| Seven Life Processes | |
| Movement Reproduction Sensitivity Nutrition Excretion Respiration Growth |
MRS NERG |
| What one MAIN characteristic do ALL organisms have in common? |
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| They’re all made of cells! | |
Category: 1st Semester
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 Purines | The Pyrimidines |
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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)
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| Adenine Nucleotide (Deoxyribose) |
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| Cytosine Nucleotide (Deoxyribose) |
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| Guanine Nucleotide (Deoxyribose) |
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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
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- 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
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 |
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| 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
- DNA helicase (enzyme) uncoils the DNA molecule
- 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
- Promoters mark the beginning of a DNA chain in prokaryotes, but mark the beginning of 1 to several related genes in eukaryotes
- The 2 DNA strands separate, but only one will serve as the template & be copied
- Free nucleotides are joined to the template by RNA polymerase in the 5’ to 3’ direction to form the mRNA strand
- mRNA sequence is built until the enzyme reaches an area on DNA called the termination signal
- RNA polymerase breaks loose from DNA and the newly made mRNA
- Eukaryotic mRNA is modified (unneeded sections snipped out by enzymes & rejoined) before leaving the nucleus through nuclear pores, but prokaryotic RNA isn’t
- All 3 types of RNA called transcripts are produced by this method
Steps in Translation
- mRNA brings the copied DNA code from the nucleus to the cytoplasm
- mRNA attaches to one end of a ribosome; called initiation
- tRNA’s attach the correct amino acid floating in the cytoplasm to themselves
- tRNA with its attached amino acid have 2 binding sites where they join the ribosome
- The tRNA anticodon “reads” & temporarily attaches to the mRNA codon in the ribosome
- Two amino acids at a time are linked together by peptide bonds to make polypeptide -chains (protein subunits); called elongation
- Ribosomes) move along the mRNA strand until they reach a stop codon (UAA, UGA, or UAG); called termination
- tRNA’s break loose from amino acid, leave the ribosome, & return to cytoplasm to pick up another amino acid
Natural Selection Activity
| Survival of the Fittest |  |
Introduction:
Within a population, organisms will vary. Charles Darwin stated that in the struggle for existence, those variant organisms that have favorable variations are “better adapted” to their environment and will survive and reproduce in greater numbers. Favorable variations may mean that they are faster, or stronger, or able to eat different types of food, or better camouflaged to avoid predators. In this lab you will simulate the effect of predation by a hawk on a large population of assorted mice. Your population of mice will consist of black, white, and speckled mice. You will represent the hawk.
Objectives:
–to simulate the effect of hawk predation on the appearance of mice
-to simulate the natural selection of traits
Materials:
large sheet of newspaper 4 hawks (students)
30 white mice (paper squares) 1 petri dish
30 speckled mice (paper squares)
30 black mice (paper squares)
Procedure:
- Open your sheet of newspaper and place it on the lab table. This will serve as the environment for your mice.
- Place the petri dish on the other side of the lab table. This will be the nest.
- Select one person from your group to act as a hawk. This person should stand by the nest.
- Spread the mice on their environment evenly.
- The hawk now swoops over and has 1 minute to pick up as many mice as possible. The hawk may only pick up one mouse at a time, and must place it in their nest (a petri dish) before flying back to pick up another. The goal is to pick up as many mice as possible in the time period.
- When the time is up record the number of mice left in the environment in the data table below.
- Repeat this procedure for each person in the lab group or 4 times.
- After all data is collected, construct a bar graph. Be sure to label the graph and its axes.
- Data:
mice |
mice |
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| Hawk #1 |
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| Hawk #2 |
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| Hawk #3 |
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| Hawk #4 |
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| Total |
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Conclusion:
Write a paragraph describing;
* the purpose of the lab
* what you thought the results would be
* what the results were (discussing numbers from data)
*how the mouse population and hawk population may change over time from natural selection
Natural Selection Peanut Activity
| Natural Selection Within a Species |  |
Introduction:
Natural selection is the evolutionary process by which the most adaptable individuals survive. An adaptation is an inherited variation that helps an organism to survive. When the organism survives, its chances of reproduction are increased as well as its ability to pass on its inherited traits. All members of a species are different from one another. In this activity, you will investigate two variations among peanut plants — length of shell and number of seeds per shell. Most shells contain a certain number of seeds which is an adaptation to its survival.
Objective:
Students will investigate natural selection in peanuts.
Materials:
50 peanuts in shells, metric ruler, pencil, graph paper
Procedure:
- Count out 50 peanuts in their shells.
- Use a metric ruler to measure the length of each shell in millimeters. Put a check mark in Table 1 in the space indicating the length of the shell.
- Open the shell and count the number of seeds inside. Put a check mark in Table 2 in the space next to the number of seeds that you counted.
- Repeat steps 1 – 3 for the other 49 peanuts.
- Set up two bar graphs using the headings from each table as the axes for each graph.
- Plot a bar graph from the data in each table.
Data:
Table 1
| Length of Shell (mm) |
Number of Shells |
| 5-10 | |
| 10-15 | |
| 15-20 | |
| 20-25 | |
| 25-30 | |
| 30-35 | |
| 35-40 | |
| 40-45 | |
| 45-50 | |
| 50-55 | |
| 55-60 | |
| 60-65 | |
| 65-70 | |
| 70-75 |
Table 2
| Number of Seeds Per Shell | Number of Shells |
| 1 | |
| 2 | |
| 3 |
Title: ________________________________________________________
Title: ________________________________________________________
Questions:
- What is the most common length of the shells you measured?
- What was the most common number of seeds in the peanut shells that you opened?
- What might happen if each shell contained fewer than normal seeds and why?
- What might happen if each shell contained more than the normal number of seeds and why?
- Was there a relationship between the most common length of shells and the number of seeds they contained? Explain your answer.
- Write 1-2 paragraphs explaining how shell length and seed number in peanuts illustrates natural selection within this species.