Biology 105                                          Chromosomes and DNA

I. Blood Types
    A. Inheritance of blood types is more complex than the traits we have discussed so far.  Blood type genetics involves both multiple alleles and codominance.
        1. A trait with _________________ alleles has more than two alleles present in the population, but each individual still only has two.  There are three human blood types alleles: ____, ____, and ____, giving the blood types A, B, AB, and O.
        2. This system shows both codominance and true dominance.  In codominance, _________ alleles are expressed in a heterozygote; neither is dominant to the other.  This is true of IA and  IB . Both, on the other hand, are dominant to i, which is a true _____________________. 
            a. This is because IA and IB  each cause the production of a _________________ on the outside of the red blood cells; i is an inactive allele that does not cause the production of any protein. 
                i. Therefore a person with IA and IB alleles will produce both A and B proteins on their red blood cells and will have the blood type (phenotype) __________. 
                ii. A person who is IA IA or IA i will produce only A proteins and will have type ____ blood.
                iii. A person who is ii will produce none of these proteins and the blood type will be _____.
    B. Blood types are also give the notation Rh+ or Rh-, which refers to the presence of another protein called ______________________.  This is inherited in the normal fashion with Rh+ dominant to Rh-.
    C. Since there are so few different blood types, they are not useful in identifying people (criminals, fathers, etc) but they can be used to rule people ______.

II. Chromosomes 
    A. Humans have _______ types of chromosomes. 
        1. Chromosomes 1-22 are the autosomes. There are two copies of each autosome in all non-gamete human cells. (Definition: An ________________ is any chromosome which is not a sex chromosome.)
        2. The 23rd type are the sex chromosomes, X and Y.  Males are _____; females are _____.   
                a. The X is much larger than the Y. (Interesting factoid: in birds _________ have two of the same chromosome and females have the different one.)
                b. So all eggs contribute an ___ chromosome to a human baby, and the father determines its gender by providing either an X or a Y chromosome. 
                    i. This was not understood by King Henry VIII of England, who divorced his wife Catherine of Aragon for failing to provide a male heir. 
    B. A ___________________________ is a picture of a person's chromosomes, taken from a dividing cell.  Each chromosome is cut out of the photo and placed next to its homolog on a chart.  
        1. A karyotype from placental cells can be used to determine the sex of a fetus and whether it has a correct set of chromosomes before it is born. There are two ways to get a prenatal karyotype:       
            a. In ________________________, amniotic fluid is removed from the uterus and fetal cells in the fluid are grown.   It is usually done during the 4th month and requires 3-4 weeks for results. 
            b. In chorionic villus sampling, a bit of placental tissue is removed and examined. It can be done in the _______ week; results require about 2 weeks, and so are available much earlier in the pregnancy than are amniocentesis results. 
    C. Human gender determination    
        1. About 1/20,000 people's karyotypes do not match their gender (_____ males or ______ females).  These "mistakes" can help us see how chromosomes are related to gender. 
        2. A gene called _____ on the Y chromosome is largely responsible for making a person male.  It causes expression of another gene, ______, or testis-determining factor.  Without TDF, testosterone cannot be made and therefore no male organs can develop.  
            a. The sry gene can be transferred to an  ____ chromosome by mistake, and then the person getting that X will be male, while a person getting the Y without its sry gene will be female.
        3. Besides needing a functional sry protein to be male, a person must also have the testosterone _____________________ protein.  If the body makes testosterone but cells can't respond to it, the person will be female, so some XY females make testosterone, but their cells don't realize it.  
            a. in some cases, there is a partial response to testosterone, which can lead to the development of "____________________" people.
    D. Sex-linked Traits
        1.The Y chromosome only carries a few genes necessary for maleness, while the ____, being much larger, carries genes affecting many parts of the body. 
            a . Since males only have one X, the concepts of dominance and recessiveness do not apply to genes on their X chromosomes, known as ________________ genes.
            b. Every trait on the X chromosome is _______________________  in males, which is why males are more likely than females to have certain genetic conditions.
            c. X-linked traits include colorblindness, Duchenne's muscular dystrophy, Norrie syndrome, and hemophilia.  A man whose X chromosome has one of these traits will express the condition; a woman who has an X chromosome with one of these traits will be a _______________.  Note: Women can express these conditions, but only if ____________ of their X chromosomes carry the same allele, because they are recessive conditions. This is often unlikely or impossible, if the condition reduces male fertility or kills boys before they grow up.
    E. To determine whether a trait is inherited as an autosomal dominant, autosomal recessive, X-linked dominant, or X-linked recessive, it is often useful to construct a pedigree. 
        1. A ________________________ is a diagram of a family.  Men are squares and women are circles.  From each couple, their children are suspended underneath, in order of oldest to youngest.   People with a genetic condition are marked by coloring in their symbol, and a deceased person is indicated by a slash.  
    
    F. Because female humans have 2 X chromosomes and males only have 1, you might think that females' cells have ____________ of the X chromosome products than males' cell do.  However, this is not so.  For humans to develop correctly their cells must have the (same) correct amount of protein gene products.  It is impossible for development to proceed correctly with a variable number of chromosomes.  Therefore, all human cells (in fact all mammalian cells) are designed to operate with only one X chromosome. 
            1. To achieve this, early in the development of all female fetuses, each cell ________________ one or the other of its X chromosomes randomly.  The chromosome turns into a small black lump called a ________ body. Each mammalian female has two types of cells: those in which her mother's X is active, and those in which her father's X is active.  
                a. This can be seen in tortoiseshell and calico cats: the gene for ____________________________ is on the X chromosome.  If a female cat inherits one black and one orange allele, her fur will have patches of color corresponding to where one or the other X was inactivated. 
    G. Chromosomal Variations
        1. Not everyone has the standard 46 chromosomes; occasionally people are born with incorrect chromosome numbers.  This causes incorrect development leading to a genetic condition, with consequences ranging from mild to deadly. 
        2. Incorrect chromosome number is due to an error in forming the gamete, and occurs more often in the ________________ than in the male. 
            a. A woman's eggs begin to form before her birth and then become _________________ until stimulated to develop, 13 - 50 years later.   This is in contrast with sperm, which are constantly made beginning in adolescence.  Eggs can be ____________________ during the years of waiting, resulting in the likelihood of chromosomal abnormalities increasing throughout the woman's childbearing years. 
            b. Chromosomal problems such as ______________ syndrome are statistically more likely to occur when the mother is older, and pregnant women over 35 are normally offered a test to determine the karyotype of the fetus.
                i. However, most Down syndrome babies are born to young women.  Why?

                Risk of Down syndrome
mother's age            chance of Down syndrome
       30                            1/885
       35                            1/365
       40                            1/109
       45                            1/25

        3. Incorrect numbers of sex chromosomes can be damaging to the individual but the symptoms are often relatively ___________. 
            a. The Y chromosome doesn't have enough on it to cause trouble.   At one time it was hypothesized that _______ males were larger and more violent than XY males but evidence has not supported that hypothesis.  Now XYY is considered a normal variant of XY (approx. 1/1000 men). 
            b. An _________ person is a subfertile male, sometimes retarded but often basically normal.  This is because the extra X in his cells can be turned off the same way the extra X in women's cells are.  
            c. A person inheriting only a single X chromosome is a sterile female. This karyotype is called ________.  The person is usually basically normal since only one X is needed per cell anyway.    
            d. ____________ is also female, and can be more severely affected, sometimes with mental retardation  as well as sterility, but often essentially normal. 
            e. An embryo conceived with only a Y and no X would not be viable.  There are many important genes on the X so this embryo would not develop. 
        4. Genetic disease is much more severe if an ________________________ is involved than if a sex chromosome is involved.          
            a. The mildest condition is Down syndrome, caused by 3 copies of chromosome _____.  People with this condition are slightly to moderately retarded, with characteristic facial features and often heart conditions.   
            b. In most other cases of extra or missing chromosomes, the affected fetus dies before birth or shortly after.  Chromosomal abnormalities are the largest cause of miscarriage; estimates vary but some experts believe that up to _________ of human conceptions are lost very early in the pregnancy due to chromosomal problems.  
        5. All of these conditions involving incorrect chromosome numbers are due to problems during the process of __________________, the type of cell division that produces gametes.

III . DNA
    A. Evidence that DNA is the ______________________ material
           1. Mendel studied genetics in the late 1800's, but the significance of what he had learned wasn't understood until ________, after his death.  In the first few decades of the 20th century many new researchers were attracted to the field, and the rules of inheritance became well known and understood
            2. A. The ______________ became the genetic research organism of choice; it was small, easy to feed and care for, and best of all, there was a new generation every two weeks.  Progress in understanding how genes were transmitted was rapid and satisfying.  
            3. A mystery remained, though ...what were genes really made of?  What __________________ brought information from the parents to the offspring?    And how did it work? 
    B. By the early 1900’s it was believed that genetic information was carried in the chromosomes, but it was not known how.  Some clever experiments showed the answer.
        1. Fred Griffith studied virulence (ability to cause disease) of pneumococcus bacteria, which cause pneumonia.  He had two strains of bacteria, S and R.  He did the following experiments on them:
                S bacteria + mice ® ________ mice
                R bacteria + mice ® ___________ mice
                heat killed S bacteria + mice ® _____________ mice. 
                Conclusion:

                heat killed S bacteria + live R bacteria + mice ® _________ mice, with live S bacteria in their bodies.
  (Note: bacteria are like people in some ways...once they die, they stay dead)
                Conclusion:

        2.  Avery, McLeod, and McCarty followed up on this observation.  They hypothesized that something in the S cells caused this genetic transformation. They did the following experiment:
                S cell extract + R cells ® _______________ mice
            a. This supported the hypothesis that something in the S cells caused the transformation.  Now they wanted to know what part of the S cell extract caused the transformation.  They hypothesized that it might be protein, RNA, or DNA, and did the following set of experiments: 
                S cell extract + R cells + protease (destroys proteins) ® ___________ mice
                S cell extract + R cells + RNAse (destroys RNA) ® _____________ mice       
                S cell extract + R cells + DNAse (destroys DNA) ® ___________ mice         
                Conclusion: 

    C. DNA structure
         1. Once it was determined that DNA was the genetic material, the race was on to understand how it was put together and how it worked.  As it turned out, once the ___________________________ of DNA had been figured out, it became obvious how it worked. 
    A. DNA is a long, unbranched chain of small molecules called _______________________, each of which itself consists of 3 parts: a sugar, a phosphate, and a base.
    B. The sugars and phosphates of all of the DNA nucleotides are the same, but there are 4 different bases.  Therefore, there are 4 different types of nucleotides.  The bases (and nucleotides)  are called ___, ___, ___, and ___.
    C. Erwin Chargaff was a chemist who made some early observations on the characteristics of DNA:
            1. He found that each member of a species has the ___________ proportions of the 4 bases. 
                 So all humans have the same % A, T, G, and C.
            2. Different species have different proportions of the 4 bases, so the %G in humans will be different than the %G in luna moths 
            3. Chargaff"s rule: the %___ in a sample = the % ___, and the % C = % G.  This was a most intriguing fact, and no one could explain it but everyone thought it was very significant. 
    D. __________ diffraction images taken by Rosalind Franklin (and used without her permission) showed that DNA was a long, thin molecule, with a constant diameter, and repetitious structure.
    E. Using Chargaff's and Franklin's data the structure of DNA was worked out by _____________ and Crick, who made models of the nucleotides and put them together in different patterns until they found one that was consistent with all of the data: the double helix.
    F. Features of the double helix
        1.  The ____________________ consists of two separate strands of nucleotides held together by complementary bonding.  This means that certain nucleotides "complement" each other or are always found together.   A always binds to T, and ___ to ___.
            a. This explains Chargaff’s rule, because for every T in the molecule there will be an A attached to it; same for C and G. 
        2. This is a perfect vehicle for carrying reproducible information.  There can be any order of bases on one strand -- unlimited possibilities.  These nucleotides are like letters which form genetic "words".  The sequence of one strand then _____________________ the other so that the information can be easily duplicated. 
 

V. DNA Replication
    A. The double helix explains heredity -- if the two strands of the DNA were separated, each could make its own complement, and you would end up with 2 double helixes both _____________________ to the original.  Each of these new double helixes would have one strand of old DNA and one strand of new DNA. This is called semi-conservative replication because the original strand is partially, but not totally, conserved.
        Demonstrate semi-conservative replication below:  

                                                                TGTCAA
                        TGTCAA      ®
                        ACAGTT

                ACAGTT   

          1. The double helix structure allows the sequence of bases on the DNA to be ________________ for each type of organism, while the chemical characteristics and the pattern of replication of the DNA is the ____________ for all. 
                a. THIS IS REALLY IMPORTANT!!  It means that all DNA works the same way!  Just like all English words work the same way.  You can read the word "blitherfussle" even if you don't know what it means.  A cell can read any DNA word, even if it doesn't know what it means. You can put human DNA in a ________________________ cell and the bacterial cell will use the DNA correctly to make a human protein, even though it can't use it.  But we can -- this is bioengineering. 
          2. Steps in DNA replication 
                a. First, the two complementary strands must ___________________.  This is easy because the bonds holding the complementary bases together are weak hydrogen bonds, much weaker than the bonds holding the bases of the same strand together.  
                b. Each single strand then attracts new ____________________________ bases.  These bases are present in the nucleus because the cell makes them all the time to have them ready for DNA replication. 
                c. The enzyme DNA ______________________ attaches the complementary nucleotides together to make a new strand. (An enzyme is a molecule that carries out biological work)
                d. The same enzyme also has the ability to tell whether the nucleotide it just added is correct.  If it is not, the enzyme will remove that nucleotide and try again.    This ability is called ____________________________ and is the main reason for the low error rate during replication.

VI. DNA fingerprinting
    A. Even though all human DNA is very similar, of course there are differences, some of which are ______________ to individuals and can be used to determine the source of a DNA sample.  
        1. These differences can allow __________________________ of a person leaving a DNA sample, for example semen, blood, saliva or even hair at a crime scene. 
        2.  Or they can be used to establish _______________________ between people, for example paternity or to reunite kidnapped children with their correct families. 
    B. If only a small amount of DNA is available, it can be amplified. 
        1. A ________ (polymerase chain reaction) machine can take a small amount of DNA and replicate it over and over, very like what happens in the cell.
            a. You take a piece of DNA, __________ it up to break the complementary bonds between strands, and then allow each single strand to form partners with complementary nucleotides.
            b. A type of DNA polymerase called ________ polymerase is used to join the nucleotides together.  Taq polymerase is unusual in that it comes from a bacteria that lives in boiling springs and therefore can work at high temperatures. 
            c. After each cycle of the machine, which only takes a few minutes, the amount of DNA is _____________.
              If you started with 100 pieces of DNA, how many would you have after 5 cycles of the machine?

    C. Once there is enough DNA to test, it is cut into pieces with molecules called _________________ enzymes. 
            1. These are useful because they cut DNA at specific sequences, called restriction sites, and convert the DNA into a reproducible set of smaller pieces.  If everyone had the same DNA sequences, everyone's pieces would be the same, but of course people differ. 
            2. One way in which they differ is in sequences called _______________, for variable number tandem repeats.  These are short DNA sequences that are repeated in different numbers in different people.  So wherever there are VNTR sequences between two restriction sites, the size of the fragment generated by the restriction enzyme will be different for different people. 
    D. The fragments are separated by size by a process called _______ electrophoresis, which we will not go into, but it ends up producing a ladder-like pattern.  Each ______________ in the ladder is a DNA fragment; the smaller the fragment is, the closer it will go to the bottom of the gel. 
    E. To determine relationship from a DNA fingerprint, remember that each individual has two fragments for each VNTR region, and that one was inherited from each _________________.