Introduction to Biological Anthropology: Notes 6 Beyond Mendel: Molecular genetics, cell division, and sex Copyright Bruce Owen 2008 Mendel s model

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1 Introduction to Biological Anthropology: Notes 6 Beyond Mendel: Molecular genetics, cell division, and sex Copyright Bruce Owen 2008 Mendel s model was completely abstract. No one had ever seen a particle of inheritance, nor anything that resembled Mendel s whole scheme of alleles randomly segregating into gametes, combining into offspring, and so on But now we know a lot about the physical mechanisms behind the abstract model he proposed today we will cover just enough about genetics to allow us to understand some processes that are important to how evolution works Living things are complex structures of many different chemical compounds mostly proteins and the functions of living things are essentially chemical processes, largely involving proteins what genes do is specify what proteins are produced, in what places and times, in order to grow the organism from an embryo and operate all the chemical reactions that make it work throughout its life proteins are a category of organic molecules a protein molecule is composed of a chain of smaller units called amino acids in the natural biological world, there are 20 different amino acids (some others can be made artificially or in non-biological processes) amino acids can form chains (proteins) in virtually any order, any combination, and any length the longest currently known in living things are about 27,000 amino acids long the sequence of amino acids in a protein is its primary structure the chain of amino acids folds and sticks to itself in a complex shape the shape is described by its secondary structure, tertiary structure, and quaternary structure, which we will not cover in detail the shape has a huge effect on the chemical properties of the protein the shape is largely determined by the sequence of amino acids: the protein s primary structure because that affects how and where the chain can bend, stick to itself, and so on Proteins have several kinds of functions some are structural proteins, which form the physical structure of the body, from cell walls, to bone, to hair, to fingernails, etc. others are motor proteins, which cause physical movement in muscles, move other molecules or structures into, out of, or within cells, and so on others are enzymes, which cause specific chemical reactions to take place the enzyme is not used up in this process; it is like a little machine that causes the reaction to happen as long as the raw materials for the reaction are present so producing an enzyme in the right circumstances is like flipping a switch to cause a particular chemical reaction to happen

2 Intro to Biological Anthro F 2008 / Owen: Molecular genetics p. 2 and other types with other functions: antibodies, signaling proteins, etc. What the genetic code codes for genes specify the primary structure of proteins: structural, motor, enzyme, etc. that is, the order of amino acids in each protein and control when, where, and how much of each protein is made The genetic code is carried on deoxyribonucleic acid, or DNA Amazing facts for your next party, not on any test: a typical complement of human DNA in a single cell is 46 strands of a long, narrow molecule just 20 angstroms (20 x meters) wide each strand is up to 12 cm long, with all 46 totaling about 2 meters long! if the DNA in one cell in your body was as large around as a human hair (75 microns, 75 x 10-6 m), the 46 pieces would total about 750 kilometers long (450 miles)! at this scale, single genes would range from 2 cm (less than 1 inch) long to about 75 meters (244 feet, or 81 yards) long (500 codons x 3 bases/codon x 3.4 angstroms/base, to 2 million codons) DNA has an unusual structure that allows the molecule to encode a huge amount of information - just what is needed for a "genetic code" double helix structure, sort of like a spiral staircase (but not exactly) two long "backbone" strands of phosphate and sugar molecules holding "stairsteps" or "rungs" made from matched pairs of nucleotide bases the bases can be in any order along the backbone but the bases join to the other side only in matched pairs; adenine only to thymine, guanine only to cytosine adenine and thymine (A and T) guanine and cytosine (G and C) [note: thymine is a base in the structure of DNA; it is not the same as thiamine (or thiamin), which is vitamin B 1 ] so each side of the DNA molecule is like an extremely long sequence of seemingly random selections of the four letters (the four bases) while the other side is its complementary, inverse image DNA works as a genetic code because the sequence of the nucleotide bases determines the sequence of amino acids in a protein (the protein s primary structure) there are 20 amino acids, but only 4 bases so the code for each amino acid is a combination of 3 nucleotide bases these combinations of three bases are like 3-letter words for example, the combination Guanine, Cytosine, Thymine (GCT) codes for the amino acid alanine each of these triplets is called a codon since each codon consists of 3 bases, and there are four possibilities for each base, there are 4 x 4 x 4 = 64 possible codons 61 of these combinations signify amino acids some amino acids are specified by more than one different codon for example, GCT, GCC, GCA, and GCG all code for alanine

3 Intro to Biological Anthro F 2008 / Owen: Molecular genetics p. 3 the remaining 3 codons indicate the beginning or end of a protein DNA physically controls the production of proteins in a complex process that we will cover only very superficially here DNA normally is inside the cell nucleus, a specialized sack of material inside the cell inside the nucleus, part of the DNA unzips into two strands, each with an exposed sequence of bases only one strand is active isolated nucleotides are floating around inside the nucleus bases that are complementary to the ones exposed on the active strand stick onto the exposed bases the new nucleotides bond to each other, then peel off as a one-stranded inverse copy of the exposed portion of the DNA this single-strand copy is messenger RNA, or mrna the mrna is then "edited" segments called introns are clipped out, and the remainder is spliced back together this seems unnecessarily complicated, but that is how it works and I have left out quite a few details already the process of producing mrna from DNA is called transcription the mrna then moves out of the nucleus into the cytoplasm, the main mass of the cell, where most of the functions of the cell are carried out in the cytoplasm, the mrna encounters a structure called a ribosome where the ribosome is in contact with the mrna, a particular reaction occurs small molecules called transfer RNA (trna) can attach to the mrna with the help of the ribosome these molecules have three bases exposed on one part and another part that can bond to one specific amino acid there is one type of trna for each possible codon and each type of trna can carry only one of the 20 amino acids so the various types of trna define the translation of codons into specific amino acids in this way, only the trna with the right three complementary bases can bond to the mrna at a given point the ribosome moves along the mrna like the head of a tape player passing along a tape at each codon, it facilitates the appropriate complementary trna to stick onto the mrna this puts an amino acid, determined by the type of trna, next to the one attached by the previous trna these bond together as the ribosome moves down the mrna, releasing the previous trna and its amino acid this forms a chain of amino acids that corresponds to the sequence of codons on the mrna a further process folds the chain up as allowed by its primary structure, and a protein has been produced there are links on the class web page to a more thorough description of the process, and to videos that cover much of this material

4 Intro to Biological Anthro F 2008 / Owen: Molecular genetics p. 4 but the level of detail in these notes is sufficient for our purposes in this class each segment of DNA that codes for a protein is a gene (actually an allele: a specific variant of a gene, like the green allele of the seed color gene) human genes range from about 500 codons long to about 2 million codons long the total human complement of DNA is about 3 billion base pairs long within which there are an estimated 30,000 to 100,000 genes yet most (over 98%) of our DNA is not genes, that is, most of our DNA does not code for proteins this is sometimes called "junk" DNA although some of it still might prove to have some purpose there are vast stretches that are simple repeating units others that are seemingly random garbage others that seem to be appropriate for making proteins, but are never used these are apparently "turned off" genes possibly ones that are damaged or no longer useful even within genes, there are the introns that get edited out before the protein is produced While many genes code for proteins that are useful in themselves, recall that others code for proteins that mostly regulate other chemical reactions these are called "regulatory genes" the action of the enzymes that these genes produce is mainly to affect the progress of other processes so regulatory genes affect whether certain other genes are activated or control overall patterns like the number of segments in the body and limbs, the relative size of structures like specific portions of the brain, the relative proportions of different parts of the face and head, and so on Cell division For an organism to grow, repair, and maintain itself, it has to be able to produce new cells the process that does this is cell division in which one cell pauses its normal functions and goes through a special procedure in order to split into two daughter cells that each have all the components needed to survive For cells to be able to reproduce, they have to be able to make a copy of their DNA for the new cell this process is called DNA replication Most of the time, the DNA in a cell is floating loose in the nucleus of the cell, like spaghetti in a fishbowl (actually, more like a huge hairball, but let's not go there) in this state, portions of the DNA strands are busily producing mrna to make proteins to maintain the cell and make it do whatever it does most cells have the full allotment of DNA that is, muscle cells and liver cells have exactly the same DNA but different parts of the DNA are active in each type of tissue

5 Intro to Biological Anthro F 2008 / Owen: Molecular genetics p. 5 so that each type of tissue has a different combination and arrangement of proteins and other components in humans, the full complement of DNA is 46 strands these strands come in pairs, so we actually have 23 paired strands of DNA in most cells when it is time for the cell to divide, the DNA undergoes replication as in DNA transcription, the DNA unzips at the center of each rung the nucleotide bases are exposed in the presence of the proper enzymes, the corresponding nucleotide bases are added to each one-sided strand creating two double-sided strands, each identical to the original piece of DNA Now the cell as a double complement of DNA, so when it divides, one set will go into each of the two resulting cells this temporarily doubles the number of DNA strands in the cell each of the 46 stands is accompanied by its duplicate this temporarily doubled allotment of DNA then condenses into chromosomes, which are visible with a microscope these are compact, sausage-like structures of tightly wound up DNA with some other proteins to hold it together each strand of DNA packs into a single chromosome the chromosomes vary in length and, when stained with certain dyes, have characteristic patterns of bands since in most cells, the DNA strands come in pairs, they form pairs of chromosomes with a microscope, you can see the pairs of chromosomes that match in length and banding these are called homologous pairs in humans, most cells have 23 pairs of chromosomes, or 46 chromosomes total other animal and plant species have more or fewer chromosomes the number does not seem to have much functional importance since each strand of DNA has duplicated itself, each chromosome appears to be two identically-banded sausages laying next to each other, joined at the waist, looking like a X at this stage, the cell temporarily has a double complement of chromosomes this is the stage in the textbook illustration on pg 27, where each chromosome is doubled The cell is now ready to divide when body cells divide for normal growth and maintenance, they do it through a process called mitosis the doubled chromosomes line up along the middle of the cell fibers from each side of the cell connect to the centers of the chromosomes then those centers joining the duplicates break apart, and one copy of each chromosome is pulled to each side of the cell the entire cell splits between the two clumps of chromosomes producing two cells, each with one complete set of chromosomes, exactly like the original cell's

6 Intro to Biological Anthro F 2008 / Owen: Molecular genetics p. 6 the two cells after division are called "daughter" cells when cell division is over, the chromosomes unravel, the DNA sprawls out through the nucleus, and it gets back to its normal role of guiding the production of proteins except that now there are two cells with the same DNA instructions this process is called mitosis: cell division that produces daughter cells that have two of each chromosome, just like the parent cell memory aid: mitosis: produces daughter cells with Two of each chromosome this is the normal kind of division that produces almost all cells in the body Sexual reproduction requires a different process parents must produce special-purpose gametes with just half the normal complement of DNA that is, gametes are haploid, with just one of each of the 23 chromosomes so that when the gametes combine to form a zygote (the first cell of the offspring), the zygote will have the normal amount of DNA that is, the zygote is diploid, like other normal body cells: it has two of each of the 23 chromosomes the zygote then divides repeatedly to create a multi-celled embryo, which develops into a fetus using the normal form of cell division discussed above (mitosis) in order for this to work, the egg and sperm must each have only half as many strands of DNA as do normal cells otherwise, when they merged, the resulting cell would have twice as many strands of DNA as either parent gametes (sperm and eggs) are created by a different kind of cell division, called meiosis meiosis produces daughter cells with half as many chromosomes as the parent cell memory aid: me1osis: produces daughter cells with 1 of each chromosome meiosis is a more complex process involving a total of three divisions the important point is that the end product is cells with not two, but just one of each chromosome: cells that are haploid see page 29 of the text for an illustrations of the overall difference between mitosis and meiosis. So, what is the point of sex? it creates offspring that have a mix of genes from each parent the offspring has a different combinations of characteristics than does either parent this creates new variants for natural selection to select from sex mixes up the genes in the offspring in two ways One: by creating a zygote that has pairs of chromosomes, one from the mother, and the other from the father so the zygote is similar in some ways to the mother, and similar in some ways to the father but is not identical to either one of them Two: the chromosomes from each parent are actually mixes of that parent s two chromosomes due to the process of crossing over during meiosis

7 Intro to Biological Anthro F 2008 / Owen: Molecular genetics p. 7 during one stage of meiosis, all of the doubled chromosome pairs physically line up next to each other for example, the two doubled chromosome 20s lay next to each other the genes on the two chromosome 20s may be different because one of these doubled chromosome 20s originally came from the individual's mother, the other from the individual's father then crossing over occurs the adjacent chromosomes physically break and swap pieces for example, the tip of one of the copies of the chromosome 20 from the mother might break off, while the tip of one of the copies of the chromosome 20 from the father breaks at exactly the same point these pieces are interchanged the result is that one of the copies of the chromosome 20 from the mother now has the tip of the chromosome 20 from the father and one of the copies of the chromosome 20 from the father now has the tip of the corresponding chromosome from the mother each copy of each chromosome may experience none, one, or multiple crossings over the result of this process is to mix up even the genes on the same chromosome into new combinations this vastly increases the possible combinations of genes in the offspring With both independent assortment of whole chromosomes, and crossing over that swaps batches of genes between chromosomes, the genes get almost completely randomly divided up into the gametes and a random pair of gametes combine to form a zygote the result is a new individual with an almost random combination of genes that is, sexual reproduction allows the offspring to have any imaginable combination of the parents genes this creates new combinations of traits in every offspring, giving selection a nearly endless supply of variation to act upon The point of delving into all this reproduction stuff it shows the physical processes through which Mendel s abstract model actually takes place how alleles on different chromosomes get randomly mixed in the offspring how alleles on the same chromosomes still get randomly mixed in the offspring through crossing over which shows how individuals can both resemble their parents (because they have their parents alleles) and always be different from their parents (because they have different combinations of those alleles than does either parent) this is exactly what Darwin (and others) observed offspring resemble their parents but there is always lots of variety for selection to work on all of which creates the variation that is necessary for natural selection to work and to cause evolution

8 Intro to Biological Anthro F 2008 / Owen: Molecular genetics p. 8 this complicated system of sexual reproduction with thorough mixing of alleles must itself have evolved this whole process of sexual reproduction seems to produce offspring that are as variable as possible combining the traits of the parents in as many different ways as possible why would that be? because it speeds up evolution! organisms that produce more variable offspring evolve more rapidly the more variants there are, the more natural selection has to select from populations that evolve more rapidly are more likely to successfully adapt to changing conditions, rather than going extinct so they are more likely to persist over time, and to be the starting points for new species when speciation events occur so natural selection would favor features that led to producing more variable offspring sexual reproduction crossing over even large amounts of junk DNA between genes because the more junk DNA there is, the more often crossing-over will cut through a section of junk, rather than a needed stretch of DNA so having lots of junk DNA should make crossing-over more successful at mixing alleles without destroying any allowing crossing over to increase the variability of offspring without causing too many errors that kill the offspring