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AP Biology Mr. Maiorana > Chapter 18-21 test > Flashcards

Chapter 18-21 test Flashcards

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1
Q

What are genomics?

A

An approach where scientists can study whole sets of genes and their interactions

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2
Q

What is bioinformatics?

A

the application of computational methods to the storage and analysis of biological data

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3
Q

What is the whole genome shotgun approach?

A

An approach to sequencing the human genome that starts with cloning and sequencing of DNA fragments from randomly cut DNA. Powerful computer programs then assemble the large number of overlapping short sequences into a single continuous sequence

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4
Q

Which 2 processes helped complete the sequencing of the whole human genome?

A

The initial methodical approach built on a storehouse of human genetic info and the whole-genome shotgun approach

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5
Q

What are the most modern sequencing techniques and how do they work? How is it different from the whole genome shotgun approach

A

Sequencing by synthesis. Many very small base pair fragments are sequenced at the same time. Cloning is not required, unlike the whole genome shotgun approach

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6
Q

What is metagenomics?

A

DNA from a group of species is collected from an environmental sample and sequenced

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7
Q

How is protein function that an unknown gene codes for determined?

A

Biochemical studies are done on the 3 dimensional structure to locate binding sites and other attributes. Functional studies are done to see how blocking or disabling the gene to see how phenotype is affected

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8
Q

What is proteomics?

A

An approach where scientists study full sets of proteins encoded by genomes

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9
Q

What is the systems biology approach? How is this approach made possible?

A

An approach that aims to model the dynamic behavior of whole biological systems based on the study of interactions among the system’s parts. This approach is made possible by bioinformatics because of the large amount of information involved

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10
Q

What is the typical genome size range for archaea and bacteria? how does this compare to eukaryotic genomes?

A

1-6 million base pairs. Eukaryotic organisms have much bigger genomes

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11
Q

Which eukaryotes have a large range of genome sizes and which dont?

A

Protists, insects, amphibians and plants have a large range of genome size and mammals and reptiles have a smaller range

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12
Q

Does genome size reveal anything about phenotype in eukaryotes?

A

no

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13
Q

Why is the number of genes in eukaryotes usually lower than expected?

A

They have large genomes, but not as many genes as base pairs

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14
Q

What allows organisms with a larger genome to get away with having the same number of genes as organisms with a much smaller genome?

A

Organisms with bigger genomes use more RNA splicing and get “more bang for their buck”, they make more proteins with fewer genes. Post translational modifications add diversity, and miRNAs and other small RNAs that serve as regulators add variety

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15
Q

Which organisms have the highest and lowest gene densities?

A

Eukaryotes have lower densities, other less complex organisms have higher densities

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16
Q

Why do eukaryotes have lower gene density?

A

They have more introns(noncoding DNA) and more non protein coding DNA between genes

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17
Q

How much of the human genome is gene related regulatory sequences and introns? What is the rest?

A

5%-20%. The rest is unique noncoding DNA such as fragments and pseudovenes(including repetitive genes)

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18
Q

What are pseudogenes?

A

Former genes that accumulated mutations over a long period of time and no longer produce functional proteins

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19
Q

What is most of repetitive DNA made up of?

A

transposable elements and sequences related to them

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20
Q

Which evidence suggests that noncoding DNA is important?

A

The high degree of sequence conservation between species.

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21
Q

What does genome organization tell us?

A

It tells us about how genomes evolved and continue to evolve

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22
Q

What are transposable elements?

A

Stretches of DNA present in Eukaryotes and prokaryotes that can move from one location to another in the genome in a process called transposition

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23
Q

How does transposition work?

A

The original and new DNA sites are brought close together by enzymes, the elements never completely detach from the cell’s DNA

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24
Q

Who discovered transposable elements and how?

A

Barbara McClintock, she identified changes in colors of corn kernels that only made sense of transposable elements existed

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25
Q

What are the type types of transposable elements?

A

Transposons: can move within the genome by means of a DNA intermediate by cut and paste or copy and paste

Retrotransposons: can move by means of an RNA intermediate that is a transcript of retrotransposon DNA, always leave a copy behind

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26
Q

Which enzymes is involved with transposons?

A

transposase

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27
Q

What are Alu elements?

A

A family of transposable element sequences that are about 300 nucleotides long(shorter than most functional transposable elements) and they do not code for protein. Many of these elements are transcribed into RNA of unknown function(if any)

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28
Q

What is LINE-1? compare to Alu family

A

Aka L1, these are retrotransposons that are much longer than Alu elements, about 6500 base pairs long. They have a low rate of transposition

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29
Q

What are some possibilities of the function of L1?

A

They effect gene expression, potentially in developing neurons

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30
Q

How does repetitive DNA, excluding transposable elements, arise? How much of the human genome consists of these genes?

A

Mistake during DNA replication or recombination. These make up 14% of the human genome

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31
Q

What is simple sequence DNA?

A

Many copies of repeated, short DNA sequences

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32
Q

What is Short tandem repeat?

A

(STR) When the unit of repeating nucleotides in simple sequence DN contains 2-5 nucleotides

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33
Q

What is a genetic profile?

A

The diversity in the number of repeating nucleotide sequences in repetitive DNA, unique to each individual since humans are diploid

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34
Q

How much of he human genome is made up of simple sequence DNA? Where are these genes usually found and why is this important?

A

3%, located at the chromosomal telomeres and centromeres, suggesting that this DNA plays a structural role and helps organize chromatin in the interphase in the nucleus(centromeres) and prevents telomere degredation

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35
Q

What are multigene families?

A

Collections of two or more very identical genes

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36
Q

What are the characteristics of multigene families with identical and nonidentical DNA sequences?

A

Identical: Clustered tandemly and have RNAs as final products(except for histone protein genes)

Nonidentical: effect gene expression by expressing versions of the same genes at different times

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37
Q

How are new species formed?

A

Meoitic accidents resulting in different numbers of chromosomes

38
Q

What is evidence of unequal crossing over and template slippage?

A

multigene families

39
Q

What are examples of genes where a gene was altered to the point where it had a totally different section?

A

genes for lysozyme and a-lactalbumin

40
Q

What is an example of genes evolving with related functions?

A

Globin families

41
Q

What are domains?

A

Functional regions of proteins, coded for by exons

42
Q

What is in example of a protein coding gene with multiple copies of exons?

A

collagen

43
Q

How do transposable elements contribute to genome evolution?

A

Promote recombination, disrupt cellular genes/control elements and carry entire genes/exons to new locations

44
Q

What do transposable elements of similar sequence do?

A

They facilitate recombination between different chromosomes by providing homologous regions for crossing over

45
Q

What is a benefit of comparing closely related species?

A

The genes of one species can accelerate the gene mapping of another species

46
Q

Which genes tend to evolve fastest?

A

Genes coding for transcription factors

47
Q

What is FOXP2?

A

A transcription factor that functions in vocalization of vertebrates and is said to be rapidly evolving

48
Q

What are single nucleotide polymorphisms?

A

(SNP’s) Single base pair sites where variation is found in at least 1% of the population

49
Q

What is evo-devo?

A

the field of evolutionary developmental biology

50
Q

What is a homeobox?

A

a 180 nucleotide sequence that specifies a 60 amino acid hemeodomain. These have to do what body development

51
Q

How do genes with homeodomains regulate development?

A

Coordinating the transcription of batteries of developmental genes, switching them on or off

52
Q

What is the Hox gene?

A

A gene responsible for development of of axes in insects and crustaceans, it also turns on different genes at different times in different species

53
Q

What is the formal definition of evolution?

A

descent with modification

54
Q

What is scala naturae?

A

A scale that aristotle concluded that all life could be placed on in terms of complexity and each organism had its own fixed rung on the ladder

55
Q

What did Carolus Linneaus do? How did Darwin argue this?

A

He developed a two part format to naming species in terms of similarity into increasingly general categories. Darwin argued that classification should be based on evolutionary relationships and that scientists using the Linnaean system often group organisms this way

56
Q

What are strata?

A

layers of sedimentary rock in which fossils are usually found

57
Q

What do Georges Cuvier do?

A

He examined strata and noticed that species in older ones were dissimilar to newer ones and that each new sediment layer was a catastrophic event. He inferred that extinctions were common and that new organisms migrated to replace old ones

58
Q

What did James Hutton and Charles Lyell do?

A

They proposed that geological events slowly changed earth over time continuously

59
Q

What two principles did Lamarck use to explain his findings that were accepted at the time

A
  1. Use and disuse

2. Inheritance of acquired characteristics

60
Q

What book did Darwin write and publish his natural selection theory in?

A

On the origin of species by means of natural selection, aka The origin of species

61
Q

What is artificial selection?

A

Modifying species over many generations by selecting individuals with desired traits

62
Q

What are Darwin’s 2 observations/inferences?

A

Observation 1: Members of a population often vary in inherited traits

Observation 2: All species can produce more offspring than their environment can support and many of these offspring fail to survive

Inference 1: Individuals whose inherited traits give them a better chance of surviving and reproducing in a given environment tend to leave more offspring than others

Inference 2: The unequal ability of individuals to survive and reproduce will lead to accumulation of favorable traits in the population over generations

63
Q

Who experiences evolution?

A

Populations(not individuals)

64
Q

How does methicillin work and which disease became immune to it?

A

It deactivates protein that bacteria use to synthesize their cell walls. MRSA became immune to it

65
Q

What is homology?

A

Similarity resulting from common ancestry

66
Q

What are homologous structures?

A

Structures that represent a variation on a structural theme that was present in a common ancestor

67
Q

What is convergent evolution?

A

the independent evolution of similar features in different lineages. This results in analogous resemblance

68
Q

What does endemic mean?

A

They are located in place and no where else in the world

69
Q

What are the pieces of evidence that support evolution?

A
  1. Direct observations of evolutionary change
  2. Homology
  3. The fossil record
  4. Biogeography
70
Q

What is phylogeny?

A

the evolutionary history of a species or group of species

71
Q

What is systematics?

A

A discipline focused on classifying organisms and determining their evolutionary relationships

72
Q

Who came up with the binomial, scientific naming system of naming organisms?

A

Carolus Linnaeus

73
Q

What is the order of taxonomy classifications from largest to smallest groups?

A 
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
74
Q

What is a taxon?

A

The named taxonomic unit at any level of hierarchy

75
Q

What is the flaw with Linnaean classification?

A

It doesnt reflect evolutionary history

76
Q

What are sister taxa?

A

groups of organisms that share an immediate ancestor, and are therefore each others closest relatives

77
Q

What does it mean if a phylogenetic tree is rooted?

A

The branch point farthest to the left represents the most recent common ancestor of the whole tree

78
Q

What is a basal taxon?

A

Taxon that diverges early in the history of a group

79
Q

What is a polytomy?

A

A branch point from which more than 2descendants emerge

80
Q

What is the point of phylogenetic trees? What can they be mistaken to reflect?

A

to reflect ancestry, no phenotype

81
Q

What are homoplasies?

A

Analogous structures that arose independelty

82
Q

How can you distinguish between analogous and homologous similarities?

A

More elements that are similar in 2 complex structures=homologous along with fossil evidence and ancestral genetic similarities

83
Q

What is cladistics and what are clades?

A

Cladistics is an approach in systematics where common ancestry is the primary criterion to classifying organisms. Biologists places species into groups called clades that include ancestral species and their descendants

84
Q

What does monophyletic, paraphyletic, and polyphyletic mean? Which one is equal to a taxon?

A

Monophyletic: clade consisting of an ancestor and ALL of its descendants. = to a taxon

Paraphyletic: consists of ancestral species and some of its descendants, most recent ancestor IS apart do the group

Polyphyletic: Includes taxa with different ancestors, most recent ancestor is NOT apart of group

85
Q

What is a shared derived character?

A

An evolutionary trait unique to a clade

86
Q

What is the outgroup and the ingroup?

A

Outgroup: species or group of species from an evolutionary lineage that is known to habe diverges before the lineage that includes the species being studied

Ingroup: Species being studied

87
Q

What is the principle of maximum parsimony?

A

A principle used to narrow the possibilities in a data set when making a phylogenetic tree, starting with the organism with the fewest evolutionary changes

88
Q

What is a molecular clock?

A

A concept that is an approach for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates assuming that number of nucleotide substitutions in related genes is proportional to the time that has elapsed since the genes branched from their common ancestor

89
Q

What causes differences in molecular clock speed?

A

Whether a gene change is neutral or not

90
Q

What are problems with molecular clocks?

A

They are very uncertain, especially when you go far back. They do not run smoothly because of natural selection and non neutral mutations.

91
Q

What is the horizontal gene transfer?

A

a process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infection, and fusions of organisms. This is how genes moved between organisms of different domains

AP Biology Mr. Maiorana (16 decks)

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