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Human genome project

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A scientific project funded by the US government. It was begun in 1990 for the purpose of mapping all of a human's genes and was successfully completed in 2003

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Genome sequencing

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The technique used to give the base sequence of DNA of a particular organism. The sequencing reaction can only identify up to around 1000 base pairs of sequence in a fragment. In order to sequence the whole genome, overlapping fragments are sequenced, then reassembled by computer software in order to generate the original sequence detail.

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Genomics

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the branch of genetics that studies organisms in terms of their genomes (their full DNA sequences), studies whole sets of genes and their interactions

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Bioinformatics

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

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what does comparison of genomes acheive

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helps provide information about the evolutionary history of genes and taxonomic groups. Complete genome sequencing exist for human, chimpanzee, e-coli etc

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Describe the goals of the human genome project

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establishment of banks of database, refining of analytical software, these database would be centralized and made readily accessible on the internet, this has accelerated progress in DNA sequence analysis by making bioinformatics available to researchers and speeding up dissemination of information

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State the 3 stages of the genome sequencing

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genetic/linkage map, physical mapping, DNA sequencing

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Genetic linkage map

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shows the linear order of markers (or genes) along a chromosome with the distance between adjacent markers proportional to the frequency of recombination between them

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cytogenetic maps

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a chart of a chromosome that locates genes with respect to chromosomal features distinguishable in a microscope

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Physical map

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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.

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genetic marker

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a specific gene that produces a recognizable trait and can be used in family or population studies, its a gene or other identifiable DNA sequence

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Recombination frequencies are used to calculate

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the order and relative distances between genetic markers

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How is a physical map made?

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By curring a DNA molecule into many short fragments and arranging them in order by identifying overlaps, this way fragments can be assigned to a sequential order that corresponds to their order ina chromosome

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What are sequencing machines used for?

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to determine the complete nucleotide sequence of each chromosome a complete haploid set of human chromosomes comsists of 3.2 billion base pairs

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Whole genome shotgun

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this was developed in 1992 by J Craig venter, this skips genetic and physical mapping and starts directly with sequencing of random DNA fragments, and then powerful computer programs are used to order fragments into a single continous sequence

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disadvantages of the two approach

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recent study has shown that whole-genome shotgun sequencing can miss some duplicated sequences, thus underestimating the size of the genome and missing some genes in those regions

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Who created NCBI?

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National library of Medicine and National institute of health created NCBI which maintains a website with extensive bioinformatics studies.

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NCBI

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National Center for Biotechnology Information.

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describe four of the programs available on the NCBI website

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BLAST(comparing of DNA sequence base by base looking for similar pairs), another program allows comparison of predicted protein sequences, third program can search any protein sequence for common stretches of amino acids (domains) for which a function is known or suspected and can even show a 3D model, another software can compare a collection of sequences, either nucleic acids or polypeptides

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What are the two websites NCBI collaborates

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European molecular biology lab, and the DNA data bank of japan

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Genbank

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An important genomic database Maintained by the NCBI, as at August 2007, it included sequences of 76 million fragments of genomic DNA, totaling 80 billion base pair. Genbank doubles its data every 18months

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Centralized resources for analysising genome sequences are

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NCBI, European molecular biology lab, DNA data bank of Japan

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What is the major difference between a linkage map and a physical map of a chromosome

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In a linkage map, genes and other markers are ordered with respect to each other, but only the relative distances are known, in a physical map the actual distances between markers expressed in base pairs are known

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How do researchers recognize protein-coding genes within DNA sequence?

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comparing the predicted amino acid sequence of the protein to that of other proteins, comparison of sequences of new genes with those of known genes in other species may help, while computer analysis of genome sequences helps identify sequences likely to encode proteins

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what does genomics studies

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genome organization, regulation of gene expression, growth and development, evolution

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proteomics

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the systematic study of the full protein sets encoded by genomes, proteins not genes carries out most activities of the cell, proteomics studies when and where proteins are produced, how they interact in networks

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Applications of systems biology

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they define gene circuits and protein interaction networks, system biology approach has been made possible by advances in bioinformatics

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Explain the cancer genome atlas (application of systems biology)

answer

this system seeks to understand how changes in biological systems lead to cancer.They are currently monitoring 2000 genes in cancer cells for changes due to mutations and arrangements,treatment of cancer and other diseases can be individually tailored ffing analysis of gene exprssion in patients suffering fromthe diseases,in future DNA sequencing may highlight predisposition to a particular illness

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Systems biology

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study of the relationships and interactions between various parts of a biological system in order to develop a model of the whole system. Seeks to understand how biological systems function.

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What is included in the just concluded completely sequenced group?

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600 genomes of bacteria, 50 archael genomes, 65 eukaryotes including vertebrates, invertebrates,protists, fungi and plants

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Compare the genome sizes of prokaryotes and eukaroytes

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genomes of most bacteria and archae range from 1 to 6 million base pair (Mb),genomes of eukaryotes are usually larger, most plants and animals have genomes greater than 100Mb, humans have 3,200 Mb. Within each domain, there is no systematic relationship between genome size and phenotype

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Number of genes in each categories

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bacteria and archae have fewer genes than eukaryotes, ranging from 1,500 to 7,500 genes, genes in eukaryotes range from 5,000 for unicellular fungi to at least 40,000 in multicellular eukaryotes

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Does number of genes correlate to genome size

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no, nematodes has 100Mb and 20,000 genes, humans have 3.200Mb and 20,488 genes, vertebrates can produce more than one polypeptide per gene because of alternative splicing of RNA transcripts

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Describe the tresnds in respect to genome suze and density

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eukaryotes have larger genomes but fewer genes, humans and other mammals have the lowest gene density or no ofgenes in a given length of DNA, multicellular eukaryotes have many introns within genes

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Introns

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a non-coding, intervening sequence within a eukaryotic gene

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Explanation of noncoding DNA in multicellular eukaryotes

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the bulk of most eukaryotic genomes consists on noncoding DNA sequences often described in the past as junk DNA,but evidence now shows that it plays important roles eg genomes of humans,rats and mice shows about 500 noncoding regions

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What part of the human genome is transcribed into proteins/RNAs

answer

1.5% codes for proteins/rRNAs/tRNAs and are called exons, 98.5% does not code for proteins

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Exons

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A coding region of a eukaryotic gene. Exons, which are expressed, are separated from each other by introns.

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Breakdown of introns percentages

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about 24% of the human genome codes for introns and gene related regulatory sequences, intergenic DNA is noncoding DNA found between genes i.e former genes that have accumulated mutations and are non functional (pseudogenes), and repetitive DNA is present in multiple copies in the genome.

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Pseudogenes

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A DNA segment very similar to a real gene but which does not yield a functional product; a gene that has become inactivated in a particular species because of mutation.

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Repetitive DNA

answer

Nucleotide sequences, usually noncoding, that are present in many copies in a eukaryotic genome. The repeated units may be short and arranged tandemly (in series) or long and dispersed in the genome. About 3/4ths (40%) of repetitive DNA is made up of transposanle elements

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Transposable elements

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Also transposoms. Mobil egenetic elements that can move around the genome by copying itself or splicing out and inserting into a different site. Half of the human genome are composed of transposable elements. Show little sequence selectivity.

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What was the first evidence of wandering DNA (transposoms)

answer

came from geneticist barbara mcclintocks breeding experiments with indian corn, she identified changes in the color of corn kernels ad postulated that some genetic elements move from other genome locations into the genes for kernel color, these transposable elements move from one site to another in a cell's DNA

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name the two eukaryotic transposable elements

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transposoms, and retrotransposoms

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Transposons

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A transposable element that moves within a genome by means of a DNA intermediate

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Retrotransposons

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Transposable elements that move within a genome by means of an RNA intermediate, a transcript of the retrotransposon DNA.

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Sequences related to transposons sequences

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multiple copies of transposable elements and related sequences are scattered throughtout the eukaryotic genome25-50% transposable elements make up a mammalian genomes,

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Alu elements

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related to transposable elements. are very short sequences. many are transcribed into RNA, function not known, they arefound in primates

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Explain transposons in the human genome

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human genome contains many sequence of a type of retrotransposon called LINE-1(L1), L1 sequences have a low rate of transposition and may help regulate gene expression

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where is L1 sequence found?

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within the introns of nearly 80% human genes, although many transposable elemenst may encode proteins, these proteins do not carry out normal cellular functions

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Simple sequence DNA

answer

contains many copies of tandemly repeated short sequences and make up 3% of the human genome, about 15% of the human genome consists of duplication of long sequences of DNA from one location to another

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Short tandem repeat

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Locations on the chromosome that contain sequences of three to seven base pairs that occur over and over within the DNA molecule.STR (2 to 5 nucleotides) is found in simple sequence DNA. The repeat no for STRs vary among sites within a genome/individual

question

where is simple sequence DNA common

answer

in centromeres and telomeres where it probably plays structural roles in the chromosomes

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Multigene families

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Collections of two or more identical or very similar genes. Some consists of identical DNA sequences, usually clustered tandemly, such as those that encode for RNA products

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How are eukaryotic genes presented?

answer

in one copy per haploid set of chromosomes, the rest of the gene occurs in collections of identical or very similar genes called multigene families

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what is a classical example of multigene of nonidentical genes

answer

are two related families of genes that encode globins alpha and beta globins are polypeptides of hemoglobin and are coded by genes on different human chromosomes

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what is the basis of change at the genomic level?

answer

mutation, which underlies much of genome evolution. the earliest form of life likely had a minimal no of genes, including only those necessary for survival and reproduction

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Have the sizes of genomes increased or decreased over time

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over evolutionary times, they have increased with the extra genetic material providing raw material for gene diversification

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Polyploidy

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A chromosomal alteration (accidents in meiosis) in which the organism possesses more than two complete chromosome sets.The genes in one or more of the extra sets can diverge by accumulating mutations, these variations persist if the organism carrying them survives and reproduces

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Explain alterations of chromosome structures

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Humans have 23 pairs while chimpanzees have 24 pairs, following the divergence of humans and chimpanzees froma common ancestor, two ancestral chromosomes

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mistakes during meiotic combination can result in

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duplications and inversions. The rate of duplications and inversions seems to have accelerated about 100 million years ago, this coincides with when large dinosaurs went extinct and humans diversified

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Duplications

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Mutations that produce extra copies of parts of a chromosome

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Inversions

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In an inversion mutation, an entire section of DNA nucleotides is reversal. A small inversion may involve only a few bases within a gene, while longer inversions involve large regions of a chromosome containing several genes.

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what does chromosomal arrangements contribute to?

answer

generation of new species, some of the recombination hot spots associated with chromosomal rearrangement are also locations associated with diseases

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Explain duplication and divergence of gene-sized regions of DNA

answer

unequal crossing over during prophase 1 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 even when their homologous sequences are not correctly alligned

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Globin superfamily

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Evolved from mutations in the original GLOBIN ANCESTRAL GENE.beta and alpha globins are monomers and are in the superfamily

question

what are the related functions of evolution of genes?

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the genes encoding the various globin proteins evolved from one common ancestral globin gene, which duplicated and diverged about 450-500 million years ago, after the duplication events, differences between the genes in the globin family arose from the accumulations in the gene copies over many generations

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Explain evolution and the terms that led to evolution of the globin superfamily

answer

subsequent duplications of these genes and random mutations gave rise to the present globin genes which code for oxygen binding proteins

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what supports this model of gene duplication and mutation?

answer

the similarity in the amino acid sequences of the various alpha and beta globin polypeptides. the amino acid sequences of the beta globins are more similar to each other than to the alpha blobin sequences, also the existence of several pseudogenes provides additional evidence:random mutations in these genes over evolutionary time have destroyed their function

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Exon shuffling

answer

occasional mixing and matching of different exons either within a gene or between two nonellelic genes owing to errors in meiotic recombination

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how does exon shuffling lead to new proteins with novel combinations of functions

answer

the copies of some duplicated genes have diverged so much in evolution that the functions of their encoded proteins have become very different eg the lysosme gene was duplicated and evolved into the alpha lactalbumin gene in mammals, lysosome is an enzyme that helps protect animals against bacterial infection and alpha lactalbumin is a non-enzyme protein that plays a role in milk production in mammals

question

how has the duplication or repositioning of exons contributed to genome evolution?

answer

errors in meiosis can result in an exon being duplicated on one chromosome and deleted from the homologous chromosome

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how does transposable elements contribute to genome evolution (coding sequence)

answer

multiple copies of similar transposable elements may facilitate crossing over between different chromosomes, insertion of transposable elements within a protein-coding sequence may block protein production, insertion of transposable elements within a regulatory sequence may increase or decrease protein production

question

How does transposable elements bring about new coding sequence

answer

during transposition, trabsposable elements may carry a gene or group of genes to a new position in the genome(this accounts for alpha and beta globinson differen human chromosomes), thay may also create new sites for alternative splicing in an RNA transcript, in all cases, changes are usually detrimental but advantageous on some occasions

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how has comparative studies in genomic sequencing helped?

answer

genomic sequencing has advanced rapidly in 20 years and has helped to advance our understanding of the evolutionary history of life, helped explain how the evolution of development leads to morphological diversity

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what has genome comparison of closely related species help us understand?

answer

recent evolutionary events

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what has genome comparison of distantly related species help us understand

answer

ancient evolutionary events.

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Realtionships among species can be represented by

answer

a tree shaped diagram

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Expain comparison of distant related species

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highly conservative genes are genes that have changed very little over time, they inform us about rships among species that diverged from each other a long time ago eg bacteria,archae and eukaryotes diverged from each other between 2 to 4 billion years ago, highly conserved gene can be studied in one model organism and the results applied to other organisms

question

Homeobox

answer

A 180-nucleotide sequence within homeotic genes and some other developmental genes that is widely conserved in animals. Related sequences occur in plants and yeasts.

question

Explain comparison of closely related species

answer

gentic differences between them can be correlated with phenotypic differences eg comparison of several mammals with nonmammals helps identify what it takes to be a mammals

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how does human and chimpanzee genome differ?

answer

by 1.2% at single base-pairs and by 2.7% because of insertions and deletions, several genes are evolving faster in humans than chimpanzees eg genes involved in defense against malaria, tuberculosis, regulation of brain size, genes that code for transcription factors

question

FOXP2

answer

the first gene linked to language production

question

how do humans and chimpanzees differ in the expression of the FOXP2 gene?

answer

humans communicate by speech..etc

question

Explain comparison of genomes within species

answer

As a species, humans have only been around about 200,000 years and have low withinspecies genetic variation

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Variation within humans is due to

answer

SNR(single nucleotide polymorphism), inversions, deletions and duplications

question

single nucleotide polymorphism

answer

the differences in homologous DNA sequences that are reflected in different lengths of restriction fragments produced when the DNA is cut up by a restriction enzyme

question

These variations are useful for studying

answer

human evolution, the differences between human populations, and the migratory routes of human populations throughout history

question

evodevo aka Evolutionary developmental biology

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is the study of the evolution of developmental processes in multicellular organisms(comparisons)

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with the advent of molecular techniques,we are beginning to realize that

answer

the genomes of related species with strikingly different forms may have only minor differences in gene sequence or regulation helping us understand the origin of the myriad diverse forms that cohabit this planet

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In both plants and animals, development relies on

answer

a cascade of transcriptional regulators turning genes on or off in a finely tuned series

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Molecular evidence supports the separate evolution of

answer

developmental programs in plants and animals

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Mads-box genes in plants are the

answer

regulatory equivalent of Hox genes in animals

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Mads-box genes

answer

Genes A, B, and C all encode regulatory transcription factors that contain this DNA-binding domain. These genes are part of the regulatory cascade that controls the floral organ identity genes.

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