Chapter 18

Question 1

Genomics allows sequencing of entire genomes

Answer 1

Genome: 
- Complete set of DNA in a single cell of an organism
Genomics - the study of genomes
- Structural genomics
- Functional genomics 
- Comparative genomics 
- Metagenomics

Question 2

Structural genomics

Answer 2

• sequencing genomes

- analyzing nucleotide sequences to identify genes and sequences such as gene regulatory elements

Question 3

Shotgun cloning

Answer 3

whole genome sequencing (shotgun cloning)

• the most widely used strategy for sequencing and assembling an entire genome
  1. Genomic DNA is cut into fragments called contigs
  2. entire chromosome is assembled by computer program
  3. fragments are aligned based on identical DNA sequences

Question 4

Contigs

Answer 4

contigs - continuous fragments

- overlapping fragments adjoining segments that collectively form one continuous DNA molecule within chromosome

Question 5

Bioinformatics

Answer 5

uses computer based approaches to organize, share, and analyze data related to:

• gene structure
• gene sequence and expression
• protein structure and function

Question 6

Applications for bioinformatics

Answer 6

• comparing DNA sequences
• finding gene regulatory regions (promoters and enhancers)
• predicting amino acid sequences
• deducing evolutionary relationships between genes

Question 7

Hallmark Characteristics of a Gene Sequence Can Be Recognized by Bioinformatics Tools

Answer 7

• several hallmark characteristics of genes (prokaryotes and eukaryotes) can be searched for using bioinformatics software
• Gene-regulatory sequences found upstream are marked by identifiable sequences such as promoters, enhancers, and silencers.

Question 8

Open reading frames (ORF)

Answer 8

• sequences of triplet nucleotides translated into amino acid sequences of a protein
• suggestive of protein- encoding gene
• typically begin with initiation sequence ATG
• end with termination sequence (TAA, TAG, TGA)

Question 9

Functional genomics

Answer 9

• Study of gene functions based on resulting RNAs or possible proteins they encode as well as regulatory elements
• Attempts to Identify Potential Functions of Genes and Other Elements in a Genome

Question 10

Predicting Gene and Protein Functions by Sequence Analysis

Answer 10

Similarity searches
–Screen databases and compare sequence to known sequence
–Genome sequence statistically similar to gene with known function likely encodes for protein with similar function.
- Compares portions of human leptin gene (LEP) with homolog in mice (ob/Lep)

Question 11

Homologous genes

Answer 11

• Genes that are evolutionarily related
• Similarity searches are able to identify homologous genes.
  Orthologs
• Genes from different species thought to have descended from common ancestor

Question 12

HumanGenomeProject (HGP)

Answer 12

• Coordinated effort to sequence and identify all genes of human genome
• Illustrates that humans and all other species share common set of genes essential for cellular function and reproduction

Question 13

Major features of human genome project

Answer 13

Two biggest surprises discovered from HGP
–There are less than 2% genome codes for proteins.
–There are probably only about 20,000 protein-coding genes.
The number of genes is lower than the number of predicted proteins.

Alternative splicing
Many genes code for multiple proteins through alternative splicing.
- Alternative splicing produces incredible diversity of proteins beyond number of human genes
- Alternative splicing patterns can generate multiple mRNA molecules = multiple proteins.

Question 14

Human genome

Answer 14

Human genomic sequence is 99.9% the same, with most genetic differences resulting from

1. Single-nucleotide polymorphisms (SNPs)
   - Single-base changes in genome
   - Variations associated with disease conditions
2. Copy number variations (CNVs)
   - Segments of DNA duplicated or deleted

Question 15

Comparative genomics

Answer 15

• Compares genomes of different organisms to answer questions about genetics and other aspects of biology
  –Incorporates study of gene and genomic evolution–Explores relationship between organisms and environment–Studies differences and similarities between organisms and how differences contribute to phenotype, life cycles, and so on.

Question 16

Eukaryotic genomes

Answer 16

Features of eukaryotic genomes not found in prokaryotes
–Gene density: Varies from chromosome to chromosome
–Introns: Variation in genomes and in genes
–Repetitive sequences: About half of human genome is repetitive DNA.

Question 17

Sea urchin genome

Answer 17

in 2006, researchers completed 814 million bp genome of sea urchin Strongylocentrotus purpuratus.

• Sea urchins have an estimated 23,500 genes.
• Contain many genes with important functions in humans
• Have nearly 1000 genes for sensing light and odor
• Sea urchins and humans share approximately 7000 orthologs.

Question 18

Dog genome

Answer 18

Dog genome completed in 2005
– Humans share 75% of their genes, as well as many genetic disorders, with dogs.
– Over 400 single-gene disorders
–Sex-chromosome aneuploidies
–Multifactorial diseases (e.g., epilepsy)
–Behavioral conditions (e.g., obsessive-compulsive disorder)

Question 19

The Chimpanzee Genome

Answer 19

Comparison of human and chimpanzee sequences
–Differ by < 2%
–Share 98% of same genes
–Analysis indicates that genome evolution, speciation, and gene expression are interconnected.

Question 20

The Neanderthal Genome and Modern Humans

Answer 20

Neanderthal (Homo neanderthalensis)
– Rough draft of Neanderthal genome encompassed 3 billion bp of Neanderthal DNA and 2/3 of genome.
– Comparative genomic analysis was used to identify where humans have undergone rapid evolution since diverging from Neanderthals.
–99% identical to humans
–78 new protein-coding sequences since divergence

Question 21

transcriptome analysis

Answer 21

Transcriptome analysis (global analysis of gene expression)
–Studies expression of genes by genome qualitatively and quantitatively
1. Qualitatively: identifies which genes are expressed and which are not
2. Quantitatively: measures varying levels of expression of different genes

Question 22

DNA microarray analysis

Answer 22

Microarrays (gene chips)
- Single-stranded DNA molecules attached to glass microscope slide complementary to all potential mRNA sequences from expressed genes

Question 23

Proteomics Identifies and Analyzes the Protein Composition of Cells

Answer 23

Proteomics
–Identification, characterization, and quantitative analysis of all proteins (proteome) encoded by genome of cell, tissue, or organism
–Used to reconcile differences between number of genes in genome and number of different proteins produced
–Allows comparison of proteins in normal and diseased tissue

Question 24

Proteomics Technologies: Two-Dimensional Gel Electrophoresis for Separating Proteins

Answer 24

Proteomics technologies: two-dimensional gel electrophoresis (2DGE)
–Technique for separating hundreds to thousands of proteins with high resolution
1.Proteins isolated from cell or tissue
2.Loaded on polyacrylamide tube gel
3.Separated by isoelectric focusing—causes proteins to migrate based on charge

DS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis)
–Second migration (after 2-D gel)
–Proteins separated by molecular mass
–Electric current applied to gel

Question 25

System biology

Answer 25

Systems biology
–Incorporates data from genomics, transcriptomics, proteomics, and other areas of biology
–Interprets genomic information in context of structure, function, and regulation
–Network map: sketch showing interacting proteins, genes, and other molecules