張學偉 生物醫學暨環境生物學系 助理教授 http://genomed.dlearn.kmu.edu.tw 僅供教學使用

If a salamander loses a leg, it can grow a new one Shortly after you drink a milk shake, bacteria living in your large intestine turn on certain genes If a salamander loses a leg, it can grow a new one Salamander蠑螈

Cancer-causing genes were first discovered in a chicken virus Lung cancer causes more deaths than any other kind of cancer

BIOLOGY AND SOCIETY: BABY’S FIRST BANK ACCOUNT In recent years umbilical cord and placental blood has been collected at birth.  store in liquid nitrogen Stem cells http://www.sciam.com.tw/read/readshow.asp?FDocNo=4 Figure 11.1

Umbilical cord and placental blood is rich in stem cells Stem cells can develop into a wide variety of different body cells  Most cells of the adult lack this ability. Figure 11.8

FROM EGG TO ORGANISM: HOW AND WHY GENES ARE REGULATED Four of the many different types of human cells They all share the same genome What makes them different? (a) Three muscle cells (partial) (b) A nerve cell (partial) (c) Sperm cells (d) Blood cells Genome (基因體;基因組):一個細胞中的所有遺傳物質 Figure 11.2

In cellular differentiation Certain genes are turned on and off Cells become specialized in structure and function It is the regulation of genes that leads to this specialization.

Patterns of Gene Expression in Differentiated Cells In gene expression A gene is turned on and transcribed into RNA Information flows from genes to proteins, genotype to phenotype The regulation of gene expression plays a central role in development from a zygote to a multicellular organism

Patterns of gene expression in specialized human cells Pancreas cell Eye lens cell (in embryo) Nerve cell Glycolysis enzyme genes Crystallin gene Insulin gene Hemoglobin gene Key: Active gene Inactive gene Figure 11.3

DNA Microarrays: Visualizing Gene Expression DNA microarray- is a glass slide carrying thousands of different kinds of single stranded DNA fragments arranged in an array. Array (grid) Glass slide 參考

DNA Microarrays: Visualizing Gene Expression A DNA microarray allows visualization of gene expression 1 mRNA isolated Reverse transcriptase and labeled DNA nucleotides 2 cDNA made from mRNA DNA microarray (each well contains single stranded DNA from a particular gene) 單股 單股 3 cDNA applied to wells 4 Unbound cDNA rinsed away Fluorescent spot Nonfluorescent spot cDNA DNA of gene DNA of gene Figure 11.4a

The pattern of glowing spots on a microarray enables researchers to determine which genes are turned on or off Figure 11.4b

The Genetic Potential of Cells- plant & animal Differentiated cells All contain a complete set of DNA May act like other cells if their pattern of gene expression is altered Clones- Genetically identically organisms

The Genetic Potential of Cells- plant Differentiated plant cells Have the ability to develop into a whole new organism Root of carrot plant Plantlet Cell division in culture Single cell Root cells in growth medium Adult plant Figure 11.5

The Genetic Potential of Cells- plant The somatic cells of a single plant can be placed in a growing medium to produce clones Clones- Genetically identically organisms

The Genetic Potential of Cells- animal Regeneration Is the regrowth of lost body parts in animals (reverse differentiated state) Re-differentiate If a salamander loses a leg, it can grow a new one

Reproductive Cloning of Animals Nuclear transplantation Involves replacing nuclei of egg cells with nuclei from differentiated cells Has been used to clone a variety of animals Scottish researchers cloned the first mammal in 1997 Dolly, the sheep

The procedure that produced Dolly is called reproductive cloning reproductive cloning (individual) & therapeutic cloning (cell) The procedure that produced Dolly is called reproductive cloning Reproductive cloning Donor cell Nucleus from donor cell Implant embryo in surrogate mother Clone of donor is born Therapeutic cloning Remove nucleus from egg cell Add somatic cell from adult donor Grow in culture to produce an early embryo Remove embryonic stem cells from embryo and grow in culture Induce stem cells to form specialized cells for therapeutic use Figure 11.6

Other organisms have since been produced using this technique, some by the pharmaceutical industry (a) Piglets (b) Banteng 白臀野牛 Figure 11.7

Therapeutic Cloning and Stem Cells Produces embryonic stem cells (ES cells) ES cells- are cells in an early animal embryo that differentiate during development to give rise to all the specialized cells in the body. Development- the process from fertilized egg to embryo

Embryonic stem cells- Can give rise to specific types of differentiated cells Liver cells Cultured embryonic stem cells Nerve cells Heart muscle cells Different culture conditions Different types of differentiated cells Figure 11.8

Adult stem cells Generate replacements for nondividing differentiated cells Are unlike ES cells, because they are partway along the road to differentiation

In 2001, a biotechnology company announced that it had cloned the first human embryo Stopped at 6-cell stage Figure 11.9

THE REGULATION OF GENE EXPRESSION How is gene expression regulated in a cell? Chromosome Unpacking of DNA DNA Gene The “pipeline” in a eukaryotic cell Transcription of gene Intron Exon RNA transcript Processing of RNA Flow of mRNA through nuclear envelope Cap Tail Nucleus mRNA in nucleus Cytoplasm mRNA in cytoplasm Translation of mRNA Breakdown of mRNA Polypeptide Various changes to polypeptide Active protein Breakdown of protein Figure 11.10 Broken down protein

Gene Regulation in Bacteria Bacteria can alter gene expression for metabolism based on environmental factors Control sequences Are stretches of DNA that coordinate gene expression An operon 操縱組 Is a cluster of genes with related functions, including the control sequences

A promoter 啟動子 An operator 操作子 Is a control sequence Is the site where the transcription enzyme initiates transcription An operator 操作子 Is a DNA sequence between the promoter and the enzyme genes [位置關係] Acts as an on and off switch for the genes

The lac operon in “off” mode Lactose absent Operon Regulatory gene Promoter Operator Lactose-utilization genes DNA mRNA RNA polymerase cannot attach to promoter Protein Active repressor (a) Operon turned off (default state when no lactose is present) Figure 11.11a

The lac operon in “on” mode Lactose present DNA RNA polymerase bound to promoter mRNA Protein Inactive repressor Lactose Enzymes for lactose utilization (b) Operon turned on (repressor inactivated by lactose) Figure 11.11b

Gene Regulation in the Nucleus of Eukaryotic Cells Eukaryotic cells have more elaborate mechanisms of gene expression than bacteria DNA unpacking Transcription 核 RNA processing RNA transport Visual Summary 11.4

The Regulation of DNA Packing Cells may use DNA packing for long-term inactivation of genes X chromosome inactivation Is seen in female mammals Involves one entire X chromosome in each somatic cell being almost entirely inactive

Tortoiseshell pattern on a cat Two cell populations in adult cat: Early embryo: Cell division and X chromosome inactivation Active X Orange fur X chromosomes Inactive X 隨機的 Inactive X Active X Black fur Allele for orange fur Allele for black fur other Orange/orange black/black Orange/orange black/black Figure 11.12

Calico cat also has white area, which are determined by another gene. 有斑點的動物[C] calico Figure 11.12x

The Initiation of Transcription The most important stage for regulating gene expression is transcription. Eukaryotic control mechanisms Involve regulatory proteins interact with DNA Regulate transcription

Model for turning on of a eukaryotic gene repressor Activator proteins Transcription factors Other proteins RNA polymerase Enhancers Promoter Gene DNA Bending of DNA Transcription Figure 11.13

Repressors are less common than activators Each eukaryotic gene Has its own promoter and other control sequences May have repressors, which turn genes off May have activators, which turn genes on Repressors are less common than activators

Transcription factors Are proteins that turn on eukaryotic genes Enhancers [DNA seq] Are bound with activator proteins as the first step in initiating transcription Silencers [DNA seq] Are repressor proteins that may inhibit the start of transcription

The “default” state for most genes in multicellular eukaryotes seems to be “off” with the exception of “ housekeeping” genes for routine activities.

RNA processing includes The eukaryotic cell Localizes transcription in the nucleus Processes RNA in the nucleus RNA processing includes The addition of a cap and tail to the RNA The removal of any introns The splicing together (join) of the remaining exons

Producing two different mRNAs from the same gene Exons DNA RNA transcript Alternative RNA splicing or mRNA Figure 11.14

Regulation in the Cytoplasm After eukaryotic mRNA is transported to the cytoplasm, there are additional opportunities for regulation mRNA breakdown Translation 細胞質 Protein activation Protein breakdown Visual Summary 11.5

(nucleotides, for example) The Breakdown of mRNA Eukaryotic mRNAs Can have different lifetimes Are all eventually broken down and their parts recycled Macromolecules (mRNA, for example) Synthesis Breakdown Monomers (nucleotides, for example) Figure 11.15

The Regulation of Translation The process of translation May be regulated by many different proteins

Post-translation control mechanisms Protein Alterations Post-translation control mechanisms Occur after translation Often involve cutting polypeptides into smaller, active final products Cutting Figure 11.16 Initial polypeptide Insulin (active hormone)

Protein Breakdown The selective breakdown of proteins is another control mechanism operating after translation

In a multicellular organism Cell Signaling In a multicellular organism Gene regulation can cross cell boundaries (Cell-to-cell signaling: is a key mechanism in the development of a multicellular organism) A cell can produce chemicals that induce another cell to be regulated a certain way

Signal transduction Is the main mechanism of cell-to-cell signaling 1 Signaling cell 1 1 Is the main mechanism of cell-to-cell signaling Secretion Signal molecule Plasma membrane Reception 2 2 3 4 Receptor protein 3 4 Signal-transduction pathway Transcription factor (activated) Target cell Nucleus 5 5 Response Tran- scription New protein mRNA 6 Translation 6 Figure 11.17

THE GENETIC BASIS OF CANCER Genes That Cause Cancer As early as 1911 certain viruses were known to cause cancer Cancer-causing viruses often carry specific genes called oncogenes Cancer-causing genes were first discovered in a chicken virus Rous sarcoma virus (RSV, chicken).

Oncogenes and Tumor-Suppressor Genes Proto-oncogenes Are normal genes that can become oncogenes Are found in many animals Code for growth factors that stimulate cell division For a proto-oncogene to become an oncogene, a mutation must occur in the cell’s DNA

Proto-oncogene DNA (a) Mutation within the gene (b) Multiple copies of the gene (c) Gene moved to new DNA locus, under new controls Oncogene New promoter Normal growth-stimulating protein in excess Normal growth-stimulating protein in excess Hyperactive growth-stimulating protein Figure 11.18

Tumor-suppressor genes Help prevent uncontrolled cell growth May be mutated, and contribute to cancer Mutated tumor-suppressor gene Tumor-suppressor gene Normal growth- inhibiting protein Defective, non-functioning protein Cell division under control Cell division not under control Figure 11.19

Genes That Cause Cancer Proto-oncogene (normal) Genes That Cause Cancer Oncogene Mutation or virus Normal protein Mutant protein Normal regulation of cell cycle Out-of-control growth (leading to cancer) Normal growth-inhibiting protein Defective protein Mutation or virus Tumor-suppressor gene (normal) Mutated tumor-suppressor gene Visual Summary 11.6

The Effects of Cancer Genes on Cell-Signaling Pathways Normal proto-oncogenes and tumor-suppressor genes Often code for proteins involved in signal transduction The proto-oncogene ras Is involved in signal transduction Can contribute to cancer if mutated

The Progression of a Cancer Colon cancer begins as an unusually frequent division of normal-looking cells in the colon lining Colon wall 1 2 3 Cellular changes: Increased cell division Growth of benign tumor Growth of malignant tumor DNA changes: Oncogene activated Tumor-suppressor gene inactivated Second tumor-suppressor gene inactivated (a) Stepwise development of a typical colon cancer Figure 11.20a

Genetic changes or mutations Result in altered signal-transduction pathways Chromo- somes 1 mutation 2 mutations 3 mutations 4 mutations Normal cell Malignant cell (b) Accumulation of mutations in the development of a cancer cell Figure 11.20b

“Inherited” Cancer Cancer is always a genetic disease because it always results from changes in DNA In some families, mutations in one or more genes predisposing the recipient to cancer can be passed on Such a cancer is familial, or inherited

Breast cancer Has nothing to do with inherited mutations in the vast majority of cases In some families can be caused by inherited cancer genes Can be caused by mutations affecting the BRCA1 and BRCA2 genes

The Effects of Lifestyle on Cancer Risk Is one of the leading causes of death in the United States Can be caused by carcinogens (cancer causing agent), e.g. UV radiation, Tobacco, Alcohol Exposure to carcinogens Is often an individual choice, but can be avoided

Table 11.1

EVOLUTION CONNECTION: HOMEOTIC GENES effect Homeotic genes Are master control genes Regulate many other genes Help direct embryonic development in many organisms Figure 11.21 Homeoboxes Are sequences of nucleotides common in many organisms Can turn groups of genes on and off during development

Homeotic genes in two different animals Fly chromosome Mouse chromosomes Fruit fly embryo (10 hours) Mouse embryo (12 days) Adult fruit fly Adult mouse Figure 11.22