chapter 20: genomics and proteomic

Question 1

define genomics

Answer 1

Field of genetics that attempts to uderstand the content, organization function and evolution of the genetic information in whole genomes

Question 2

genetic maps

Answer 2

• approximation of the location of genes relative to other genes
• based on recombination
  -use cM or map units

Question 3

what are come characteristics of genetic maps

Answer 3

• low resolution
  -not always accurate
• based on rates of crossing over

Question 4

physical maps

Answer 4

based on the direct analysis of dna and they place genes in relation to distances
- measured in number of base pairs, kilobases, or mega base

Question 5

high recombination=

Answer 5

father genes

Question 6

• 3. List some problems associated with sequencing of an entire genome

Answer 6

• whole genome sequencing
• only small fragments can be sequenced at a time
• must fragment genome into millions of small overlapping fragments
• how to order them after fragments are sequenced

Question 7

goals of human genome project

Answer 7

• developing sequencing technology
• sequence genomes of model organims
• determine sequence of the human genome
• identify all genes in human genome

Question 8

what were the two projects of the human genome project

Answer 8

• internatinoal human genome sequencing (public effor)
• celera genomics (private effort)

Question 9

• Give the percent similarity between two humans

Answer 9

99.99%

Question 10

• Define single nucleotide polymorphisms and haplotype (fig 20.8)

Answer 10

SNP: mutation where a single base pair in a DNA sequence differs
haplotype: A haplotype is a group of alleles in an organism that are inherited together from a single parent. Haplotypes are groups of SNPs that are inherited as a single block.

Question 11

• Explain how SNPs can be used for genome wide association studies

Answer 11

• can help tell you the overall risk of developing a disease

Question 12

how many base pairs in the human genome

Answer 12

3.2 billion

Question 13

how many base pairs difference between you and your neighbor

Answer 13

4000cM

Question 14

○ What is a contig

Answer 14

§ Set of two or more overlapping dna fragments that form a continuous stretch of dna

Question 15

what is bioinformatics

Answer 15

molecular biology + computer science
- identify genes
-annotate genes

Question 16

how is bioinformatics useful to identify a gene

Answer 16

-exract the useful information from sequencing projects
- ab initio approach

Question 17

define annotation in bioinformatics

Answer 17

○ Linking its sequence information to other information about its function and expression
○ The protein it encodes and similar genes in other species
Computer programs are available for determining whether similar sequences have been found

Question 18

Define metagenomics

Answer 18

§ Sequencing genomes of a entire group of organisms that share a common environment
Applied mostly to microbial communities

Question 19

What issues does metagenomics address

Answer 19

Study of microbes that can’t be cultured in a lab
Study of the structure of microorganisms

Question 20

why does this field exist

Answer 20

• some bacteria can’t be cultured in a lab
• it can extract DNA from their environment to answer multiple ques

Question 21

how are snps helpful in studying the genome

Answer 21

use them across the genome to find genes of interest

Question 22

what is functional genomics

Answer 22

• characterizes what sequence do their function
  -goal is transcriptome and proteome

Question 23

what is trnascriptome

Answer 23

rna molecules transcribed from a genome

Question 24

what is proteome

Answer 24

all the proteins encoded by a genome

Question 25

Define homology search and explain how this can be used to understand the function of a gene

Answer 25

○ Conmparisons of dna and protein sequeinces from the same species and from different species
○ Computational methods that search for similar evolutionary related homologous genes
Genes that are related = homologous genes

Question 26

differentiate between ortholog and paralog

Answer 26

ortholog: Homologous genes in a different species that evolved from a common ancestor
paralogs: § Homologous genes in the same organism that arose through duplication

Question 27

list two techniques that can be used to study the expression of a gen

Answer 27

1. microarrays
2. rna sequencing

Question 28

describe how microarrays can be used to examine gene expression

Answer 28

○ Used to study expression of so many genes
○ A microarray consists of dna probes fixed to s olid support such as a nylon membrane or glass slide
○ Each spot consists of a different dna probe

Question 29

describe the process of rna seq as below

Answer 29

collect total cellular rna from cells (isolate)
-isolate mRNA
- reverse transcribe into cDNA
-fragment cDNA
sequence with next gen sequencing
-assemble sequences into rna transcripts