Bio Chapter 21

gene density

how many genes there are in a given length of DNA more introns = less dense in addition to introns, multicellular organisms have a vast amount of non-protein-coding DNA between genes

genomics

study of genes and their interactions

homeobox

A 180-nucleotide sequence within homeotic genes (dictate the identity of body segments) that specifies a 60-amino-acid homeodomain in the encoded proteins. very similar between different species.

whole-genome shotgun approach

A faster method than the 3 step approach to sequencing an entire genome, first used by the Human Genome Project. A method for determining the DNA sequence of an entire genome. After a genome is cut into small fragments, each fragment is sequenced and then placed in the proper order. WHOLE-GENOME SHOTGUN APPROACH 1. Cut the DNA from many copies of an entire chromosome into overlapping fragments short enough for sequencing 2. Clone the fragments in plasmid or phage vectors 3. sequence each fragment 4. order the sequences into one overall sequence with computer software

linkage map

A genetic map based on the frequencies of recombination between markers during crossing over of homologous chromosomes.

physical map

A genetic map in which the actual physical distances between genes or other genetic markers are expressed, usually as the number of base pairs along the DNA. fragments (created by DNA cloning) can be assigned to a sequential order that corresponds to their order in a chromosome.

Human Genome Project

An international collaborative effort to map and sequence the DNA of the entire human genome. started in 1990. THREE STEP APPROACH Steps: (page 473) pre-steps: cytogenetic maps based on karyotyping that revealed chromosome numbers and banding patterns and a few gene loci 1. linkage map 2. physical map 3. DNA sequencing WHOLE-GENOME SHOTGUN APPROACH 1. Cut the DNA from many copies of an entire chromosome into overlapping fragments short enough for sequencing 2. Clone the fragments in plasmid or phage vectors 3. sequence each fragment 4. order the sequences into one overall sequence with computer software

homeotic gene

Any of the genes that control the overall body plan of animals by controlling the developmental fate of groups of cells.

bioinformatics

Application of mathematics and computer science to store, retrieve, and analyze biological data

metagenomics

DNA from a group of species is collected from an environmental sample and sequenced all sequenced by computers the ability to sequence the DNA mixed populations eliminates the need to culture each species separately in the lab, a difficulty that has limited the study of many microbial species

DNA sequencing

Determining the exact order of the base pairs in a segment of DNA

genome evolution

Duplication of entire chromosome sets: sometimes polyploidy organisms survive for the better. as long as one copy of an essential gene is expressed the divergence of another copy can lead to its encoded protein acting in a novel way, thereby changing the organism's phenotype Alterations of chromosomal structure: duplications and inversions and fusions of chromosomes and rearrangements. ex: chimpanzee chromosomes 12 and 13 fused together to form the human chromosome 2, we think. unequal crossing over can result in one chromosome with a deletion and another with a duplication slippage, when a template shifts with respect to the new complementary strand, and a part of the template strand is either skipped by the replication machinery or used twice as a template

number of genes

bacteria and archaea: 1,000-7,500 genes plants and animals: 5,000-40,000 does not necessarily determine the genome size/length (both affect gene density) introns affect length, but not the genes

FOXP2

In humans, the gene helps control mouth movement and sequences of mouth movement during speech as well as controlling comprehension of speech. It is a transcription factor which activates some genes while suppressing others page 490

copy-number variants

Loci where some individuals have one or 3+ copies of a particular gene or genetic region, rather than the standard two copies. Result from regions of the genome being duplicated or deleted inconsistently within the population.

transposable elements

Segment of DNA that can move from one location to another within the genome "jumping genes" HOWEVER, they never completely detach from the cell's DNA INSTEAD, the original and new DNA sites are brought together by enzymes and other proteins that bend the DNA two types: transposons and retrotransposons usually hundreds to thousands of base pairs long, scattered throughout eukaryotic genomes ex: Alu elements, LINE-1 (L1)

short tandem repeat

Short sequences of DNA repeated many times in a row.

proteomics

Study of proteins, study of the full sets of proteins encoded by genomes proteins, not the genes that encode them, actual perform most of the activities of the cell we must therefore study them if we are going to understand the functions of cells and organisms

THREE STEP APPROACH

THREE STEP APPROACH Steps: (page 473) pre-steps: cytogenetic maps based on karyotyping that revealed chromosome numbers and banding patterns and a few gene loci 1. linkage map 2. physical map 3. DNA sequencing

gene annotation

The identification of protein coding genes within DNA sequences in a database

Rearrangements of Parts of Genes: Exon duplication and exon shuffling

a particular exon on a gene could be duplicated on one chromosome and deleted from the other. the double copy of the exon would code for an altered protein and its function would change- could be more stable and able to bind to a particular ligand better, or alter some other property exon-shuffling=the occasional mixing and matching of different exons (either within a gene or between two different (non allelic) genes) owing to errors in meiotic recombination.

transposition

a transposable element moves from one site in a cell's DNA to a different target site by a type of recombination process

Cancer Genome Atlas

aims to determine how changes in biological systems lead to cancer

multigene families

collections of two or more identical or very similar genes in multigene families that consist of identical DNA sequences, those sequences are usually clustered tandemly and, with the notable exception of the genes for histone proteins, have RNAs as their final products an example of identical genes of multigene families is the genes that code for ribosomes to quickly make the millions of ribosomes needed for active protein synthesis and example of nonidentical genes of a multigene family are related families of genes that encode globins- the two different types page 483

repetitive DNA

consists of sequences that are present in multiple copies in the genome, 75% of all repetitive genes is made up of units called transposable elements and sequences related to them

simple sequence DNA

contains many copies of tandemly repeated short sequences much is located at chromosomal telomeres and centromeres, which suggests it has a structural role

most useful things to look at for studying human evolution

copy-number variants, SNPs, and variations in repetitive DNA such as short tandem repeats

Globin Family Genes

duplication and then mutation of the duplicated genes is most likely what gave way to the different globin genes

pseudogenes

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

genome size

most bacterial genomes have between 1 and 6 million base pairs genomes of archaea are within the same size range as bacteria (although few genomes have been sequenced of archaea) genomes of single celled yeast has about 12 million most plants and animals, multicellular eukaryotes, have at least 100 Mb Humans 3,000 Mb so far, no systematic relationship between genome size and an organism's phenotype

retrotransposons

move by means of an RNA intermediate that is a transcript of the retrotransposon DNA. always leave a copy behind during transposition, since they are initially transcribed into an RNA intermediate. THEN to insert at another site, the RNA intermediate is first converted back to DNA by reverse transcriptase, an enzyme encoded by the retrotransposon.

transposons

move within a genome by means of a DNA intermediate cut and paste mechanism, which removes the element from the original site, or copy and paste mechanism, which leaves a copy behind in the original site both mechanisms require an enzyme called transposes, which is generally encoded by the transposon

genome organization

tells us much about how genomes have evolved and continue to evolve once the human genome was sequenced, we say that only 1.5% of it codes for proteins or is transcribed into rRNAs or tRNAs GENE-REGULATED DNA (coding/non-coding): 25% - gene regulatory sequences: 5% - introns: 20% - coding DNA: 1.5% NON REGULATED: unique noncoding DNA, such as gene fragments and pseudogenes: 15% repetitive DNA w transposable elements/related sequences: 44% repetitive DNA unrelated to transposable elements: 14% large-segment duplications: 5-6%

evo-devo

the field of evolutionary developmental biology, studies/compares developmental processes of different multicellular organisms

How transposable elements contribute to genome evolution

they can promote recombination (between different chromosomes!), disrupt cellular genes or control elements, and carry entire genes or individual exons to new locations depending on where the gene is carried, the transposition can have different affects: if it jumps to the middle of a protein coding sequence, it will prevent the production of a normal transcript of the gene. if a transposable element inserts within a regulatory sequence, the transposition may lead to increased or decreased production of one or more proteins. most are harmful, some can be beneficial and provide a survival advantage