Biology Term 1 Notes
Living Characteristics/Viruses
Requirements are MRS CHEGG ( Metabolism, Reproduction, Stimulus response, Cells, Homeostasis, Evolve, Growth & development. )
Living organisms have to have a form of genetic code (DNA/RNA)
Viruses are usually considered nonliving, but scientifically it is a grey area as they show both living and nonliving characteristics.
Viruses lack the following : The ability to reproduce by themself, a stimulus response, membrane bound organelles, and homeostasis.
Viruses have TWO viral cycles : Lysogenic and Lytic.
Lysogenic happens when the virus enters the cell but doesn’t fully overrule the cells system
Lytic occurs when the virus enters the cell and overrules the cell. This leads to the death of the cell.
Viruses can only affect certain hosts.
Antibiotics don’t work on viruses, only bacteria.
Scientists and their discoveries
Hooke discovered the dead plant cells
Schwann discovered that all animals have cells
Schleiden discovered that all plants have cells
Virchow discovered that all cells come from other cells
Prokaryotic VS Eukaryotic
Prokaryotic cells are the smallest and simplest organism.
Single celled and lacks a nucleus, along with other organelles.
Many have flagella to move around.
Bacteria is a type of prokaryote.
DNA is one giant strand
Eukaryotic cells are larger and much more complex than prokaryotic cells.
Have both a nucleus and membrane bound organelles.
The cytoskeleton supports the cell shape and the movement
Animals & plants are eukaryotic
DNA is linear and coiled
Cell Organelle and Membrane
The cytoplasm IS an organelle.
Qualities of the cytoplasm : Flexible & fluid, Bilayer, All cells have a membrane, Made of many parts , Selectively Permeable
1. Phosphate group Lipid
Head is hydrophilic Makes up the tail, hydrophobic
Cholesterol
Makes up marker ID’s, Transports things through the membrane, Receptor
Proteins
Provides stability in the membrane, Prevents tails from sticking together
Passive/Active Transport / Tonicity
Facilitated Diffusion is the passive transport of proteins.
Channels allow larger molecules to pass through membrane
Carriers change shape to allow specific molecules to pass through
Overtime, substances move from high concentration on one side to lower concentration on the other side. Theses molecules will bounce into each other until it reaches equilibrium.
Simple diffusion requires no energy since it is a type of passive transport. It moves with the concentration gradient (High —> Low). EX: Since water molecules are small, most can simply squeeze through the bilayer.
Proteins help transport materials across the membrane by changing shapes. Mainly found in facilitated diffusion.
Facilitated diffusion is a type of passive diffusion. It requires the help of proteins to pass through the membrane. EX : Passes through aquaporins , charged ions use protein channels.
The movement from low to high concentration requires ATP.
Endocytosis fuses substances into the cell membrane by using vesicles.
Exocytosis gets rid of cell waste which allows for cell materials to leave.
TYPE | DEFINITION | WHAT OCCURS IN ANIMALS | WHAT OCCURS IN PLANTS |
Isotonic | Amount of solute is the same in and out of the cell. | Water flows in and out of the animal cells equally. (Stable) | Water flows in and out of the plant cells.(Unstable) |
Hypertonic | Amount of solute is higher outside. | The cell shrivels up and dies. | Water flows out. (Plasmolysis) |
Hypotonic | Amount of solute is lower outside. | The cell explodes | Turgor Pressure. |
The types of tonicity
Isotonic : Animal cells remain stable while plant cells die. Same amount of water found inside and outside of the cell
Hypertonic : Animal cells and plant cells with both shrivel up and likely die. Water flows out of the cell and towards the environment, since it has the higher amount of solute. (Hyper = High)
Hypotonic : Animal cells with gain water and explode. Plant cells will thrive. The solute is lower than inside the cell. (Hypo = Low )
Cellular Transport
Main functions of the cell membrane :
Regulation
Protection
Communication.
Structures found in the Cell Membrane :
Colesterol
Phospholipid
Protein
Types of Proteins
Transport ( Moves the items )
Marker ( Identification )
Receptor ( Communication )
The cell membrane is sometimes referred to as the Fluid Mosaic Mode as it describes the structure of the cellular membrane.
SELECTIVELY PERMEABLE :
Made of phospholipids & different types of proteins. Membrane spanning protein is interlocked with the phospholipid bilayer. Surface proteins are found only on the inside or outside of the cell. Small polar or non-polar molecules more across the membrane. These molecules pass through the phospholipids.
FACILITATED DIFFUSION :
The membrane spanning proteins remain gated or ungated (the gaps in the protein is the channel). A hormone attaches to the channel and opens it to allow glucose or other things to pass through. Facilitated diffusion is referred to in this way as it requires help to let things pass in and out of the cell.
ACTIVE TRANSPORT :
Active transport requires the use of ATP. It goes against the concentration gradient (L —> H). The protein channels are found in the phospholipid bilayer. These channels use ions & other hormones to ‘unlock’ the gate and allow substances to enter or leave the cell.
Metabolism, Anabolism, & Catabolism
Metabolism :
The chemical reaction in the body’s cells that change food into energy. (Metabolism is the combination of Anabolism and Catabolism)
Anabolism :
Metabolic processes that build complex molecules from simpler ones, requiring energy to form chemical bonds. ( Building up )
Catabolism :
Metabolic processes that break down large, complex molecules into smaller and simpler ones. ( Breaking down )
Mechanical Digestion :
Chewing your food
Chemical Digestion :
Saliva breaking things down
Enzymes
Enzymes are used to break down and build different things. When ‘-ase’ is used at the end of the word, it is classified as an enzyme. They lower the activation energy needed for chemical reactions. We need them to help speed up reactions. If we lacked enzymes, the process would take to long and we would end up dead.
Activation energy is the term used for the start of a chemical reaction.
Photosynthesis
Light Dependent :
When plants rely on the sun for photosynthesis. Sunlight and water (H2O) enter the plants thylakoids. This process releases oxygen (O2), ATP, and NADPH.
Light Independent :
Plants that don’t rely on sun are light independent. Carbon dioxide (6CO2), ATP, and NADPH+ all enter the cell during this process. These chemicals enter the cells stoma. Glucose (C6H12O6), ADP, NADP+ are thing that exit the cell during this process.
Cellular Respiration
Process where all organism break down glucose to create ATP (Energy).
C6H12O6 + 6O2 ——> 6CO2 + 6H2O + 38 ATP
Glycolysis
Located in cytoplasm
First step in cycle
Anaerobically makes 2 ATP
Krebs Cycle (Citric Acid Cycle)
Located in mitochondrion matrix
Aerobic
Creates 2 ATP
Electron Transport Chain
Located in the cristae of mitochondira
Aerobic
34 ATP
Anaerobic Respiration
Fermentaion occurs after glycolysis oxygen is unavailable. Yeast uses alchoholic fermentation other organisms use lactic acid fermentation.
Aerobic Respiration
Glycolysis breaks down glucose and passes pyruvic acid to the Krebs Cycle, which releases CO2. ATP is made at each step, but primarily in the Electron Transport Chain along with H2O.
DNA Structure
DNA is the molecule of heredity. It contains the genetic blueprint of life.
Blue is a phosphate, orange is a Deoxyribose sugar, and green is the nitrogen containing base
Four bases are Adenine, Thymine, Cytosine, and Guanine ( Found in DNA )
Adenine - Thymine
Cytosine - Guanine
** When in RNA, the bases are Adenine, Uracil, Cytosine, and Guanine
Adenine - Uracil
Cytosine - Guanine
Hydrogen Bonds are very weak; Covalent Bonds are very strong
Transcription is the copying of a gene. RNA polymerase adds new RNA nucleotides. mRNA leaves the DNA and goes to the ribosome.
Hydrogen bonds break
Strands of the DNA separate
Free nucleotides are drawn to exposed bases on DNA
Hydrogen bonds in nucleotides form
DNA stands for deoxyribonucleic acid. DNA is shaped like a double helix. It can have bases of adenine, thymine, cytosine, or guanine. The replication of DNA is semi-conservative. Nitrogen bases are paired with hydrogen bonds.
PROTEIN SYNTHESIS
TRANSCRIPTION
The first process
Creates mRNA by transcribing DNA
Occurs in the nucleus
RNA polymerase adds complimentary RNA nucleotides
Delivers the mRNA to other parts of the cell after leaving the nucleus
FINAL PRODUCT IS A mRNA STRAND
TRANSLATION
The second process
All 3 types of RNA (tRNA, mRNA, rRNA)
The mRNA is translated into an amino acid sequence
Occurs in the cytoplasm/ribosomes
rRNA bonds amino acids into polypeptides
tRNA transfers the amino acids to the right place
FINAL PRODUCT IS A PROTEIN
Mutations are errors in the genetic coding sequence. They change the genetic material of a cell. Most are neutral & cause little harm to people/animals. Some may end up being beneficial and something. Some are harmful and may make life harder for people and animals. (Essentially natural selection)
Epigenetic’s & Biotechnology
Epigenetic’s is the study is the study of how the environment and behaviors can change how your genes function without changing the genetic sequencing.
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Epigenetic tags are added to histones
When histones are separated, the genes are ‘turned on’ or expressed. (internally/externally)
When histones are wound tightly, the genes are ‘turned off’ or are unable to go through transcription.
Environmental factors after birth can affect your cells
Biotechnology is the use of technology to manipulate biological organisms. It often involves the use of microorganisms (virus’ & bacteria) to benefit humans.
Penicillin is a mold, however biotechnology made it an antibiotic
Modern biotechnology relies on the ability to manipulate DNA
The Human Genome Project helped identify different genetic variations
We’ve only determined 2% of our protein codes
½ of the human genome is a repeated sequence
DNA is able to be taken out with a restriction enzyme
Gel Electrophoresis (STR) makes creating a fingerprint effective
Copies of DNA can occur with Polymerase Chain Reactions (PCR)
Helps identify family relationships
Plasmids and CRISPR-Cas9 can change an organisms genetics
Biotechnology PT. 2
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Applications of DNA Technology
Identification of Relationships
Medical Diagnosis
Forensics & Archaeology
Tracking Disease Outbreaks
Trade and Agriculture
1A. Paternity testing, helping establishing relationships
2A. Viral diagnostic tests, DNA sequencing
3A. Identifying + matching DNA to a suspect
4A. Tracking infectious diseases as they mutate
5A. Verification of consumer goods
Selective Breeding
Humans have been altering genetics through selective breeding for thousands of years. The use of plasmids and CRISPR-Cas9 system are now more efficient ways to transform genetics of an organism.
Transgenic Organisms
Transgenic organisms incorporate DNA from more than one species. Cloning creates exact copies of a gene or organism. Somatic cell nuclear transfer is one process of creating these clones.
Biological Molecules
All life depends on the properties and reactions of four classes of organic (carbon based) compounds — carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates are sugar. Saccharides are a monomer, or a building block. (Polymers are made of smaller molecules). Carbon, Hydrogen, Oxygen build the molecule in a 1:2:1 ratio.
FUNCTION : Quick Energy
Lipids are fats, oils, and waxes. Monomers of lipids are fatty acids and glycerol. Carbon, Hydrogen, Oxygen build the molecule with no set ratio. Straight Chain.
FUNCTION : Long term energy storage.
Proteins are our monomers. Carbon, Hydrogen, Oxygen, and Nitrogen makeup the molecule. Proteins help repair the tissues and muscles in the body. R-group is responsible for the substrate shape (amino acid).
FUNCTION : Regulating chemical reactions
Nucleic Acid monomers are nucleotides. (DNA and RNA are examples). Carbon, Hydrogen, Oxygen, Nitrogen and Phosphates make nucleic acids. DNA’s code A-T, C-G. RNA’s code A-U, C-G.
FUNCTION : Store and transmit genetic information.
Nitrogen Cycle
1. Nitrogen Fixation (The "Unlocking" Stage)
Since plants can't use nitrogen gas from the air, they need help "fixing" it into a solid form.
Bacteria: Tiny bacteria living in the soil or on the roots of plants like beans and peas (legumes) do the heavy lifting. They turn gas into ammonia .
Lightning: A huge bolt of lightning has enough energy to break nitrogen gas apart, which then falls to the ground with rain.
2. Nitrification (The "Makeover" Stage)
Ammonia is a bit "toxic" for many plants, so soil bacteria give it a makeover. They turn the ammonia into nitrites and then into nitrates. Nitrates are the "gold standard"—this is the form of nitrogen that plants love the most.
3. Assimilation (The "Lunch" Stage)
This is where nitrogen finally enters the food chain.
Plants soak up the nitrates through their roots to grow.
Animals eat the plants. Now, that nitrogen is officially part of our bodies, helping us grow and stay healthy.
4. Ammonification (The "Recycling" Stage)
Everything that lives eventually dies or poops. When plants and animals die, or when animals leave waste, decomposers (like fungi and bacteria) go to work. They break down the organic matter and turn the nitrogen back into ammonia in the soil.
5. Denitrification (The "Return" Stage)
To keep the cycle going, some nitrogen has to go back into the air. Special "denitrifying" bacteria in the soil take the extra nitrates and turn them back into nitrogen gas. It floats back up into the atmosphere, and the whole cycle starts all over again.
DNA and Protein: Without this cycle, you couldn't make the proteins that build your muscles or the DNA that makes you you.
Fertilizers: Farmers use nitrogen-rich fertilizers to help crops grow faster, but if too much gets into the water, it can cause "algae blooms" that hurt fish.
Carbon Cycle
1. The Life Loop
This part happens quickly, moving carbon between the air and living things in days or years.
Photosynthesis: Plants, algae, and some bacteria take carbon dioxide out of the air and use sunlight to turn it into "food" (glucose/sugar).
Consumption (Eating): Animals eat the plants. Now the carbon is inside the animal, being used to build muscle or provide energy.
Respiration : Both plants and animals "breathe out" carbon. When we use energy, we break down those sugars and release carbon back into the atmosphere.
Decomposition: When plants or animals die, fungi and bacteria break them down. This releases their carbon back into the soil or the air.
2. The Rock Loop
This part takes millions of years to complete.
Ocean Absorption: The ocean is a giant "sink." $CO_2$ from the air dissolves into the water. Tiny sea creatures use it to build shells and skeletons.
Sedimentation: When those sea creatures die, they sink to the bottom. Over millions of years, they get buried and pressed into limestone or fossil fuels (like coal and oil).
Volcanoes: Eventually, through plate tectonics, these rocks melt deep underground. Volcanoes then erupt and burp that carbon back into the atmosphere as gas.
3. The "Human Factor"
Normally, the slow cycle keeps carbon "locked away" for a long time. However, humans have changed the speed of the cycle:
Combustion (Burning): When we burn fossil fuels (coal, oil, gas), we are taking carbon that was supposed to stay underground for millions of years and dumping it into the atmosphere all at once.
Deforestation: Cutting down trees means there are fewer "machines" to pull carbon out of the air, making the carbon pile up in the atmosphere
Water Cycle
1. Evaporation
The sun is the engine of the water cycle. It heats up water in oceans, lakes, and rivers, giving the molecules enough energy to turn from a liquid into an invisible gas called water vapor.
2. Transpiration
Plants also contribute to the air's moisture. They soak up water through their roots and release it as vapor through tiny holes in their leaves.
3. Condensation
As water vapor rises higher into the atmosphere, the air gets colder. When the vapor cools down, it loses energy and turns back into tiny liquid water droplets. These droplets cling to pieces of dust in the air to form clouds.
4. Precipitation
When too many water droplets gather in a cloud, they become too heavy for the air to hold them up. Gravity pulls them down to Earth as precipitation. Depending on the temperature, this could be:
Rain (Liquid)
Snow, Sleet, or Hail (Solid)
5. Collection and Runoff
Once water hits the ground, it has a few places to go:
Runoff: Water flows over the surface of the land, eventually reaching streams, rivers, and the ocean.
Infiltration: Water soaks into the soil. Some stays in the top layer for plants, while some sinks deeper to become groundwater stored in underground rock layers called aquifers.
Accumulation: Water gathers in large bodies like lakes or the ocean, where the sun can start the whole cycle over again.