Study Guide- Mid Term.pdf

Scientific Method

Scientific method is simply the way people are supposed to conduct experiments, observe, and draw inferences based on experimental data.

There are 6 steps in the method. These steps are pretty straightforward, so they are shown here:1. Ask a question2. Do background research based on the question presented3. Create a hypothesis (what you think will happen) in If… then… form (for

example, if this happens, then that should happen)4. Test your hypothesis by doing an experiment5. Read your data and make inferences6. Results and reflect (did you hypothesis turn out to be correct?)

Life Functions

Imagine that you have discovered a new entity, but don’t know whether it is living or not. How do you figure out whether it is living or not? To make it easier for people to identify something as living, scientists identified 8 functions that an entity must carry out to be considered living. It doesn’t have to include ALL the characteristics, but most of them.

A living organism must be able to:• Grow: the organism must be able to increase in size or create more

of itself. • Attain Nutrition: the organism must be able to use energy to grow

or fix injuries, damages, etc.• Transport: move materials throughout the body so that resources

are distributed.• Synthesize: create complex structures or molecules using simpler

substances or structures.• Excrete: remove wastes and byproducts of nutrition or other

processes. • Maintain Homeostasis: keep conditions within the organism at a

suitable level for life. This includes adjusting to temperature changes, pressure changes, light level changes, etc.

The organism does not necessarily need to reproduce; mules don’t reproduce but they aren’t considered to nonliving!

Study Guide: Mid Term

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Organisms and Organization of Animals

An organism is a part of a species, which is a part of a population, which is a part of community, which makes an ecosystem. In an ecosystem, every organism plays a key role or has a biological niche in the system. This way, every organism is dependent on each other for survival. All the organisms have relationships to each other.Remember: Niche is a role, or occupation, in an environment

Symbiosis

Symbiosis is a type of relationship where two organisms live closely.

There are 3 types:•Parasitism: Where one organism benefits (parasite), the other is harmed(host)•Commensalism: Where one organism benefits, the other is not affected •Mutualism: Where both organisms benefit

Flow of Energy & Biomass

All energy comes from the sun. That’s it. The ultimate energy source is the sun. Plants use it to convert carbon dioxide and water to make glucose and oxygen in a process called photosynthesis. From there, animals eat the plants, and larger animals kill the smaller ones to get energy. Because energy is used in one organism, some energy escapes the system (it is NOT destroyed; you will find out why in physics)

As you can see in the pyramid to the right, Producers make most of the pyramid, followed by Primary Consumers. This is also true in the real world. The animals at the top





of the pyramid get the least energy. This is because 90% of the energy escapes the system from trophic level to trophic level.

Biomass is also a very important thing in flow of energy (biomass is how much tissue is there in one trophic level) Since energy becomes less and less as we go up the pyramid, there would be very little to feed the upper levels in land ecosystems (NOT water ecosystems) Therefore, the upper trophic levels stay the same for a land ecosystem. In a water ecosystem, however, the biomass pyramid is upside down, meaning there is more upper trophic level creature mass than there is of lower ones.

Here’s a list of words you may need to know:• Autotroph/Producer: an organism that could feed itself• Consumer/Heterotroph: an organism that gets energy by eating another

organism• Predation: eating other animals to get energy

Population

The population refers to number of organisms in one area. This is affected by many factors:• Death Rate• Birth Rate•Food Supply (important)•Water Supply (important)





Components in population graph (previous page):(1)Lag Time: period of time where little growth occurs in the system(2)Exponential growth: period of time where growth is constant(3)Carrying Capacity: the maximum amount of organisms that could besupported in the community• Decline (not shown): if a population deceases, this part shows the populationgoing down.*Carrying Capacity could change if any of the factors are altered

Abiotic Factors/Environment

The environment affects the individual as well as the organisms in the community.

Water, Carbon, & Nitrogen Cycles

All organisms require water, carbon, and nitrogen to live. Water is primarily used as a “medium of transport” (thing used to move stuff around), carbon for providing the energy, and nitrogen is required for nucleic acids as well as amino acids





Water Cycle:

Nitrogen Cycle:





Carbon Cycle (Super Simplified):*There is also a Phosphorus Cycle, but it is the least important cycle, so it was not included.

Effects of Organisms on EnvironmentThe environment is not only a factor in the life of an organism; it also is affected by them. Organisms could drastically change an environment

Ecological SuccessionAn ecological succession is changes that occurs in a community over time. There are several types of successions (only land described here):•Primary (Land): This occurs where there is no soil in the area or region at first. Pioneer species (first species in a region) usually make this region habitable for later species.•Secondary (Land): A change that occurs from the destruction of a previous community.

Land Biomes and their Characteristics

Biomes are ecosystems/environments that have a set of abiotic factors that differentiates them from another. Biomes are usually defined by their climate, which is:• Temperature: whether the place is cold or hot• Precipitation: the amount of snowfall and/or rainfall in the area





Sometimes, small places have slightly differing climate than the rest of the region. This is considered a microclimate1.

Biomes have other abiotic factors that define them. They include things like soil quality, humidity (although it’s associated with climate), and light. Don’t include these in the test unless there are no other option.

Major Land Biomes

There are 10 major biomes defined by their climate and its organisms. They include:• Tropical Rain Forests: Hot and wet all year-round with nutrient

lacking soils. (For organisms, check page 100 in Miller Biology) Found in Central & South America (ex. Amazon Rain Forest), Southeast Asia, Core of Africa, and Northern Australia.

• Tropical Dry Forests: Mostly hot throughout the year with wet and dry periods throughout the year. (For organisms, check page 100 in Miller Biology) Mostly where rain forests are found and tropical islands.

• Tropical Savanna: Warm temperatures and seasonal rainfall. Not as wet as dry forests. (For organisms, check page 101 in Miller Biology) Found in Africa (eastern), southern Brazil and Australia.

• Desert: Extremely dry; Very little rainfall (less than 25cm/year). TEMPERATURE DOESN’T MATTER; Antarctica is considered a desert and it’s a frozen ice cube! (For organisms, check page 101 in Miller Biology) Found in Africa (ex. Sahara Desert), Asia (ex. Gobi Desert), Middle East, United States, Mexico, South America, & Australia (near inside of the continent)

• Temperate Grassland: Warm summers with good rainfall. Fertile soils (great for farming) (For organisms, check page 102 in Miller Biology). Central Asia, North America, Australia, parts of Europe and South America.

• Temperate Woodland/Shrubland: Warm & dry during summers, cool & wet during the winters. Soil lacks nutrients. (For organisms, check page 102 in Miller Biology) These biomes are typically found in the Americas (western edge), near the Mediterranean Sea (Europe), South Africa, and Australia.

• Temperate Forest: Warm Summers & Cold Winters; Precipitation occurs throughout the year (not as much as tropical rain forest). Soils are fertile. (For organisms, check page 103 in Miller Biology). Commonly found in eastern United States (near Tennessee and such states), southern Canada (away from the cold northern area), majority of Europe & East Asia.



1 Remember: micro-small climate-temperature + precipitation



• Northwestern Coniferous Forest: Medium temperature (not too hot, not too cold, just right) All the seasons have rainfall except dry summer. Acidic soils (not necessarily sterile). (For organisms, check page 103 in Miller Biology) Western North America.

• Boreal Forest: Extremely cold winters, with short and cool summers (For organisms, check page 104 in Miller Biology) Found in far north regions.

• Tundra: Little precipitation, long and cold winters with wet (and short) summers. Permafrost (permanently frozen soil) present. Not fertile land. (For organisms, check page 104 in Miller Biology) Found in far north regions.

Water Biomes and their Characteristics

Aquatic biomes are similar to land biomes in that they both involve temperature. However, aquatic systems are also grouped according to the depth of the ecosystem, content of water, and movement of water.

Salt vs. Fresh water

Saltwater and freshwater ecosystems are different in that one system has

more dissolved salt. The presence of salt in water affects the organisms living in the ecosystem because the salt may dehydrate freshwater organisms and the absence of salt may saturate saltwater organisms. Both of these are harmful to the creature and could lead to death of the organism.

The following diagram illustrates this:





In the diagram, you can see that there are three words. These refer to the water salinity (amount of salt in the water):• Hypertonic: If the water (or solution) has too much salt. (If the solution

has less water than the cell)• Isotonic: There is a balance in salt and water. (If the solution has a

similar amount of water than there is in the cell)• Hypotonic: If the solution has too much water. (If the solution has a

higher quantity of water than the cell)

Freshwater Ecosystems

Freshwater ecosystems consist of two subgroups. They include systems with flowing water and still water. You might also find this good to know: fresh water makes up only 3% of earth’s surface water.

Flowing Water Ecosystems

Flowing water ecosystems include rivers and streams. These ecosystems are characterized by their motion and the fact that they are filled with freshwater instead of saltwater. They are also less deep than still water ecosystems. The organisms are adapted to floating around in the fast-moving water. The organisms may also have several ways to keep themselves locked down, such as using hooks to latch themselves onto plants. They may also use suction cups (or similar) to keep themselves in one place.

Still Water Ecosystems

Still water ecosystems have little to no flowing water. Flowing water ecosystems usually flow into still water ecosystems. They are usually deeper than flowing water ecosystems. Although they have no flowing water, the water does move around and moves resources around for the organisms to use. The types of organisms that are found in these systems include plankton. These are (usually) microscopic organisms that can’t swim rapidly enough to live in flowing water systems. There are two types of plankton:• Phytoplankton: single celled plants that use nutrients floating in the

water to turn into energy and nutrition for higher trophic levels.• Zooplankton: tiny animals that can’t produce their own food and uses

phytoplankton to get energy and nutrients.





Saltwater/Marine Ecosystems

Saltwater ecosystems are very large, as they include oceans and seas. Due to its size and depth, there are many regions to the ecosystem.

Regions according to Depth

Depth is extremely important when it comes to marine ecosystems. Due to the loss of light and energy as the depth increases, the zones are divided according to the amount of light received in the region. There are two zones according to light level:•Photic Zone: region in

a marine ecosystem where light penetrates and is able to provide energy to plants to do photosynthesis. Usually occurs at the topmost layer, up to 200 meters.

•Aphotic Zone: region where there is no light and plants are unable to produce food for higher tropic levels.

Regions according to distance from Land

The regions of a marine ecosystem is also named according to distance from land. These regions are known as:• Intertidal Zone: this

place can be flooded with water one moment, the next dry. This is because tides bring or remove water into/from the land. Organisms must adapt to living in both water-filled conditions as well as waterless.

• Coastal Ocean: costal ocean ecosystems start from low-tide mark (the area that marks the lowest a tide could be) and goes all the way to the continental shelf (shown in diagram). This zone is almost completely under the photic zone. This means that plankton and algae are able to





live and bring energy into the food chain here. This area is the place that has the most organisms in the ocean. You can compare it to the “city of the ocean”.

• Open Ocean: this zone extends from the continental shelf and goes into the ocean. This area has water extending all the way to aphotic zones, which makes plants unable to produce food for other organisms. Therefore, this place has the least densely populated areas of the ocean.

Wetlands

These ecosystems are sort of a mix of salt water and freshwater ecosystems. They are places where water covers up to the surface of the soil. Wetlands include swamps, marshes, and bogs. These systems often look like flooded versions of land biomes.

Human Interactions

Humans altered the earth more than any other organism. This has good as well as bad effects. There are several things that humans have done that has affected the environment

Hunting and Gathering

The earliest things humans started doing that had an impact on the biosphere (the earth) involved hunting and gathering. This means that humans have killed animals and collected plants for food. Although this isn’t as effective as modern methods, it still caused extinctions of many animals in certain areas. To maintain a balance in what humans consume and what they give back, we started relying on subsistence hunting. In this system, only what is required to live is taken and the rest is left untouched. However, hunting and gathering often didn’t provide enough food for the human race, so they turned to agriculture.

Agriculture

Agriculture is the practice of farming. In this field, people grow crops and animals. Since hunting involved going out and finding food, and agriculture involved growing your food on demand, agriculture allowed people to have a stable food supply. As a result of more food becoming available in one area, humans eventually settled and farming became extremely important. However, when humans started demanding much more food than that was produced, people started the green revolution





Green Revolution

The green revolution was simply many strategies that helped increase the amount of food produced through agriculture. A strategy that was used (and in many places, are still used today) include monoculture. This is a method where a single plant is planted repeatedly, rather than plant several different ones each time. This has allowed for mass production of certain crops. However, it also brought many disadvantages, such as transportation of water to the farmland (irrigation).

Industry

As an increasing amount of people settled down and eventually got jobs, the industry became a huge part of people’s lives. With the increasing number of industries came more products. However, the industries also produced a lot of wastes, which is a major change that humans caused.

Renewable and Nonrenewable Resources

There are many resources on earth that could be used by humans. However, they could be split into two categories: • Renewable: these resources could easily regenerate fast. Since they

could be used and there would still be more of them being produced, they could be used almost forever.

• Nonrenewable: these resources cannot regenerate quickly. Since they don’t regenerate (or take a significant amount of time to regenerate), they can’t be reused.

Sustainable Use

To use our resources well, nonrenewable as well as renewable, we must learn sustainable use. In this idea, people must learn to use their resources wisely so that they won’t be depleted quickly. If we fail to use our resources sustainably, then there could be major problems, such as:• Soil Erosion: resources such as soil could be lost due to lack of plant life

to hold them in place.• Desertification: large areas of land could become desert. • Acid Rain: acid could replace water in rain. This would harm plant and

animal life, which could falter our steady food supply.• Smogs: fogs of smoke and unhealthy gases that could harm humans,

plants, and animals that breathe it.





In order to stop this from happening, we must limit many things, such as farming. We must only farm in places that are meant to be farmed in. We must also address the issue of deforestation, which is eliminating forests that hold soil in place.

Pollution is also a very important result of not using our resources wisely. When we use fossil fuels and burn them, we release the excess wastes into the air, water, or land. This releases pollutants, or harmful substances that could cause damage, into the environment.

Biodiversity

One of the most important resources on earth is biodiversity. This simply is the variation between animals, organisms, and ecosystems. This topic is very general, so there are three parts of biodiversity, which are:•Ecosystem Diversity: the variation between ecosystems and the

processes that occur within them•Species Diversity: the variation between species of organisms•Genetic Diversity: the variation between the genetic information

passed between organisms

Why is biodiversity an important resource?

Biodiversity is an important resource because the differing species on earth all have something to offer to humans, the earth, or each other. This helps the earth stay as one community that flourishes.

How is it being threatened?

It is being threatened by many things, such as:• Habitat Fragmentation: the splitting of habitats and greatly reducing

the size of a unique ecosystem. Examples of this include surrounding patches of one ecosystem by another different ecosystem. This greatly reduces the amount of space available to the reduced ecosystem, which results in the ecosystem’s organisms to have less space to live. Smaller populations of organisms that were originally in the system may not have enough resources or space to live as a result





• Biological Magnification: the increase in pollutants or dangerous chemicals as the trophic level increases

• Invasive Species: the introduction of a foreign species into an ecosystem. This could end up with the elimination of the invading species, or the invading species might be more successful and use too much of the limited resources in the ecosystem.

•Demand for wildlife products• Increase in urban cities

When these factors are included in the ecosystem, the organisms may become endangered (the population of the species decreases considerably; could be followed by extinction) or even extinct (the species no longer has any living members; they all died out).

Conservation

To preserve biodiversity, we could limit our use of wildlife products. In addition, we could set up areas where ecosystems are endangered and not have industries or other human factors interrupt the natural processes. Remember, biodiversity is also considered a resource, so sustainable use is applicable here.

Problems

Although there are several ways humans can prevent all sorts of issues with the environment, there are still problems that humans created. These include global warming and the thinning and eventual depletion of the ozone layer.

Global Warming

Global warming is the gradual increase in the temperature of the earth. Earth naturally varied temperatures over the billion years it was in existence, but humans also have a profound influence in this. Greenhouse gases (gases that trap heat on earth and retain it), which come from the burning of fossil fuels, have increased throughout the years following the industrial revolution. If this issue isn’t addressed, there could be problems with species as biomes are transformed from temperature change. Droughts, floods, and other natural disasters are inevitable if we don’t change our





habits. Polar ice cap melting is another clue that is telling us if we don’t change our habits, we might destroy the earth.

Things we can do to prevent this include using hybrid cars, public transportation, or just walk. You could also prevent excessive electronic use and save the earth!

Ozone Depletion

The ozone layer is a layer in the atmosphere that is mostly composed of ozone gas. This gas absorbs UV c rays, which is harmful to humans and other animals. However, this layer is steadily decreasing in volume due to use of CFCs (Chloroflourocarbons). If the ozone layer continues to lose volume in such a high rate, then we would be virtually unprotected from UV c light, which could result in more damage in organisms on earth. So far, CFCs have decreased in usage, but the ozone layer is recovering at an extremely slow rate.

Organization of Organisms

There are countless organisms that live on earth. However, many of these organisms have similar traits and others that are unique to them. To identify organisms (not based on their local name, or the name given by the native language in the area), scientists devised a way to organize organisms based on similar traits and uniqueness. This is called taxonomy, or the assignment of a name that is universally known to an organism.

Before the Theory of Evolution

Before we learned about the theory of evolution, we thought that organisms were defined by their species name and that their traits within a species would never change. Using





this principle, a Swedish biologist named Carolus Linnaeus created a system that helped organize life on earth. He divided the species based on 7 categories, which is based on 7 levels of similarity. The organisms in the first category, kingdom, have the least in common with each other. The next level, phylum, has more in common with its organisms than does kingdom. Then comes class, with even similar organisms than phylum. As each level progresses downward, the creatures have a lot in common. For example, order is more specific than class, family is more specific than order, genus is more specific than family, and species is more specific than genus. Using this, scientists at the time used these 7 categories to identify a creature.

Binomial Nomenclature

However, using 7 words to describe one organism can be very tedious, so Linnaeus devised another system that

was easier to describe organisms. It is still based on his system of taxonomy, but it was shortened to two words; its genus followed by the species name. This is called binomial nomenclature. (If you find this hard to remember, just note down: bi = 2 nominal = name nomenclature = naming) In this system, the genus’ first letter is capitalized, and the species is lowercased.

After the Theory of Evolution

Linnaeus’s methods were pretty successful before the discovery of evolution. However, this system relied solely on structural aspects of a species. Ever since technology advanced, we have found out many things that could aid us in organizing organisms. For example, when scientists found that species evolve over time, grouping started to include evolutionary classing. Evolutionary classing is the grouping of organisms based on the species’s history. Evolution is not the only factor used to differentiate species. There is also DNA and RNA similarities that come into play. This could be tracked using Molecular Clocks, or the tracking of mutations within the genetic code as it evolves throughout the existence of a lineage of a species. As a result, we could define species based on many factors, not just structural differences.





Due to similarities between several kingdoms, scientists decided to include a higher level of classification, called Domain. This is more general than kingdom. There are currently 3 domains, identified in the next section.

Classification Today

Today, there is not two kingdoms, but 6. They are Eubacteria, Archaebacteria, Protista, Fungi, Plantae, and Animalia. These kingdoms in turn comprise three domains with the names Bacteria, Archaea, and Eukarya. The domains Bacteria and Archaea have organisms that are unicellular, or are organisms that have only one cell. The cells could also be one of two types:

Prokaryotes Eukaryotes

Simplest type of cell Complex structures

No organelles or nucleus present

Nucleus and organelles present

Contains cell membrane and cytoplasm

Contains cell membrane and cytoplasm

Here are a few diagram for each domain that explains the properties of the organisms within that domain:

Domain: Bacteria

Kingdom Eubacteria

Cell Type Prokaryote

Cell Structure Cell Walls present

Number of cells Unicellular

Nutrition Autotroph

Domain: Archae

Kingdom Archaebacteria

Cell Type Prokaryote





Kingdom Archaebacteria

Cell Structure Cell Walls present

Number of cells Unicellular

Nutrition Autotroph

These organisms could live in harsh conditions with acids, bases, extreme pressure, heat, etc. This domain is the domain where extremophiles probably are in abundance.

Domain: Eukarya

Kingdom Protista Fungi Plantae Animalia

Cell Type Eukaryote Eukaryote Eukaryote Eukaryote

Cell Structure Cell walls present;

Chloroplasts could be

included in cells

Cell walls present

(made of chitin)

Cell walls present

(cellulose); Chloroplasts

present

No cell walls or

chloroplasts (we are not little green

people)

Number of cells

Unicellular; could be colonial

Multicellular (few

unicellular, like yeast

Multicellular Multicellular

Nutrition Autotroph/Heterotroph

Heterotroph Autotroph Heterotroph

Atoms

Atoms compose molecules. But what makes them make molecules? A simple answer to that is that they chemically bond. A chemical bond is the attraction of atoms due to electrons (a subunit of atoms) or the charge of the atom.

Semantics of Atoms

All atoms consist of a nucleus, that has protons and neutrons, and an electron cloud that consists of electrons. The number of protons will always be the same for an element, which is the atomic number. The





number of neutrons might differ (but is usually the same number as protons). If the number of neutrons differ from the number of protons in an atom, it is known as an isotope of the atom. In a regular atom, (meaning it’s not an ion), the number of electrons is also the same number as there are protons. Since protons have a charge of +1, and electrons have a charge of -1, there is usually the same number of protons as there are electrons because opposite charges attract.

Happy and Unhappy Atoms

Atoms have electrons in their electron cloud. Big deal; we all know that now. But why does it matter? The electrons are grouped into energy levels with a capacity for the number of electrons on one level (to see what level has what capacity, look at the table). For an atom to be happy, it has to have its topmost shell, better known as an “octet”, filled.

Now, some atoms won’t have the luxury of having its topmost shell filled. This will result in

some pissed of atoms. To prevent this, they will bond with other atoms to be happy.

Bonding

There are two (actually three, but weak hydrogen bonds are not strong enough to be a true bond) types of bonds that link atoms to form molecules. The first, covalent bonds, are bonds that are formed when two (or more atoms) share electrons. The number of electrons that the atom needs to fill is the number of covalent bonds it could make. Sometimes, atoms aren’t nice and decide to steal electrons from one another. But in this situation, the atom that loses the electron is happy to lose it. When an atom steals an atom to make a full octet, it gains a -1 charge. Similarly, the atom that is jacked gains a +1 charge. This would only work if the atom that loses the



Energy Level

Capacity(Electrons)

1 2

2 8

3 8



electron is happy, and it will be happy if it loses enough electrons to deplete its uppermost octet. As long as the lower energy shell is left alone, the atom will not complain. After the electron snatching is over, since the atoms have different charges and different charges are attracted to each other, the two atoms will come together and form what is known as an ionic bond.

Chemicals in Biology

All chemicals are composed of molecules. Molecules are also composed of a smaller subunit, known as the atom. Atoms could be used to organize the chemicals into two categories based on its presence. The two categories are:• Organic Molecules: These molecules have both (can’t stress it enough)

carbon and hydrogen in their chemical formula.• Inorganic Molecules: These molecules are what the organic molecules

aren’t. They may contain carbon or hydrogen, but not both. Otherwise, the molecule would be considered organic.

There are several million (or more) organic molecules, but they are a part of 4 main groups. They are:•Carbohydrates•Proteins•Lipids•Nucleic Acids

Before we begin… Here’s a few terms and concepts you’ll find useful:• Isomer: two chemicals that have the same chemical formula, but

different chemical arrangement.• Polymer: A chemical that is composed of parts that repeat.• Monomer: A chemical that is not composed of parts that repeat.• Dehydration Synthesis: The process of combining chemicals to form a

larger chemical by removing a water molecule.• Hydrolysis: The opposite of Dehydration Synthesis; The process of

breaking chemicals into its subunit by adding water to the chemical formula.

Carbohydrates

Carbohydrates are any organic chemical that has a Hydrogen to Oxygen ratio of 2:1 (the same as water). (And has only C, H, and O) Carbohydrates could be sugar or starches, for example.





The most simplest carbohydrates are simple sugars, or monosaccharides. These include Glucose, Fructose, and Glactose (C6H12O6). When you use dehydration synthesis on these chemicals, you will end up with a disaccharide. You can remember this by noting that “di" means two in Greek or Latin, whatever it is. So, there are two monosaccharides in a disaccharide. Now, if you repeat the disaccharides like a dozen or so times, (maybe even a thousand), you will get a polysaccharide. Starches, cellulose (the material the cell wall of a plant cell is made of), and chitin are a few examples of polysaccharides. This is a polymer, and neither the disaccharide, nor the polysaccharide will be able to pass the cell membrane.

(Important to know: Simple sugars and starches each have indicators. They include Benedict’s solution [for sugar] and Lugol’s solution [for starch]. When a solution has the chemical the indicator is used for, it’s color changes.)

Proteins

Proteins are polymers made from amino acids that are bonded using peptide bonds. Let’s rewind for a second; Amino acids are basically an amino group (NH2), a carboxyl acid group (CHO2), a hydrogen atom, and an R group attached to a central (or alpha) carbon atom. Don’t get it? Here’s a diagram:

Still don’t get it? Well, I don’t have anymore diagrams, so read the paragraph again.

Now, the R-Group is where amino acids differ. There could be practically anything there (no, seriously) and this is what makes each protein different. Now, peptide bonds are bonds where the OH part of the carboxyl group of one amino acid is removed, while the O part of the other amino acid is removed. The remaining space is joined for each amino acid. When two amino acids are joined like this, it becomes a dipeptide (same thing as before, “di" some language for two). Now, if these





dipeptides are repeated over and over again, they become a protein, a polymer.

Lipids

This chemical type is used to store energy longer than carbohydrates. They are not soluble in water, but in order to break lipids into its components, hydrolysis is required. To make the lipid and water mix, an emulsifier (oil mixer) is used (like bile). Anyways, lipids are composed of 3 fatty acids connected to a glycerol molecule. Lipids are not polymers (they are not composed of repeating monomers). Lipids include fats in its group; there are two types of them, which are:•Saturated fats: These are the more unhealthy types of fat. They have

each carbon atom attached to two other carbon atoms (so the bonds will

look something like this for each carbon atom, just not at the end): Saturated fats are usually solid at room temperature.

•Unsaturated fats: These are much healthier than saturated fats. They usually have a hydrogen atom missing (I seriously don’t know how…) and it is liquid at room temperature. That means olive oil and vegetable oils are healthy!

Nucleic Acids

We finally come to nucleic acids. These monsters (when unraveled) are 3 feet in length. Nucleic acids include RNA and DNA, which store genetic information. They are composed of a sugar (deoxyribose for DNA, and ribose for RNA) connected to a phosphorus ion. A nitrogenous base is connected to the sugar also. Sounds like a different language? To sum it up, DNA and RNA is made up of a backbone of sugar connected to a phosphorus atom. The sugar is also connected to a base that changes based on the organism that the DNA is made for. Before we get deep into the bases and stuff, here’s a diagram that will make everything clearer: “D” in the diagram is the sugar (deoxyribose for DNA, ribose for RNA)“P” is for the Phosphorus ion“T, A, C, & G” are the bases





RNA and DNA have 3 common bases, known as “Adenine”, “Guanine”, and “Cytosine”. Guanine and Cytosine pair up and make up roughly 52% of the molecule. However, DNA has “Thymine” (which pairs with Adenine) instead of “Uracil” (which also pairs with Adenine, but in RNA). Adenine and Thymine (or Uracil, in RNA) make up 48% of the molecule.

The Digestive System

The digestive system is a very crucial system in the body. It is the system that provides energy and nutrition to the rest of the human body. Since the rest of the body’s cells can’t break down food into usable components, the digestive system takes care of this for us. The process of breaking down food into smaller components outside of a

cell is called “extracellular digestion”. This is the opposite of “intracellular digestion”, where the digestion occurs within the cell itself.

Components of the Digestive System

The digestive system consists of the oral cavity, salivary glands, esophagus, stomach, small intestines, large intestines, rectum, gall bladder, liver, and pancreas.





Oral Cavity

The food starts in the oral cavity, where the food is mechanically digested through chewing. Mechanical digestion is when food turns from a solid to liquid, but doesn’t chemically break down. In the mouth, salivary glands produce saliva that mixes with the food and chemically digest carbohydrates using an enzyme known as “amylase”.

Esophagus

After the food is done being chewed, it is swallowed and it goes into the esophagus. The esophagus is lined with muscles that push food into the stomach. But, before it reaches the stomach, it goes through the epiglottis, which is located in the pharynx. The epiglottis is a flap in the esophagus that closes the trachea (a tube that brings air into the lungs) so that food will go into the stomach and not the lungs. The esophagus is also designed so that the muscles that surround it bring food into the stomach through contractions through a process called peristalsis. But, if the food is to toxic (the liver or stomach can’t handle it), the contractions will reverse in direction and you will throw up (ew...)

But wait! It still doesn’t go into the stomach until it goes through a structure called a “sphincter”. This structure prevents a fluid from getting into an organ from one direction. The sphincter in the esophagus is called the “cardiac sphincter”, because it is located near the heart. This specific sphincter stops stomach acid, or gastric juice, from getting into the esophagus. However, if this sphincter decides to not work, it will cause a burning sensation near the heart. This is known as heartburn.

Stomach

After the food passes through the cardiac sphincter, it enters the stomach. This organ chemically breaks down proteins into simpler proteins called peptides through chemical digestion. The chemical breakdown is aided by an enzyme called “pepsin”; this enzyme is exclusive to the stomach due to the stomach’s low pH. The low pH is due to the acid that is present in the stomach, which is also responsible for helping with digestion. The acid it uses to chemically digest the food is a very





strong acid known as hydrochloric acid; in fact, it is so strong that the stomach would digest itself if it wasn’t covered with mucus on the stomach walls. Forget about your stomach, did you know that this thing can melt through a car door? If the mucus wasn’t there, the stomach would digest itself. This is similar to how ulcers form; the stomach doesn’t have enough mucus in one area and the acid (painfully) digests parts of your stomach. But, apart from using an acid that could literally burn a whole through it, the stomach also aids the breakdown of other materials through further mechanical digestion. It mechanically digests other foods by grinding the food using its strong muscles. By mechanically breaking down the foods, the stomach could increase the surface area of the food to allow for the chemicals to digest the foods faster.

Small Intestines

After it passes through the stomach, the food is mostly liquid, and is now called “chyme”. It goes through another sphincter called the “pyloric sphincter” and into the small intestines. Over here, the intestinal fluid digests the peptides that the stomach broke down into amino acids (to

check which enzymes break down which chemicals, check the chart to the left) It also digests lipids using bile from the liver to break the lipids into glycerol and fatty acids, and it also breaks carbohydrates like starches into simple sugars like glucose. (Note that bile doesn’t chemically break down lipids; rather it breaks bile into water soluble droplets through a process

called “emulsification”) In the small intestines, the nutrients are absorbed through structures called “villi”. In the villi, there are blood vessels that absorb the nutrients, along with a structure called the “lacteal”, which absorbs fatty acids and glycerol. The villi on the outside look like little folds. The small intestine’s inside is simply covered with these little folds. It is shaped like this because there is a higher surface area for nutrients to be absorbed. As you can see, it has blood vessels that absorb nutrients through



Enzyme Substrate

TrypsinPeptides/

Simple Proteins

Lipase Lipids/Fats

Amylase Carbohydrates



diffusion. The blood gets nutrients from the digested materials and transports it to the rest of the body.

Large Intestines

The large intestine, or the colon, doesn’t digest anything. All it does is absorb the remaining water in the waste. If it doesn’t absorb enough water, the waste will be released as diarrhea. If the opposite happens, people will experience constipation, where too much water has been removed from the feces. The parts that aren’t digested, or could not be digested (like cellulose in our bodies), are stored in the rectum. Finally, they are removed after enough waste accumulates in the rectum.

Accessory Organs

What happened to the other digestive organs? Well, they are used, but food doesn’t pass through them. These organs shouldn't be called accessory organs, because without them, we’d be dead! They do many important things for the body.

Liver & Gallbladder

The liver is one of the most important accessory organs. This is also a mysterious one; it is the only organ that could regenerate itself.

One of the main functions of the liver is to be a poison control center; it breaks down poisons (if there is a small amount of it) into harmless chemicals. In addition to this, the liver assists the digestion of lipids by producing bile that is stored in the gall bladder. The gall bladder releases the bile into the small intestine to digest foods.

Pancreas





The pancreas is also an accessory organ. This organ is located behind the stomach and it does many things, such as produce hormones. These hormones control movement, energy release, etc. Along with this, it also produces enzymes that break down nutrients, which get funneled into the small intestines.





Documents

Study Guide- Mid Term.pdf