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IB Biology Study Guide
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Contents
1 Biotechnology
1.1 Block 1B
1.2 Block 3B
1.3 Block 4B
2 Cellular Biology
2.1 Block 1B
2.2 Block 3B
2.3 Block 4B
3 Cell Division
3.1 Block 1B
3.2 Block 3B
3.3 Block 4B
4 Genetics
4.1 Block 1B
4.2 Block 3B
4.3 Block 4B
5 DNA
5.1 Block 3B
5.2 Block 4B
6 Photosynthesis/Respiration
6.1 Block 1B
6.2 Block 3B
6.3 Block 4B
7 Chemistry
7.1 Block 1B
7.2 Block 3B
7.3 Block 4B
8 Evolution
8.1 Block 1B
8.2 Block 3B
8.3 Block 4B
9 Classification/Ecology
9.1 Block 1B
9.2 Block 3B
9.3 Block 4B
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Biotechnology
[edit]
Block 1B
PCR
PCR, or Polymerase Chain Reaction, was developed by Kari Mullis as a means to
amplify DNA obtained from crime scenes. In short, it's replication GONE CRAZY. In
just a few hours, DNA can be replicated millions of times. In the procedure, DNA
Polymerase uses nucleotides and primers to replicate a small sequence of DNA so that it
is visible when comparing DNA obtained from a crime scene with samples. There are
four steps to the process:
1. Denaturation - breaks Hydrogren bonds, splits them with heat
2. Anneal - adds primers, cools DNA
3. Extension - DNA Polymerase adds nucleotides to the DNA sequence
4. Repeat - in three hours, one can obtain three million copies of the DNA.
The DNA polymerase of Thermus aquaticus, a bacterium that lives in hot springs, is
often used during PCR because the enzyme is able to survive the extremely hot
temperatures needed to break hydrogen bonds in the DNA. One can replicate specific
sequences of the DNA by utilizing specific primers in the replication process.
Gel Electrophoresis
Gel electrophoresis is a method of separating the strands of DNA based on their
charge and size. Based on charge, DNA molecules have a negative charge. When placed
on a magnetic field, the DNA strands move toward the positive pole. In addition, they
can be separated based on size. Larger DNA molecules move much slower than small
ones, so different sized DNA strands stop at different points along the magnetic field.
Through this technique, the DNA leaves a distinctive pattern, and it can be compared
with other samples to match DNA.
Restriction Enzymes
Restrictions enzymes, or molecular scizzors, are used to cut DNA molecules in
specific places. Bacteria produce restriction enzymes for the purpose of seeking out and
destroying bacteriophage DNA. Researchers use these restriction enzymes to cut DNA
at specific points, called palindromes, into manageable segments. Later this DNA can
be inserted into a vector molecule, which will take the plasmids (DNA segments) into
the cell. Once inside the nucleus of the cell, this plasmid DNA is replicated and
distributed to any daughter cells. Restriction enzymes cut the DNA in a staggered
pattern, producing sticky ends to which other DNA molecules which have been cut with
the same restriction enzyme can bind.
Recombinant DNA
When DNA is spliced into a vector, the newly-formed product is known as
recombinant DNA. Genetic engineering enables individuals to change viruses so that
they can more easily introduce DNA into cells of more complex organisms, creating
more complex and advanced recombinant DNA.
Human Genome Project
The human genome project aims to find the location of all of these genes on the
human chromosomes and the base sequence of all of the DNA that makes them up. The
project is an international cooperative one, with laboratories in many countries
involved. The sequencing of the entire human genome will make it easier to study how
genes control human development. It will allow easier identification of genetic diseases
and the production of new drugs bases on DNA base sequences of genes or the structure
of proteins coded for by these genes. It is estimated that the project could contain
anywhere from 30,000 to 40,000 different individual genes.
Cloning
Cloning produces an organism with and identical genotype as to its host/donor. A
clone is a group of genetically identical organisms or a group genetically identical cells
derived from a single parent. Two types of cloning exist: cloning by embryo splitting,
an earlier procedure, and cloning by nuclear transfer, used to clone the sheep Dolly. To
clone the sheep Dolly, udder cells were taken from a donor sheep and unfertalized egg
cells were taken from another sheep. The nucleus was removed from each egg, which
were then fused with the donor cells using electricity. The fused cells developed into
embryos, which were then implanted into a surrogate mother. The mother gave birth to
a sheep genetically identical to that of the donor cell organism. Cloning by embryo
splitting is an earlier method with differences in the method by which a clone is
achieved. First, the actual egg cell of an animal is removed to be fertilized in a petri
dish. In the dish, the zona pellucida is a chemical coating that promotes cell division.
After the first division, this zona pellucida is removed by an enzyme and the two cells
separate to become two individual cells. Within the petri dish, an artificial zona
pellucida is added to the individual eggs and they continue development separately.
This method is often used in cloning favorable livestock. Livestock are often selected
for cloning based on favorable commercial qualities, including wool, meat, or milk
productivity.
Use of Reverse Transcriptase in Biotechnology
In the biological world, reverse transcriptase is an enzyme used mostly by viruses to
convert single-stranded RNA molecules into double-stranded DNA molecules. In terms
of biotechnology, reverse transcriptase is utilized in reverse transcription PCR. In this
way, by converting RNA to DNA before beginning the process of PCR, RNA can be
examined in the same way that DNA can be through the process.
Bio Tech Ethics
There are many controversial issues concerning biotechnology. Cons- 1. New
chemicals can kill agriculture
2. Some people have allergic reactions, sometimes fatal to biotech engineered food
3. Cloning (Hot political issue*) can be seen as trying to "be God"
4. Cloning can casue some genetic problems
Pros- 1.With Biotech, we can ffed the rapidly growing world population better
2. Products can grow faster, bigger, and better
3. Cloned animals such as cows can produce more milk to better the American
market
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Block 3B
PCR: Polymerase Chain Reaction: The polymerase chain reaction is used to amplify
DNA in a small amount of time. There are four basic steps that outline this
amlpification. Denaturation: heat(extreme) is used to break hydroge bonds and separate
the strands of DNA; Anneal: Primers are then added to the separated strands during this
step; Extension: Thermus aquaticus provides the enzyme DNA polymerase; Repeat:
The process is then repeated multiple times. Each hour yields approximately 1 million
copies. (5 hours = about 5 million copies)
Restriction Enzymes
Restriction enzymes are DNA scissors. They cut both strnds at specific bases in order
to remove needed genes and open bacterial plasmids. By cutting at certain bases, they
can create sticky ends, helpful in the creation of recombinant plasmids (i.e. insulin).
Gel Electrophoresis:
Gel electrophoresis is used to separate DNA according to size and charge. Due to the
phosphate groups that make up DNA, DNA has a negative charge. Therefore, DNA will
migrate towards the postively charged pole. In addition, large molecules will move
slower then the smaller molecules.
Reverse Transcriptase
Reverse Transcriptase is used to create DNA from RNA. It is found in retroviruses.
Biotechnology uses this to create DNA without the garbage introns from RNA.
The Human Genome Project The Human Genome Project was started by United
States scientists in 1990. Although originally planned to last for fifteen years because of
the extensive amount of work that was planned to be done, it only took until 2003. The
Human Genome Project successfully determined the sequences of over 3 billion base
pairs in DNA and identified all of the genes in DNA. The ultimate goal of the Human
Genome Project was to map out human DNA so that it would be easier to cure diseases
and sickness.
Cloning
Dolly is the name of a sheep that was cloned by nuclear transfer. Another way of
cloning is embryo splitting.
Recombinant DNA After a specific section of DNA is spliced off, it can be inserted
into an organism via a vector. A vector is a means of transporting this DNA fragment,
such as a gene gun or bacteriophage (which we steal to inject the recombinant DNA).
This allows us to insert new genes into organisms, forming the basis for genetic
engineering.
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Block 4B
Restriction enzymes are “molecular scissors” used to cut DNA molecules in specific
places. Restriction enzymes cut DNA in a staggered manner, which produces pieces
with identical, complementary, single-stranded “sticky ends”. These “sticky ends” can
pair up with single-stranded ends of other DNA molecules that have been cut with the
same restriction enzyme.
PCR is also known as the Polymerase Chain Reaction. It was created/discovered in
1983 by Kary Mullis. The main purpose of PCR is to make many many many copies of
DNA (1 to over 3 million in 3 hours!!). THe first step is Denaturation which breaks the
Hydrogen bonds and separates the strands of DNA using Heat. Then there is Anneal,
which adds DNA Primers using DNA Poymerase. The final step is Extension where
DNA Polymerase adds nucleotides(dNTPs).
Gel Electrophoresis is an example of DNA profiling that is used to separate strands of
DNA based on charge and size. Smaller molecules move much faster than the larger
molecules. When DNA has a negative charge, because of the phosphate groups, it will
migrate towards a pole with a positive charge.
Recombinant DNA is formed when DNA is spliced into a vector, it is the DNA that
has been created artificially. Engineered viruses are used to introduce DNA into the
cells of more complex organisms.
The Human Genome Project was a project launched officially in 1990 at a cost of 3
billion US dollars with a coalition of countries such as the U.S., U.K., Germany, France,
Japan, and China. The purpose of this project was to identify all of the 20000-25000
genes in the human DNA, determine sequences, store the information in the database,
improve tools for analysis, among other goals. The sequence of the last chromosome
was published in 2006; although, the genome itself was finished in 2000. With the
completion of the project, scientists are closer to their goal of isolating genes that could
cause certain diseases/ disorders.
Gene Therapy is used to treat genetic diseases by altering the genotype. In theory, it
would be possible to eliminate genetic diseases in the future by changing the base
sequence of the allele that causes the disease. For example, if the disease-causeing allele
is recessive, one could insert the dominatn allele that would prevent the disease into the
cells that have been infected. Although this procedure could be done at several different
stages during the human life cycle, the best cells to use are stem cells. They can divide
repeatedly to replace lost body cells.
Gene Mutation is any change to the base sequence of a gene. Although there are
several types of gene mutations, the smallest possible change that can occur (when one
base is replaced by another) is called a base substitution. One of the most notable
examples of a gene mutation is non-dysjunction in chromosome 21 (trisomy-21),
otherwise known as Down Syndrome.
Cloning Cloning is a process by which a genetically identical copy is made of
something. The most famous example to date is Dolly the Sheep. Dolly was the product
of somatic cell nuclear transfer where 1) the nucleus from a somatic cell is placed inside
an egg cell, which has had its nucleus removed 2)An eletrical shock intiates the egg that
contains the somatic cell's nucleus to begin dividing 3)It will eventually form a
blastocyst, which has almost identical DNA to the original organism.
Scientist have said that it is possible to clone Humans, but the process is considered
controversial. On the positive side cloning of embryos would allow scientist to screen
for genectic diseases earlier. Then infertile couples would have a more successful
chance if their mbryos were cloned. On the negative side those groups who were
genectically identical might suffer psychological problems. Also, if differentiated cells
could cause a high risk of fetal abnormalities and a high rate of miscarriages. Then
differentiated cells have already began ageing and it might cause the humans clones to
grow old quickly.
Reverse Transcriptase is the molecule which allows a single strand of RNA to be
made into a double strand of DNA.
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Cellular Biology
[edit]
Block 1B
Viruses/Reverse Transcriptase
Viruses are non-cellular infections agents that must have a host cell to replicate. They
are also considered non-living; however, this is debated, as the current definition for life
may be contestable. Viruses are self-propogating, and they undergo some of the same
biological processes that other classied living organisms do. Viruses also contain
nucleic acid (either DNA or RNA) which is surrounded by a protein coat, or capsid. An
argument against viruses being considered living organisms is that they rely on other
cells to perform metabolic activities, with no independence. The most widely accepted
theory for the origin of virusis is that they are bits of nucleic acid that have escaped
from cells. Phages are viruses that invade bacteria.
Reverse transriptase, also known as RNA-dependent DNA polymerase, is a DNA
polymerase enzyme that transcribes single-stranded RNA into double-stranded DNA.
Normal transcription involves the synthesis of RNA from DNA, hence reverse
transcription is the reverse of this.
Prokaryotic/Eukaryotic Cells
Eurkaryotic cells feature membrane-bound organelles, compared to prokaryotic cells
which do not. Prokaryotic cells feature both a cell wall and a cell membrane, while
eurkaryotic cells feature only the membrane. Prokaryotic cells are also typically smaller
than eurkaryotic cells and likely evolved first. Prokaryotic cells feature circular DNA
which is naked, while eukaryotic cells contain linear DNA contained within a nucleus.
Lastly, prokaryotic cells feature 70s ribosomes, in contrast to 80s ribosomes found in
eurkaryotic cells.
Plant/Animal Cells
Plant cells feature chloroplasts and mitochondria, while animals cells only contain
mitochondria. Plant cells are surrounded by a cell wall made of cellulose, whereas
animal cells only have the cell membrane. Plant cells contain one large vacuole to store
water, while animal cells have many smaller vacuoles for the storage of other
substances. Lastly, animal cells have cilia and flagella to promote movement, while
plant cells are stationary.
Cellular Organelles: Functions, Structure
Nucleus - Contains DNA, regulates cell processes
Nucleolus - Creates ribosomes
Chloroplast - Site of photosynthesis
Mitochondria - Make energy
Endoplasmic Reticulum (rough or smooth) - Pathway for transport of materials
throughout cell
Ribosomes - Synthesize proteins
Lysosome - Digests food, recycles organic material, suicice sac, contains digestive
enzymes
Golgi Apparatus - Packaging center for proteins
Vacuole - Storage, disposal of waste
Vesicles - Transfers proteins through cytosol
Plasma Membrane - Selectively permeable membrane that allows the passage of
materials in and out of the cell
Cell Wall - Maintains shape, water intake, and protection for the cell
Cilia/Flagella - Provide movement
Microtubule - Structure
Centrioles - Assist in cell division
Plasma Membrane/Structure
Plasma membrances for cells are made of a phospholipid bilayer. Each phospholipid
is made up of two faty acid chains linked to a glycerol molecule.
Cell Cycle
INTERPHASE
GROWTH 1 (or G0) - 11 hours long (longest phase), rapid growth of organelles
SYNTHESIS - 7 hours, DNA replication
GROWTH 2 - 13 hours (I'm not sure why G1 is the longest phase, but that's what my
diagram says), growth continues, final preparation for mitosis, spindles form
MITOSIS - 1 hour (shortest phase), Prophase, Metaphase, Anaphase, Telophase
Cytokinesis then leads back to >>>>>>>> INTERPHASE
Cells
Cells are the building blocks of all living things
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Block 3B
Prokaryotic/Eukaryotic Cells
Prokaryotic cells and eukaryotic cells have many differences, such as the following:
Prokaryotic cells have circular DNA/Eukaryotic cells have linear DNA Prokaryotic
cells have 70 Svedburg Ribosomes/Eukaryotic cells have 80 Svedburg Ribosomes
Eukaryotic cells have membrane-boung organelles, while prokaryotic cells do not.
Animal and Plant Cells
Plant Cells • Surrounded by both Plasma membrane and rigid cell wall • Contain
mitochondria and chloroplasts • Rigidly held in place by cellulose wall • Has one single
large vacuole that holds mostly water and offers structural support. Animal Cells •
Surrounded by plasma membrane only • Retains the ability to move (cilia/flagella) •
Has many small vacuoles sporadically sprinkled throughout the cytoplasm
Cellular organelles: • Nucleus: Used to control protein synthesis and hold DNA. "The
brain." •Nucleolus: Used to make ribosomes • Chloroplast:The site of photosynthesis in
plants • Mitochondria: Site of cellular respiration, which is the catabolic process that
generates ATP by extracting energy from other sugars, fats, and other fuels with the aid
of oxygen)"The Powerhouse" • Rough Endoplasmic Reticulm: Holds the ribosomes
which create proteins for export • Smooth Endoplasmic Reticulum: The site for the
synthesis of lipids and detoxification • Ribosomes: Manufacture Proteins • Lysosomes:
They digest unwanted material and waste in the cell • Golgi Apparatus: The packaging
center that receives and transports vesicles • Vacuole: Stores material and for plants it
provides structure • Vesicles: Membrane bound transportation sacs • Plasma Membrane:
Selective and permeable barrier that controls the movement of materials into and out of
the cell
Endosymbiosis
Endosymbiosis is a theory that attempts to explain how cell organelles developed to
form eukaryotes.Lynn Margulis is credited as the founder of this theory. Endosymbiosis
states that early prokaryote cells engulfed other prokaryote cells, which formed a mutual
symbiosis in which the outer cell provided protection, while the inner cells produced
energy. This explains how mitochondria and chloroplasts developed as seperate cells
which later evolved into their present organelles. There are several "proofs" claimed for
endosymbiosis. Chloroplasts and mitochondria have several characteristics of early
prokaryotes
Circular DNA
70S Ribosomes
Undergo Mitosis on their own
Seperate membranes
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Block 4B
Organisms can either be unicellular or multicellular. It is the unicellular organisms,
however, that are needed to carry out life functions. The cells in multicellular organisms
are unique in that they can they are able to carrout specialized functions by expressing
certain genes, but not others.
Robert Hooke first discovered cells. Antecdote to help remember said fact: While
looking at the small entities, their compartmentalized appearance reminded him of tiny,
conneted rooms (also known as "cells" during this time). Hence he decided to name the
entities "cells".
Virues need a host cell to replicate in. Retroviruses use reverse transcriptase to insert
the virus DNA into the host DNA, making the virus unrecognizable from the host. One
of the most notable retroviruses of today is HIV.
Plant cells have a cell wall, chloroplast and a plasma membrane but do not have
centrioles.Plant cells also contain a central vacoule, for water storage.
Animal cells do not have a cell wall, chloroplast or plasma membrane but have
centrioles. Animal cells also can have movement organelles, such as flagella.
Cell Size
A cell's rate of metabolism is equal to the ratio mass:volume. Likewise, the rate of
material exchange is equal to a cell's surface area. It's vital that a cell has a high surface
area to volume ratio. It can only do this by remaining small, because it's surface area
increases much more slowly than its volume. If a cell becomes to large, it will lose its
ability to maintain levels of homeostasis. Microvilli can help to increase a cell's surface
area without changing it's size. The type of microscope used to view a cell can
significantly change the viewers image of the cell. A light microscope is used to view
living organisms, uses color images, has a large field of view, has a low resolution with
a magnification of 1000x, and is relatively inexpensive, and portable, as well. An
electron microscope, on the other hand is used to view dead organisms, uses
monochrome images, has a small field of view, has a high resolution with a
magnification of 250,000x, is rather expensive, and cannot be moved.
Components of the Prokaryotic Cell
Cell Wall-Provides protection & support; made of peptidoglycan.
Plasma Membrane-Allows for the regulation of intra/extra material in the cells.
Mesosome-Located in the infolding of the plasma membrane. DNA replication occurs
here.
Cytoplasm-Intercellular fluid that suspends organelles.
Ribosomes-Involved with protein manufacturing.
Nucleoid region-"Naked" DNA is located here.
Components of Eukaryotic cells
Cytoplasm-watery material that contains materials involved in cell metabolism
Endoplasmic Reticulum (ER)- pathway for the transportation of materials throughout
the cell; associated with synthesis and storage
Nucleus-control center for cell metabolism and reproduction
Ribosome-site of protein synthesis
Lysosomes- digestion of food within the cells
Mitochondria- "powerhouse" of the cell; site of cellular respiration. It has two
membranes (inner, outer). All eukaryotic cells have mitochondria.
Golgi bodies- packages and secrets products of the cell
Centrioles- cell division in animals
Vacuoles- Fluid filled organelles sheltered by the membrane, holds stored food and
waste
Nucleolus- site of the production of ribosomes
Nucleur membrane- controls movement in and out of nucleus
Cell wall- gives shape and provide production in plants
Cilia- hairlike structure that helps the cell move. Composed in a 9x2 arrangement of
microtubules.
Flagellum- long, hairlike tail used for movement. Composed in a 9x2 arrangement of
microtubules.
Chloroplast- site of photosynthesis
Cell plate- new cell wall that begins to form during cytokinesis
Chlorophyll-traps light and used to reproduce in plants
microtubles-microscopic cylinders that give cell shape. They are larger than the thin
microfilaments
microtubules-transport chromosomes during cell division, as well as organelles and
vesicles throughout the cell.
chloroplast-site of photosynthesis. It contains the pigment chlorophyll. The
chloroplast has three membranes (inner, outer, thylakoid). Plants, algae, and some other
protists carryout photosynthesis with the chloroplast.
There are numerous enzymes that are actually imbedded in membranes. The
following membranes are a part of the endomembrane system: ER, nucleus, Golgo
complex, lysosome, vacuoles, and plasma membrane. Eukaryotic cells have a
cytoskeleton that provides shape and allows for locomotion.
Prokaryotic cells: circular DNA, mesosome, lack membrane bound organelles, 70S
ribosomes, smaller
Eukaryotic cells: linear DNA, no mesosome, contain membrane-bound organelles,
80S ribosomes, larger
Cell Cycle I: Interphase- longest phase G: Growth (transcription and translation
occur) S: synthesis of DNA (replication occurs)
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Cell Division
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Block 1B
Mitosis: Purpose? Stages?
Purpose - growth and repair; allows for direct replication of a cell
Stages - Interphase, Prophase, Metaphase, Anaphase, Telophase1
Meiosis: Purpose? Stages?
Purpose - reproduction; allows for the formation of haploid gamete cells
-Germ cells of Eukaryotes produce gametes
-2 Divisions ending in 4 cells that are different from each other and parents
Stages
INTERPHASE
-chromosomes replicated in the S-phase
PROPHASE I
-nucleus and nuclear membrane break down
-centrioles move towards opposite poles
-tetrads formed
METAPHASE I
-homologous pair line up along equator
ANAPHASE I
-homologues seperate and move to opposite poles
TELOPHASE I
-chromosomes at opposite poles
-new cell membranes form through cytokeneisis
PROPHASE II
METAPHASE II
ANAPHASE II
TELOPHASE II
When homologous chromosomes meet at the equator to form a tetrad, crossing over
can sometimes occur among sister chromatids. In crossing over, the genes switch
chromosomes at the chiasma and travel with their new chromosomes through the
remained of the process of meiosis. The term tetrad refers to the structure formed when
these two homologous chromosomes come together. Independent Assortment refers to
the quality that chromosomes will sort into different cells during meiosis independent of
one another. Both crossing over and independent assortment increase genetic variation
in reproduction of a species, allowing for evolution. Species which reproduce by mitosis
have less genetic variation, which can only be achieved through mutations.
MICROTUBULES
Microtubules are one of the components of the cytoskeleton. Microtubules serve as
structural components within cells and are involved in many cellular processes
including mitosis, cytokinesis, and vesicular transport.
CENTRIOLES
A centriole in biology is a barrel shaped microtubule structure found in most animal
cells and algae though not often in plants. It constitutes the compound structure known
to cell biologists as the centrosome. Centrioles are very important in the cell division
process. They organize the pericentriolar material (PCM) which plays a role in
organizing the mitotic spindle, which in turn helps the cells to divide. The mitotic
spindle functions in the chromosomes. During cell division the centrioles are duplicated,
so that there will be a pair for each daughter cell.
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Block 3B
Mitosis The purpose of mitosis is to make two identical cells by chromosome
duplication. Stages are the following: -Interphase -Prophase -Prometaphase -Metaphase
-Anaphase -Telophase -Cytokinesis
Meiosis: The purpose is to create four haploid germ cells (such as sperm/eggs). This
process ensures genetic variation in offspring. The daughter cells are genetically differnt
from the parent cell, unlike in mitosis. Meiosis can be broken down into roughly nine
steps: Prophase I-Metaphase I- Anaphase I - Telophase I- Prophase II - Metaphase II Anaphase II- Telophase II- Cytokinesis
Microtubules Microtubules are hollow fillament structures in eukaryotic cells that
help chromosomes move to opposite sides of the cell (especially in anaphase of
mitosis)They also aid int eh structue and support of a cell.
Variation There are several ways that Meiosis produces variation in organisms.
Crossing Over - When a tetrad forms, the tips of the homologous chromosomes can
switch, allowing for random variation during Prophase I.
Mutations - Random freak genetic accidents can mutate genes.
Insertion - DNA put in
Deletion - DNA taken out
Inversion - DNA reversed
Translocation - DNA cut out somewhere and stuck back in somewhere else
Independant Assortment - Chromosomes line up independently during meiosis,
creating a near infinite amount of combinations.
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Block 4B
Mitosis Mitosis is asexual reproduction. It creates two new, identical nuclei. Stages:
Prophase-the chromosomes condense and become visible.
Metaphase-chromosomes line up at the meta pkate and the spindle fibers attach
to the centromeres
Anaphase:Spindle fibers shorten, chromotids separate.
Telophase-cytokinesis! two new identical cells.
Cell Cycle
The cell cycle begins in the first gap phase, also known as the G1 phase. This phase of
growth is the longest phase of the cell cycle. Near the end of this phase, the enzymes
that allow the cycle to move into its second phase become increasingly active. Some
cells do not divide, and are stuck in this phase of the cell cycle, which, in that case,
would be G0. The next phase, the S phase, DNA is synthesized, along with some
chromosomal proteins. This is also the stage in which the complex process of
chromosome replication takes place. Upon the completion of the S phase, the cell enters
it's second gap phase, the G2 phase. As the cell prepares for division, more proteins are
synthesized. This phase is relatively short compared to the previous two phases. The
final stage of the cell cycle, mitosis, occurs next. Although it is the shortest phase of the
cell cycle, this is the part in which the most action takes place. Near the conclusion of
mitosis, the cytoplasm divides to form two cells in a process called cytokinesis.
Cytokinesis overlaps into the G1 phase, which starts the cycle over again.
Mitosis is the process in which a cell duplicates its chromosomes to generate two,
identical cells. It is associated with growth and asexual reproduction. Stages: Interphase
(uncondensed chromosomes), Prophase (chromosomes condense), Metaphase
(chromosomes line up at the metaphase plate), Anaphase (chromatids seperate),
Telophase (2 new identical cells).
Crossing over allows for genetic variation in gametes. It occurs on non-sister
chromatids. The chiasma is the site of crossing over.
Tetrads form only during Meiosis and consists of 2 homologous chromosomes.
Chromosome= DNA+Protein
Variation occurs during meiosis because of two things. The first being because of
crossing over. Crossing over provides a new arrangement of genectic information,
which then increases the chance for variation. The other method that variation occurs is
because of the law of independent assortment. In the law of independent assortment
alleles of different loci are randomly distributed into gametes.
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Genetics
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Block 1B
GENETIC TERMS
- Homozygous: Having two identical alleles of a gene
- Locus: The particular position on homologous chromosomes of a gene
- Codominant Alleles: Pairs of alleles that both affect the phenotype when present in a
heterozygote.
- Test Cross: Testing a suspected heterozygote by crossing it with a known
homozygous recessive.
- Carrier: An individual that has a recessive allele of a gene that does not have an
effect on their phenotype.
- Phenotype: The observable physical of biochemical characteristics of an organism,
determined by both genetic make up.
- Heterozygous: Having two differents alleles of a gene.
- Dominant Allele: An allele that has the same effect on the phenotype wheter it is
present in the homozygous or heterozygous state.
- Recessive Allele: An allele that only has an effort on the phenotype when present in
the homozygous state.
- Genotype: The combination of alleles located on homologous chromosomes that
determines a specific characteristic or trait. md
Linked Genes are located on the same chromosome and are inherited together. They
do not assort independently. Linked genes will only fom recombinants if crossing over
has occured
Genetic Recombination: production of offspring with different traits than the parents
Recombination Frequency: (# recombinants)/(total # offspring) x 100%
Mutation- a change, different from the parents', that occurs on a chromosome that
marks for a specific trait
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Block 3B
Genetic terminology: “Allele”- one of two expressions of a gene that occupies a single
locus on a chromosome.
“Dominant” – a gene that, once inherited, results in the occurrence of a specific
phenotype (ex. Having the dominant gene for a widow’s peak means you have a
widow’s peak on your forehead)
“Recessive”- a gene that results in the absence of the stated phenotype (ex. Being
recessive for the widow’s peak means you DO Not have one),
“Homozygous”- describes a gene with two identical alleles, either dominant of
recessive (ex. HH or hh)
“Heterozygous”-describes a gene containing one dominant allele and one recessive
allele (ex. Hh)
“Polyploid”- referrs to the posesion of more than one set of chromosomes. [Polyploid
organisms, especially plants, are larger than normal and have larger cells. Affected
animals are often abnormal in appearance and usually infertile.]
Polygenic Inheritance
Polygenic inheritance refers to traits that are determined by more than one gene. For
instance, skin color, hair color, or eye color. There isn't just black or blonde hair, but
varying shades of each due to polygenic inheritance.
Sex-linked Traits A sex-linked trait is due to a gene found only on the X chromosome,
otherwise known as the sex chromosome. One example is colorblindness, which males
are more likely to get because they have two X chromosomes to a female's one, thus, in
effect, doubling their chances of being affected.
Karyotype A karyotype is a picture of an individual's chromosomes. Karyotypes are
used to identify certain genetic disorders. For example, if the karyotype reveals trisomy
on chromosome 21 then the person has down syndrome.
Linkage Group: Genes in a particular chromosome that tend to be inherited together.
A one to one ration should be obtained if the genes are linked. They will from
recombinants solely in the event that crossing over has occured. In order to calculate the
frequency one can use the formula: % Recombinants/total offspring x 100%=
recombination (in percent, centimorgans, or map units)
[edit]
Block 4B
Genotype-alleles on a homologous chromosome that show the characteristics of the
trait that the homologous chromosome codes for
Phenotype- The observable physical characteristics determined by genes
Locus-The position of a gene on a chormosome
Homozygous- two identical alleles of a gene [ gene with two identical alleles, either
dominant of recessive (ex. HH or hh)]
Heterozygous- two different alleles of a gene [one dominant allele and one recessive
allele (ex. Hh0]
Dominant Allele- an allele that is dominant in regards to the phenotype whether it is
part of a homozygous or heterozygous combination
Recessive Allele- An allele that does not show if a dominant allele is present, but
shows when an organism has a trait that is homozygous recessive
Test Cross-Testing for a heterozygote by crossing it with a known homozygous
recessive organism
Genetic Recombination-offspring that has different genotypes from its parents
Carrier- An organism that has a recessive allele of a gene that does not effect it, but
that it may pass down to its offspring
Codominant Alleles-Pairs of alleles that equally affect the phenotype even though
they are heterozygote
Linked genes -genes that are located on the same chromosome.
Karyotype - the chromosome composition of an indivdual and a photomicrograph
showing the composition (generally numbered in order of size)
P Generation: Parent Generation F1 Generation: The offspring of the parent
generation F2 Generation: The offspring of the F1 Generation
Multiple alleles-three or more alleles of a single locus. ex.blood types
The phenotypic ratio of a monohybrid cross is 3:1. The phenotypic ratio for a dihybrid
cross is 9:3:3:1.
Sometimes when traits are crossed people end up getting traits that are known as
Hybrid Vigor. This is when superiority arises froom the heterozygote as oppose to
homozygous genotypes. Some examples of hybrid vigors are mules, and Sickle cell
when it is a heterozygote because the people can not get malaria, but they can still carry
oxygen.
Polygenetic inheritance is when multiple independent pairs of genes have similar and
additive effects on the same trait - Coded for by more than one gene - Appear in a
normal distribution curve Examples: Skin, eye, hair colors
Mutation- a change on the chromosome or in the gene that gives the offspring
different DNA/ traits from the parents.
Polyploid organisms have more than two copies of each chromosome
Polygenetic inheritance is when multiple independent pairs of genes have similar and
additive effects on the same trait - Coded for by more than one gene - Appear in a
normal distribution curve Examples: Skin, eye, hair colors
Diploid: having the full set of chromosomes (2n or 46 chromosomes) Haploid:
gametes (egg and sperm) only half the number of chromosomes (n)
Mathematics & Genetics
Probability - The fraction, percentage, or ratio that is used to describe the chance of an
event occuring. In genetics, probabilities predict phenotypes and genotypes that come
from genetic crosses.
Product Rule - The probability that two or more independent events will occur
together is found using the product of the individual probablilies of each event. If the
probility of a cross between a tall pea plant and a short pea plant producing a short pea
plant is 25%, what is the probability of three short plants being produced in a row? The
answer can be found using the product rule: 0.25x0.25x0.25=0.015625 or 1/64. So there
is a 1 in 64 chance that three short plants will be produced in a row.
Hardy-Weinberg principle - Named after English mathematician Godfrey Hardy and
German physician William Weinberg, this principle shows the expected frequencies of
different genotypes in a population. Though this rule represents an ideal population in
which there is random mating, no mutation, a large population size, no migration
(emigration of immigration) and no natural seleciton, it helps us understand that in large
populations, the process of inheritance does not cause changes in allele frequencies
alone. There are two equations used in Hardy-Weinberg: p2 + 2pq + q2 = 1 and p + q =
1, where p2 is the dominant genotype frequency (AA), 2pq is the heterozygous
genotype frequency (Aa) and q2 is the recessive genotype frequency (aa). Therefore, p
represents the dominant allele (A) while q represents the recessive allele (a).
[edit]
DNA
Bold text===Block 1B=== Structure DNA's structure is quite complicated (I know,
lame attempt at a topic sentence). STRUCTURE
The structure of DNA is illustrate by handed double helix, with about 10 nucleotide
pairs per helical turn. Each spiral strand, composed of a sugar phosphate backbone and
attached bases, is connected to a complementary strand by hydrogen bonding (noncovalent) between paired bases, adenine (A) with thymine (T) and guanine (G) with
cytosine (C).
Adenine and thymine are connected by two hydrogen bonds (non-covalent) while
guanine and cytosine are connected by three.
This structure was first described by James Watson and Francis Crick in 1953.
Transcription
-Occurs in the nucleus
-Occurs in a 5'-3' direction
-RNA Polymerase recognizes the start point at the promoter region. Ribonucleoside
triphosphate supply the energy for transcription and become RNA nucleotides by losing
a phosphate. Transcription ends at the terminator region. RNA undergoes splicing to
remove introns before it leaves the nucleus. Before splicing mRNA = hn RNA. After
splicing mRNA = mature m RNA
Translation
-Occurs in the cytoplasm/ribosomes
-Occurs in a 5' - 3' direction
-tRNA activating enzyme binds a specific amino acid to tRNA using ATP energy. At
the 3' end of every tRNA are the three nitrogenous bases: CCA. Translation consists of
initiation, elongation, and termination. The start codon is always AUG.
DNA = Deoxyribonucleuic Acid DNA is the blueprint for who we are and for who we
have become
[edit]
Block 3B
DNA is shaped as a double helix. One strand of Dna contains a sugar and phosphate
backbone and a base. The subunits of DNA are Nucleotides. The bases are adenine,
guanine, cytosine, and thymine. Adenine and guanine are purines. Thymine and
cytosine are pyrimidines. Adenine pairs with Thymine and guanine pairs with cytosine.
Most of DNA is repetitive sequences that don't code for anything, only a small portion
is coding. The nucleotides are held together by phosphodiester bonds which links the
sugar and the phosphate. DNA strands also run anti-parallel. Basically, this means that
on any give strand, one end of the phosphate is attached to a 5' carbon and the other to a
3' carbon. When two DNA strands join the 5' carbon attaches itselelf to the 3' carbon
end.
Structure
Chromosome Composition Chromosomes are made up of DNA and protein. The
DNA is coiled around the proteins (histones) and then folded over itself. Histones make
up a nulceosome, which is a complete coil of DNA around the histone core (8 histones)
held together by one histone stabilizing protein.
DNA Replication DNA replication is semi-conservative. This means that each new
DNA molecule has half of the original. In order to begin replication, DNA is unwound
(unzipped) by DNA helicase. Helix-destabilizing proteins keep the helix in the unzipped
position until the complimentary bases are added. DNA Polymerase III catalyzes the
linking together of nucleotide subunits in a 5' to 3' direction as always. The energy and
nucleotides are provided by Deoxynucleoside Triphosphate. When replication is about
to begin, RNA primase lays down RNA primers which are replaced by DNA by DNA
Polymerase I before replication is complete. Replication is initiated at many points and
is discontinuous in one strand and continuous in the other. The lagging strand moves
away from the replication fork and is synthesized in fragments because DNA
polymerase cannot move too far away from the rpelication fork and the leading strand
goes toward it. The fragments on the lagging strand are known as Okazaki fragments
and the fragments are joined together by DNA ligase.
quiz yourself! can you label every number in the picture below?
Polysomes and Nucleosomes A polysome is a bunch of ribosomes bounded together
by mRNA. A nucleosome is made up of eight histones with DNA wrapped around it
and a stabilizing histone on top. Nucleosomes package DNA into chromosomes.
Transcription: In a general sense, transcription is the process of copying the specific
needed recipe from the huge cookbook, slimming off all the excess and sending out to
be made. *happens within the nucleolous and cytoplasm *always occurs in 5’-3’
direction How its done: 1.RNA polymerase finds the specific base-coded unit called the
“promoter” it’s a start sign written in A’s T’s G’s and C’s. 2.The RNA polymerase then
lays down the needed coinciding base units on the anti-sense strand. 3.this strand of
RNA is known now as hnRNA, it still has introns. 4.In the open are of the nuclear
membrane, the strand is “spliced” all of the intron garbage is removed, and it is now
called mature DNA. 3 bases of said strand is called one codon, or one amino acid.
Translation:
Translation is the actual cooking of the recipe. It is the process of ribosomes reading
the specific amino acids and sending the instructions out into the cell. This whole
awesome process goes down in the cytoplasm.
Remember: INITIATION, ELONGATION, TERMINATION.
How it all goes down:
• The start codon, AUG meets • between the two parts of the ribosome : The large and
small sub units. The anit codon (UAC) connects with the codon at the Peptide station on
the large s.u. • The enzyme peptydil transferase then moves this connected unit from the
P to the A area, thus sending the chain down the line. • This process continues until all
the little jellyfish are made.
[edit]
Block 4B
The structure of DNA, its double helix shape, was discovered by Watson and Crick.
DNA is a nucleic acid (polymer) made from nucleotides (the monomers of nucleic
acids). Each nucleotide is made made of a phosphate, a sugar, and a base. The base is
bonded to the sugar which is bonded to phosphates. The sugars and phoshpates bond
together (phosphodiester bond) in an alternating pattern the forms the backbone of
DNA. The nucleotides of DNA contain 4 bases, the purines encompasing Adenine and
Guanine and the pyrimidines which include Cytocene and Thymine. These nucleotides
combine to form a strand of DNA. DNA is a double stranded molecule. The strands are
held together by hydrogen bonds between the bases. Adenine bonds with Thymine and
is held by two hydrogen bonds, and Cytocene bonds with Guanine and is held together
by three hydrogen bonds. It is this difference in bond number and thus strength that
accounts for the helicle shape. Due to the phosphates in the DNA strnad a DNA
molecule of DNA has a slightly negative charge.
Chromosome composition includes DNA (genes) and a protein.
DNA Synthesis begins at specific based sequences termed the ORIGINS OF
REPLICATION (there are many)...The replicaion fork occurs at both ends so DNA
replication proceeds in bot directions.
DNA Replication
There are three types of replication:
1. Semi-conservative replication - The new DNA molecules have half the genetic
material as the original.
2. Conservative replication - The new molecules havw all the genetic material of
original.
3. Dispersive replication - Each molecule contains a mixture of genetic material in
various regions on each strand.
Replication of DNA begins at certain sites on the DNA molecule known as origins of
replication. The Y-shaped structure at which both DNA strands are replicated
simultaneosly is known as the relplication fork. There is a lagging strand, which is
always leaving the replication fork, as well as a leading strand, which continously
moves toward the fork. The lagging strand, however, is synthesized in an irregular
fashion since the DNA polymerase, which catalizes the linking of DNA subunits,
cannot be too far from the replication fork. As a result, small Okazaki Fragments are
created & synthesized.
Replication occurs in the nucleus, always in a 5’ to 3’ direction.
1)Helicase unwinds and unzips DNA.
2)Primase then lays down a primer.
3)DNA Polymerase I replaces RNA primers with DNA
4)DNA Polymerase III adds the nucleotides
5)Ligase joins together the Okazaki fragments, which form because the DNA
Polymerase III cannot move too far away from the replication fork. Okazaki fragments
are present on the lagging strand, where replication is discontinuous. Replication on the
leading strand is continuous.
A nucleosome is made up of DNA that is wrapped around 8 histone proteins, where
one of the histones stabilizes the structure.
DNA Transcription occurs in a 5'-3' directio in the nucleus. First the promotor reginon
allows RNA polymerase to recognize the start point. Then Ribonucleoside Triphosphate
supplies the energy that is used in transcription and will then become Rna nucleotides
by losing a phosphat. Tracnsciption is done when it reaches the terminator region. In
order for it to leave the nucleus it must be spliced(the removal of the non coding
introns) transforming it from hnRNA to mature RNA
[edit]
Photosynthesis/Respiration
[edit]
Block 1B
Photosynthesis occurs in the chloroplast, which is found in plant cells. The lightdependent reactions occur in the thylakoid membrane, located in the chloroplast.
Photons, which are packages of light from the sun, first go to photosystem II. The photo
activation of photosystem II occurs due to the light activating it. The accessory
pigments found in the photosystem absorb the light and give the energy to chlorophyll,
which is another pigment that is also absorbing light. The chlorophyll then gets excited
with the energy it received and loses two electrons. Chlorophyll wants to regain the two
electrons it lost, so a water molecule splits into two hydrogen and one oxygen using a
process called photolysis, where light is used to split a water molecule. The chlorophyll
then takes the two hydrogen in order to become more stable and replace the two
electrons lost. Meanwhile, the two electrons lost go to the Primary Electron Acceptor,
and then travel down the Electron Transport Chain. The electrons go through the
Electron Transport chain in one direction, thus creating energy. The energy made is
used to undergo photophosphorylation where ADP combines with Phosphate to make
ATP. The ATP is then needed to help take the hydrogen out of the stroma and undergo
chemiosmosis where ATP synthetase is a protein channel that allows the hydrogen to
move through and out of the thylakoid membrane. The process creates more ATP. Back
to the electron traveling through the Electron Transport Chain, the electrons then go to
Photosystem I, which is photo activated. In Photosystem I, there are accesory pigments
absorbing energy and giving it to chlorophyll that then loses two electrons. The
chlorophyll does not need replace the two electrons by using hydrogen from photolysis
because more electrons are coming from the Electron Transport Chain. The two
electrons go to the Primary electron Acceptor and then go to Ferrodoxin. Ferrodoxin, a
protein, transfers the electrons to NADP that then undergoes reduction because it uses
the electrons to combine with a Hydrogen and become NADPH. With light-dependent
reactions, there is also cyclic and non-cyclic photophosphorylation. Non-cyclic
photophosphorylation is the normal light-dependent process that produces ATP and
NADPH; however, cyclic phosphorylation is different and not normal. Cyclic
photophosphorylation is a process where electrons go through the Primary Electron
Acceptor, down the Electron Transport Chain, and into Photosystem I. The accessory
pigments in Photosystem I absorb the energy and give it to chlorophyll. The chlorophyll
then has energy and gets excited so that it loses two electrons. The two electrons then go
to the Primary Electron Acceptor, and the process repeats itself. Cyclic
photophosphorylation cannot go on continuously and produces only NADPH. Lightindependent reactions take place after light-dependent reactions. Light-independent
reactions occur in the stroma. RuBP carboxylase helps in combining carbon dioxide and
RuBP in a process called carbon fixation. The process produces a 6 carbon intermediate.
The 6 carbon intermediate then becomes two 3 GP carbon compounds. ATP and
NADPH created from the light-dependent reaction are used to change the arrangement
of atoms so that GP undergoes reduction and creates two 3 TP. The ATP and NADPH
oxidize and become ADP and NADP, which can be used again in light-dependent
reactions. Five of the six carbons in TP are used to recreate RuBP and the other carbon
helps in producing a carbohydrate.
One may increase the rate of photosynthesis by increasing the temperature, sunlight,
or CO2 in the atmosphere
One may decrease the rate of photosynthesis by increasing the amount of wind on the
plant
CAM/C4
C4 and CAM plants both have an enzyme called PEP (phospoenolpyruvate). This
enzyme can fix CO2 at very low concentrations.
C4 patway:
CO2 + PEP (3C) yields oxaloacetate (4c) Oxaloacetate is converted into malate (using
NADPH) Malate enters itno the bundle sheath cells and is decarboxylated into Pyruvate.
Pyruvate (3c) is converted into PEP (using ATP) The CO2 goes into the Calcin Cycle
(light independent cycle) just as it does in the normal c3 pathway.
CAM pathway
CAM plants only open their stomata at night. They join co2 with PEP forming
oxaloacetate and convert this into malate in the same method that c4 plants use. Hower,
they store the malate in a vacuole until daytime and decarboxylate in to gain the co2
needed for the Calvin Cycle.
CHEMIOSMOSIS
Chemiosmosis is the diffusion of ions across a membrane. More specifically, it relates
to the generation of ATP by the movement of hydrogen ions across a membrane. An Ion
gradient has potential energy and can be used to power chemical reactions when the
ions pass through a channel. Hydrogen ions (protons) will diffuse from an area of high
proton concentration to an area of lower proton concentration.
ATP synthase is the enzyme that makes ATP by chemiosmosis. It allows protons to
pass through the membrane using the kinetic energy to phosphorylate ADP making
ATP. The generation of ATP by chemiosmosis occurs in chloroplasts and mitochondria
as well as in some bacteria.
[edit]
Block 3B
Xerophyte and Hydrophytes have several differences that enabel them to survive in
their given enviroment. Xerophytes (arid plant):Thick cuticle to retain water, Deep,
branching roots, Few stomata for gas and water exchange, Greatly reduced leaves (they
can have spines, be rolled, or hairy); Hydrophytes (aquatic plant), Thin/no cuticle,
Shallow, short roots, Many stomata, Large and finely divided leaves.
Cytochromes are used to transport the electrons down the electron transport chain.
Oxidation is loss, reduction is gain. A neat way to remember this is: OIL RIG.
Glycolysis, The Krebs Cycle, and the Electron Transport Chain are the main three
steps in Cellular Respiration, which mainly takes place in the mitochondria.
Photophosphoylation
A really long complicated word that really just means making energy with light.
Noncyclic vs Cyclic Photophosphorylation Noncyclic
What normally occurs during photosynthesis.
Produces a normal amount of ATP
Can occur forever (theoretically)
Produces NADPH
Cyclic
Unnaturally occurs when there is not enough H20
Produces abnormally high ATP
Cannot go on forever
Produces no NADPH
PII and PI
Photosytem II
-An excited pigment loses two electrons when it is struck by a photon of sunlight Chlorophyl breaks open a water molecule to get the two missing electron, thus turning
the water molecule into floating hydrogens and oxygens (called Photolysis) - The first 2
electrons bounce down the ETC, fueled by ATP.
Photosystem I
-The 2 electrons bounce off the ETC and into the next chlorophyll just as its pigment
loses them to the photon again. -These 2 electrons in turn aid ferrodoxin in turning
NADP and H into NADPH
[edit]
Block 4B
Chemiosmosis is the movement of hydrogen ions through the thylakoid membrane
(where the photosystems I &II are located).
Xerophytes:thick epidermis, sunken stomatas, dry habitats
Hydrophytes: stomata on surface, often floating or submerged, moist habitats
Light Energy
Light emission is an important part of photosynthesis. Visible light is a small part of
the electromagnetic spectrum. Light travels in waves. A wavelength is the distance from
one wave peak to the next one. Light is also made up of packets of energy called
photons. A photon's energy is inversly proportional to its wavelength.
When a molecule absorbs on of these photons, one of its electrons become energized,
shifting the electron from a lower-energy orbital to one of higher energy that is farther
from the nucleus. The electron then either returns to its ground state or leaves the atom
to be accepted by and electron acceptor molecule (the latter occurs in photosynthesis).
Chlorophyll
A leaf is made up of a green pigment called chlorophyll, which is also the main
pigment of photosynthesis. It absorbs light mostly in the blue and red areas of the
visible light spectrum, since most green light that hits the leaves is reflected, giving
plant leaves a green appearance. There is more than one type of chlorophyll.
Chlorophyll a initiates the light-dependent reactions of photosynthesis. Chlorophyll b is
an accessory pigment that absorbs and reflects light in a way that gives it a yellow-green
appearance, while chlorophyll a has a more bright-green appearance. The spectrum of
light that can provide energy for photosynthesis can be broadened with another
accessory pigment called a cartenoid, which can be yellow or orange. Chlorophyll can
be excited by light directly by photons or indirectly by energy it recieves from these
accessory pigments. The absorption of light is often monitored by graph. A pigment's
absorption spectrum is a graph of its absorption of light of different wavelengths. The
action spectrum shows the effectiveness of certain wavelenghths of light. It can be
obtained by measuring the rate of photosynthesis ar each wavelength for leaf cells or
tissues that have been exposed to light of one wavelength (monochromatic).
Photosynthesis takes place in the chloroplast, while respiration takes place in
mitochondria. Plants and algae carry out photosynthesis. Respiration occurs in all
eukaryotes.
Key Idea to Remember: Oxidation is loss and Reduction is Gain (OIL RIG)
Cellular respiration has three metabolic stages. The first is Glycolysis cycle, is the
splitting of sugar and occurs in the cytosol, the fluid between membranes. This process
is anaerobic and is at substrate level phosphorylation. It begins with 6C Glucose and
becomes 2 (3C) Pyruvate while gaining 2 ATP and 2 NADH, thus is it demonstrating
oxidation. The gaining of 2 NADH is the reduction of a co-enzyme. The second stage is
the Krebs Cycle occurs in the mitochondria. This stage begins with pyruvate (3C) and
decarboxylates (loses CO2) to become 2C Acetyl CoA. Then 4C is added to form 6C
intermediatie which decarboxylates into 5C which decarboxylates into 4C which begins
the cycle again. There is a link reaction between the 4C oxaloacetate and the 3C
pyruvate. This process is also oxidation as it gains NADH, 2 ATP and FADH2. One
turn of the Krebs/Citric Cycle yields 2CO2, 3NADH, FADH2, and ATP. The third and
final stage is the Electron Transport Chain which occurs in the inner mitochondria
membrane and yields 32 ATP. It transports 2 hydrogens and 2 electrons from FADH2
or NADH to molecular oxygen forming water, which eventually makes ATP. Oxygen is
the final electron acceptor in the ETC.
The rate of photosynthesis increase as the amount of light increase, until it reaches a
certain point then it will stay constant not increasing or decreasing. It will also increase
as the rate of Co2 concentration increases, but photosynthesis does not occur at very
low Co2 concentrations and will eventually level out at very high concentrations. As the
temperature increases the rate of photosynthesis will continue to increase until it reaches
its optimum rate, then the rate of photosynthesis will rapidly decline. ALL PLANTS
need water and oxygen to survive
[edit]
Chemistry
[edit]
Block 1B
Water is an important part of the chemistry of all living things as well. Some of the
main characteristics of water are as follows:
POLAR- thus, it is the universal solvent
COHESION- water molecules stick to themselves, helps provide surface tension
ADHESION- water molecules stick to other surfaces which allows capillary action
and movement agaist the pull of gravity
TRANSPARENT- essential for underwater plants to receive the light they need for
photosynthesis
HIGH HEAT OF VAPORIZATION- when water evaporates, as in sweat, it has a
cooling effect because of the heat it draws from the body
HIGH SPECIFIC HEAT- water stays warm for a long time after it is heated, but
takes a long time to heat. This is essential for organisms living in water so that their
environment does not change too quickly before they can adjust.
ELEMENTS
Elements are substances that cannot be broken down into simpler substances. The
three most frequently occurring elements found in living systems are carbon = C,
oxygen = O2 and hydrogen = H2. Other important elements include nitrogen = N2,
phosphorus = P, iron = Fe, calcium = Ca, potassium =K, and magnesium = Mg.
[edit]
Block 3B
The three most common elements are carbon, oxygen, and hydrogen. Hydrogen is the
most abundant element on earth and carbon is found in all life. Examples of Organic
Molecules: Lipids (they have twice the energy of Carbs.)-Monomer=Glycerol/Fatty
Acids, Bond= Ester, Uses= cushioning/insulation/energy storage/structure,
Examples=Fats/Oils/Waxes Carbohydrates' 'MonomerGlucose or monosaccharide Uses
break down of protein, storage of energy, energy Examples: Amylose, sucorse, ribose,
glucose..any protein with -ose instead of -ase. Carbohydrates have -ose' Proteins contain
carbon, oxygen, hydrogen, sulfur, and other organic elements. Their monomer is amino
acid which is written as OHHNRCHCOHH, where R represents a functional group,
specific to that protein. Uses include storage, protection, muscles. Are bonded by
peptide bonds which form through a linkage of carbon and nitrogen with a byproduct of
water.
Redox reactions
Oxidation: When a molecule LOSES an electron. Reduction: When a molecule
GAINS an election.
OIL RIG: Oxidation is Loss, Reduction is Gain.
[edit]
Block 4B
The three most common elements in organic chemistry are Carbon, Hydrogen, and
Oxygen.
Other Important Elements
Nitrogen-Used in DNA, proteins, and enzymes.
Calcium-Helps build strong bones, & used in sending nerve impulses.
Phosphorus-Used for ATP.
Iron-Transports oxygen.
Sodium-Keeps a balance of H20. Also used for nerve impulses and muscle
contractions.
ORGANIC MOLECULES
Carbohydrates
monomer-monosccharide
ex. glucose, galactose
Proteins
monomer-amino acid
ex. enzymes, structural, hemoglobin
Lipids
monomer-fatty acids
ex.fats, phospholipids, waxes,oils
Nuclei Acids...phosphodiester bonds
monomer-nucleotide(sugar, phosphate, base)
ex.DNA,RNA
Fatty Acid: CH3-CH2-C=O (also branching off from the C on right is an OH by a
single bond)
Polar bonds are the result of covalently bonded atoms that have unequal
electronegativity. Non-polar bonds are the result of covalently bonded atoms that have
equal electronegativity. Water is a polar molecule- one end of the molecule has a partial
positive charge and the other end has a partial negative charge.
More Bonding
Covalent bonds: Electrons are shared between atoms so that each atom has a filled
valance shell.
Electronegativity measures the attraction of an atom to shared electrons in a bond.
Ionic bonds: Form as a result of the attraction between a cation and an anion.
Hydrogen bonds: Bonds between a partially-charged negative atom and an atom in a
hydrogen bond with either oxygen or nitrogen. Can form between two molecules or two
parts of one molecule.
Organic molecules: Carbohydrates are used for energy and stored energy. There
chemical makeup has a 1:2:1 ratio of carbon to hydrogen. Monomers include glucose
and monosaccharides. Proteins are connected by peptide bonds. They are used for
structural movements, like muscles. They are also used for transport (hemoglobin),
storage, protection, and regulation. Protein’s monomers are amino acids, of which there
are twenty. Lipids are insoluble in water. Monomers include glycerol and fatty acids.
Ester linkages bond lipids. Lipids are used for insulation, energy storage, cushioning,
and have structural purposes (cell membranes). Examples include fats, oils, waxes,
carotenoids, phospholipids, and steroids. Nucleic acids store information. RNA is used
for transmission. DNA is responsible for expression of genetic information. Nucleic
acids are linked by phosphodiester bonds. Nucleic acid monomers are nucleotides,
which are composed of a sugar, a phosphate, and a base.
[edit]
Evolution
[edit]
Block 1B
Lynn Margulis proposed the theory of Endosymbiosis, which provides a possible
explanation for the formation of eukaryotic cells. It is believed that mitochondria and
chloroplast, which are located in eukaryotic cells today, were once on their own like
prokaryotic cells. There is evidence that the two organelles were prokaryotic because
mitochondria and chloroplast contain circular DNA just like prokaryotic cells. Also,
mitochondria and chloroplast have 70s ribosomes that is similar to the 70s ribosomes of
prokaryotic cells. The theory provides the explanation that the prokaryotic cells took in
the mitochondria and chloroplast and a symbiotic relationship formed. The prokaryotic
cell provided shelter and protection, and the chloroplast made food and the
mitochondria broke down the food in order to make energy that the cell could use. Thus,
the creation of eukaryotic cells occurred.
MILLER AND UREY
They conducted an experiment which would change the approach of scientific
investigation into the origin of life. Miller took molecules which were believed to
represent the major components of the early Earth's atmosphere and put them into a
closed system. The gases they used were methane (CH4), ammonia (NH3), hydrogen
(H2), and water (H2O). Next, he ran a continuous electric current through the system, to
simulate lightning storms believed to be common on the early earth. Two percent of the
carbon had formed some of the amino acids which are used to make proteins. Perhaps
most importantly, Miller's experiment showed that organic compounds such as amino
acids, which are essential to cellular life, could be made easily under the conditions that
scientists believed to be present on the early earth. This enormous finding inspired a
multitude of further experiments.
Human Evolution
-Features that define humans as primates:
digits with nails
eyes in front of the head
5 grasping digits with opposable thumb
long, slender limbs that rotate freely at the hips and shoulders
acute hearing
relatively large sized brain
long life spans
-Evidence for bipedalism:
curvature of spine provides better weight distribution
foramen magnum is centered in the base of the skull
increae in the legth of legs in comparison to the arms
shorter, broader pelvis for attachment to leg muscles
alignment of the big toe with the rest of the toes
-Genus Australopithecus: the immediate ancestors of the genus Homo
Darwin-Wallace Theory of Natural Selection
Evolution is based on four observations about the natural world:
1. Overproduction: each species produces more offspring than will survive
2. Variation: individuals in a population exhibit variation
3. Limits on population growth: environmental factors limit growth, causing a
struggle for existance
4. Differential reproductive success: those with the most favorable characteristics are
more likely to survive and reproduce
Modern Examples of Evolution
-In response to the widespread use of the Warfarin pesticide, some species of rat have
become immune/resistant
-Penicillin resistant strains of bacteria due to the widespread use of the antibiotic
-Some mosquitos resistant to DDT
-Evolution of Peppered Moth due to predation and changes in environment
Other Theories of How we got here
Panspermia- The theory that a life form came from another planet, treveling on a
coment or asteroid and landed on earth, leading to the evolution to humans
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Miller and Urey’s experiments: What you need to know: •Miller and Urey conduced
experiments to test if life could have formed in the primordial soup •They used"
W-ater H-ydrogen A-mmonia M-ethane
•They boiled the water and used electric shocks to simulate the various stages of
heating and cooling and lightning that were likely present on early earth’s surface •They
produced organic molecules form this experiment, but no life. However, such a find
sent a wave through the science community
Exogenesis (sick word), but more commonly known as panspermia, originates as far
back as the Greek philosopher Anaxagoras (sweet name). The actual theory of
panspermia speculates that life came to earth from another planet, perhaps being carried
by a meteorite that crashed here. This theory solves the time gap that we currently have
in our evolution chart, but it only moves the problem to another planet, so it really
doesn't solve anything.
The Darwin-Wallace Theory of Evolution has four key points. The first is that
individuals in a population exhibit variation. Next is overproduction, the reproductive
abilities of a species causes an increase (geometric) over time. Then, there are limits on
population growth caused by things such as; food, water, light, growing space, and
other resources. Lastly, the individuals that have the most favorable traits and
adaptations are more likly to survive and reproduce (differential reproductive success).
Natural Selection
Natural Selection is the principle that nature tends to favor organisms with certain
traits. These organisms therefore have a greater chance of survival in that environment
than other organisms without the trait. This gives the organisms with the trait a
significant advantage in the environment. Because it has a greater chance of survival,
and organism with the trait is less likely to die young and has a greater chance of
reproducing early and often to spread its genes. It then can pass on this beneficial trait,
allowing the trait to proliferate throughout the species. In this way, natural selection
favors organisms with certain traits, giving them a greater chance to survive and pass on
these traits so that more of the population can surivive using this favorable trait.
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Modern examples of evolution include: pepperd moth, DDT resistance in some
mosquitos, penicillin resistant strains of bacteria as a result of the widespread use of the
antibotic and a warfarin strains of rat in response to the widespread use of the pestcide.
Evolution is the change in a populations overall traits and usually refers to the genes
passed on from generation to generation. Evolution is used to map out the growth of a
population as well as the mutations that affect/ change it. Natural selection is one way
of causing a population to evolve and natural selection means that heritable traits that
are more helpful to survival are the ones most likely to be passed on from generation to
generation
Evolution as a theory was first developed by Darwin and Wallace. Before that, there
was the Lamarckian theory which stated that traits acquired during a lifetime would be
passed on to the next generation.
Some reasons why it is believed that Humans evolved from Primates: -5 Digit
Hands...Pentadactyl -Grasping Ability -Erectness -Stereoscopic Vision
Recombination and assortment allow for variation (and mutations) in a population.
Miller and Urey simulated the conditions on pre-biotic Earth in order to test for
chemical evolution. They sealed Water, Hydrogen, Ammonia, and Methane in a flask
(WHAM) in order to model the conditions. Electrodes were used to simulate lightning.
Humans have evolved from mammal-like reptiles that existed over 200 million years
ago. Early humans were classified under the genus Australopithecus. The species
include: afaransis, africanus, and robustus. Next came the genus Homo. Species include:
habilis, erectus, neanderthalensis, and sapiens. Current humans are classified as Homo
sapien sapiens.
Okay Panspermia basically rules because it says life may have come from another
planet. If you watch Star Trek there was an episode discussing this. It also linked
several species such as Andorians, Klingons, Vulcans, Romulans, and most importantly
Humans to a common ancestor from another planet.
Other then Panspermia and evolution, another theory that is used to explain evolution
is creationism. This describes how God created the Earth and everything that surrounds
it. Another theory that describes evolution is the theory of intelligent design. This talks
about some higher being created everything on Earth and is guiding them through their
existence.
Endosymbiosis is the theory proposed by Lynn Margulis which suggests that
eukaryotic cells evolved from prokaryotic cells.
Okay basically endosymbiosis states that a prokaryotic cell consumed other
prokaryotic cells, in this case mitochondria and chloroplasts. They grew to have a
symbiotic relationship and eventually went on live together in peace. The reason this is
believed to be true is because mitochondria and chloroplasts have their own DNA.
Darwinism
Adaptation: An evolutionary modification that causes thechances of survival and
successful reproduction much higher.
Natural Selection: Organisms that are better adapted have a greater chance of being
able to survive and bring forth the next generation.
Charles Darwin - Darwin believed that the Earth was very old and its form had
transformed over a period of time. Artificial selection supposedly could allow breeders
to choose traits that they liked. Darwin used this process to explain a similar process
that occurs in nature.
Alfred Wallace - Sent Darwin a published paper of his ideas, which were quite similar
to those of Darwin himself. Thus, the Darwin-Wallace Theory of Evolution was born,
This theory held that four key aspects of life lead to evolution: population variation,
overproduction, limits on population growth, and defferential reproductive success.
Thomas Malthus - Wrote An Essay on the Principle of Population as It Affects the
Future Improvement of Society. In it, he stated that growth in a population is not always
desirable. Populations can increase exponentially, while the population's food supply
can only increase arithmetically. Because of this problem between food supply and
population, famine, disease and war can occur, halting population growth.
Evidence for Evolution: - Geological Distribution of living organisms - FossilizationRadioactive Dating - Biochemical evidence: the universality of DNA and protein
structures - Embryo evidence because all embryos look alike in the early stage of
development - Pentadactyl limb
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Classification/Ecology
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Classification is pretty much the single greatest thing since sliced bread. Maybe even
before sliced bread. It allows organisms to be grouped together based on their similar
characteristics. There are a lot of organisms, so this is important. This variety of
organisms (and their ecosystems!) is known as biological diversity. The study of said
diversity is systematics. Classifying and naming organisms is known as taxonomy. We
use a binomial nomenclature when referring to organisms. The binomial nomenclature
was designed by Carolus Linnaeus and consists of an organisms genus and species.
Both words have latin roots.
In case you were wondering, the system of classification is as follows: kingdom
phylum class order family genus species
Wait a minute? WHAT'S A SPECIES? Well, let me tell you. [please do so] A species
is a potentially interbreeding population. Remember, the offspring must also be able to
reproduce. A population is a group of the same species. A community is a group of
populations, cohabitating. This habitat is known as the ecosystem. A group of
ecosystems makes up a biome (think temperate forest, or tundra!) The entire world,
and/or all the biomes and life and everything, makes up the biosphere.
PLANTS
There are four major groups of plants:
Bryophytes
- Non vascular
- Dominant Gametophyte generation
- Seedless plants
- Small, require moist environment, reproduce by spores
- mosses, liverworst
Filicinophytes
- Vascular
- Dominant Sporophyte generation
- Seedless plants
- Reproduced by Spores
- Ferns, Horsetails
Coniferophytes
- Vascular
- Dominant Sporophyte Generation
- Seed plants (naked seeds)
- reproduce by seeds
- Conifers, Cycads, Ginkgoes
Angiospermophytes
- Vascular
- Dominant sporophyte gen
- Seed plants (seeds encased in fruit)
- Reproduce by seeds
- Flowering plants, monocots, dicots
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Classification System
A classification system is something that helps scientists to organize animals, plants,
and other life into categories so that we can see similarities and differences.
Our modern classification system consists of:
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Binomial Nomenclature
This is the specific system of naming in which scientists derive names of organisms
with respect to their Genus and Species. For instance, humans are classified as Home
(Genus) Sapiens (Species). This allows for a continuity and common ground for naming
organisms throughout science, facilitating research and building a foundation for further
study into biology.
Plants can be catergorzed into several different groups: 1. Bryophtyes- Non-vascular
seedles plants that are small and require moist enviroments. Such examples are mosses
and liverworts and their dominant generation is the gameophyte. 2. Tracheophtyes
which are broken down further into --> a.) Filicinophtyes- Vascular seedless plants that
reproduce by spores. The dominant generation id the sporophtye and examples are ferns
and horsetails. b.) Coniferophtyes- Vascular seed plants (naked seeds!! hehe) that also
reproduce by spores. Examples are conifer and ginkgo tree and the dominant generation
is the sporophtye. c.)Angiospermophtyes- Vascualr seed plants (encased in fruit) that
reproduce by spores. The dominant generation is also sporophtye and examples are
monocots and dicots.
Plants
Bryophytes
-nonvascular
-Dominant Gametophyte generation
-seedless
-small
-thrives in moist environments
-reproduce by spores
-E.x.: mosses (hornwarts etc)
Filicernophytes
-vascular
-Dominant Spor. generation
-seedless
-reproduce by spores
Coniferophytes
-vascular
-Dom. Spor. Gen.
-seeds (but naked seeds)
-E.x. COnfers (ginkoes, Cyands...)
Angiosperophytes
-vascular
-Dom. Spor. Gen.
-have seeds, in fruit
-reproduce by seeds
-e.x. Flowering plants (daffodills, roses, monocots, dicots)
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Block 4B
Classification is how scientists group different organisms and thier species. They can
be determined through different methods.
This is how a regular classification system works:
Domain=> Kingdom=> Phylum=> Class=> Order=> Family=> Genus=> Species
A way to remember this although its really dirty is
King Philip Came Over For Gay Sex
FOR HUMANS: Animalia, Chordata, Mammalia, Primate, Homindae, Home, Sapien,
Cro-Magnon/ Sapien
Species-a particular kind of organism; members posess similar automatical
characteristics and have the ability to interbreed and produce fertile offspring.
There are four main groups of plants. Filicinophytes, Coniferophytes, and
Angiospermophytes are grouped together under a larger set called Tracheophytes.
Bryophytes and Filicinophytes reproduce by spores, while Coniferophytes and
Angiospermophytes reproduce by seeds. The seeds in Angiospermophytes are encased
in fruit, while Coniferophytes have naked seeds. Examples: Bryophytes- moss,
liverworts, hornworts; Filicinophytes- ferns, club mosses, horsetails; Coniferophytesconifers, cycads, ginkgoes; Angiospermophytes- flowering plants, monocots, dicots.
Plants and the Cell
Plants show Alteration of Generation in which they spend some of their lives in a
haploid stage, and another part in a diploid stage. In the gametophye generation, the
haploid stage leads to gametes through mitosis, while meiosis is used in the sporophyte
generation, where the diploid state leads to haploid spores. Gametophytes produce a
small gametangia called antheridia (the female version is called archegonia). The zygote
forms when an egg and sperm cell unite. The first stage in the sporophtye generation,
the newly-formed diploid zygote, divides by mitosis and becomes a young,
multicellular sporophyte plant. Once it matures, it gains special cells that divide using
meiosis to form haploid cells known as spores. These spores divide by mitosis,
producing a multicellular gametophyte, thus restarting the cycle.
Seed Germination- 1. Imbibition- Seed absorbs water 2. Embryo releases Gibberellic
Acid (GA) 3. GA triggers the alueron layer to release amylase 4. Amylase digests
amylose into maltose 5. Maltose is used by embryo to grow
Every seed needs water and oxygen to grow. Other things that might be necessary
include: Light, digestion by mammal birds, bacterial digestion, and/or fire.
In the seed their consists many differetn parts. The first one that people meet is the
testa(seed coat), then there is the aleurone layer. Because the embryo has to go through
these two layers that is why germination takes so long. Then in the seed is the cotyledon
and the embryo. The embryo is made of the embryonic shoot and the embryonic root.
Binomial nomenclature is the formal system of naming species. It involves names for
the genus, then the species. The name for the genus is always capitalized, but the
species name is lower case. Both names are italisized however. For example: Passer
domesticus
Biological Organization: Organism, Population, Community, Ecosystem, Biome,
Biosphere