Name: ___________________________________

DNA Unit Workbook 

I.   DNA and RNA

     Notes….                                              Pages  2 – 4

     Section I Questions….                       Pages 5 – 7

     Section I Matching and T/F….         Page 8

II.  DNA Replication          

      Notes….                                              Page 9
 
      Section II Questions…                      Page 10

      Replication Diagram…                     Page 11

      Replication Active Reading….        Pages 12- 13

III.  Protein Synthesis

Notes….                                              Page 14

Section III Questions….                    Pages 15 – 16

Triplet WS…                                       Page 17

Protein Synthesis WS…                    Pages 18- 19

IV.  Mutations (selected reading)

Reading…                                          Page 20

Section IV Questions…                    Page 21

I. DNA & RNA

  A.  History of DNA Science:

    1. Genetic Molecule: Protein or DNA?
        Hershey and Chase: ‘Marked’ proteins and DNA to see which viruses injected.  
        Finding:  DNA, when injected, allowed virus to take over a host cell.

                 

    2. Chargaff’s Base-Pairing Rule: Discovered amounts of A = amounts of T,
         while amounts of C = amounts of G.  Reasoned they must pair in DNA molecule.

    3. Rosyln Franklin and Wilkins : X-ray crystallography indicated DNA molecule was a spiral/helical molecule.
  
    4.  Watson and Crick: Successful model DNA in  1953.  Given credit for double helix model.

  B. DNA Structure: 

                       

    1. Nucleotide: Basic building block of DNA.  Consists of one sugar (deoxyribose), 
                                                        one phosphate, and one   nitrogen-containing base.
  
          How many nucleotides in the DNA molecule pictured above?

    2.  Backbone of DNA consists of alternating deoxyribose sugars and phosphates.
  
          Circle the backbone of the DNA molecule above.

    3. ‘Rungs’ of ladder consists of nitrogenous bases paired together.  

    4. Bonds in DNA
      a. Backbone: Sugar + Phosphate connected with covalent bonds (between two nonmetals)
      b.  Nitrogenous Bases: Hydrogen bonds (weaker than covalent bonds)

     Draw a DNA molecule with 6 nucleotides and label the sugar, phosphate and nitrogenous base.

  C. RNA: Ribose Nucleic Acid
        RNA vs DNA:
 
        1.  Uracil (U) instead of Thymine (T)

        2. Ribose sugar rather than Deoxyribose

        3. Single strand of nucleotides rather than double strand.

List three similarities and three differences between DNA and RNA in the Venn Diagram below:
                                             DNA                                                         RNA

Section I Questions
1.	What are the 4 bases of DNA?

2.	How are purines different than pyrimidines?

3.	What two molecules make up the backbone of DNA?

4.	What kind of bonds bind nitrogenous bases together?
5.	Below is an image of a single nucleotide.  Circle and label each of the following: the phosphate group,  the deoxyribose sugar and the nitrogenous base.

                                           
6.	Recall from the chemistry of life chapter that covalent bonds form between two non metals while ionic bonds usually form between a metal and nonmetal.  Below is the periodic table (recall “H” is a nonmetal although it is on left side of table). 

               

a) For each atom in the nucleotide below, label it as a metal or nonmetal.  

b) Would you expect covalent or ionic bonds to form in a molecule of DNA?

                                    

7.	a.  How many nucleotides in the strand of DNA pictured below?

b.  Circle all the nitrogenous bases in the image below:

                     

    

8.	For the image below, color all sugars blue, all phosphates black and all nitrogenous bases purple. Draw all covalent bonds black and all hydrogen bonds red.

9. The structure of proteins is determined by the order and type of their
    (a) nitrogen bases.                                    (b) pyrimidines.
    (c) amino acids                                          (d) nucleotides.

10. The central dogma of molecular biology is best represented by
     (a) DNA + RNA = Protein                 (b) DNA ! RNA + Protein.
     (c) DNA ! RNA ! Protein.                  (d) Protein ! RNA ! DNA.

11. What makes up the “steps” of the DNA spiral staircase?
     (a) sugars                                               (b) phosphates
     (c) sugars and phosphates                   (d) nitrogenous base pairs

12. Pyrimidines include
      (a) uracil.                                                (b) thymine.
      (c) cytosine.                                           (d) all of the above.

Section I Matching

____ 1. uracil
____ 2. Watson and Crick
____ 3. DNA
____ 4. gene
____ 5. nucleotide
____ 6. purine
____ 7. pyrimidine
____ 8. alternating sugars and phosphates
____ 9. RNA
____ 10. Hershey and Chase

  a. monomer of all nucleic acids
  b. double-stranded nucleic acid
  c. thymine or cytosine
  d. nitrogenous base found only in RNA
  e. backbone of DNA
  f. single-stranded nucleic acid
  g. segment of DNA that codes for a protein
  h. correctly modeled DNA
  i. adenine or guanine
  j. proved DNA is genetic molecule
 
Section I T/F

Write true if the statement is true or false if the statement is false. If false, correct statement to make it true.

______ 1. Proteins give organisms their traits.

______ 2. The function of proteins is determined by their structure.

______ 3. Franklin and Wilkins proved conclusively that DNA is the genetic material.

______ 4. The backbone of DNA consists of base pairs.

______ 5. In DNA, the complement of ATC is TAG.

______ 6. In RNA, guanine always bonds with uracil.

______ 7. RNA is found only in the cytoplasm of the cell.

______ 8. RNA molecules are smaller than DNA molecules.

______ 9. Messenger RNA carries instructions to the cytoplasm.

______ 10. Ribosomal RNA brings amino acids to the ribosome.

II. DNA Replication

    A. Steps of Replication (occurs during S phase of mitosis):
   
         1. DNA uncoils and unzips (done by DNA Helicase).
  
         2. New nucleotides are added to exposed  strand and added by 
             DNA polymerase (an enzyme).
     
         3. Each new strand is half new, half old  (semiconservative).

     B. Where?  Replication: Occurs in the nucleus; 

     C. Why? Process of DNA creating an exact replica of original strand.

         Is the strand below DNA or RNA?  How do you know?

              ATTACGCGTACTACTAGC

Section 2- DNA replication

1.	What is the purpose of DNA replication?

2.	Give the complementary bases for the following DNA strand.  
                                     AATACGATTAGCCTAGGA

3.	Where in the cell does replication occur?

       4.     During DNA replication, the two new strands of DNA are built
               (a) in opposite directions                    (b) in the cell cytoplasm.
               (c) from amino acids.                           (d) at a ribosome.

5.	Explain the role of the following enzymes in DNA Replication:

a.	DNA polymerase:

b.	DNA helicase:

c.	DNA ligase:

      6.  What does “semiconservative” replication mean?

7. Which of the following nitrogenous bases will tend to hydrogen bond with adenine in DNA?	
	 	A.	guanine	
	 	B.	cytosine	
	 	C.	thymine	
	 	D.	uracil	

8. Which of the following is a nitrogenous base found in RNA, but not DNA?	
	 	A.	thymine	
	 	B.	guanine	
	 	C.	uracil	
	 	D.	adenine	

9. What is the correct sequence of the replicated DNA created from the following strand of DNA?
                              3' CAC GTC GAA 5'	
		A.	5' GTG CAG CTT 3'	
	 	B.	5' GUG CAG CUU 3'	
	 	C.	5' TGT ACT AGG 3'	
	 	D.	5' GTG CUG CTT 3'	

III. Protein Synthesis

A.	Central Dogma of Biology: “DNA make RNA makes Protein”

   B. Transcription occurs in the nucleus.  DNA to RNA.

  C. Steps of Transcription:
       1. DNA unzips,
       2. RNA Polymerase (an enzyme) adds  complimentary nucleotides.
       3. New RNA molecule leaves nucleus.

  D. Transcription makes three types of RNA:
      1. mRNA (messenger RNA): Long strand that carries message from nucleus to ribosome.
      2. rRNA (ribosomal RNA): Makes up ribosomes (along with proteins).
      3. tRNA (transfer RNA): carries amino acids to ribosomes.

E. Translation: Going from DNA code to Amino Acid Sequence.

F.  Steps of Translation:
     1. DNA transcription leads to segement of mRNA.
     2. mRNA leaves nucleus, goes to ribosome (in cytoplasm).
     3.  tRNA meets mRNA at ribosome, produces AA sequence (protein).

G. Details of Translation:
    1. three nucleotides in a row make a ‘command’ for mRNA, known as a codon.
    2. tRNA carries amino acid and anticodon (which matches with a condon).

        If DNA reads,  ACCTAGACGACCGAT
   
                a) What would the mRNA read?
  
                b) How many codons are on this mRNA?

         If the DNA reads ATG CAG GAC CCG, 

a)	what is the mRNA? 

b)	What are the anticodons?

1. What is one role in protein synthesis that is played by RNA polymerase?
  (a) It carries information out of the nucleus.
  (b) It begins the transcription process.
  (c) It forms a subunit of the ribosome.
  (d) It acts as a stop codon in RNA.

2. What happens during transcription?
   (a) A new polypeptide is created.
   (b) RNA is scanned by a ribosome.
   (c) A new copy of DNA is produced.
   (d) A complementary copy of RNA is made.

3. A codon is a(n)
    (a) nucleotide.                            (b) amino acid.
    (c) nitrogen base.                      (d) three-base sequence.

4. Which code word signals “start” in the genetic code?
   (a) UAT                 (b) AUG
   (c) UGA                 (d) UAA

5. How many amino acids does one codon code for?
     (a) 20                  (b) 4
      (c) 3                    (d) 1

6. When a protein is made in a cell, the instructions for the protein are first copied from
DNA to
   (a) rRNA.             (b) tRNA.
   (c) mRNA.           (d) none of the above.

7.  What is the purpose of protein synthesis?

8.  Where are the directions for making proteins stored?

9.  Where does transcription take place?

10.  Where does translation take place?

11.  What is the monomer of proteins?

TEST PREP:
12. What is the correct sequence of the mRNA created from the following coding strand of DNA?

3' TAC TTC ATT 5'	
	 	A.	5' ATG AAG TAA 3'	
		B.	5' AUG AAG UAA 3'	
	 	C.	5' CGT CCT GCC 3'	
	 	D.	5' UTG UUG TUU 3'	

13. During the process of protein synthesis, a portion of the DNA molecule opens and the messenger RNA molecule makes a near replica of the DNA strand. Using the base pair sequence of the DNA molecule shown below, what would be the corresponding sequence on the RNA molecule from left to right?

	 	A.	T-T-A-G-C-C-G	
	 	B.	U-U-A-C-G-G-C	
	 	C.	A-A-U-G-C-C-G	
		D.	U-U-A-G-C-C-G	

Write true if the statement is true or false if the statement is false. If false, change sentence to make it true.

______ 14. Transcription is “RNA to DNA.”

______ 15. There are 64 different amino acids in proteins.

______ 16. All codons code for amino acids.

______ 17. The reading frame in translation consists of four bases.

______ 18. The same genetic code is found in all organisms.

______ 19. Proteins may be modified after protein synthesis.

Types of Mutations
In multicellular organisms, mutations can be subdivided into germline mutations, which can
be passed on to descendants, and somatic mutations, which cannot be transmitted to the
next generation. Germline mutations change the DNA sequence within a sperm or egg cell,
and therefore can be inherited. This inherited mutation results in a class of diseases known
as a genetic disease. The mutation may lead to a nonfunctional protein, and the embryo
may not develop properly or survive. Somatic mutations may affect the proper functioning
of the cell with the mutation. During DNA replication, the mutation will be copied. The
two daughter cells formed after cell division will both carry the mutation. This may lead to
the development of many cells that do not function optimally, resulting a less than optimal
phenotype. Cancers are generally caused by DNA mutations in somatic cells.  Various types 
of mutations can all have severe effects on the individual. These include point mutations, 
frameshift mutations and chromosomal alterations.

Chromosomal Alterations
Chromosomal alterations are large changes in the chromosome structure. They occur
when a section of a chromosome breaks and rejoins incorrectly, or does not rejoin at all.
Sometimes the segment may join backwards or reattach to another chromosome altogether.
These mutations are very serious and usually lethal to the zygote or embryo. If the embryo
does survive, the resulting organism is usually sterile and thus, unable to pass along the
mutation.

Point Mutations
As the name implies, point mutations occur at a single site within the DNA.  Consider this example: 

THE BIG FAT CAT ATE THE RED RAT.

A change at any one position could result in a sequence that does not make sense. Such as:

THE BIG FAT SAT ATE THE RED RAT.

As shown above, point mutations exchange one nucleotide for another and are known as
base substitution mutations. These mutations are often caused either by chemicals, environmental factors such as X-rays or UV light, or by a spontaneous  mistake during DNA replication. A transition exchanges a purine for a purine (A for G) or a pyrimidine for a pyrimidine, (C for T), and is the most common point mutation. Less common is a transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a
purine.  Some point mutations have no effect on an organism as multiple codons code for the same amino acid.

Frameshift Mutations
In the case of framshift mutations, a nucleotide is added or deleted, throwing off all codons downstream.

THE BIG FAT CAT ATE THE RED RAT.

Add a guanine at the beginning:

GTH EBI  GFA  TCA  TAT ETH ERE DRA T

Questions
1. What are germline mutations?

2. Define chromosomal alterations, and explain why chromosomal alternations are often
lethal.

3.  Define point mutations, and give an example.

4. Common mutagens (factors causing mutations) include
     (a) X-rays.                   (b) chemicals.
      (c) ultraviolet light.    (d) all of the above.

3. A point mutation in which one purine is exchanged for another purine is called a(n)
    (a) amplification.       (b) transversion.
    (c) transition.              (d) inversion.

4. Removing nucleotides or adding nucleotides results in a
    (a) point mutation.       (b) proto-oncogene.
    (c) base substitution.    (d) reading frame shift.

5.  Germline mutation
     (a)  mutation in the DNA of a body cell
     (b)  mutation in the DNA of a gamete
     (c)  mutation that adds multiple copies of a chromosomal region
     (d) mutation that reverses the order of nucleotides of a chromosomal region

6.  Somatic mutation
     (a)  mutation in the DNA of a body cell
     (b)  mutation in the DNA of a gamete
     (c)  mutation that adds multiple copies of a chromosomal region
     (d) mutation that reverses the order of nucleotides of a chromosomal region

Write true if the statement is true or false if the statement is false.

______ 7. It is possible for mutations to occur spontaneously.

______ 8. Only somatic mutations can be passed on to offspring.

______ 9. A mutation that changes C to G is a transition mutation.

______ 10. Some mutations have no significant effect.

______ 11. Nearly all cancers are caused of mutations in DNA.