dorsal

2. ventral

3. Lateral-Right

4. Lateral-Left

5. Anterior

6. Posterior

<p>1. Dorsal</p><p>2. ventral</p><p>3. Lateral-Right</p><p>4. Lateral-Left</p><p>5. Anterior</p><p>6. Posterior</p>
85
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*** EXAM 2: Match the Developmental Stage to the best set of corresponding events.

Formation of the notochords

Neurulation

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*** EXAM 2: Match the Developmental Stage to the best set of corresponding events.

Fusion of male & female gametes

Fertilization

87
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*** EXAM 2: Match the Developmental Stage to the best set of corresponding events.

Formation of advanced organ structures

Organogenesis

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*** EXAM 2: Match the Developmental Stage to the best set of corresponding events.

Formation of the germ layers

Gastrulation

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*** EXAM 2: Match the Developmental Stage to the best set of corresponding events.

Rapid cell division

Cleavage

90
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EXAM 2: What are the two different correct ways you could end up with a "French Flag" coloring-like phenotype in an embryo based on one morphogen and two thresholds.

1. Red default. White activated above B (covers red), Blue activated above A covers both Red and White

2. Blue default, Blue repressed below A and White activated, White repressed below B and Red activated

<p>1. Red default. White activated above B (covers red), Blue activated above A covers both Red and White</p><p>2. Blue default, Blue repressed below A and White activated, White repressed below B and Red activated</p>
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P.FINAL: Select the correct order of parts in a typical gene

5' UTR, Promoter, Exon, Intron, Exon, 3' UTR

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P.FINAL: ___________ is the observable properties of an organism produced by its genotype

Phenotype

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P.FINAL: a major reason we discussed for studying changed in phenotypes in mutant organisms is to determine the function of the mutated ___________

Gene

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P.FINAL: indicate whether the following are terms used to describe either a gene or protein:

Promoter

Gene

95
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P.FINAL: indicate whether the following are terms used to describe either a gene or protein:

Transmembrane Domain

Protein

96
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P.FINAL: indicate whether the following are terms used to describe either a gene or protein:

TATA Box

Gene

97
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P.FINAL: indicate whether the following are terms used to describe either a gene or protein:

Cellular Targeting Sequence

Protein

98
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P.FINAL: the effect of this type of mutation can be more adverse or detrimental than a null mutation in which there is complete loss of gene function

dominant negative

99
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P.FINAL: a major reason we discussed for studying changes in phenotypes in transgenic organisms is to determine the function of the altered _________

gene

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P.FINAL: Which of the following is a specific benefit of using CRISPR methodology in genetics research?

a. single DNA strand replacement

b. site directed DNA editing

c. nuclear targeting

d. promotor editing

e. the ability to stop epigenetic effects

b. site directed DNA editing