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BIO 1306 Spring 2025 > Chapter 21 - Genomes & their Evolution > Flashcards

Chapter 21 - Genomes & their Evolution Flashcards

1
Q

Definition of Genome

A

An entire set of DNA instructions found in a cell (required for development & functions of organisms)

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2
Q

How much of DNA is noncoding?

A

98.5%

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3
Q

What percentage of genes are for proteins & RNA?

A

1.5%

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4
Q

(1990) Human Genome project purpose

A

to determine the complete nucleotide sequence of each chromosome

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5
Q

(Human Genome project) Who was the molecular biologist that sequenced the entire genome using an alternative whole-genome shotgun approach?

A

J. Craig Venter

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6
Q

What is the whole-genome shotgun approach (WGS)?

A

He used cloning & sequencing of DNA fragments followed by assembly into a single continuous sequence via tech

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7
Q

What is J. Craig Venter associated with?

A

– Sequenced entire human genome
– Whole-genome shotgun approach (WGS)

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8
Q

When was the human genome published?

A

2006

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9
Q

What does WGS do?

A

Sequence data from a given organism

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10
Q

Step 1 of WGS

A
  1. Cut the DNA into overlapping fragments short enough for sequencing
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11
Q

Step 2 of WGS

A
  1. Clone the fragments in plasmid (can clone, transfer, & manipulate genes) or other vectors
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12
Q

What is plasmid?

A

A small, circular double-stranded DNA molecule. They’re used as tools to clone, transfer, and manipulate genes.

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13
Q

Step 3 of WGS

A

Sequence each fragment (arrange in a particular order)

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14
Q

Step 4 of WGS

A

Order the sequences into 1 overall sequence w/ computer software

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15
Q

Today, WGS is still used, but newer techniques are contributing to…

A

…the faster pace & lowered cost of genome sequencing

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16
Q

“Next-Generation” techniques

A

–Don’t require cloning step
–Facilitates metagenomics approach
–Can generate large amt of data in short time

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17
Q

Tf does metagenomics do?

A

It can generate large amounts of data in a short time & DNA from a group of species in an environmental sample is sequenced (so it’s like WGS except it has an automatic sorter for different creatures’ DNA)

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18
Q

What is metagenomics

A

the study of the structure and function of entire nucleotide sequences isolated and analyzed from all the organisms (typically microbes) in a bulk sample (usually for studying specific community of microorganisms)

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19
Q

What is Genomics?

A

the study of whole sets of genes & their interactions

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20
Q

Complete ________ exist for human, chimps, E. coli, brewer’s yeast, corn, fruit fly, elephant shark, and many other organisms.

A

…genome sequences…

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21
Q

Comparisons of genomes among organisms provide…

A

…insights into evolution & other biological processes

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22
Q

Scientists use ______ to analyze genomes & their functions

A

…bioinformatics…

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23
Q

What is Bioinformatics?

A

Storage, analysis, and distribution of biological data, most often DNA & amino acid sequences

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24
Q

Bioinfo resources are provided by several internet sources, which are…

A

–(NLM) National Library of Medicine & (NIH) National Institutes of Health maintains the (NCBI) National Center for Biotechnology Information
–European Molecular Biology Lab
–DNA Data Bank of Japan
–BGI in Shenzhen, China

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25
GenBank __________ is constantly updated w/ the data it contains increasing rapidly
...the NCBI database of sequences...
26
what does NCBI's "BLAST" stand for?
Basic Local Alignment Search Tool
27
What does NCBI BLAST let peeps search for/do?
--specific DNA sequence --predicted protein sequence --common stretches of amino acids in a protein --3-D protein structures --The ability to compare a DNA sequence in GenBank, base by base --Sequence for conserved(common) stretches of amino acids(domains) for which a function is known or suspected
28
What are domains (amino acids)?
Distinct functional and/or structural units in protein/DNA --usually responsible for particular function/interaction
29
What is Proteomics/Systems biology?
An approach to studying large sets of proteins & their properties
30
What's a proteome?
The entire set of proteins expressed by a cell/group of cells
31
Scientists have begun to compile catalogs of genes & proteins and focus on...
...their functional integration in biological systems
32
Computer software can...
...map genes to produce a network-like "functional map" of their interactions (genes & proteins)
33
What is Gene Annotation?
The identification of protein-coding genes w/in DNA sequences in a database (automated)
34
What do computers for during gene annotation?
translational start, stop signals, RNA splicing sites, promoter sequences, etc.
35
Comparison of sequences w/ unknown... ...may help provide clues abt their function
...genes w/ those of known genes in other species...
36
Functional studies involving ____ the gene function can show how the phenotype is altered
...knocking out...
37
The Cancer Genome Atlas project was completed in 2018 w/ publications called the...
...Pan-Cancer Atlas
38
Cancer Genome Atlas project significance?
--many interacting genes & gene products were analyzed together as a group --Pan-Cancer Atlas contributed significantly to understanding how, where, and why tumors arise
39
______ on glass/silicon chips and, increasingly, RNA-seq are used to analyze gene expression in patients with cancers/other diseases.
DNA microarrays...
40
...lets physicians to tailor treatment to unique genetic makeup of patient & cancer
Analyzing which genes are over/underexpressed in a cancer...
41
Genomes of most bacteria & archaea range from...
1-6 million base pairs (Mb)
42
What does Mb stand for?
Million base pairs
43
Free-living bacteria & archaea have...
1500-7500 genes
44
______ ...genomes tend to be larger
Eukaryotic...
45
Most plants & animals tend to have genomes greater than...
100 Mb
46
Humans have...
3000 Mb
47
of genes is NOT proportional to...
...genome size in eukaryotes
48
Multicellular eukaryotes have a lot of...
...noncoding DNA & many multigene families
49
_____ & ______ have the lowest gene density/# of genes in a given length of DNA
Humans & mammals
50
Multicellular eukaryotes have many introns w/in genes and a large amount of _____ btwn genes
modeling DNA (non-coding DNA that doesn't code protein/filler material in genes)
51
Sequencing of human genome revealed that __ doesn't code for proteins, rRNAs, or tRNAs
98.5%
52
_______ & ________ account for 5% & 20%, respectively, of the human genome
Gene regulatory sequences (5%) & introns (20%)...
53
Noncoding DNA found btwn genes includes...
Pseudogenes & repetitive DNA
54
What are psuedogenes?
former genes that accumulated mutations & are nonfunctional
55
Repetitive DNA is present in ___ ____ in the genome
...multiple copies...
56
A high lvl of _________ in some noncoding DNA among humans, rats, and mice suggests that these regions have IMPORTANT functions
...sequence conservation...
57
Prokaryotes & eukaryotes have stretches of DNA that can move from 1 place to another w/in the genome called...
...transposable elements
58
Abt _____ is made up of transposable elements
...75% of human repetitive DNA...
59
1st evidence of transposable/mobile elements came from _____ breeding experiments w/ Indian corn (maize)
...Barbara McClintock's...
60
Duplication, rearrangement, and mutation of DNA contribute to...
...genome evolution
61
The basis of change @ the genomic lvl is...
...mutation, which underlies much of genome evolution
62
THe size of genomes has increased over evolutionary time, w/ the extra genetic material providing raw material for...
...gene diversification
63
Accidents in ____ can lead to extra chromosomes (AKA polyploidy)
...meiosis...
64
The genes in one or more of the extra sets of chromosomes can diverge by accumulating...
mutations
65
These variations (aka mutations) may persist if the organism carrying them...
...survives & reproduces
66
Unequal crossing over during _____ can result in one chromosome w/a deletion and another w/ a duplication of a particular region
...prophase 1 of meiosis...
67
Transposable elements can provide _____________ btwn non-sister chromatids
...sites for crossover...
68
Transposable elements may carry ________ to a new position
...a gene/groups of genes...
69
Multiple copies of similar transposable elements facilitate...
...recombination/crossing over btwn different chromosomes
70
Transposable elements may create...
...new sites for alternative splicing in an RNA transcript
71
Insertion of trans elements w/in a protein-coding seq may block...
...protein production
72
Insertion of trans elements w/in a _______ may inc/dec protein production bc (1) genes in one or more of the extra sets can diverge by accumulating mutations, (2) variations may persist if organism survive & reproduce, and (3) genes w/ novel functions can evolve bc of 1 & 2
...regulatory sequence...
73
The rest of the genes occur in ________ collections of 2 or more identical/very similar genes
...multigene families...
74
example of multigene families of NONIDENTICAL genes:
alpha globins & beta globins are hemoglobin polypeptides coded by genes on different human chromosomes and are expressed at different times in developments. The genes for the different globin proteins evolved from one common ancestor, which duplicated & diverged after the accumulation of mutations
75
Humans have 23 pairs of chromosomes while chimps have...
24
76
Following the divergence of humans & chimps from a common ancestor, _______________ fused in the human line
...2 ancestral chromosomes...
77
Chromosomal rearrangements are thought to contribute to...
...the generation of new species
78
One copy of a duplicated gene can undergo mutations/alterations that lead to a...
...completely new function for the protein product
79
Example of a mutated duplicated gene w/ a new function:
lysozyme gene duplicated & evolved into smth that encodes alpha-lactalbumin in mammals (nonenzymatic protein related to milk-production in mammals)
80
What is lysozyme?
an enzyme that helps protect animals against bacterial infection
81
Highly conserved genes have changed...
...very little over time & can be studied in one model organism and the results apply to other organisms
82
What does FOXP2 gene do?
regulates genes that function in vocalization in vertebrates
83
What do mutations in FOXP2 cause?
severe language & speech impairment in humans
84
Mice w/ "disrupted" FOXP2 gene have...
...malformed genes & fail to emit normal ultrasonic vocalization
85
What does evolutionary developmental biology (evo-devo) do?
Compares developmental processes of different multicellular organisms
86
What are Homeotic genes/Hox genes?
encode transcription factors w/a DNA-binding domain called a homeo box & regulate development of body plan
87
An identical/very similar nucleotide seq discovered in hox genes of...
...both vertebrates & invertebrates as well as other developmental genes that are highly conserved from species to species

BIO 1306 Spring 2025 (5 decks)

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