Chapter 21 - Genomes and Their Evolution Flashcards Preview

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Flashcards in Chapter 21 - Genomes and Their Evolution Deck (30):
1

What is genomics?

The study of whole sets of genes and their interactions

2

What is bioinformatics?

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

3

What is proteomics?

The complete set of proteins translated in a cell

4

What is metagenomics?

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

5

What are some sources that provide bioinformatics resources?

- National Library of Medicine and the National Institutes of Health (NIH) created the National Center for Biotechnology Information (NCBI)
- European Molecular Biology Laboratory
- DNA Data Bank of Japan
- BGI in Shenzhen, China

6

What are some sources that provide bioinformatics resources?

- National Library of Medicine and the National Institutes of Health (NIH) created the National Center for Biotechnology Information (NCBI)
- European Molecular Biology Laboratory
- DNA Data Bank of Japan
- BGI in Shenzhen, China
- Genbank, the NCBI database of sequences, doubles its data approximately every 18 months
- Software is available that allows online visitors to search Genbank for matches to; a specific DNA sequence; a predicted protein sequence; common stretches of amino acids in a protein; design PCR primers
- The NCBI website also provides 3-D views of all protein structures that have been determined

7

What is gene annotation?

Given a long DNA sequence from a database such as GenBank, scientists aim to identify all protein-coding genes in the sequence and ultimately their functions

8

What is a proteome?

The entire set of proteins expressed by a cell or group of cells

9

What is systems biology?

An approach which aims to model the dynamic behavior of whole biological systems based on the study of the interactions among the system's parts

A very efficient way to study emergent properties at the molecular level

10

Discuss the applications of systems biology to medicine.

- The Cancer Genome Atlas project, started in 2010, looked for all the common mutations in three types of cancer by comparing gene sequences and expression in cancer versus normal cells
- It’s been extended to 10 other common cancers
- Silicon and glass “chips” have been produced that hold a microarray of most known human genes
- These are used to study gene expression patterns in patients suffering from various cancers or other diseases

11

How many genes are contained in the human genome?

Researchers predicted the human genome would contain about 50,000 to 100,000 genes; however the number is around 21,000

12

How can vertebrate genomes produces more than one polypeptide per gene?

Vertebrate genomes can produce more than one polypeptide per gene because of alternative splicing of RNA transcripts

13

Discuss gene density and non coding DNA.

- Humans and other mammals have the lowest gene density, or number of genes, in a given length of DNA
- Multicellular eukaryotes have many introns within genes and a large amount of noncoding DNA between genes
- Sequencing of the human genome reveals that 98.5% does not code for proteins, rRNAs, or tRNAs
- About a quarter of the human genome codes for introns and gene-related regulatory sequences

14

What are pseudogenes?

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

15

What is repetitive DNA?

Consists of sequences that are present in multiple copies in the genome (44% of the entire human genome)

16

What are transposable elements?

Stretches of DNA that can move from one location to another within the genome; during the process called transposition, a transposable element moves from one site in a cell's DNA to a different target site by a type of recombination process

17

Where did the first evidence for wandering DNA segments come from?

- The first evidence for mobile DNA segments came from geneticist Barbara McClintock’s breeding experiments with Indian corn
- McClintock identified changes in the color of corn kernels that made sense only if some genetic elements move from other genome locations into the genes for kernel color
- These transposable elementsmove from one site to another in a cell’s DNA; they are present in both prokaryotes and eukaryotes

18

What are transposons?

A eukaryotic type of transposable element which move within a genome by means of a DNA intermediate; transposons can move by a "cut and paste" mechanisms, which removes the element from the original site, or by a "copy and paste" mechanism which leaves a copy behind

Both mechanisms require an enzyme called transposase

19

What are retrotransposons?

Most transposable elements n eukaryotic genomes are of this second type, which move by means of an RNA intermediate that is a transcript of the retrotransposon DNA

Retrotransposons always leave a copy at the original site during transposition

20

Discuss the sequences related to transposable elements.

- Multiple copies of transposable elements and related sequences are scattered throughout eukaryotic genomes
- In primates, a large portion of transposable element–related DNA consists of a family of similar sequences called Alu elements, which make up approximately 10% of the human genome
- 17% of the human genome is made up of a type of retrotransposon called LINE-1, or L1

- Transposable elements and related sequences make up 25-50% of most mammalian genomes

21

What is simple sequence DNA?

Contains many copies of tandemly repeated short sequences

22

What is a short tandem repeat?

STR; a series of repeats only 2-5 nucleotides long

The repeat number for STRs can vary among sites (within a genome) or individuals

23

How much of the human genome consists of duplication of long sequences of DNA?

About 15% of the human genome consists of duplication of long sequences of DNA from one location to another

24

Where is simple sequence DNA common?

Simple sequence DNA is common in centromeres and telomeres, where it probably plays structural roles in the chromosome

Telomeres prevent genes from being lost as the DNA shortens with each round of replication; telomeric DNA also binds proteins that protect the ends of a chromosome from degradation and from joining to other chromosomes

25

What are multi-gene families?

Collections of two or more identical or very similar genes

- Many eukaryotic genes are present in one copy per haploid set of chromosomes
- The rest of the genes occur in multigene families, collections of identical or very similar genes
- Some multigene families consist of identical DNA sequences, usually clustered tandemly, such as those that code for rRNA products

26

Discuss the duplication and divergence of gene sized regions of DNA.

- Unequal crossing over during prophase I of meiosis can result in one chromosome with a deletion and another with a duplication of a particular region
- Transposable elements can provide sites for crossover between nonsister chromatids

27

Discuss genome comparisons.

- Genome comparisons of closely related species help us understand recent evolutionary events
- Relationships among species can be represented by a tree-shaped diagram

28

What is the FOXP2 gene function?

Functions in vocalization in vertebrates

29

Compare distantly related species?

- Highly conserved genes have changed very little over time
- These help clarify relationships among species that diverged from each other long ago
- Bacteria, archaea, and eukaryotes diverged from each other between 2 and 4 billion years ago
- Highly conserved genes can be studied in one model organism, and the results applied to other organisms

- Human and chimpanzee genomes differ by 1.2% at single base-pairs, and by 2.7% because of insertions and deletions
- A number of genes apparently evolved faster in the human than in the chimpanzee or mouse; i.e. genes involved in defense against malaria and tuberculosis; regulation of brain size
- Humans and chimpanzees differ in the expression of the FOXP2 gene, whose product turns on genes involved in vocalization
- Differences in the FOXP2 gene may explain why humans but not chimpanzees communicate by speech

30

What is exon shuffling?

The occasional mixing and matching of different exons either within a gene or between two different genes; this process can sometimes lead to new proteins with novel combinations of functions