Biology (Semester I)

Biology (Semester I)
Evolution
Selection
Natural Selection
Natural selection is the process of which an individual with a trait
that favours its environment will be more suited to live in it and
thus those who don't have said trait will perish.
A simple example would be how if a mutation occured on an insect who lived in a
grassy environment and was normally brown that made it green, it would be less
susceptable to predators finding it and thus that trait will survive while others don't.
When a species is divided and put in different
environments, the environment will greatly differ
the species from one another.
Sexual Selection
Evidence for Evolution
Primate and Human Evolution
Inheritance of Genotypes and Phenotypes and Genetic Disorders
Traits
There are many traits that can
be passed down from your
parents.
Depending on the trait, there will be
traits that are either dominant or
recessive.
For example, brown eyes are a dominant eye
colour while blue eyes are a recessive eye
colour.
The phenotype, which is the
technical name for a trait
Phenotypes are defined by your
genotype.
Determining a Trait
Your parents will carry the trait themselves, and
depending on where they stand on it you can take
on that trait or an entirely different one.
If the genotype for your trait is homozygous, then
it is either completely dominant or completely
recessive.
If it is heterozygous, you have both a dominant
and a recessive showing and thus the dominant
trait will show.
To determine the probability of what trait
a child could have, we use Punnet
Squares.
A Punnet Square is a visual method
that helps us determine trait
possibilities.
Generally, you make a column and a row for each gene that
affects the trait, and then put every possible combination in each
column and row, then combine them in the squares to show if you
are homozygous or heterozygous.
Mendelian Genetics
Gregor Mendel
Ended up using pea plants, pea plants are good
because they have a number of characteristics
that are easily definable and can breed quickly.
Mendel's Laws
Law of Segregation
Law of Independent Assortment
The name of the first generation is
always called the P generation for the
parents.
They're children are the F1 generation
and the grandparents are the F2
generation.
Mendel noticed that sometimes when the P had
a purple and a white flower, the F1 is also
purple.
Mendel observed many different traits in the
pea plants including pea colour, pod colour,
rounded vs. wrinkled pod, etc.
He observed that some traits, such as a rounded
pea, would show up more than a different trait,
such as a wrinkled pea.
This is because some traits show
dominance over other traits, which would
be recessive.
However, sometimes two traits will show
codominance where the two traits both show up,
such as in blood type when a type A and a type B
give a type AB child.
Incomplete dominance is where both traits are "there" such as a
red and white flower making a pink flower. Contrasted with
codominance, codominance would show red and white spolches
of colour on the flower in the same situation.
Genetic Disorders
Sex-Linked
Some disorders are located on certain sexes
because they are located on the 23rd
chromosome, also called the sex chromosome.
These disorders are harder to predict, but
males are very susceptable to these
diseases.
This is because women have two X chromsomes, allowing for
any disorders to be easily corrected. Men do not have the
second X, so they are more susceptable to the diasease not
being corrected.
In other words, Girls 1 Boys 0
You can still use a Punnet Square to
determine the likelihood, however it isn't
perfect.
Sex-Linked Disorders
Colour blindness is sex-linked
and more susceptable with
males.
Others include hemophilia, Duchenne
muscular dystrophy, and Turners
syndrome.
Lupus has been linked to mostly females, and while we don't
have much information on how disorders are linked with certain
genes, research in this is helping advance all areas of disorder
research.
Dominant
As long as there is there is one copy of the
mutated gene, it will show up in the genotype
as dominant.
Huntington's Disease is a very infamous one
because you do not show symptoms till you are at
least 40 years of age, allowing you to pass it on
easily.
Anthropomorphism, or dwarfism,
is a dominant condition as well.
Recessive
In order for a recessive disorder to be passed, it
must show two copies of the mutated gene or it
will not be passed down.
Sickle cell anemia, which is a one letter mistake
in genetic code, is recessive and will only show
up if it is a homozygous recessive.
Other recessive disorders include
cystic fibrosis Tay-Sachs disorder, and
PKU.
Nonharmful phenotypes are determined
the same way, such as wet vs. dry
earwax.
Molecular Biology and DNA Manipulating Equipment
Micropipettes
Micropipettes are used to to take a small
amount of fluid and get exact measurements
with various substances
There are four different types of micropipettes,
each with a different range of how much liquid
they can hold. This is measured in microliters
(μ)
Centrifuge
Mixtures are stored in microtubes
when they need to be stored in small
amounts.
These microtubes, if the substances they hold want
to be seperated, are loaded into a centrifuge which
spins them at high velocties and sperates the
chemicals
This is a device often used in seperating blood
cells from other things in blood like plasma,
etc.
A centrifuge must be balanced, or
it will destroy the motor and not
work.
Gel Electrophorisis
If you need to identify the components of a
substance using suspected chemicals, you can
use gel electrophorisis.
Loading substances into small wells formed in gel and running
electricity through it seperates the substances by polarity, size,
and charge.
Is generally used for substance identification and DNA
matching, seeing if DNA on a person matches someone else
DNA or if parental DNA matches the child.
Genetics (DNA Coding)
DNA
DNA Structure
The DNA helix is like a spiraled ladder. The
sturdy backbone is made of sugars and
phosphate groups.
Linking across the bases are
four different types of
nucleiotides.
Adenine, Thymine, Cytosine, and Guanine
Adenine will ONLY link with Thymine, vice versa,
and Cytosine with ONLY link with Guanine, vice
versa.
DNA Replication
DNA repliction occurs in the middle of
interphase, during a part of it called the S
phase.
Enzymes unzip DNA like a zipper and nucleotides
come in, binding with the now available RNA and they
have to be identical because of how nucleotides
bond.
Transcription
When a cell is working, it generates protiens to
make up more cells and do other functions,
etc.
In order to make proteins, a code has to be given.
This code is the DNA. However, DNA cannot fit
through nuclear pores, so a different process must
occur.
Enzymes unzip the section of DNA where
proteins will need to be coded for. Then the
strand of RNA is sent out of the nucleus and the
DNA is repaired.
Before the RNA is sent out, it is matched by a set of
nucleotides, however anything that will be thymine is
replaced with Uracil. This will happen twice to the
strand.
Translation
Once the RNA is out, it floats around until it finds
one of the many ribosomes litered throughout the
rough endoplasmic reticulum.
Once it goes through a ribosome, groups of three nucleotides
called "codons" are matched with an anticodon that has the
nucleotides that match it on one end and an amino acid on the
other.
These amino acids link together with peptide bonds
and form the protein that the DNA codes for.
Photosyntesis, Glycolysis, and Cellular Respiration
Photosynthesis
The first thing that happens is
a photon hits the plant
In the chlorophyll, the photon excites an electron
through photoexcitation, causing the electron to break
off, thus starting the process. Because of this, two
things happen.
The electron is taken around by
the electron transport chain.
Proteins that are designed to move electrons
transfer electrons and use them to turn NAP+
into NAPH
The chlorophyll freaks out over
the fact it lost an electron.
Using the water the plant is given, it splits the
water molecule and stores hydrogen isotopes,
or just the protons
The oxygen is a by-product that
gets released through the
stomata.
The protons are sent to the thylakoids, where they
build up in energy till they can't take it anymore and
have to leave through an enzyme called ATP synthase
This creates ATP for energy
Photosynthesis utilizes three
things and transforms it
The three things are glucose,
sunlight, and water
Plants really dig the colours red
and blue
They make oxygen (which we
breath) as a byproduct of this
Glycolysis
The general breaking down of sugars and is anaerobic, while
the rest of cellular respiration is aerobic and requires oxygen
Fermentation
Fermentation takes different forms. There are
mainly two types of fermentation, alcoholic
fermentation, and lactic acid fermentation.
In alcoholic fermentation, alcohol is the by-product
of NAD+ mixing with pyruvates in certain
species
In other species, such as every single mammal,
lactic acid fermentation does the same thing,
only lactic acid is produced.
Lactic acid is responsible for
making our muscles sore after a
workout
The process breaks up the glucose into two pieces of
pyruvic acids
Glycolysis uses 2 ATP and some glucose to yield 4ATP, 2
pyruvates, and 2 NADH
Cellular Respiration
Cellular respiration is the set of metabolic reactions responsible
for turning biochemical energy from nutrients into adenosine
triphosphate. (ATP is REALLY IMPORTANT.)
Kreb's Cycle
The Kreb's cycle takes the pyruvate molecules
and reworks them into 2 more ATP molecules
(per glucose molecule)
It works by, first, oxygen binds with one of the carbons from the
pyruvate moleclue, leaving behind something called acetyl
coenzyme A with a by-product of carbon dioxide
Some NAD+ is floating around, so it might as well be turned into two more
molecules of NADH
1 glucose molecule can yield six NADH molecules and two
FADH2 molecules
Some energy is also created
Citric acid is a by-product of this
process, so it is also called the "Citric
Acid Cycle"
Electron Transport Chain
In the membrane of the mitochondria, electrons
from the NADH are sent to power electron
pumps.
Protons from within the mitochondria are sent
through the chain into an area with very little
room to move around.
The electrons diffuse through an enzyme called
ATP synthase, where the electrons' energies are
used to squish ATP together.
The Cell Membrane and Transport
The Cell Membrane
The cell membrane is made of a
bunch of phospholipids lined up
to create a membrane
The lipid molecules have a polar head
and a non-polar tail.
There are two layers of this with the
heads pointing in opposite directions.
This the the phospholipid bilayer.
The bilayer is set up like this for
"selective permeability", making sure
only stuff the cell wants gets in.
In between these two layers in floating
cholesterol.
The membrane is littered with
random channel proteins.
Channel proteins use passive
transport to allow water and oxygen
in
They are basically gaps where water
can get in, and water knows to do it
because the insides are hydrophilic.
Transport
Active Transport
Most chemicals get into the cell
using active transport.
Active transport is normally used to battle
diffusion and combat the concentration
gradient.
Almost any movement your cells do
when transporting needs a handy little
molecule of ATP to power it.
Many channel proteins are more like gateways. You fill the inside
of the protein up with your chemical, you then pay a small fee of
ATP, and your chemical is allowed in, picking up stuff that needs
to go out and then letting it out when the next customer comes.
Cytosis
Using vesicles (also made of
phospholipids) helps gets things in and out
of the cell.
Exocytosis
The cell uses a vesicle to carry a chemical to
the phospholipid cell membrane, where the
vesicle and membrane fuse, releasing the
chemical
An example of this is this is the way your body
releases neurotransmitters like dopamine and
serotonin.
Endocytosis
Phagocytosis
This happens with white blood cells, where they will detect a
harmful invader, capture it, suck it inside of them and use
vesicles to take it to a place where it will get an "unholy beat
down of enzymes and chemicals"
Pinocytosis
It consumes things like in phagocytosis, only it
does this only with substances that have been
desolved enough.
Receptor Mediated Endocytosis
Receptors receive small concentrations
of things that gather up until a vesicle
is formed and can take it away.
Passive Transport
Using passive transport does not
require any energy! This is useful
so water and oxygen can get in.
This happens through nature wanting
everything to be in equilibrium.
When you drop a drop of water,
most of the time it is going to
spread as far out as possible
because of diffusion.
Osmosis is the diffusion of water,
even if the water is a solution with
something else.
If the concentration of a solution with water
inside a cell is higher than outside, than it is
hypotonic.
If the concentration is lower inside
than outside, then it is hypertonic.
If both have the same
concentration (which is naturally
attempted by diffusion) then it is
isotonic.
Meiosis
There are two different types of
cells, diploid cells and haploid
cells.
Diploid cells tell to be body cells. Body cells are also
called somatic cells. Diploid cells hold 46
chromosomes (IN HUMANS) and generally go through
mitosis.
Haploid cells are normally sex cells, and have 23 chromosomes
(again, HUMANS), which is the same amount of PAIRS of
chromosomes that diploid cells have, making diploid cells have
twice as many as haploid cells
Seperated into two steps, with
the same exact names.
One is labeled I and the other II
Homologous pairs are formed from chromatids that match their
parents' traits. For example, the chromosome that has the trait for
hair colour in your mother matches with the chromosome in your
father.
These pairs are ripped apart, leaving the end sex
cell with hall the chromosome that came from
the father and half from the mother.
Sex chromosomes are different, depending on the sex chromosome the
first sex cell has, you can be XX or XY. XX is a girl, and this pair is
happy, however in XY, the X hates the stumpy little Y and they don't for a
pair, changing DNA depending on whether the child would be a girl or a
boy.
Sometimes, DNA replication will mess up and create
an extra or forget to make a certain chromosome. We
get strange effects from this.
If there are 47 chromosomes and the extra one
appears in, say, the 21st pair, then we see Down
Syndrome, or Trisomy 21
Klinefelter's Syndrome happens when sex
chromosomes mess up so there is an extra X
chromosome and we get an XXY
II is exactly like mitosis
Mitosis
Cell Cycle
Interphase
Longest period a cell is in
The cell can be developing in this
stage, making new DNA molecules,
or just working
Phases G1 and G2 are used for
growing while phase S
synthesizes DNA
Mitosis
A small amount of the time, after
interphase, a cell will enter mitosis, which
has five main phases.
Prophase
The nucleolus fades and chromatin
gets compressed into chromosomes
Each chromosome has two chromatids
Microtubules start to breakdown
Metaphase
Tension applied by the spindle fibers
aligns all chromosomes in one plane at
the center of the cell.
Anaphase
Spindle fibers shorten, the kinetochores
separate, and the chromatids are pulled apart
and begin moving to the cell poles.
Cleavage furrow appears
Telophase
The daughter chromosomes arrive at the poles and
the spindle fibers that have pulled them apart
disappear.
Cytokenesis
The spindle fibers not attached to chromosomes begin breaking
down until only that portion of overlap is left. It is in this region that
a contractile ring cleaves the cell into two daughter cells.
Microtubules then reorganize into a new cytoskeleton for the return
to interphase.
Nobel Prizes of 2012
Medicine and Physiology
The award was given jointly to
Sir John B. Gordon and
Shinya Yamanaka
They were awarded this for the discovery
that there is a cell with the ability to
reprogram mature cells back to the point to
where they were pluripotent.
This advances stem cell research immensely
and leaves behind the controversy from
Embryonic Stem Cells
Physics
Was awarded to Serge Haroche and David J.
Wineland.
They were awarded for "ground-breaking
experimental methods that enable measuring
and manipulation of individual quantum
systems"
There were two different methods, one of
them including trapping a photon in a box of
mirrors and sending in things to manipulate it.
Chemistry
Robert J. Lefkowitz and Brian K Kobilka were
awarded for their work on G-couple-protein
receptors, which is a receptor that works with
sensing light, flavour, and odour.
Literature
Novelist Mo Yan won the prize for his writing,
including one of his best novels "Life and
Death Are Wearing Me Out".
His writings have been described as being
hallucinatory, historic, and other things.
World Peace
European Union is the receiver of this prize.
This means 500,000,000 million people
actually win this prize and split a $1,200,000
prize.
Many think of trade and such when the Union
is brought up, but since the Union was
created, war as been at bay for a majority,
which was its essential use.
Economics
Operating a Microscope
The Microscope
A light microscope uses a beam of
light to project the image
An electron microscope utilizes a
beam of electrons to project an
image
A scanning electron microscope is used to
study cell surfaces
A transmission electron microscope is used to
study the inside of cells
A "micrograph" is a photograph taken
via microscope
"Magnification" is the zoom setting,
and "resolving power" measures
clarity
How to operate the light microscope (similar microscopes that work with this
method as a guideline include microscopes such as the dissecting microscope)
Step 1: Turn on light
Step 2: Place slide on stage
Step 3: Adjust to least magnification
Step 4: Adjust height of stage (coarse focus)
Step 5: Adjust resolving power of microscope
(fine focus)
Anatomy of a Cell
Common to most eukaryotes
Nucleus
Nucleolus in the nucleus creates
ribosomes that are sent to rough
endoplasmic reticulum
Contains DNA
Ribosomes
Created in the nucleolus and
sent to the rough
endoplasmic reticulum
Endoplasmic Reticulum
Rough ER
Rough ER are dotted with ribosomes, and
proteins synthesized on the ribosomes
are sent through the ER
Smooth ER
These ER synthesize lipids, phospholipids, and
steroids, making them a very essential part of a
cell, especially in cells meant for hormone
development.
These lack ribosomes
Golgi Apparatus
The Golgi apparatus puts the finishing touches
on the macromolecules produced, then
organizes then sends them out of the cell out
to where they should go.
Mitochondria
The mitochondria are the power sources of
cells. They give them power to move, divide,
and basically make it function.
A mitochondrion combines sugars from
carbohydrates and mixes it with oxygen to
create ATP, the main energy source for a cell
to power.
Cytoskeleton
Pushes cell membrane and makes it secure
Plant Cell
Chloroplasts
Turn solar energy, carbon
dioxide, and water into glucose
Main parts of cells that deal with
photosynthesis in the plant
Cell Wall
The cell wall is very rigid and is the main thing
in keeping a plant cell together
Found in prokaryotes as well
Vacuole
Central vacuole takes up at least
half of the cell and serves the
purpose as basically a large
lysosome
The vacuole helps with intracelluar
digestion
Found in animal cells too, but smaller
Bacteria Cell
Flagellum
Can also be found in animal cells, helps the
cell move around
Pili
They help attach bacteria to surfaces so they
don't fall and can spread faster
Nucleoid
Where the DNA is held
Plasma Membrane
What holds the nucleoid together
Capsule
The outer wall that holds together the cell and
connects the pili to the cell
Animal Cell
Lysosomes
These are transfer vesicles much like vacuoles
to plant cells and carry certain things from the
ER to the Golgi apparatus
Macromolecules
Monomers and Polymers
Monomers bind together to form polymers
These bind together using hydrogen bonds
Bonds can be formed through "dehydration
synthesis", the act of removing water in order
to enable a hydrogen bond
This act can be reversed through "hydrolysis",
rendering no need for a hydrogen bond, thus
breaking it apart
Carbohydrates
Monosaccharides
Monosaccharides have one monomer
Can be detected by Benedict's solution or
a glucose test strip
Glycogen stores energy for short bursts in
muscle tissue
Common monosaccharides are glucose and
fructose (basically the same thing but still)
Disaccharides
Disaccharides have two monomers
A common disaccharide is sucrose, lactose,
and maltose
Polysaccharides
Polysaccharides can have
thousands of monomers
Commonly referred to as "starches"
Can be detected by iodine
Nucleic Acids
DNA and RNA are composed of nucleic acids
RNA is a single helix
DNA is a double helix
that creates proteins
These two form our genetic makeup
A virus contains one DNA or RNA strand with a
protein shell
Nucleic acids are composed of nucleotides
Aside from composing our DNA and RNA,
nucleotides help with signaling cells and help
with enzymatic reactions
They are generally made up of a varying
number of phosphates, sugars, and have a
nitrogen base
Proteins
Amino acids are the essential building blocks
of everything biological
Different amino acids form different proteins,
which are the main pieces of building things
There are twenty different amino acids
An amino acids carbon base allows it to bond
with many other molecules, this variable is
called the R-group
This R-group determines what
type of amino acid it will be
Enzymes are proteins that catalyze a
substrate so it can change into a number of
products
An enzyme can only act when the substrate
reaches the activation site
The enzyme is unique to the chemical reaction.
Depending on the chemical reaction you can
have numerous enzymes that will only work
with that substrate
Sort of like a lock and key, once you have the
"lock", the substrate at the activation site, the
"key", the enzyme, can unlock the products
These products do everything from produce
essential things for the body to diffusing toxins
You can denature an enzyme with
"denaturation", which changes the
shape of an enzyme, rendering it
useless. This can can be done in a
variety of methods.
Enough heat (boiling is suffice)
Chemical changes
High concentration of other substance, low
concentration of enzyme
Salt
Lipids
Four types of lipids
Steroids
Any hormone created by a living thing fall under
this category.
Cholesterol
Cholesterol has been classified as a waxy
steroid of fat, however, it acts differently in
some respects
Although essential to our health, cholesterol is
a terrible thing to have in access as it directly
relates to cardiovascular disease
Fatty Acids
These make up triglyceride, one fatty acid
attached to each of the three molecules in
glycerol
Phospholipids
Phospholipids are extremely useful as they
make up the membranes of our cells
A pool of phospholipids will ALWAYS end up forming a lipid
bilayer, because of the polar head and nonpolar tail
Stores energy
Fats are packets of energy that are being
stored for later use
Energy from complex carbohydrates is broken
down here and stored, also
Unlike glycogen, this is only released when
needed, while glycogen releases it for an extra
boost
Saturated and unsaturated fats
When a fat is plentiful with hydrogen, we call
that saturated, and when it lacks hydrogen, it
is unsaturated.
Trans fat doesn't have anything to do with these
A saturated fat is a solid, and an unsaturated
fat is a liquid
Changing the above molecule by replacing
one of the fatty acids with a phosphate group
will create a phospholipid
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