Category: Curriculum Map

Preap Nucleic Acid Study Guide

Nucleic Acids, Protein Synthesis, & DNA Technology Study Guide

1. What are purines & pyrimidines and give examples of each?

2. Which scientists determined the structure of DNA?

3. DNA and RNA are named by their __________.

4. What three things make up a nucleotide?

5. Describe the structure of DNA.

6. An organism’s characteristics are coded for by molecules of __________.

7. What are the subunits called that make up DNA?

8. Sketch the basic structure of a nucleotide.

9. What 2 things are found on RNA, but are not found on DNA molecules?

10. What is the primary function of DNA?

11.What did Rosalind Franklin’s x-ray photographs of DNA crystals tell us about this molecule?

12. State Chargaff’s rule.

13. What happens to tRNA anticodons during translation?

14. What is a codon & where are they found?

15. What is the function of rRNA?

16. What bases pair with each other on: a) DNA?   b) RNA?

17. Name the 3 types of RNA & tell the function of each.

18. What is the function of DNA polymerase?

19. If the code on DNA is TTAGCCTGA, what will be the code on the complementary section of DNA when it’s copied during replication?

20. List all the ways that RNA differs from DNA?

21. Where does mRNA go for proteins to be made in a cell?

22. What is transcription?

23. What is translation?

24. Which RNA carries instructions for making proteins?

25. What is the function of DNA helicases?

26. What is the job of restriction enzymes?

27. What are “sticky ends” and how are they helpful?

28. What is the difference between introns & exons?

29. What is an operon and in what type of cell would they be found?

30. What does RFLP stand for?  How is this process used?

31. What is meant by cloning?

32.What is DNA fingerprinting and how can it be used?

33. How is recombinant DNA formed?

NOTES                STUDY GUIDES

Nucleotide Model preap

 

Model of a Nucleotide

 

Introduction

Nucleotides consist of three parts — a pentose sugar, a nitrogen-containing base, and a phosphate group. A pentose sugar is a five-sided sugar. There are 2 kinds of pentose sugars — deoxyribose and ribose. Deoxyribose has a hydrogen atom attached to its #2 carbon atom (designated 2′), and ribose has a hydroxyl group atom there. Deoxyribose-containing nucleotides are the monomers of DNA, while Ribose-containing nucleotides are the monomers of RNA.

A nitrogen-containing ring structure is called a base. The base is attached to the 1′ carbon atom of the pentose. In DNA, four different bases are found — two purines, called adenine (A) and guanine (G) and two pyrimidines, called thymine (T) and cytosine (C). RNA contains The same purines, adenine (A) and guanine (G).  RNA also uses the pyrimidine cytosine (C), but instead of thymine, it uses the pyrimidine uracil (U).

 

The PurinesThe Pyrimidines

The combination of a base and a pentose is called a nucleoside.  A phosphate group is attached to the 5′ carbon of the pentose sugar.

Objective

Students will construct a 3-dimensional model of a single nucleotide, the monomer of which nucleic acids are composed.

Materials

Various materials may be used for the atoms that make up a nucleotide such as styrofoam balls, plastic coke bottle caps, beads, etc. Bonds between atoms may be made from toothpicks, plastic stirring sticks, popsicle sticks, etc. Single & double bonds must be represented by the correct number of “sticks”. The atoms and bonds may NOT be made of any food item. Your model should be glued together to make the model rigid for hanging. Attach string and a label with the nucleotide’s name to your model. Models must be sturdy, light weight, and small enough to hang from the ceiling.

Color Code for atoms:

CARBON –BLACK
HYDROGEN – YELLOW
OXYGEN – RED
NITROGEN –BLUE

Structural Formulas of Nucleotides:

Uracil Nucleotide (Ribose ) & Thymine Nucleotide (Deoxyribose)

 

Adenine Nucleotide (Deoxyribose)
Cytosine Nucleotide (Deoxyribose)
Guanine Nucleotide (Deoxyribose)
 

 

 

Nucleic Acids & Protein Synthesis

Nucleic Acids and Protein Synthesis
All Materials © Cmassengale

Cell   à   Nucleus    à    Chromosomes   à   Genes    à     DNA 

Proteins

  • Organic molecules (macromolecules) made by cells
  • Make up a large part of your body
  • Used for growth, repair, enzymes, etc.
  • Composed of long chains of small units called amino acids bonded together by peptide bonds
  • Twenty amino acids exist

DNA

  • Deoxyribonucleic acid is a coiled double helix carrying hereditary information of the cell

  • Contains the instructions for making proteins from 20 different amino acids
  • Appears as chromatin when cell not dividing

  • Structure discovered by Watson & Crick in 1953
  • Sides made of pentose (5-sided) sugars attached to phosphate groups by phosphodiester bonds
  • Pentose sugar called Deoxyribose

  • Steps or rungs of DNA made of 4 nitrogen-containing bases held together by weak hydrogen bonds
  • Purines (double carbon-nitrogen rings) include adenine (A) and guanine (G)
  • Pyrimidines (single carbon-nitrogen rings) include thymine (T) and cytosine (C)

  • Base pairing means a purine bonds to a pyrimidine   (Example:  A — T   and   C — G)
  • Coiled, double stranded molecule known as double helix
  • Make up chromosomes in the nucleus
  • Subunits of DNA called nucleotides
  • Nucleotides contain a phosphate, a Deoxyribose sugar, and one nitrogen base (A,T,C, or G)

  • Free nucleotides also exist in nucleus
  • Most DNA is coiled or twisted to the right
  • Left twisted DNA is called southpaw or Z-DNA
  • Hot spots which can result in mutations occur where right & left twisted DNA meet

 

History of DNA discovery

  • Freidrich Miescher (1868) found nuclear material to be ½ protein & ½ unknown substance
  • 1890’s, unknown nuclear substance named DNA
  • Walter Sutton (1902) discovered DNA in chromosomes
  • Fredrick Griffith (1928) working with Streptococcus pneumoniae conducted transformation experiments of virulent & nonvirulent bacterial strains
  • Levene (1920’s) determined 3 parts of a nucleotide
  • Hershey & Chase (1952) used bacteriophages (viruses) to show that DNA, not protein, was the cell’s hereditary material
  • Rosalind Franklin (early 1950’s) used x-rays to photograph DNA crystals

 

Click for larger picture!

 

 

  • Erwin Chargraff (1950’s) determined that the amount of A=T and amount of C=G in DNA; called Chargaff’s Rule
  • Watson & Crick discovered double helix shape of DNA & built the 1st model

Click for larger picture!

 DNA Replication

  •  Process by which DNA makes a copy of itself
  • Occurs during S phase of interphase before cell division
  • Extremely rapid and accurate (only 1 in a billion are incorrectly paired)
  • Requires many enzymes & ATP (energy)
  • Begins at special sites along DNA called origins of replication where 2 strands open & separate making  a replication fork

 

  • Nucleotides added & new strand forms at replication forks
  • DNA helicase (enzyme) uncoils & breaks the weak hydrogen bonds between complementary bases (strands separate)
  •  DNA polymerase adds new nucleotides to the exposed bases in the 5’ to 3’ direction

  •  Leading strand (built toward replication fork) completed in one piece
  • Lagging strand (built moving away from the replication fork) is made in sections called Okazaki fragments

 

OKAZAKI FRAGMENTS

  •  DNA ligase helps join Okazaki segments together

  • DNA polymerase proofreads the new DNA checking for errors & repairing them; called excision repair
  • Helicase recoils the two, new identical DNA molecules

RNA

  • Ribonucleic acid
  • Single stranded molecule  

  • Found in nucleus & cytoplasm
  • Contains ribose sugar
  • Contains the nitrogen base uracil (U) instead of thymine so A pairs with U
  • Base pairings are A-U and C-G
  • Three types of RNA exist (mRNA, TRNA, & rRNA)

mRNA

  • Messenger RNA
  • Single, uncoiled, straight strand of nucleic acid
  • Found in the nucleus & cytoplasm
  • Copies DNA’s instructions & carries them to the ribosomes where proteins can be made
  • mRNA’s base sequence is translated into the amino acid sequence of a protein
  • Three consecutive bases on mRNA called a codon (e.g. UAA, CGC, AGU)
  • Reusable

tRNA

  • Transfer RNA
  • Single stranded molecule containing 80 nucleotides in the shape of a cloverleaf
  • Carries amino acids in the cytoplasm to ribosomes for protein assembly
  • Three bases on tRNA that are complementary to a codon on mRNA are called anticodons (e.g. codon- UUA; anticodon- AAU)
  • Amino Acid attachment site across from anticodon site on tRNA
  • Enters a ribosome & reads mRNA codons and links together correct sequence of amino acids to make a protein
  • Reusable  

rRNA

  • Ribosomal RNA
  • Globular shape
  • Helps make up the structure of the ribosomes  
  • rRNA & protein make up the large & small subunits of ribosomes
  • Ribosomes are the site of translation (making polypeptides)

  • Aids in moving ribosomes along the mRNA strand as amino acids are linked together to make a protein

Amino Acids

  • 20 exist
  • Linked together in a process called protein synthesis in the cytoplasm to make polypeptides (subunits of proteins)
  • DNA contains the instructions for making proteins but is too large to leave the nucleus
  • Three consecutive bases on DNA called a triplet (e.g. TCG, ATG, ATT)
  • mRNA codon table tells what 3 bases on mRNA code for each amino acid (64 combinations of 3 bases)
  • Methionine (AUG) on mRNA is called the start codon because it triggers the linking of amino acids
  • UAA, UGA,  & UAG on mRNA signal ribosomes to stop linking amino acids together

Genetic Code (RNA)

 

 Amino Acid 3 Letter
Abbreviation		 Codons
 Alanine Ala GCA GCC GCG GCU
 Arginine Arg AGA AGG CGA CGC CGG CGU
 Aspartic Acid Asp GAC GAU
 Asparagine Asn AAC AAU
 Cysteine Cys UGC UGU
 Glutamic Acid Glu GAA GAG
 Glutamine Gln CAA CAG
 Glycine Gly GGA GGC GGG GGU
 Histidine His CAC CAU
 Isoleucine Ile AUA AUC AUU
 Leucine Leu UUA UUG CUA CUC CUG CUU
 Lysine Lys AAA AAG
 Methionine Met AUG
 Phenylalanine Phe UUC UUU
 Proline Pro CCA CCC CCG CCU
 Serine Ser AGC AGU UCA UCC UCG UCU
 Threonine Thr ACA ACC ACG ACU
 Tryptophan Trp UGG
 Tyrosine Tyr UAC UAU
 Valine Val GUA GUC GUG GUU
 Start AUG
 Stop UAA UAG UGA

 

 

  Practice Table:

DNA
Codon 		mRNA
Codon 		tRNA
Anticodon 		Amino
Acid

GCU

TAC    
    AUU
  UUU  
TCA    
    UCU
CTT    
  ACU
ACU  

Protein Synthesis

  • Consists of 2 parts — Transcription & Translation
  • Begins in the nucleus with mRNA copying DNA’s instructions for proteins (transcription)
  • Completed in the cytoplasm when tRNA enters ribosomes to read mRNA codons and link together amino acids (translation)

 Steps in Transcription

  1. DNA helicase (enzyme) uncoils the DNA molecule
  2. RNA polymerase  (enzyme) binds to a region of DNA called the promoter which has the start codon TAC to code for the amino acid methionine
  3. Promoters mark the beginning of a DNA chain in prokaryotes, but mark the beginning of 1 to several related genes in eukaryotes
  4. The 2 DNA strands separate, but only one will serve as the template & be copied
  5. Free nucleotides are joined to the template by RNA polymerase in the 5’ to 3’ direction to form the mRNA strand
  6. mRNA sequence is built until the enzyme reaches an area on DNA called the termination signal
  7. RNA polymerase breaks loose from DNA and the newly made mRNA
  8. Eukaryotic mRNA is modified (unneeded sections snipped out by enzymes & rejoined) before leaving the nucleus through nuclear pores, but prokaryotic RNA isn’t
  9. All 3 types of RNA called transcripts are produced by this method

Steps in Translation

  1. mRNA brings the copied DNA code from the nucleus to the cytoplasm
  2. mRNA attaches to one end of a ribosome; called initiation
  3. tRNA’s attach the correct amino acid floating in the cytoplasm to themselves
  4. tRNA with its attached amino acid have 2 binding sites where they join the ribosome
  5. The tRNA anticodon “reads” & temporarily attaches to the mRNA codon in the ribosome
  6. Two amino acids at a time are linked together by peptide bonds to make polypeptide -chains (protein subunits); called elongation
  7. Ribosomes) move along the mRNA strand until they reach a stop codon (UAA, UGA, or UAG); called termination

  1. tRNA’s break loose from amino acid, leave the ribosome, & return to cytoplasm to pick up another amino acid

Click here for an animation of Translation 

Osmosis & Diffusion in Egg Lab

 

Osmosis & Diffusion in an Egg

 

Objective:
In this investigation, you will use a fresh hen’s egg to determine what happens during osmosis & diffusion across membranes.

Materials: (per lab group)
1-2 fresh hen eggs in their shells, masking tape & marker, distilled water, clear sugar syrup (Karo, for example), vinegar, clear jar with lid, tongs, electronic balance, paper towels, paper, pencil

Procedure:

Day 1   

  1. Label the jar with your lab group & the word “vinegar”.
  2. Mass the egg with the electronic balance & record in the data table.
  3. Carefully place the raw egg into the jar & cover the egg with vinegar.
  4. Loosely re-cap the jar & allow the jar to sit for 24 to 48 hours until the outer calcium shell is removed.

Day 2   

  1. Open the jar & pour off the vinegar.
  2. Use tongs to carefully remove the egg to a paper towel & pat it dry.
  3. Record the size & appearance of your egg in your data table.
  4. Mass the egg on an electronic balance & record.
  5. Clean and re-label the jar with your lab group & the word “distilled water”.
  6. Carefully place the egg into the jar & cover the egg with distilled water.
  7. Loosely re-cap the jar & allow it to sit for 24 hours.

Day 3   

  1. Open the jar & discard the distilled water.
  2. Use tongs to carefully remove the egg to a paper towel & pat it dry.
  3. Record the size & appearance of your egg in your data table.
  4. Mass the egg on an electronic balance & record.
  5. Clean and re-label the jar with your lab group & the word “syrup”.
  6. Carefully place the egg into the jar & cover the egg with clear syrup.
  7. Loosely re-cap the jar & allow it to sit for 24 hours.

Day 4   

  1. Open the jar & pour off the syrup.
  2. Use tongs to very carefully remove the egg & rinse off the excess syrup under slow running water.
  3. Pat the egg dry on a paper towel.
  4. Record the size & appearance of your egg in your data table.
  5. Mass the egg on an electronic balance & record.
  6. Clean up your work area & put away all lab equipment.

Data:

 

RESULTS OF DIFFUSION

Original MassFinal MassAppearance of Egg
VINEGAR
WATER
SYRUP

 

 

Questions & Conclusion:

1. Vinegar is made of acetic acid & water. Explain how it was able to remove the calcium shell.

 

2. (a) What happened to the size of the egg after remaining in vinegar?

(b) Was there more or less liquid left in the jar?

   (c) Did water move into or out of the egg? Why?

 

3. (a) What happened to the size of the egg after remaining in distilled water?

(b) Was there more or less liquid left in the jar?

   (c) Did water move into or out of the egg? Why?

 

4. (a) What happened to the size of the egg after remaining in syrup?

(b) Was there more or less liquid left in the jar?

   (c) Did water move into or out of the egg? Why?

 

5. Was the egg larger after remaining in water or vinegar? Why?

 

6. Why are fresh vegetables sprinkled with water at markets?

 

7. Roads are sometimes salted to melt ice. What does this salting do to the plants along roadsides & why?

 

 

 

 

Mitosis Activity

 

Stages of Mitosis

Introduction

Mitosis, also called karyokinesis, is division of the nucleus and its chromosomes.  It is followed by division of the cytoplasm known as cytokinesis.  Both mitosis and cytokinesis are parts of the life of a cell called the Cell Cycle.  Most of the life of a cell is spent in a non-dividing phase called Interphase.  Interphase includes G1 stage in which the newly divided cells grow in size, S stage in which the number of chromosomes is doubled and appear as chromatin, and G2 stage where the cell makes the enzymes & other cellular materials needed for mitosis.

Mitosis has 4 major stages — Prophase, Metaphase, Anaphase, and Telophase. When a living organism needs new cells to repair damage, grow, or just maintain its condition, cells undergo mitosis.

During Prophase, the DNA and proteins start to condense. The two centrioles move toward the opposite end of the cell in animals or microtubules are assembled in plants to form a spindle. The nuclear envelope and nucleolus also start to break up.


Prophase

During Metaphase, the spindle apparatus attaches to sister chromatids of each chromosome. All the chromosomes are line up at the equator of the spindle. They are now in their most tightly condensed form.


Metaphase

During Anaphase, the spindle fibers attached to the two sister chromatids of each chromosome contract and separate chromosomes which move to opposite poles of the cell.


Anaphase

In Telophase, as the 2 new cells pinch in half (animal cells) or a cell plate forms (plant cells), the chromosomes become less condensed again and reappear as chromatin. New membrane forms nuclear envelopes and the nucleolus is reformed.


Telophase

Objective: 

In this lab, you will determine the approximate time it takes for a cell to pass through each of the four stages of mitosis. You may use your textbook and class notes to help you identify the stages of mitosis as seen under the microscope. 

Materials:

Microscope, prepared slide onion root tip or whitefish blastula, textbook, lab worksheet, pencil

Procedure:

  1. Set up a compound light microscope and turn on the light.
  2. Place a slide containing a stained preparation of the Allium (onion root tip) or Whitefish blastula.
  3. Locate the meristematic or growth zone, which is just above the root cap at the very end of the tip or
  4. Focus in on low power, and then switch to medium or high power. Below find micrographs of the four stages of mitosis. Use them to help you identify the stages on the microscope slide.


Prophase (onion)

 


Metaphase (onion)

 


Anaphase (onion)

 


Telophase (whitefish)

 

  1. Now count the number of cells found in each stage of mitosis and place the data in the chart below.
  2. Determine the percentage of time each cell will spend in each stage of mitosis. Divide the number of each cell by the total number of cells and multiply by 100 to determine the percentage. Place these values in the chart below.

 

Stage of MitosisNumber of CellsPercent of time in each stage =

# of cells in stage     X  100%
Total # of Cell

Prophase%
Metaphase%
Anaphase%
Telophase%
Interphase
(Not a Mitotic Stage)		%
Total # cells100%

 

  1. Line graph the data you have just collected.  Be sure to label the X and Y axis & include the units of measurement.

Title: __________________________________________________

Graph Legend:

 

Questions:

1. Of the four stages of mitosis, which one takes the most time to complete? 

 

2. Which is the shortest stage in duration?

 

3. What would happen if the process of mitosis skipped metaphase?  telophase?

Further Study:

Normal Cell Division may be observed in onion root tips. Many of the processes are similar to those in animal cells. However, in plant cells, the cell plate between daughter cells forms from the Golgi.

Find all of the stages of mitosis and  interphase in the above picture. Make a sketch of each stage and briefly describe what is occurring. Count and record the number of cells you see in each stage.

Projects
Notes