Exam 1: Lecture 6

Question 1

Comparison of Nuclear Gene Content

Answer 1

• genomes of diverse organisms can harbor very different numbers of genes
• idea that more complex organisms would have dramatically higher numbers of genes than simple organisms is not true in all circumstances
• Craig Venter and Francis Collins leaders of private and public efforts sequence human genome

Question 2

Gene Duplication (What?)

Answer 2

• one path to acquiring new genes
• some cases individual genes are duplicated while in other situations large segments of chromosomes can be duplicated
• often occur as result of error in homologous recombination or from movement of transposable element
• rare cases entire chromosome or genome is duplicated which result from errors in chromosome segregation and cell division

Question 3

Gene Duplication (When?)

Answer 3

• can occur during formation of gametes during meiosis as well as mitosis
• several cancers are due to gene duplications in isolated tissues

Question 4

Gene Duplication (Happens? sub-functionalization)

Answer 4

• immediately after, both daughter genes are identical in sequence, structure and function
• as time proceeds random mutations knock out complementary functions in two daughter genes thereby leaving each daughter gene to execute subset of tasks that were controlled by ancestral gene

Question 5

Gene Duplication (Happens? neo-functioanlization)

Answer 5

• random mutations alter function of only one of two daughter genes.
• results in one daughter carrying out all ancestral functions while other daughter gene acquires new functions

Question 6

Mutatioin That Lead to Neo-functionalization

Answer 6

• can affect regulatory models or coding sequences
• note: in hypothetical example in note two daughter genes carrying out same function (coding sequence not altered) but they are doing it indifferent tissues.
• If coding sequence is changed then the actual function of the encoded protein will diverge

Question 7

Gene Gain and Loss

Answer 7

-can have profound influence–>lead to evolution of bacterial pathogens and marine phytoplankton from putative brown algae

Question 8

Comparison of Modern Primates

Answer 8

• indicates 100’s of genes that have been lost and gained over last 48 million years
• losses and gains could be underlying causes for some of difference that are observed between various primates
• differences between the species can also be cause by differences in DNA sequences of common genes, expression patterns, transcriptional levels and protein modifications

Question 9

Organization of Human Genome

Answer 9

• contains approximately 30,000 genes (note each gene found in two copies)
• only 1.5% is taken up by coding portion (exons) of genes
• rest made up of non-coding segments like introns, regulatory and untranslated sequences, intergenic DNA, pseudogenes, gene fragments and satellite sequences.
• last category is made up by remnants of transposable elements
• simpler organisms have higher gene density and thus fewer stretches of non-coding DNA
• also contains mitochondrial genome

Question 10

Mitochondrial Genome

Answer 10

-portion of genome is efficiently organized. Contributes 37 genes and almost no non-coding DNA

Question 11

DNA Organization: Sea Urchin

Answer 11

• discovered that mRNA transcripts contained only a fraction of the sequences that were found within genomic DNA
• for the first time showed that the nuclear genome contained a significant portion of non-coding sequences
• presaged several discoveries including the identification of exons and introns and the process of RNA splicing
• • Sequencing of the Drosophila, mouse, and human genomes confirmed that similar relationships existed in other complex organisms

Question 12

Non-coding DNA

Answer 12

• the vast majority of the human genome is comprised of non-coding DNA
• this is true of nearly all eukaryotic organisms
• exception:yeast which is a single celled eukaryote
• yeast genome has high gene density and fewer non-coding DNA segments than other eukaryotes
• Bacterial genomes are even more compact: their genomes are fairly devoid of introns, transposable elements, pseudogenes and repetitive sequences

Question 13

Pseudogenes

Answer 13

• inactive genes that are either no longer expressed due to a mutation in regulatory element or is dysfunctional due to a mutation within coding sequences
• can be recognized since they contain sequences that are similar to functional gene
• formation is very common after gene duplication and significant portion of eukaryotic genomes is comprised of inactive pseudogenes
• arise from duplications located relatively close to sister genes while those born from retrotransposition can be located at considerable distances

Question 14

Psudeogene: mutation in regulatory element

Answer 14

-duplication event takes place which is then followed by accumulation of deleterious mutations in one of daughter genes

Question 15

Psudeogene: mutation within coding sequence

Answer 15

• messenger RNA is converted into cDNA clone by the reverse transcriptase enzyme.
• this DNA copy inserted into genome via retrotransposition.
• original mRNA lacks enhancer and promoter elements, newly integrated cDNA copy cannot be transcribed and is inactive in genome

Question 16

Example of Pseudogenes

Answer 16

• analysis of hemoglobin genes
• during evolution globin genes have been duplicated several times
• some genes transcribed during fetal development while others expressed only in adulthood.
• few globin genes expressed during both phases.
• in addition to these active genes several of duplication products have been inactivated by random mutations.
• sit idle within genome on chromosome 11 and 16

Question 17

Transposable Elements

Answer 17

• makeup significant portion of eukaryotic genomes
• ancestors of bacteriophages and viruses
• continue to exist and infect both prokaryotic and eukaryotic cells
• bacterial genomes contain very few transposbale elements
• yeast contains a few more but overall number still small
• in genomes of higher organisms (humans and maize) percentage of genome comprised by these elements increases significantly

Question 18

Varigated Coloration of Corn

Answer 18

-due to localized movement of transposable elements around genome
some instances the element will insert itself into gene that is required for normal color of kernel
-inactivation of these genes which happens on a cell by cell basis results in the variegated pattern.