Genome Content (Lec 16)

Question 1

organization and sequence of genetic information contained within a genome is called what?

Answer 1

structural genomics

Question 2

approximate locations of genes, relative to the location of other genes, based on the rates of recombination is called what?

Answer 2

genetic maps

Question 3

what are the limitations of genomic maps?

Answer 3

low resolution or detail; do not correspond to physical distances between genes

Question 4

Define contig

Answer 4

a set of overlapping fragments that form a continuous stretch of DNA

Question 5

Define single-nucleotide polymorphisms

Answer 5

site in the genome where individual members of a species differ in a single base pair

Question 6

The specific set of SNPs and other genetic variants observed on a chromosome is called a what?

Answer 6

haplotype

Question 7

In regards to structural genomics determining the DNA sequences of entire genomes, the number of copies of DNA sequences (greater than 1000 bp) varies from people to people. This is referred to as?

Answer 7

copy-number variations

Question 8

In regards to structural genomics determining the DNA sequences of entire genomes, markers associated with DNA sequences that are expressed as RNA are called what?

Answer 8

expressed-sequence tags

Question 9

In regards to structural genomics determining the DNA sequences of entire genomes, molecular bio + computer science = ?

Answer 9

bioinformatics

Question 10

This aspect of structural genomics may include deletions or duplications; most contain multiple genes and potentially affect the phenotype; have been found to be associated with psoriasis schizophrenia, autism, and mental retardation

Answer 10

Copy-number variations

Question 11

This aspect of structural genomics may be obtained by isolating RNA from a cell and subjecting it to reverse transcription, producing a set of cDNA fragments; cDNA fragments are sequenced and the sequence identifies the DNA fragment

Answer 11

Expressed-Sequence tags

Question 12

How does a cDNA sequence differ from the genomic sequence?

Answer 12

no introns

Question 13

What is the Ab initio approach of bioinformatics?

Answer 13

scans sequence looking for features usually found within a gene

Question 14

What is the comparative approach of bioinformatics?

Answer 14

looks for similarity between a new sequence and sequences of known genes

Question 15

Define metagenomics

Answer 15

sequencing genomes of entire communities of organism- for example, the flora of the human gut

Question 16

Define synthetic biology

Answer 16

the creation from scratch novel organisms

Question 17

Define functional genomics

Answer 17

characterizes what the sequences do, The Encode project

Question 18

All the RNA molecules transcribed from a genome are called what?

Answer 18

transcriptome

Question 19

All the proteins encoded by the genome are called what?

Answer 19

proteome

Question 20

Genes that are evolutionary related are called what?

Answer 20

homologous

Question 21

Homologous genes in different species that evolved from the same gene in a common ancestor are called what?

Answer 21

orthologs

Question 22

Homologous genes arising by duplication of a single gene in the same organism are called what?

Answer 22

paralogs

Question 23

What is the difference between orthologs and paralogs?

Answer 23

orthologs are in different organisms; parallels are in the same organism

Question 24

In regards to gene expression and microarrays, using a known DNA fragment as a probe to find a complementary sequence is called what?

Answer 24

nucleic acid hybridization

Question 25

What is a reporter sequence?

Answer 25

encoding an easily observed product used to track the expression of a gene of interest

Question 26

What does a microarray consist of?

Answer 26

DNA probes fixed to a glass slide

Question 27

How can genes encoding a particular trait or function be identified?

Answer 27

mutagenesis screen

Question 28

In a mutagenesis screen, progeny with normal phenotypes are mated with wild type fish, the following progeny are ____ to reveal ____ mutations

Answer 28

backcrossed; recessive

Question 29

How do prokaryotic genomes evolve?

Answer 29

genome size and number of genes; horizontal gene transfer; function of genes

Question 30

Define horizontal gene transfer

Answer 30

exchanging genetic information from closely related distantly related species over evolutionary time

Question 31

How do eukaryotic genomes evolve?

Answer 31

genome size and number of genes; segment duplications and multilane families; noncoding DNA; transposable elements; protein diversity; homologous genes; collinearity between related genomes

Question 32

True or false? | A very low degree of homology occurs in eukaryotic genomes

Answer 32

false; tremendous degree

Question 33

Mice and humans have about ___% of their genes in common

Answer 33

99

Question 34

About 50% of genes in ___ ___ are homologous to genes in humans

Answer 34

fruit flies

Question 35

Plants have about ___% of their genes homologous to human genes

Answer 35

18

Question 36

Define colinearity

Answer 36

presence of many genes in the same order in related genomes due to evolution from a common ancestral genome

Question 37

Chromosome number in grasses ranges from __ to ___

Answer 37

4; 266

Question 38

The rice genome consists of only about ___ million bp, whereas the genome of wheat contains ___ billion bp

Answer 38

460; 17

Question 39

The ___ genome consists of 25 linkage blocks, consisting of groups of linked genes

Answer 39

rice

Question 40

What is the total average length of gene in the human genome?

Answer 40

27,000 bp

Question 41

What is the average size of coding region in the human genome?

Answer 41

1,340 bp

Question 42

What is the average number of exons per gene in the human genome?

Answer 42

8.8

Question 43

The total length of the entire human genome is how long in bp?

Answer 43

3.2 billion bp

Question 44

It was previously thought that only 25% of the DNA in the human genome was transcribed into RNA. The percentage is actually probably closer to ___%

Answer 44

80

Question 45

Less than 2% of the human genome does what?

Answer 45

encodes protein

Question 46

___ genes are often separated by vast regions of noncoding DNA, much of which consists of repeated sequences derived from ____ elements

Answer 46

Active; transposable

Question 47

The human genome does not encode substantially more protein domains, but the domains are combined in more ways to produce a relatively ___ ___

Answer 47

diverse proteome

Question 48

The human genome with approximately 24,000 genes, might encode 72,000 or more mRNAs. How is this possible?

Answer 48

because a single gene often encodes multiple proteins through alternative splicing; each gene encodes on average two or three different mRNAs

Question 49

Which three chromosomes have the highest densities?

Answer 49

17, 19, and 22

Question 50

Which chromosomes have the lowest densities?

Answer 50

X, Y, 4, 13, and 18 | X,Y, brett favre, kurt warner, peyton manning

Question 51

Some proteins encoded by the human genome that are not found in other animals include those affecting what?

Answer 51

immune function; neural development; structure and function; intercellular and intracellular signaling pathways in development; hemostasis; apoptosis

Question 52

True or false? | Transposable element are much more common in the worm, plant, and fruit fly than the human genome

Answer 52

false; more common in human genome

Question 53

In one region of the X chromosome, __% of the DNA is made up of transposable elements, whereas other regions are largely devoid of these elements

Answer 53

89

Question 54

The human genome contains a variety of types of transposable elements. Name 4.

Answer 54

LINEs, SINEs, retrotransposons, and DNA transposons note: most appear to be relatively old and are defective, containing mutations and deletions making them no longer capable of transposition

Question 55

One technique used in the determination of cellular proteins is called what?

Answer 55

mass spectrometry

Question 56

Affinity capture (interactome), protein microarrays, and structural proteomics are three techniques that are used to analyze what?

Answer 56

the complete set of proteins found in a cell

Question 57

True or false? | Protein microarrays can be used to study protein-protein interactions of thousands of proteins at once

Answer 57

true