Substance Sugar Protein Virus Bacterium Time to di use 1 m 1 msec 10 msec 100 msec 1 second Time to di use 10 m 100 msec 1 second 10 seconds 100 seconds D Knecht Di usion The spread of parJcles through random moJon Water molecules are in constant moJon They bump into each other and other molecules in soluJon causing random movement Brownian moJon i e there is NO direcJonality The larger the molecule the slower the movement As distance increases the Jme for it to move that distance increases as a square funcJon 100x longer to get 10x as far How does the cell move large biological materials nucleic acids proteins organelles from one place to another through a very crowded cytoplasm The cytoskeleton The cytoskeleton drives cell shape changes and motor proteins help move cargo around Cell Size Shape Most eukaryoJc cells are 10 30 m in diameter but vary greatly in shape Small molecules move into and out of cells by di usion through the membrane O2 and nutrients must di use into the cell and CO2 and waste products di use out of the cell As a spherical cell gets larger its cytoplasmic volume increases as a cubic funcJon V 4 r3 3 while its membrane surface area increases as a square funcJon 4 r2 The amount of transport is limited by the amount of surface area Surface area cannot keep up with volume This is a limit to the size of metabolically acJve cells Growth is oien coupled with division to maintain cells at a manageable size Cell Size Cell Shape and Di usion 1 All living creatures are made of one or more cells 2 The cell is the basic structural unit of living things 3 On today s Earth cells can only arise by division from preexisJng cells Cell Biology is based on the Cell Theory Note Not all cells have to have all of these properJes Many cells in our bodies cannot reproduce for example Being composed of proteins lipids carbohydrates and nucleic acids Having a high degree of complexity Encoding informaJon in genes Being delineated from the rest of the world by a membrane Being able to reproduce themselves Being able to acquire and uJlize energy Being able to carry out a variety of chemical reacJons Being able to carry out mechanical acJviJes Being able to respond to sJmuli Being capable of self regulaJon Being capable of evolving Basic properJes of cells include The Central Dogma Proteins are the workhorses of cells they directly do many things cells do and catalyze the producJon of non protein consJtuents of cells Changes in DNA produce heritable changes in protein structure funcJon and expression Enzymes which carry out chemical reacJons Structural proteins which provide organizaJon Regulatory molecules which provide informaJon Proteins fold into speci c shapes to make Genes can be alternaJvely spliced proteins can be cleaved into mulJple acJve species DNA codes for mRNA mRNA codes for protein sequence DNA also codes for small RNA species that regulate the stability of mRNA i e miRNA siRNA In general but not always one gene codes for one protein GeneJc InformaJon Flow Prokaryote minimum 477 in Mycoplasma parasite Typically 1000 4000 Eukaryote Simple single celled 6300 Complex mulJcellular 30 000 We now know the complete sequence of the genomes of many organisms We can read the gene sequences to predict the complement of proteins the proteome of many organisms What we are sJll trying to do is gure out how all those proteins interact in cells to give rise to quite complex behaviors How many di erent proteins does it take to make a cell Genomes genes and proteins All the cells of an organism contain the same DNA So why do we have such a variety of cell types and funcJons Remember a cell whether a single celled organism or a cell in a mulJcellular organism does not express all of its genes all of the Jme In any given cell some genes are turned on some are turned o Some are expressed at high levels some low This is known as di erenJal gene expression TranscripJon factors are proteins that bind DNA and can acJvate or repress the transcripJon of genes So depending on which genes are being transcribed the transcriptome and translated a cell will express a parJcular suite of proteins One of the central goals of cell biology is to understand how all those proteins interact with themselves and with other cellular components to carry out cell funcJons or to respond to changes inside or outside of the cell The response to internal external sJmuli occurs through cascades or pathways of interacJons between proteins lipids nucleic acids and other biochemicals in the process of signal transducJon Not all of the informaJon in a cell is encoded directly in DNA in a form we can read Some cellular responses may act through the exisJng proteins of a cell In addiJon since transcripJon factors themselves can be targets of signal transducJon pathways some responses lead to changes in gene expression that changes the suite of proteins in the cell As transcripJon factors can regulate the expression of other transcripJon factors cells can develop complex gene regulatory networks TranscripJonal changes are oien temporary and reversible in response to sJmuli In other situaJons the DNA and its associated histone proteins can become chemically modi ed i e by methylaJon or acetylaJon causing the underlying genes to be held in a transcripJonally acJve or inacJve semi permanent state SomeJmes these modi caJons can be stably inherited from one cell to another Such changes in the geneJc potenJal of a cell without changes to the underlying DNA sequence are the topic of epigeneJcs In this course we will not focus on transcripJon factor networks and changes in gene expression in response to sJmuli GeneJcs Developmental Biology Advanced Cell Biology This course will explore the interacJons of proteins lipids nucleic acids and biochemicals that underlie the amazing diversity of funcJons and behaviors exhibited by cells Prokaryotes Bacteria and Archaea lack a nucleus and internal membranes Eukaryotes MulJcellular animals plants and fungi and unicellular proJsts have a nucleus and an extensive internal membrane system This course will focus almost exclusively on eukaryoJc cells There are two basic types of cell on earth Plasma Membrane lipid bilayer boundary of cell that allows it to create an internal environment di erent from the external environment Special systems exist to transport both small and large molecules cross this barrier Cytoplasm the soluble internal contents of the cell Nucleoid area in which circular DNA