Digital Analysis of the Genome

A major shock to emerge from the completion  of the human genome sequence was the discovery of only about ______ genes. Of these genes, roughly 21,000-23,000 encode proteins, while the remainder are transcribed into _____ that are not __________, such as _____ and _____ that participate in translation, and the _______ that function in spliceosomes

These numbers are much lower than expected. Estimates made before the initiation of the Human Genome Project had suggested that there might be _______ or more genes. Many of these estimates anticipated that because humans have much ______ biological complexity than simpler model organisms such as bacteria, yeasts, nematodes, and fruit flies, our genomes must have many more ____

The total length of genomes varies much more markedly over the course of evolution than the number of genes (compare the genomes of human, mice vs other simple euks like worms and flies). Why does this generalization hold?

The vast majority of DNA sequences instead are found in _______, in the spaces between genes (______ regions), in ________ ______ that can move from one chromosomal position to another, and in structural features like ______ and _________

The tremendous variation seen in the size of genomes of different species is thus mostly due to expansions and contractions of ________ DNA outside of the _____, rather than changes in gene ______ and ______

Students sometimes assume that all the genes on a chromosome are transcribed in the same direction, always using the same strand of double-stranded genomic DNA as the template. Why is this wrong?

Why does RNA polymerase use the chromosome's "Watson" strand as the template for some genes, while for other genes, the template is the "Crick" strand?

On average, the density of a gene in the human genome is slightly less than 1 gene in every 100 kb of DNA (25,000 genes in 3,000,000 kb genome); however, this rough value obscures the fact that the packing of genes can be very different in various parts of the _______. Some regions on some chromosomes are _____-rich, with little space between densely packed genes

The most gene-rich region of the human genome is a 700 kb stretch of chromosome 6 that contains 60 genes encoding _________ proteins with diverse functions

Chromosomal regions that have many more genes than expected from average gene _______ over entire genome are gene-rich regions. Example in human genome is the class III region of major ________ complex. ______ ______ are regions of >1 Mb that have no identifiable genes and they make up 3% of human genome. Do they exist simply because the genes are hard to identify (e.g. big genes)?

Genomes continually undergo many different kinds of DNA sequence changes that provide the raw material for ______ _______

Genome annotation has revealed that exons often encode discrete _________ domains, each of which is a linear sequence of ______ _____ that folds up in ______-dimensional space so as to act as a _____ ______ ______

Genes with multiple exons often encode proteins with multiple _______ analogous to the cars of a train. Each train is composed of multiple different cars, and each kind of car has a discrete function.

Similarly, many genes are composed of multiple ______ that encode discrete protein domains. The shuffling, addition or deletion of exons during evolution can create new genes whose protein products have novel ____ architectures (different numbers and kinds of ____ in different orders) and thus can assume ____ roles in cells and organisms

The fig. shows domains associated with various transcription factors, proteins that bind to regions of DNA such as enhancers that control the _______ of nearby genes. Exon ______ over evolution has produced different transcription factors with differing domains that enable these proteins to ______ particular DNA sequences and also to interact uniquely with _______ such as other proteins

The mechanism of RNA splicing facilities this kind of exon rearrangement in euk genomes (aka creation of new genes) because _______ does not have to be precise. 

Multigene families

Examples of gene families include the genes that encode the hemoglobin that allow us to transport _______ in our blood, the _______ (antibodies) that help us ward off infections, and the ________ receptors critical for our sense of smell

With the use of bioinformatics, researcher can see that each gene family evolved by a process of ________ and _______ from an ________ gene. The two DNA sequence products of a duplication event, which start out _______, eventually _______ as they accumulate different ________

The duplication and divergence process is critical for the creation of new raw material. Once a gene has duplicated, divergence allows either or both of the copies to assume new specialized but _______ functions, as long as one or both of the copies still fulfills the role of the _______ gene

The genes in such families may be _______ on one chromosome or _______ on several chromosomes. In the case of the hemoglobin family, the α-globin gene cluster, aka the ______ _____, on chromosome 16 contains five functional genes, while the β-globin (aka _____ _____)  cluster on chromosome 11 also has five genes

The sequences of all α-like genes are ______ similar to each other than they are to the β-like sequences, and vice versa. The β-like genes are exactly the same ______, and the five β-like genes have two _____ at exactly the same position; in fact the α-like genes also have two _______ at the same position

These comparisons suggest that all of the globin genes can be traced back to a single ______ DNA sequence. Hundreds of millions of yrs ago, this ancestral globin gene _____, and one copy moved to another ________. With time, one of the two copies gave rise to the ______  and the other to the ________

Each lineage then underwent further ______ to generate the present array of α-like and β-like genes in humans. By comparing genomes of different organisms, it is possible to estimate when these various _____ events occured

Orthologous genes (define) usually retain the same _______.

The genes for the ε-globin in humans and chimps are orthologs (why?)

By contrast paralogous genes (define) arise by _______

The genes for δ-globin and ε-globin in the human β-globin locus are close _______, and both are more distant ________ of genes in the α-globin cluster

Homology (define)

All hemoglobin genes in all species are thus _______, and all these genes share _____ homologies with myoglobin genes encoding more ______ related oxygen-carrying proteins in muscle tissues rather than red blood cells

The duplications that gave rise to multiple functional hemoglobin genes also produced genes that eventually lost the ability to ______. Molecular geneticists made this last deduction from data showing two additional α-like sequences within the α locus and one β-like sequence within the β locus that no longer have the capacity for proper ________

Pseudogenes

Why do pseudogenes accumulate mutations at a faster rate than coding or regulatory sequences of a functional gene?

Eventually, nearly all pseudogene sequences mutate past a boundary beyond which it is no longer possible to identify the ______ genes from which they have been derived. Continuous mutation can thus turn a once functional sequence into an essentially ______ sequence of DNA

The mouse and human genomes, which diverged 85 million years ago, exhibit striking similarities and differences not only in the _______ of individual genes, but also in the ______ of those genes on the chromosomes

Syntenic blocks

Within syntenic blocks, the order of genes is very ______  in humans and mice. However, the orders of these blocks along the chromosmes are totally ______ in the two organisms. It is as if one genome had been cut into 180 pieces of _______ size and then ______ assembled into the other genome

Conserved synteny (define) also exists between the human and puffer fish genomes , which diverged more than 400 million yrs ago. In this case the _____ _____ are relatively small

What causes the apparent cutting and reassembling of chromosomal blocks accompanying evolution?
translocations 
inversions

The farther back in time two species last shared a common ancestor, the ______ chromosomal rearrangements accumulate in each separate lineage that will alter the order of genes. As a result, the avg size of syntenic blocks becomes ______ with _______ evolutionary distances between species

Combinatorial amplification (define) can increase info and generate diversity. State two strategies

T cells undergo ________ of DNA coding for antibodies. By _______ the V, D and J segments, there can be increased ________. Approximately a thousand combinations are possible

Three neurexin genes, which encode proteins that help bind neurons at _______ illustrate ______ combinatorial strategies. Each gene has two _______ regions (producing α and β class mRNAs) and five sites at which ______ _____ can occur. Together, these three genes can probably generate more than 2000 ________ ______ forms of mRNA. Not all of the combos are ________

GenBank database
RefSeq

Suppose you have identified a gene (from Drosophila) and would like to know whether the human genome contains a homolog of this fly gene. Nam a tool you would use and what does it do?

In this typical output of a BLAST search, we are looking for a human _____ that share ______ with the fly _______ of interest. The Query is the sequence you already know; here, the ______ ____ sequence of the fly ______ is written in the one letter code

The subject is the ________ sequence found by the BLAST program; in this case, the related human ______. The row between the Query and the Subject indicates the conserved amino acids, with a + symbol denoting ______ amino acid replacements (missense substitutions in which an amino acid is replaced by a different amino acid with similar chemical props)