Columbia College Biology 110 - Study Guide
Dr. Simon Duffy
January 2017
The following guide is to help you in reviewing. However, you are responsible for thouroughly STUDYING every detail of the course material.
January 2017
The following guide is to help you in reviewing. However, you are responsible for thouroughly STUDYING every detail of the course material.
Table of Contents
Lesson #1 - The CellLesson #2 - The Cell Surface
Lesson #3 - DNA Replication
Lesson #4 - Cell Cycle and Intro to Mendelian Genetics
Lesson #5- Mendelian Genetics
Lesson #6 - Chromosomes
Lesson #7 - DNA as Genetic Material
Lesson #8- Transcription and Translation
Lesson #9 - Gene Expression
Lessons #10 and 11 - Evolution Theory
Lesson #12 - Speciation
Lesson #13- Taxonomy/Prokaryotes
Lesson #14- Kingdom Protista
Lesson #15 - Kingdom Plantae: Seedless Plants
Lesson #16 - Kingdom Plantae: Seed Plants
Lesson #17 - Kingdom Animalia
Lesson #18 - Invertebrate Animals
Lesson #19 - Animal Phylum Chordata
Lesson #20 - Kingdom Fungi
Lesson #21 - Population Ecology
Lesson #22 - Community Ecology
Lesson #23 - Energy Flow
Lesson #1 - The Cell
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Concept #1 Cells are Small
1. What is a cell? The (two words) theory provide a formal definition of a cell.2. Which of the following statements best describes the theory in Question #1?
3.
Why
is the
cell small?
The
first question to ask is why does the surface AREA of the cell matter?
Next, what is the relationship between cell surface area
and cell volume?
So
the consequence is...
Both
the surface area and volume of
the cell increase but, since the volume increases faster than the
surface area there comes a point where the cell does not have enough
surface area to meet the transport and metabolic needs of the cell.
4.
What are the
appoximate sizes of cells (Eukaryote vs
Prokaryote)?
A
prokaryotic cell is typically about
(enter number, not words) microns, whereas a eukaryotic cell ranges
from
microns to
microns
in diameter.
Concept #2 Different Cell Types
1. What are the differences between prokaryotic and eukaryotic cells? Select whether each trait is unique to either prokaryote, eukaryote or both.Has a double-membrane bound nucleus | |
Has a non-membrane bound nucleoid | |
Synthesizes protein using ribosomes | |
Has endosymbiont 'organism' living inside | |
Has single-membrane bound cytoplasmic organelles | |
Has a cellular endomembrane system |
2. What are the differences between plant and animal cells? Select whether each trait is unique to either prokaryote, eukaryote or both.
Has a centrosome structure with centrioles | |
Has a cell membrane | |
Has a cell wall made of cellulose sugar | |
Has many lysosomes to digest food | |
Has mitochondria | |
Has chloroplast | |
Has a large central vacuole that keeps the cell inflated and controls the osmotic potential (water balance) inside the cell |
For more information and practice click here.
Concept #3 Components of the Cell
1. How do we know what is inside a cell? Consider the differences between light and electron microscopy. Write down your answer, THEN ...Click here >>>
While we think of
light as something that moves in a straight line, it
actually vibrates back and forth, like a wave. The 'wobbling' of light
is called its wavelength and the maximum resolution of light is one
half its wavelength. The wavelengths of light range 400-700 nm, meaning
we could never see anything less than ~350 nm. In reality, the
practical limit of light microscopes is 1,000 nm (or one micron).
Since prokaryotes are typically less than one micron in size, we need to use an electron microscope. At high energy, electrons do not vibrate nearly as much as light. This lower wavelength means that we can get high resolution for viewing even the smallest parts of cells.
Since prokaryotes are typically less than one micron in size, we need to use an electron microscope. At high energy, electrons do not vibrate nearly as much as light. This lower wavelength means that we can get high resolution for viewing even the smallest parts of cells.
2. What is the endomembrane system? This concept is described in lecture but you can also watch a video to help, here: What is the endomembrane system?
3. What is 'endosymbiosis'? This topic is discussed in the following video: What is endosymbiosis?
4. What are the parts of the cell and what do they do?
Review the following material: Components of the cell
A) Name:
Function #1 Function #2 B) Name: Function #1 Function #2 C) Name: Function #1 Function #2 D) Name: Function #1 Function #2 E) Name: Function #1 Function #2 F) Name: Function #1 Function #2 |
G)
Name:
Function #1 Function #2 H) Name: Function #1 Function #2 I) Name: Function #1 Function #2 J) Name: Function #1 Function #2 K) Name: Function #1 Function #2 _ L) Name: Function #1 Function #2 |
Lesson #2 - The Cell Surface
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What are the key features of the cell membrane?The cell membrane is a cellular barrier composed of a bilayer of the moleculeEach of these molecules is hydrophobic on one end and hydrophilic on the other end. The term is used to describe molecules with this property.A classical view of the cell membrane is the fluid-mosaic model, where the component of the membrane represents the 'fluid' component and the component of the membrane represents the 'mosaic' component of the of the membrane. Hint: What's a 'mosaic' anyway?Membrane fluidity is influenced by temperature as well as two key elements of the cell membrane:
- The formation of cis-double bonds in the phospholipids - cis-double bonds are special bonds that bend the fatty acid hydrocarbon and make the membrane more fluid.
- The presence of cholesterol in the membrane (1) reduces the fluidity of the membrane at high temperatures and (2) increases the fluidity of the membrane at low temperatures
-
What are the functions of the membrane proteins?I provided the mnemonic I-SCATE but you have to be very careful in applying my mnemonics on an exam. Here are my rules:
- When asked, "what are the functions of membrane proteins?"... If you answer "I-SCATE" you get zero marks. Referring to the mnemonic does not indicate that you can use it effectively. If you memorize and regurgitate the phrases that I gave you, you get zero marks. For example, "signal transduction" gets you zero marks because you have not demonstrated what this term means.
- You may be given this question in the form of multiple choice, multi-select or
matching questions. In this case, you would simply need to
identify the function and memorizing the mnemonic would be useful for
this kind of question. Do you remember the mnemonic...?
I stands for:
S stands for:
C stands for:
A stands for:
T stands for:
E stands for: - At some point, you will be likely asked to describe two or three of these functions. Take some time to research and come up with some unique sentences that would describe the function. Example: "One function of membrane proteins is signal transduction, where the outside surface of the cell interacts with the environment. This interaction produces a signal, either chemical or electrical, that passes through the membrane and tells the cell to respond in some way to the environment."
-
Membrane TransportSince the cell membrane only allows some molecules to cross and not others it is considered to be permeable.
The cell membrane separated the fluid outside the cell from the fluid inside the cell. This means that you can have higher concentrations of a particular molecule on one side, compared to the other side of the cell. When you have two spaces with different concentration of a substance, the molecules will tend to from the region of (hint: options are lower or higher) concentration to the region of concentration.
If a molecule is too large to cross the cell membrane by istelf or is hydrophilic or charged. Transport proteins may form "tunnels" to allow the molecules to cross the membrane. Since the molecules are being moved along their concentration gradient and no added energy is expended, this is called membrane transport.
Imagine a situation where a cell wants to absorb sugar from its environment but there is already more sugar inside the cell than in the environment. In this case the cell will transport sugar against its concentration gradient from a region of concentration to a region of concentration. Proteins that transport these sugar molecules against their concentration gradient need extra energy (e.g. ATP) to accomplish transport of the molecules.
More on passive transport: watch the following video.Notice how channel proteins are simply holes or 'pores' through the cell membrane. The can have gates that allow the cell to open and close them as needed.Carrier proteins are more complex in that they actively bind a molecule on one side of the membrane and then change shape to deliver that molecule to the other side. Carrier proteins are often far more specific to a particular molecule.
More on active transport: There are two types of active transport, called primary and secondary. Primary active transport uses ATP to drive the active transport of molecules. Secondary active transport uses the passive diffusion of one molecule across the membrane to drive the transport of another molecule. In the case of human cells, the cell actively pumps sodium ions out of the cell. This means that sodium 'wants' to diffuse back into the cell. Sodium is co-transported with glucose, where the energy release from sodium diffusion along its concentration gradient is transferred to glucose transport against its concentration gradient. -
How does the cell transport substances that are MUCH larger than a single molecule?The cell can consume very large substances (even whole other cells) by folding the cell membrane around it and then fusing the membrane to form a bubble (or 'vesicle') inside the cell. This process is called . Inside these vesicles, the substance can be digested into individual molecules and absorbed by passive or active transport. Waste can also be pumped into these vesicles and then the bubble of waste can be transported in bulk out of the cell by .
If the substances being consumed are liquids, this process may be called while if the substances being consumed are solid (like whole cells), this process may be called . -
What are the key concepts involving the cytoskeleton?The cytoskeleton is important because it holds the organelles in place, maintains the shape of the cell and allows the cell to move. There are three different protein networks that form the cytoskeleton. They are named based on their diameter and/or structure.
- Microfilaments are the thinnest cytoskeletal filaments, formed from two strands of proteins wound around one another. Microfilaments are important in rapid changes in shape associated with movement or the contraction of a muscle.
- Intermediate filaments are thicker than microfilaments but thinner than microtubles. These thick coils of proteins make some cells very rigid. In humans, intermediate filament is commonly found in skin cells or hair fibers. The thick scales of fish and reptiles are also rich in intermediate filament . If you look at dead skin, the rest of the cell has degraded and only the intermediate filament scaffold remains.
- Microtubules are the thickest cytoskeletal fibers and are named because they form hollow tubes of protein. Microtubules are important in forming the flagella (tails) or cilia (hairs) that help cells move. We will see that microtubules play a very important role in cell division.
-
What are the key features found on the OUTSIDE surface of the cell membrane?Plant cells have a cell membrane AND a rigid that is made primarily of the carbohydrate .
Animal cells have a cell membrane AND a fibrous that is composed of proteins like that are achored to the cell membrane by membrane proteins. -
How are individual cells joined together within a tissue?Plant cells are largely joined together by stacking and interconnecting their cell walls but the individual cells may form tunnels from the cytoplasm of one cell to the cytoplasm of another cell. These cell junctions are called .
Animal cells have three ways in which they are joind together.
- Like the tunnels between cells in plants, animal cells can join the cytoplasm of neighboring cells using junctions.
- In your stomach, for example, where the tissues do not want toxic fluids to enter the body the cells bind very tightly using junctions.
- Sometimes cells are just loosely tethered, like a balloon on a string. These associations are called junctions.
Lesson #3 - The Cell Surface
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What are the key terms associated with DNA Structure?Let's start off easy! In a eukaryote, the human genome can be found in the:
The terms "chromosome" and "chromatin" are confusing. Do you remember what I told you about the suffices -some and -in? Use this knowledge to apply the correct term in the following sentence:
-- When you look at a cell under the microscope at metaphase, you see dark spots or 'bodies' in the nucleus. These dark spots represent a three-dimensional structure that is collectively called a . While that term describes the structures the actual molecule, composed of DNA and protein, would be called .
Get your flash cards out! There is no escaping the need to memorize some names in this section. you should be able to identify all of the structures in the following image:
#1 =
#2 =
#3 =
#4 =
#5 =
Associated with the centromere is a structure that the mitotic spindle uses to bind onto the chromosomes.
-
Getting to know the human genome ...The human genome is diploid, meaning that there are (use words, not number) copies of each chromosome in most cells. In total, there are (use number this time) chromosomes in the typical human cell.
Human cells can be classified into two groups: (1) The cells of the body, referred to as cells, which divide into two daughter diploid cells by the process of , and (2) the (two words) cells (also, "gametes", "egg and sperm") that divide into daughter haploid cells by the process of .
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Cell Cycle of Somatic CellsIt's important to carefully review the cell cycle. Specifically, we discussed in class (1) What happens at each stage? and (2) How the cell cycle is regulated?
Recall that interphase include G1, G2 and S phases of the cell cycle and contitute 90% of the cell cycle.
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In which stage of the cell cycle is DNA copied?
At the end of which stage of the cell cycle would the chromosome not be 'X' shaped?
Which stage of the cell cycle will proceed faster if the cell is stimulated by platelet-derived growth factor (PDGF)?
During which stage of the cell cycle does the cell stop to confirm that DNA has been replicated without error?
During which stage of the cell cycle would you observe spindle fibers?
Which stage of the cell cycle will proceed faster if the cell is stimulated by maturation promoting factor (MPF)?
Cells at which stage of the cell cycle will likely never divide and will simply continue to die off?
A karyotype is usually performed during metaphase, which occurs at which stage of the cell cycle?
Cytokinesis occurs at which stage of the cell cycle?
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Mitotic Cell DivisionMitosis and cytokinesis represent 10% of the cell cycle. The best way to begin to understand this process is to memorize the order of events. Review the mnemonic and type the mitotic stage below before proceeding.
Stage 1 - .
Stage 2 - .
Stage 3 - .
Stage 4 - .
Stage 5 - . -
Mitosis, in detail...The best way to learn mitosis is to create a story with images and to keep track of what happens to DNA throughout the process. Look at the images below. From the pull-down menu select the options that best describe what you see. Try not to choose the same option twice!
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
Lesson #4 - Cell Cycle and Intro to Mendelian Genetics
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What are the differences between haploid and diploid cells as well as haploid and diploid organisms?Hint: most of the answers below are either the words 'haploid' or 'diploid'
You are a dominant organism, meaning most of your cells has two copies of each chromosome. Your germ line cells represent a short period of your life cycle, which are haploid cells because they are produced by a form of cell division, known as .
Haploid reproductive cells can be divided into two groups: (1) gametes (egg and sperm) and (2) spores. The key difference is that gametes fuse to form a cell, called a zygote, which grows into an organism. Alternately, spores are haploid cells that undergo mitosis to produce a organism.
When you are looking at a human, you are looking at a organism.
When you are looking at a fungus, you are looking at a organism.
When you are looking at a plant you may be looking at either a haploid or diploid organism because plants undergo (three words), where one generation of plant might be diploid and the next generation haploid. We call the specific plant generations sporophytes and gametophytes.
Sporophytes are plants that produce (spores? gametes?). These cells then divide by mitosis to generate plants called gametophytes. Gametophytes produce haploid (spores? gametes?) that fuse and give rise to another generation of sporophytes. Did you notice how the names of the plants match the cells they produce? -
What are the stages of mitosis? Mitosis?Mitosis and cytokinesis represent 10% of the cell cycle. The best way to begin to understand this process is to memorize the order of events. Review the mnemonic and type the mitotic stage below before proceeding.
Stage 1 - .
Stage 2 - .
Stage 3 - .
Stage 4 - .
Stage 5 - . -
How is Meiosis I different from Mitosis?Before you do this exercise, make sure you have carefully reviewed Mitosis in Lecture #3
Prophase I
Like Prophase of mitosis, In Prophase I each chromosome has a sister chromatid, giving it an 'X' shape and these chromosomes are condensed.
However, unlike mitosis, the each homologous pair of chromosomes become fused together to form a structure, called a . In other words, you have two copies of chromosome #1 but these chromosomes become stuck together during Prophase I. So, your 46 chromosomes become 23 (same answer as previous box).
The positions where the chromosomes are attached are called and these attachments allow DNA to be swapped between chromosomes, in a process called -over.Prometaphase I
Like Prometaphase of mitosis, this is when the kinetochore forms and the centrioles extend into asters. However, only one kinetochore forms per chromosome rather than one per chromatid. You will see in Anaphase I that Meiosis I involves the separation of chromosomes, no chromatids.
Metaphase I
Like metaphase of mitosis, the chromosomes line up along the metaphase plate. However, make note of the fact that they are tetrads that are lined up. On a test, could you tell the difference between Metaphase and Metaphase I, based on an image?
Anaphase I
Remember how Anaphase of meiosis pulled sister chromatids to either side of the cell? In Anaphase I each of the homologous pairs is drawn to the edge cell.
Telophase I
Again, the nucleus reforms and the cleavage furrow begins to split the cells (in animals).
Recall that the output of Mitosis were two diploid cells, with 46 chromosomes.
The output of Meiosis I is two haploid cells with 23 chromosomes (one of each homologous pair) but each chromosome still has two sister chromatids.
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How is Meiosis II different from Mitosis?Short Answer: Not much different !
The main difference is that the cell starts as a haploid cell.
- Prophase II - chromosomes condense, nucleus begins to dissolve, centrioles start to polarize
- Prometaphase II - asters and kinetochores appear
- Metaphase II - The chromosomes line up at the metaphase plate, waits until spindle attachment is confirmed
- Anaphase II - Sister chromatids are separated to each side of the cell
- Telophase
II - nucleus
re-forms and cleavage furrow appears
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Who was Gregor Mendel and what is 'Mendelian' Genetics?Gregor Mendel studied the how traits might be inherited from one organism to another. This is not an easy thing to do because different traits are inherited in different ways. Mendel addressed this problem by ignoring all traits except those that were discontinuous.
Which of the following statements best describes a discontinuous trait?
Mendel's first challenge was to make genetically pure populations of plants. He took advantage of the fact that he could mate pea plants against themselves in a process called (two words).
One example of his experiments was that Mendel bred plants with violet (purple) flowers to plants with white flowers. This kind of experiment was called .
These purple and white flowers were called the Parental or "P" generation. After mating these plants, all of the next generation (F1 or filial) had flowers because purple was the trait and white was the trait.
So, that's it! When you mate two organisms, one trait dominates the other and the genetic information of the recessive trait is lost, right? Wrong !!! When he mated two purple plants from the F1 generation, most of the offspring were purple as expected but 25% of the offspring had white flowers! -
What were Mendel's Conclusions and Laws?
Observation Conclusion or Law Plants can have two versions of a trait - alleles. When two pure-bred plants are mated both alleles are retained. While only one allele is expressed, the plant has genes for both alleles. Offspring inherit a gene for the trait from each parent and each organism has two copies of each gene.
The pure-bred plant is homozygous - meaning both copies of the gene code for the same variation of the trait.
The plant that has two different alleles is heterozygousMating of heterozygous plants suggests that each gamete (sperm and egg) receives one copy of the gene (allele) and the division, or segregation, of alleles into gametes is random. Mendel's First Law - Law of Segregation
When gametes form, the alleles segregate and each gamete receives one of these two alleles.If Mendel mated a plant that was tall and purple, tall plants were not always purple or always white. These two traits were inherited in a way where the inhertance of one did not affect the inheritance of the other. Mendel's Second Law - Law of Independent Assortment
Genes for different traits segregate independently into gametes, so they are inherited independently of one another.Some traits are dominant and others are recessive Mendel's Third Law - Law of Dominance
Lesson #5 - Mendelian Genetics
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What are the key terms used to describe Mendelian Genetics?Does Mendelian genetics describe continuous or discontinuous traits?
- This means that a trait either has one characteristic or another, but not a mixture of both.
This happens because we have two chromosomes and therefore two genes for each trait. If genes code for the same gene (e.g. flower colour) but give different properties (purple vs white), these different gene variants are called a .
Mendel hybridized true bred organisms to generate an individual that was , meaning the have one copy of each variant. In his pea plants, he observed that the purple flower had a purple phenotype. However, if we represent the purple allele as P and the white allele as p the genotype of this hybrid is .
Mendel developed a method to determine if an individual is homozygous dominant or heterozygous. This method involves hybridizing against an individual with the homozygous individual. This process is called a cross. -
Practice for Punnett SquareThe Punnett square is usually the easiest problem to perform. There are a lot of online resources and practice questions.
- http://www.athro.com/evo/gen/geframe.html
- http://tcet.unt.edu/tegs/chapter2/fires.html
- http://www.dnaftb.org/5/problem.html
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Pedigree AnalysisPedigree analysis is used to trace genetic trends within a family. Below are a tutorial and pedigree exercise.
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How do statistics relate to genetics?Here's a good description of probability laws: https://www.youtube.com/watch?v=y4Ne9DXk_Jc
Lesson #6 - Chromosomes
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Mendelian Genetics and Human DiseaseMendelian genetics is useful in understanding some human disesases.
- Dominant - dwarfism, polydactyly, Huntington's disease
- Recessive - sickle cell, albino, cystic fibrosis
Most genetic diseases are recessive because people with disease are less likely to survive to have large families.
Why do these diseases not just disappear through evolution?
- Partly because people who are heterozygous, called , can survive without the disease but can transmit the genes to the next generation.
- Partly because communities may be isolated and have no alternative but to have children with close family. These consanguineous matings, or "in-breeding" result in an increase in frequency of recessive traits.
Thomas Morgan - Chromosomes
-
Why did Morgan study fruit flies?
- Fruit flies reproduce quickly - he could do lots of experiments in a short time
- Fruit files have simple genetics - only three pairs of autosomes and one pair of sex chromosomes
- Fruit flies have X and Y chromosomes - Other animals have different genetic systems (Chicken ZW, Bee haplodiploid, grasshopper XO).
-
What did Morgan learn that was not already described by Mendel?Recall that Mendel only studied genes that assorted .
Morgan discovered that some genes are , meaning that every time one allele is inherited all other alleles on that chromosome are also inherited.
Morgan found that the best way to describe these genetics were to study sex chromosomes. The genes inherited on sex chromosomes are called sex linked genes.
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What did Morgan discover about Sex-linked genes?Genes can be either X-linked (on the X-chromosome) or Y-linked (on the Y-chromosome).
If a male has an allele on the either the X or Y-chromosome, there is no second copy because there is no homologous pair. These alleles are not homozygous or heterozygous, but rather .
You should be able to do a Punnet square for sex linked traits.
https://www.youtube.com/watch?v=h2xufrHWG3E
In some circumstances, even a female cell can be hemizygous. This is when X-inactivation causes the chromosome to conense into a Barr body.
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How did Morgan end up mapping genes in the genome?Okay ... so Morgan was trying to show that some genes are linked.
Consider the cross: AaBb x aabb
If they are independent (Mendel), the cross would yield:
1 AaBb : 1 aaBb : 1 Aabb: 1 aabb
If they are linked on the same chromosome (Morgan), the cross would yield:
1 AaBb : 1 aabb
Morgan found that some genes do in fact appear linked.
However, at very low frequency, he observed that linked genes crossed over from one chromosome to another.
Genes that are farther apart are more likely to cross over. Allowed Morgan to map the distance between each gene pair.
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The number of chromosomes may cause human disease.How do cells end up with either too many or too few chromosomes? During stage of mitosis and meiosis, the cell normally pauses to ensure that the spindle is attached to the .
When they don't, the homologous chromosomes or chromatids are all pulled to only one side of the cell. This is called non- .
An abnormal number of a chromosome is called while, when there is an abnormally high number of chromosomes it is called .
Match the following disorders with the chromosomal abnormality.
Down's Syndrome
Turner Syndrome
Kleinfelter Syndrome
Cris-du-Chat
Philidelphia Chromosome
Lesson #7 - DNA as Genetic Material
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Establishing DNA as Genetic Material
- A key term is DNA transformation. What does this term mean?
- Match the scientists below with their finding:
- Fredrick Griffiths
- Oswald Avery
- Hershey and Chase
- DNA is a polymer made up of monomers
- Which of the following are pyramidines?
- Consider the following nucleic acid: 10% A, 25% T, 35% G and 30% C. This molecule is .
- The explanation for the question above is HERE
- First, determine whether the molecule is DNA or RNA. Recall that DNA consists of the bases A,T,G and C while RNA consists of A,U,G,C.
- Next, recall that in double stranded DNA A=T, G=C. If this is not the case, the DNA is single stranded.
- In semi-conservative DNA replication, each DNA strand consists of .
Consider the Following DNA sequence:
5' - ATA CGC AAA TGT GGC -3'
- Without spaces, type in the complementary sequence:
- Without spaces, type in the sequence of the other DNA strand: 5' - - 3'
- RNA is transcribed as a reverse complement of the DNA. With this in mind, type the sequence of RNA that would be transcribed from the sequence: 5' - - 3'
- Hint: Did you remember to convert
thymine to uracil?
DNA Replication
- Which of the following is not a valid difference between prokaryote and eukaryote DNA replication? .
- Here is an animation of DNA replication along with three multiple choice quizzes: QUIZ #1 QUIZ #2 QUIZ #3
- Which form of DNA synthesis involves Okazaki fragments? .
DNA Packaging
- While the center of the eukaryotic chromosome is called the centromere, the end of the eukaryotic chromosome is called the ___.
- Eukaryotic DNA is wrapped aroung proteins called histones to form a ___ structure.
- Tightly packed chromatin is called while loosely packed chromatin is called .
Lesson #8 - Transcription and Translation
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Expression of Genes
- The Central Dogma of Biology states that genetic information flows in what order?
- To what do the following characteristics of the genetic code refer?
- The genetic code is non-overlapping
- The genetic code is degenerate
- The genetic code is universal
- The genetic code is unambiguous
- The mutation that typically has the greatest effect on gene expression is called a shift
Trascription of RNA
- Initiation of Transcription
- Directly before the part of a gene that codes for a protein is a DNA sequence that coordinates when the gene is "on" or "off". This regulatory region is called the .
- Within this region, the enzyme RNA polymerase binds a sequence called the box.
- In prokaryotes, the factor helps the RNA polymerase bind the DNA while in eukaryotes this process involves a number of proteins called (two words).
- When RNA polymerase is bond to the DNA and begins to unwind the template, the enzyme and associate proteins are called the transcription initiation complex.
- Elongation of Transcription
- The RNA polymerase adds monomers to the -prime (number, not word) end of the RNA strand.
- Termination of Transcription
- Prokaryotes have a specific termination sequence, where transcription ends
- Eukaryotes transcription continues for 1,000 to 2,000 bp and is later cut.
- Post-transcriptional Modification of the RNA
- Steps #1-3 make a molecule called pre-mRNA
- To make the mRNA molecule more stable, it is modified by a -prime cap and a _-primer poly-A tail
- The mRNA is also processed to remove "junk" sequence, called introns. The remaining exons are fused together and this process is called RNA .
- After addition of 7-metG cap, poly-A tail and after intron splicing, the RNA is called mature mRNA and is ready to be exported from the nucleus.
Translation of Protein
- The ribosome has three key subunits used in synthesis of polypeptides (proteins). How are they normally written, from right to left? (Think: tail-less monkey)
- There are 20 different amino acids and each one is fused to a specific tRNA to make a molecule called an amino acyl tRNA. The enzyme that fuses these molecules is called amino acyl tRNA .
- The tRNA delivers the amino acid to a specific codon of the mRNA because it has its own triplet sequence that is complementary, called an .
- There is no tRNA for the STOP codon, instead the codon is bound by a protein called the factor.
- Not all proteins are made in the rough endoplasmic reticulum. The proteins made in the rER are destined to be secreted out of the cell, on the outer surface of the cell membrane or inserted into certain organelles (e.g. lysosome). The proteins made in the polysome will function in the cytosol or on the inner surface of the cell membrane.
Lesson #9 - Gene Expression
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Organization of a Gene
- For the most part, what is the function of a gene? To give instructions for the cell to make
- This part of the gene is actually called the 'coding' region or 'open reading frame'
- The simplest gene would be a monocistronic gene in prokaryotes. See the following monocistronic gene:
- What is the role of the promoter region?
- What is the role of the coding region?
- What is the role of the downstream non-coding region?
- A more complex organization of genes in prokaryotes
is polycistronic and
is called an
See the following gene: - The difference between a monocistronic and a polycistronic gene is that multiple open reading frames (ORFS) are controlled by a single promoter. They turn on together and they turn off together.
- Each ORF codes for a different __.
- There are two polycistronic genes that we discussed in class and they are named using the three letter notations andenter in the order they appear in the lecture notes).
- Eukaryotes generally do not have polycistronic genes but their single coding region can produce multiple different proteins because of RNA splicing. In RNA splicing, the segment of the RNA is removed and the segements are fused together.
Upstream Promoter Region | Coding Region | Downstream Non-coding Region |
Upstream Promoter Region | ORF 1 | ORF 2 | ORF 3 | Downstream Non-coding Region |
Operons
Operons are specific genes, found in prokaryotes. Proteins that are involved in the same cellular function are normally expressed ("turned on") together. This is achieved by placing multiple open reading frames (ORF) under the control of a single promoter. All ORFs will be transcribed onto a single RNA molecule. It is the ribosome that reads the RNA and produces a different polypeptide (protein) for each ORF.- The ORFs of the trp operon are all involved in allowing the cell to make the amino acid
- When this amino acid is at high concentration in the cell, the trp operon is turned .
- This is because the repressor protein is activated by this amino acid. It binds part of the promoter of the operon (called "operator") and prevents the RNA polymerase from entering the coding region.
- The ORFs of the lac operon are all involved in the import and breakdown of the sugar .
- If this sugar binds to the repressor, the repressor protein changes shape so that it bind the gene's operator.Whenever the repressor is bound to the operator, the gene is turned OFF.
- In addition to the repressor, the lac operon is controlled by the catabolite acivator protein (CAP).The sugar does not bind to the promoter. Transcription does not start unless CAP is bound.
- So, in order for transcription to occur there must be a concentration of glucose, CAP bind to the operator and the of lactose causes the repressor protein to be removed from the operator. Tricky isn't it?
Chromatin Structure and Gene Expression
- Chromatin can take two forms: which is highly condensed and which is loosely packed.
- Like a scroll, genes can be read by the transcription protein complex when it is uncoiled and cannot be read when it is coiled up. Do you think that genes are actively transcribed during metaphase of mitosis?
- This structural change in chromatin is not something that is controlled by a 'gene' and is therefore called regulation of gene expression.
- DNA, particularly the base cytosine (C), can be . This causes the chromatin to become more condensed.
- The histones that wrap DNA within a nucleosome can be . This causes the chromatin to be uncoiled.
Transcription Factors
- Proteins that bind the promoter of eukaryotic genes and affect the rate of transcription are called transcription factors (TFs).
- These TFs bind to DNA sequences close to the gene, called regulatory sequences and more distant sequences called regulatory sequences.
- Those sequences far away from the gene are further divided into elements that increase gene expression and elements that reduce gene expression.
- These transcription factors not only influence whether RNA polymerase can bind and move along the DNA but also affect the folding of the chromatin DNA.
mRNA Processing
- Even when a DNA gene is transcribed at a high level to mRNA, this transcript may not make a lot of protein. One reason is that, in eukaryotes, mRNA must travel from the nucleus to the ribosomes and the molecule may break down along the way.
- The mRNA is a linear nucleic acid molecule (like a string) that is most fragile at its two ends. To protect the 5' end, the mRNA molecule is protected by a 7-methylguanosine and the 3' end is protected by a poly-A
- Also, protein called (three words) bind to both the 5' and 3' ends to protect them from damage.
Post-Translational Regulation
- Even when a gene is both transcribed to mRNA and translated to protein, the resultant protein may still be degraded or may be inactive within the cell.
- Some proteins may have to be phosphorylated or dephosphorylated in order to make them functional.
- Alternatively, expressed proteins can be tagged for removal from the cell. This involves ligating (or 'attaching') a molecule called is ligated ("attached") to the protein, tagging the protein for destruction by the proteasome. The ligation of this moelcule is like leaving a chair in the hallway saying "please throw out" and the proteasome is like the garbage can that in ends up inside.
Cancer
- Cancer involves dysregulation of genes, especially those invovled in regulating the cell cycle.
- Genes that normally promote the cell cycle are called proto-
- When these genes are mutated so that they cause uncontrolled growth of cells they are called oncogenes.
- Other genes are important in slowing the cell cycle. These genes are called tumor suppressors. However, if tumor suppressors are mutated and no longer slow the cell cycle they can also cause uncontrolled cell growth.
- When the cells grow, they form a mass of tissue called a that grows into a mass. If the tissue mass stops growing it is called and is not considered harmful but if it continues to grow it is called and is considered hazardous.
Lessons #10 and 11 - Evolution Theory
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Pioneers of Evolution Theory
- Match the following philosophers and scientists with each description
- Cuvier
- Lamarck
- Darwin
- Plato
- Aristotle
- Linnaeus
- Hutton
- Darwin noted that since individuals in a population vary, and more offspring are produced than can be supported by current resources. Some offspring die and those with greater ability to survive and reproduce are selected for.
- An organism's capability to survive and reproduce is called it's .
- When species evolve better fitness it is called .
- When species evolve to accomodate changes in their natural environment it is called selection, whereas humans can selectively breed animals to promote selection.
- Most evolution involves species becoming progressively more different, termed evolution. But, in some cases, bird and bat wings develop in unrelated species. This latter case is called evolution.
Population Genetics
- Match the following terms with the best description:
- Gene pool
- Fixed Allele
- Microevolution
- Macroevolution
- Average Heterozygosity
- Cline
- Hardy-Weinberg Equilibrium - Developed a model of populations that are not evolving. This model makes a series of assumptions that make it impossible but the model represents an estimation about real populations.
- Which of the following is not an assumption of Hardy-Weinberg equilibrium?
- Dwarfism is a dominant Mendelian trait. If a population of 500 individuals is at equilibrium and there are 375 dwarfs how many of those are carriers?
- How many people in the population are not dwarf?
- What proportion of people in the population are not dwarf?
- What proportion of the population are heterozygous?
- How many people in the population are heterozygous? (round up)
- Real populations change in ways that cannot be predicted by Hardy-Weinberg equilibrium:
- They under go non-random mating, called (two words).
- Sometimes natural disasters can eliminate a large segement of the population to create an evolutionary effect.
- Gametes may cross from one population to another, called (two words).
Lessons #12 - Speciation
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Speciation
- Populations diverge into new species when they are form one another.
- Mating of individuals in a population may be prevented in many ways by are broadly divided based on whether the barrier to mating occurs before or after the formation of the .
- If two populations are separated by geography, the isolation is considered patric.
- If two populations exist in the same geography but mate a different times, this would exemplify isolation.
- If two populations of insect are in the same geography but one lives on the ground while the other lives in trees, this would exemplify isolation.
- The inability for a male Chiwawa dog to mate with a female german shepherd would be an example of isolation.
- Horses and donkeys are not the same species because their offspring, the mule, is an example of reduced hybid .
- In plants, many speciation events occur because of , which involves mating tetraploid plants of the same species, or , a change in chromosome number resulting from inter-species mating.
Hybrid Zones
- Which of the following statements describes the term 'hybrid zone'?
- There are three possible outcomes for species at the hybrid zone:
- The hybrids might outcompete the parental species, leading to only survival of the hybrid species. This is called .
- The hybrid zone may become a stable region where hybrids keep arising because of mating between closely related species. This is called hybrid .
- The hybrids may not be fit and the two parental species will continue to diverge until they can not longer mate. This is called .
Rate of Speciation
- New species emerge on average every million years but this can range dramatically depending on the number of genes that must change to generate a new species.
- Most of the time, evolution follows a gradual speciation model but some times the changes happen very quickly, called the (two words) model.
Lessons #13 - Taxonomy/Prokaryotes
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Taxonomy
- Review the mnemonic and enter the Taxonomic rankings from
Domain (on top)
to species (no bottom).
Enter all of the
taxonomic classifications for a human.
Taxonomic Rank Human Classification
- Use your knowledge of humans
to complete the following table:
Apple tree Kingdom = Kangaroo Class = Chimpanzee Order = Lizard Class = Whale Phylum = Salmon fish Phylum = Whale Class =
Taxonomic Trees
- Taxonomic trees may also be called cladograms. The following video gives nice description of how you might put one together: http://viewpure.com/_C6cqsOf2mI. Pick some random animals and try to make trees of your own.
- Review the image below and answer the following questions:
- In this tree, what is the sister taxon to the bird?
- What is the basal taxon?
- What is the outgroup?
- How many branch points are in this tree?
- In the image above, if we group the animals based on whether they lay eggs, this group would include all of the animals except the mammals. This would be considered a phyletic group.
- One of the challenges with making evolutionary trees is that some species have similar traits, called . These traits, rather than being homologous, are considered because they arise from evolution.
- This challenge can be overcome by looking at molecular characteristics, like DNA sequence. We typically examine mutations that arise in a single gene, such as the traits. However, sometimes genes duplicate and you get multiple version on the same DNA strand.
- Ideally, we can match the appearance of specific mutations with fossil evidence or radioisotope decay so that we can develop a (two words). This answers the question of when a specific speciation event happened.
- DNA is not a perfect way to measure evolution because it is not always transmitted from parent to child. The transmission from parent to child is called transmission of genetic information.
- However, DNA can also be transmitted (for example) by viruses that carry the information from one organism to another. This can cause DNA to be shared across species and is called transmission of genetic information (see the example of plasmids below).
Prokaryotes
- Cell surface
- What structures could a prokaryote use to adhere ("stick") to a substance?
- Like human sperm cells, prokaryotes can have a long tail-like extension called a . However, where this structure is made from in eukaryotes, it is made of the protein in prokaryotes.
- The Gram stain involves the use of crystal to stain the cell wall of some bacteria. This divides all bacteria into either Gram positive or Gram negative species.
- Prokaryotes do not have organelles. How then do they create isolated chambers within their cell?
- Prokaryotes and their environment
- Some prokaryotes are extremophiles. For example, bacteria grow at very high temperature and bacteria grow in very salty environments.
- Under good conditions the bacteria can rapidly reproduce by fission but under poor environmental conditions they can form rigid and resistant structures called the .
- Another way that prokaryotes adapt to their environment is by sharing genetic information (Horizontal gene transfer).
- As we know from the Griffith's experiment, bacteria can take up DNA from their environment in a process called .
- DNA can be carried from one cell to another by virus vectors in a process called .
- Finally, bacteria can extend sex pilli that fuse so that they can share small DNA molecules called plasmids. This is called .
- Bacteria play a critical role in obtaining or circulating nutrients in our environment.
- While some prokaryotes are , which obtain carbon by consuming organic matter, others are that absorb carbon from the air.
- While some prokaryotes are and obtain energy by consuming organic matter, others are that get energy from sunlight.
- Some bacteria are and need oxygen while others are and do not need oxygen.
- While most organisms struggle to get nitrogen in a usable form, some prokaryotes can absorb nitrogen from the air by (two words).
Prokaryotes and their relationships with other organisms
- Cells of the same species can specialize in different functions, resulting in a . Alternatively, multiple species of bacteria can live together and cooperate as they grow in a .
- Prokaryotes often form symbiotic relationships with organisms of other species. In most symbiotic relationships both groups benefit. However there are three classes of symbiotic relationships:
- is when both species beenfit.
- is when one species benefits and the other neither benefits or is harmed.
- is when one species benefits but the second is harmed.
- Prokaryotes and other microbes that harm other organisms (e.g. humans) are often called pathogens. Gram- bacteria are relevant in medicine because they make that harm specific organs and tissues (e.g. neurotoxins). Alternatively, Gram- bacteria can potentially induce life threatening . There is significant fear that these organisms are developing resistance to our current anti-microbial drugs.
- Prokaryotes are not all pathogens. Some prokaryotes can be used to clean up the environment, in a process called .
Lessons #14 - Kingdom Protista
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Protist Taxonomy
- The classification 'Protista' refers to which taxanomic rank?
- Because classification of protists is especially difficult,
they have been more generally classified into supergroups.
Consider the mnemonic U-CARE. In this order, name each supergroup and
select the appropriate description: (in an exam, I might ask you to
recognize but not necessarily to spell each supergroup name)
Multicellular Protists
- An important question in Biology is "when did organisms become multicellular?" Based on extant protists, it appears that multicellularity multiple times evolved independently.
- Animals and Fungi: (1) Amoeba live as single-celled predators, (2) slime moulds evolved to undergo mitosis but not cytokinesis. So, a large multinucleate cell forms the reproductive fruiting body, (3) slime moulds evolved that live as single celled amoeba that later cooperate to form a multicellular fruiting body, (4) animals and fungi emerge that are multicellular throughout their entire lifecycle.
- (1) Single celled protists use chloroplast endosymbiont to perform photosynthesis. (2) "Algae" is a general term for photosynthetic protists and is the result of convergent evolution in both chromalveolata (golden and brown algae) or archaeplastida (red and green algae). (3) In both supergroups, the algae collected into colonies and later formed multicellular "seaweed". (4) A particular green alga called is the closest extant relative of land plants.
Important Protists
- In the supergroup there are the following relevant protists:
- The malaria parasites of the genus , which is transmitted through mosquito bite and kills more than 1 million people per year.
- The protist that is responsible for red tide fever, a potentially fatal disease that arises from consuming toxins that accumulate in molluscs. This same protist can also cause water to glow with light, using a process called .
- The is a protist that is a common single celled predator in freshwater ponds. It is commonly used to show how complex a single cell can be because it had special structures like cilia and a contractile vacuole.
- Some of the protists in this supergroup are photosynthetic algae. algae resemble land plants in that they have alternation of generations but it is not believed that these algae are the ancestors of plants.
- In the supergroup there are the following relevant protists:
- Space ships use hydrogen gas as fuel in "fuel cells" to make electricity. are protists that may be very important in space exploration because they have hydrogenosomes that respire sugar to hydrogen gas instead of CO2.
- Trypanosomes are important protists in this group because they cause sickness, a potentially fatal disease that is spread through the bite of hte Tsetse fly.
- Some in this group live as symbionts inside of termites, where they digest wood and share the sugar byproduct with the host termite.
Lessons #15 - Kingdom Plantae: Seedless Plants
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Why did land plants evolve?
- Plants perform photosynthesis by absorbing (Two words). This gas is more abundant in air than in water.
- As the tide washes up onto land, bring nutrients onto the shoreline
- Water absorbs and block , the source of energy for photosynthesis. On land, the plants have direct access to this energy.
- Before plant colonized land, there were very few (animals that would eat them).
What conditions did plants have to overcome in order for algae/plants to colonize land?
- Plants tend to dry out on land, a process called . This is a HUGE problem for any organism that lives on land.
- One response to drying out was for plants to coat their spores in
- Another adaptation was the formation of a waxy around the stem of the plant, to prevent water loss.
- Land plants are called because they protect their embryo from drying out by keeping inside the parent plant and providing nourishment to it using transfer cells.
- Ferns became , meaning they developed xylem vessels to allow water to flow from the deepest root to the tallest shoot of the plant.
- Plants produce , special pigments that protect them from the damaging ultraviolet rays of the sun.
- Plants needed to anchor themselves to the ground to prevent being carried away by the .
- Moss had structures that anchored them to the ground but vascularization allowed fern sporophyte to the develop true that grew deep into the ground and anchored them.
- Plants needed to develop greater structural support to overcome the force of .
- Vascularization also involved the incorporation of into the cell wall of plant stems, which made them capable of growing much taller
Why do we think that plants evolve from charophytes?
- BOTH charophytes and plants have cell walls composed of .
- BOTH charophytes and plants undergo similar cytokinesis. A cell plate forms from the .
- While some algae have non-motile sperm, carried by water currents, BOTH charophytes and seedless plants have sperm that a propelled by .
- While many algae have peroxisomes, the in the peroxisomes of BOTH charophytes and plants are particularly similar.
- More recently, analysis of the DNA sequence for charophytes and plants has been found to be similar.
Moss (Bryophytes)
- Bryophytes are plants with a dominant lifecycle.
- The gametophyte consists of a body, or , that is anchored to the ground by structures.
- The gametophyte develops dedicated (male) and (female) gametangia.
- The sperm is flagellated and swims to female gamete, where fusion occurs and a sporophyte grows on top of the parent thallus.
- The sporophyte remains attached by a , through which it draws nutrients.
- The stem of the sporophyte is called a and ends with a structure that is full of spores.
- Unlike the gametes that can swim, the spores are released into the wind.
Ferns (Monilophyta)
- Monilophyta are plants with a dominant lifecycle.
- The gametophyte consists of a microscopic -shaped body, or , that is anchored to the ground by structures.
- The gametophyte is bisexual and has both (male) and (female) gametangia.
- The sperm is flagellated and swims to female gamete, where fusion occurs but a sporophyte grows beside the parent thallus.
- The sporophyte is anchored to the ground by true and can more efficiently perform photosynthesis because it has true .
- On the under side of the fern leaf are yellow circular structures, each called a . These structures contain spores that are dispersed by wind and that grow into gametophytes.
- Unlike the gametes that can swim, the spores are released into the wind.
Lessons #16 - Kingdom Plantae: Seed Plants
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Seed vs Seedless Plants
- There are three relevant plant reproductive structures, that divide the seed and seedless plants: Spores, Pollen and Seeds ... these are NOT the same things!
- Let's talk SPORES
- Moss and Ferns are , meaning that there is no morphological difference between the spores that grow into male gametophytes and spores that grow into female gametophytes.
- Gymnosperms and angiosperms are , meaning that (smaller spores) grow into male gametophytes and (larger spores) grow into female gametophytes.
- Moss and ferns primarily spread their offspring by releasing spores into the wind.
- Gymnosperm and angiosperms instead spread their offspring by spreading pollen and seed.
- Let's talk POLLEN
- Moss and fern gametophytes are independent plants. In fact, in moss the gametophyte is the dominant plant generation.
- In gymnosperms and angiosperms, the microsporophytes and male gametophyte is reduced to a small cluster of cells that is contained inside of pollen.
- A single conifer tree typically has male cones and female cones on the same tree. The cone releases pollen and distributes it on .
- A single angiosperm has a reproductive organ called the flower. The male reproductive structure is the anther, which produces pollen. The pollen is often distributed on .
- Let's talk SEED
- Moss and fern do not have a seed.
- In gymnosperms the megasporophyte and female gametophyte is located in the ovulate cone. A single scale of the cone can carry the seed on the wind.
- In angiosperms the megasporophyte and female gametophyte is located at the base of the flower carpels. The ovary enlarges into a fruit with one or more seeds within it.
- The angiosperm seed may be dispersed by the wind but is often spread by animals who eat the fruit.
- When seeds grow into young plants, the process is called .
Seed Plant Diversity
Complete the following table:Plant | Classification | Description |
Black Pepper | ||
Ephedra | ||
Carrot | ||
Ginko | ||
Douglas Fir | ||
Grass | ||
Cycad | ||
Water Lily |
Angiosperm Diversity
Monocots and Eudicots
Historical note: Plants were originally divided into monocots and dicots based on physiological characteristics. DNA evidence showed that some dicots (e.g. Magnolia flowers) do not belong in this group. Since then, the true or eudicots have been more formally recognized. You'll hear biologist (perhaps, even me) use the term dicot out of habit but we generally mean eudicot.
Examine the following characteristics and indicate whether it describes a monocot, eudicot, neither or both:
- The plant has a symbiotic relationship with honey bees -
- Two leaves in the embryo -
- Leaf veins that run parallel to one another -
- The plant has vascular tissue composed of both xylem and phloem -
- There is both an ovulate cone and a pollen cone on a single plant -
- Vascular tissue is scattered randomly throughout the stem -
- There is one large main root, called a tap root -
- The pollen grain has a single opening -
- The plant does not develop a flower -
- Flowers of the plant are arrange in fives -
Lessons #17 - Kingdom Animalia
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What is an Animal?
- It's easy to say that a cow is an animal, or a dog. However, some animals like a sea sponge are not so obvious.
- Animals are that move (are motile) at some stage of their life. Animals are and typically reproduce sexually.
- Animals have a common developmental pathway
- Animals, fungi and plants have a zygote but animal cells divide, in a process called cell , and expand into a large hollow ball called a . The first part of the animal that develops is the gut, which develops through a process called .
- Most (but not all) animals start out as and then undergo a transition to adulthood through a process called .
- Unlike plants and fungi, animals have a complex body plan. The body develops in a way specified by a set of genes called the genes (three letter name).
Animal Diversity
M: | P: | E: |
R: | B: | A: |
C: | D: | P: |
L: | E: |
The first three broadly divide animals into "after/beyond animals", "near animals" and "true or well animals". If you can't remember, refer to this list of Greek and Latin roots.
- "M" encompasses all animals.
- "P" includes the sea sponge, phylum , is barely an animal because it does not have true tissues or body symmetry and is not motile. (Hint: it does not feed through a mouth but instead through pores throughout its body).
- "E" includes all other "true" animals.
- The "true" animals are divided by symmetry, either radial or bilaterial. Animals in the phylum (e.g. jellyfish) have radial symmetry, meaning they are symmetrical at all angles when viewed from above.
- The bilateral animals are divided based on the number of tissue layers in the embryo. Diploblastic animals have two layers while triploblastic animals have three layers. Diploblasts are flat while triploblasts have a large cavity in the body called a coelom. This division covers "A" and "C" above.
- An example of a diploblast is the flatworm in phylum .
- The animals with a coelom are divided based whether the mouth "stoma" or anus develops first. Do you remember what proto means?
- During gastrulation, your anus developed first from the blastopore. Your phylum is and you are most closely related to the deuterostome starfish in the phylum .
- The protostomes are divided into those that molt, including insects (phylum ) and roundworms (phylum ), and those that do not.
Phylum Porifera
Imagine an "animal" with no mouth and that does not move. The sea sponge is a porous tube with a hole on the top. Choanocytes are cells that wave a cellular extension, called a . Water is drawn into the hollow body, or spongeocoel, and nutrients are filtered out of the water.Phylum Cnidaria
Jellyfish (class ), hydra (class ), box jellies (class ) and sea anemone (class ) all have common features, such as stinging cells called and a single cavity for digestion called a cavity.Like the sea sponge, these animals may not be motile during the stage of their lifecycle. However, these animals developed the ability to move, which occurs during the stage of their lifecycle.
Corals are an incredibly important part of many marine ecosystems and represent cnidarians of the class .
Cnidarians of the class produce one of the most toxic poisons known.
Lessons #18 - Invertebrate Animals
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Glossary of Terms
Before we tackle taxonomy, it helps to define some root terms:- Gas- means
- Ptera- means
- Pod- means
- Aster- means
- Poly- means
- Oligo- means
- Myriad means
- Hexa- means
- Cephalo- means
Evolution of Animals
Now, let's place animals into their defining categories. Practice making the tree based on My PERl BAC DAPLE and use this mnemonic to fill in this table.Common Name | Body Structure | Embryonic Tissues | Coelom? | Digestive System | Blastopore
becomes... |
Superphylum |
Sea Sponge | n/a | n/a | n/a | n/a | n/a | n/a |
Jellyfish | n/a | |||||
Sea anemone | n/a | |||||
Hydra | n/a | |||||
Planarian | n/a | |||||
Tapeworm | NONE!!! | n/a | n/a | |||
Fluke | n/a | |||||
Roundworm | ||||||
Snail | ||||||
Earthworm | ||||||
Honey bee | ||||||
Starfish | n/a | |||||
Human | n/a |
Taxonomy
Now, let's tackle the taxnomic classification of animals. First of all, ALL ANIMALS belong to the domain and the kingdom . This exercise is more difficult than you would see on an exam. However, if you can identifiy the major phyla and extend the glossary of terms above to identify the other taxonomic groupings, you will be in a strong position.Animal | Phylum | Subphylum | Class | Order |
Sea Sponge | --- | --- | --- | |
Jellyfish | --- | --- | ||
Sea anemone | --- | --- | ||
Box Jelly | --- | --- | --- | |
Planarian flatworm | --- | --- | --- | |
Blood fluke | --- | --- | ||
Snail | --- | --- | ||
Octopus | --- | --- | ||
Centipede | --- | --- | ||
Honey Bee | ||||
Crab | --- | --- | ||
Spider | --- | --- | ||
Horseshoe crab | --- | --- | ||
Roundworm | --- | --- | --- | |
Earthworm | --- | --- | --- | |
Common Starfish | --- | --- | ||
Sea cucumber | --- | --- |
Lessons #19 - Animal Phylum Chordata
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Defining Characteristics of Chordates
Not all chordates are vertebrates.
Instead, they are defined based on four key characteristics. Chordates
have all four characteristics at some
point in their life cycle.- Post anal
- Dorsal hollow (two words... there's no 'H' )
- Flexible (there is an 'H' )
- slits
Evolution of Chordates
The key to understanding the taxonomy of chordates is to trace the major evolutionary steps. First. these animals developed a . The next adaptation was the , followed by a . Even before transitioning to land, the fish swim bladder developed into the and the fish acquired the . Amphibians lay, fertilize and hatch their eggs under water while reptiles, birds and mammals have a specialized egg called an egg.Animal | Vertebrate? | Jaw? | Bony Skeleton? | Egg? | Amniote? | Calcified Egg? | Endotherm? | Hair? |
Lancelet | ||||||||
Tunicate | ||||||||
Hagfish | ||||||||
Lamprey | ||||||||
Shark | ||||||||
Tuna fish | ||||||||
Coelocanth | ||||||||
Frog | ||||||||
Lizard | ||||||||
Eagle | ||||||||
Dinosaur | ||||||||
Platypus | ||||||||
Kangaroo | ||||||||
Human |
Taxonomy
Animal | Subphylum | Infraphylum | Superclass | Class | Order |
Lancelet | --- | --- | --- | ||
Tunicate | --- | --- | --- | ||
Hagfish | --- | --- | |||
Shark | --- | ||||
Tuna Fish | --- | ||||
Frog | |||||
Salamander | |||||
Lizard | |||||
Crocadile | |||||
Turtle | |||||
Eagle | --- | ||||
Platypus | |||||
Kangaroo | |||||
Rat | |||||
Bat | |||||
Wolf | |||||
Human |
Primates and Paleoanthropology
- Some key features of primates are the thumb, nails, snout and brain.
- Monkeys are divided between -world (Asia and Africa) and -world (South America) monkeys.
- Apes are separated from monkeys because apes lack a .
- Apes are divided in various genera, inlcuding humans (Genus ), chimpanzees (Genus ), gorillas (Genus ) and orangutans (Genus ).
- The hominids include Homo habilis, who developed (two words) and Homo erectus, who developed , and Homo sapiens, who developed the ipad.
Lessons #20 - Kingdom Fungi
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Defining Fungi
- Like animals, fungi are and . However unlike animals, fungi do not have a digestive system, they just secrete digestive enzymes outside their body and absorb the nutrients.
- Fungi have a cell wall composed of .
- Fungi can grow as single cells, called , or as a multicellular with a body called a .
- Multicellular fungi grow as long strands called , but these strands form larger bundles that are each called a .
- Multicellular fungi are also divide based on whether their cells are fused, called fungi, or divided, called septate fungi.
Reproduction
Fungi generally have a dominant lifecycle and can reproduce sexually os asexually.Instead of "males" and "females", the mating types of fungi are called "+" and "-"
Fungal gametes first fuse to form a cell with two nuclei. This process is called and the resultant cell is refered to as .
Later, the nuclei fuse through the process of .
Fungal Phyla
Match the fungal phylum with the most appropriate description:Basidomycota | |
Ascomycota | |
Chytridamycota | |
Glomeromycota | |
Zygomycota |
Importance of Fungi
Match each organism/tissue with its relationship with fungi:Leaf cutter ("Farming") ant | |
Lichen | |
Mycorrhizae | |
Endophyte | |
Human skin | |
Human urinary tract | |
Staphylococcus |
Lessons #21 - Population Ecology
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Population Size
- Population size is often measured using mark-recapture experiments. If 50 animals are marked and released into the wild. When 1000 animals were recaptured 10 had the markings. How many animals are there in the population?
- Population size is a function of birth, death, immigration and emmigration. In a population of 500 individuals, 7 are born, 3 die, 4 immigrate and 9 emmigrate. How many remain? .
- Animals often adopt different dispersion patterns. Territorial animals often adopt distribution, mating animals often adopt distribution and wind-dispersed plants often adopt distribution.
Demographics
- Ecologists often collect information, called statistics, and enter these data for a cohort of individuals in a table.
- The trend that is often observed is that animals conform to one of three survivorship patterns
- Type I survivorship curve represents animals that
- Type II survivorship curve represents animals that
- Type III survivorship curve represents animals that
Growth Rate
- If a population is at zero growth and the bird rate is 20% of the total population (per year). What is the death rate? %
- You often see a zero growth population when the population conforms to a growth curve and has reached the capacity for its habitat.
- In contrast, founders that enter a habitat with abundant resources often show growth.
- Growth strategies often conform to one of two strategies: (1) parity involves rarely reproducing but making as many offspring as possible; (2) parity involves producing few offspring but often.
- Organism that make many offspring, which each have a low chance of surviving, are call -selected, because this letter represents the growth rate. -selected species make few offspring and invest in them, which is avantageous when the population reaches the carrying capacity.
- This causes population numbers to change over time, called population . An example is the variation of predator population along with the population density of their prey.
- The human population is experiencing population growth. However, the past 30 years has seen the growth rate slow.
- The slowing of human population growth produces an population, where there are not enough young people to support the relatively high number of elderly. In Canada, we see that our elders are retiring later in life and there are fewer jobs for our youth.
Lessons #22 - Community Ecology
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Niche
- A niche is when two species occupy different parts of a habitiat or use different within the same habitat.
- The maximum niche that a population can occupy is called its niche. However, in a community the population only occupies a smaller niche because of interspecific competition.
- Competition between species often drives speciation.
Self Defense
- Animals often use body colouration as a form of communication or warning
- Aposematic colouration involves
- Cryptic colouration involves
- Mullerian mimicry involves
- Batesian mimicry involves
Symbiosis
- Mitochondria are an example of .
- Bird nests are an example of .
- Honey bees are an example of .
- Malaria protists are an example of .
- Epiphytes are an example of .
- Facilitation is not symbiosis because the organisms are not in direct contact. However, some species facilitate others indirectly.
Species Diversity
- The number of species is called species while the size of a species population is called species .
- Foundation species are typically abundant and form the structure of the habitat, while species may be rare but play an essential role in maintaining the habitat.
- Beavers are an example of ecosystem .
- Fires and pathogens are often examples of ecological . Some disturbances are useful. Consider a fire: warm air rises and can distribute conifer seeds.
- Species that are introduced into an ecosystem may be species, which may be severe disturbances that offset the balance of the entire ecosystem. Don't discard of your turtle in the nearest park.
Food Web
- There are two major food webs: (1) the food web originates with photosynthetic organisms while (2) the food web originates from decaying matter.
- The length of food webs may be limited by (1) the waste of energy at each trophic level and (2) top level predators easily become extinct if the prey population dwindles.
- A diverse ecosystem requires a rich source of energy and organic carbon. The base of the food web becomes more stable during ecological , where weeds transition into bushes and then rich forests.
Lessons #23 - Energy Flow
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Laws of Nature
- Prepare a clear definition of 'ecosystem'.
- Nature is based on the laws of physics and chemistry. Energy and matter are never created or destroyed.
- Nature's energy ultimately comes form the .
- To key drivers in biology are light and water.
- The ecosystem has plenty of water but limited light.
- The ecosystem has plenty of light but constant desiccation.
Trophic Levels Revisited
- A wolf would be a .
- A cow would be a .
- Grass would be a .
- A mushroom on a decaying log would be a .
Energy Budget
- Enough sunlight beams on the Earth in a single day to supply all the energy consumed by humans in years.
- Photosynthesis captures 1% of that energy because the rest is lost to reflection, clouds, etc.
- What is the difference between gross and net primary production?
- Primary production is limited by light and nutrients, like (N) and (P).
- Agricultural run-off and sewage can provide these nutrients and cause phytoplankton to bloom. While this may seem like a good thing, the organisms that decompose phytoplankton end up consuming the that fish need to survive.This phenomenon is called .
- While it varies by organism, approximately percent of the energy is transferred from one trophic level to another.
Biogeochemical Cycles
- Matter is not created or destroyed but it can be captured in , such as the capture of carbon in fossils (peat, coal, oil).
- Water, nitrogen and carbon cycles are all similar in that the matter cycles as a gas. When nitrogen and carbon are captured from the atmosphere, they are "fixed".
- Carbon naturally cycles but excess carbon has been buried underground as oil and coal. As well burn fuels, we are releasing 100s of millions of years of stored carbon into the atmosphere.
- Commercial fertilizers largely provide a synthetic nitrogen source, which normally limits plant growth.