 An ecosystem consists of all the living and non-living factors in a  defined area

what is origin of life?

o Living: Biotic ingredients

 Organic molecules, proteins, nucleic acids, fats,  

carbohydrates

o Non-living: Abiotic ingredients

 It took about 10 billion years for living things to come to  come into existence, so until that happened abiotic  

ingredients came about

 Atoms

 Hydrogen was the first stable atom that was formed  

as the universe aged

 More reactions occurred to make bigger atoms

 Origins of life

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o Within waters, complex substances began to form that became  organic molecules

 Some of these contained at least one carbon and one  hydrogen atom hydrocarbons

o Biotic ingredients came together and compounds were formed  Created our common ancestors

 We came from a single common ancestor

 Components of this ancestor

what is symbiosis?

o Cell membrane

 Fatty inside, water-loving outside

o Inheritance/DNA

o Reproduction

 Asexual or sexual (exchanging genetic  

information)

o Detecting and responding to environment

o Energy—all organisms need it, use it, and store

it

o Growth and Development

o Sustainability

 Homeostasis

o Evolution and Reproduction

 Evolve as a living organism

 Commonalities between “friends”

o Endosymbiosis

 One organism lives inside of the other

o What is symbiosis? Don't forget about the age old question of 11) Why are action potentials usually conducted in one direction?

 When two or more different species live together and  interact; they have a very close association with each other  It is not always beneficial!

o Associations

 Competition

 Two species interact but what they are doing is  

harmful to both of them

 We forced this in food production with the use of  pesticides, fertilizer, etc  stresses other species in  the area

what is food?

 75% of antibiotics = used by farmers 

 Niche: everything you need to live

 Combination of all abiotic and biotic needs of a  

species or population to survive and reproduce

 During a competition, some part of the niche is  

interrupted

o “Friend” Relationships

 Exploitation

 One is harmed, one benefits

o Examples:

 Herbivores eat plants

 Predators kill other animals for food

 Parasiteslive in and on the organisms  

eaten

 They often cause harm

 Pathogens

 The average American is prescribed 17  

doses of antibiotics by the age of 20 

 Equivalent to 30,000lbs 

 Commensalism

 One species benefits and the other is unharmed/does not cost them

o Example: Barnacles on whales

 Mutualism

 Both species benefit  

 Survival and reproduction are both increased with  both species

 Microbiome:

 All organisms which live in symbiotic relationships  with humans

o Affects digestion/absorption, immune system,  

stress/psychological issues, development

 Have enzymes that digest substances we cannot  Communicate with our immune cells

 Amphibiosis:

 Transitions of one type of species-species interaction  to another

o Example: switching from commensalism to  

exploitation

o This is based on population size and other  

present microbes

 Trophism:

 Movement of food from one organism to another

o Producers to consumers

 Food  

o It is an organic substance, meaning it is a hydrocarbon o Inorganic source = CO2

o Organic products are produced from inorganic sources by  organisms

 Who makes food and who eats food?

o Autotrophs: produce their own food

 Chemoautotrophs

 These are prokaryotes

 They transform light energy into chemical energy

 Photoautotrophs

 These are prokaryotes, protists, plants…. Or anything green or that has color and can make their own food  

from sunlight

o Heterotrophs: eat food produced by autotrophs humans are  heterotrophs

 Photoautotrophs

 These are prokaryotes

 Chemoautotrophs

 Can’t make their own food

 Rely on autotrophs to make food for us in the form of  sugar, which we then use to make other substances

 Humans, prokaryotes, plants, fungi, protists, animals   Prokaryotes

o Single celled organisms that have a simplistic structure and  function

 Include archaea

 Live in many extreme environments

 Include bacteria

 Live everywhere

o When they are pathogens, they can harm us

 Can be intracellular

 Enter into our cells and survive

o They produce a substance that causes harm

o They kill the cell that causes it to burst

 Apoptosis: cell death

 Can be extracellular

 They multiply outside

o Produce a substance that causes harm

o Cause an imbalance in our normal flora  

(microbiome)

 Can be toxins

 Endotoxins

o Something structural that is there for a  

different purpose and unintentionally helps the  

cell

 Example  lipopolysaccharide

 Exotoxins  

o Produce mainly as a defense

 Proteins

 Top disease-causing foodborne pathogen? 

 Viruses: 58% 

 Salmonella: 11% 

 Top hospitalizations? 

 Salmonella: 35% 

 Viruses: 26% 

 Top deaths? Salmonella: 28% 

 How to prevent foodborne illness:

 Cooking food properly (ie not prepping veggies and  

raw meat on same cutting board

 Salting

 Pickling

 Drying  

 Being clean

 Eukaryotes

o A cell that absorbed energy from another in the form of sugar  produced oxygen as a byproduct

o More mitochondria in muscle cells because they are the ones  that contain energy

o Protists

 Examples

 Algae

o They are photosynthetic

 Phytoplankton

 Zooplankton

o Plants

 Ferns

 Gymnosperms

 Angiosperms

 A flowering plant

 Mostly what we consume

 If it is green, it is a photoautotroph!

 Roots exist below the ground

o Circulatory system involves moving minerals  

and water to the photosynthetic cells

 Shoots exist above the ground

o Includes the leaves and stem cells

o Perform photosynthesis

 Uses sunlight and pigments

 Stomata (pores) of leaves allow CO2 in

 What we eat:

 Below ground vegetation

o Tubers, roots, and bulbs

 Above ground vegetation

o Leafy greens

o Fruit (this is really the ovaries of the plant)

o Fruit

 Flowers

 Production of flower attracts pollinators and then  

seed dispersal can occur  

 Most are hermaphroditic, meaning they have both  

male and female parts

o Male parts include a stamen, which has a  

filament that can project out of the flower and  

project the anther (contains the sperm pollen)

o Female parts are collectively referred to as the  

carpel

 Stigma: the top part that has a sticky  

substance that the pollen can stick to

 The sperm travels down the style, into  

the ovary, and then into the ovule, where

individual eggs are

 Different types of fruit

 Simple fruit

o From a flower that has one ovary, such as the  

pea fruit

 Aggregate fruit

o From one flower with multiple ovaries, such as  

a raspberry

 Multiple fruit

o From many flowers, such as a pinapple

 Photosynthesis

o To make food:

 Photosynthetic eukaryotes have specialized organelles  called chloroplasts

 Sunlight is needed

 Water and minerals come from roots

 CO2 is taken in through pores

 Pigments come from the chloroplasts

o Step 1: light reactions

 Photosystem

 Light energy is converted to electrical energy and  

then to chemical energy

o Photons, packets of energy, are measured in  

wavelengths and are part of the  

electromagnetic spectrum

 Antennae complex reaction center

 Arrangement of pigments

o Any substance that can absorb light energy

o Color is determined by wavelength it reflects

o Light is converted into heat, light, or chemical  

energy

o The most important one is chlorophyll a

 Electron Transport Chain

 Lost electron is replaced

o H2O splits to produce O2 and H+

 ATP and NADPH are produced

 Electron from chlorophyll a is energized

 Energy carriers

 ATP has three groups of phosphates

o Tridi

 They receive, store, and deliver energy

 Electron carriers are NADH, FADH2, NADPH

 The first two pick up electrons and hydrogen atoms  

that have been released and NADPH deliver energy  

by providing electrons and hydrogen atoms

o Dark reactions

 Transforms chemical energy into food via the Calvin Cycle  4 steps

o Carbon fixation

 Remove carbon from CO2 by Rubisco  

(enzyme) and it is fixated to RuBP

o Energize sugar to incorporate it into existing  

substance

o Sugar exits

o Recycle RuBP

 What type of relationship doesn’t exist within your microbiome? o Competitive  

 Fungi

o Decompose and release nutrients that would otherwise not be  available

 Can be single celled, like yeast, or multicellular

 These are chemoheterotrophs

o Metabolism

 Facultative: switch from oxygen-producing metabolism  Anaerobic cellular respiration = fermentation

 Fungi can live by either aerobic or anerobic cellular  

respiroation

 Why do leaves turn colors in the fall? 

o Pigments are broken down which changes the light reflected  Animals

o Cells do not have a cell wall, which plant cells do have  Allows animals to have flexibility

o Invertebrates and vertebrates

o Mollusks

o Arthropods

o We consumed 200lbs/meat/person in 2014 

o What do we consume?

 Fish

 Both freshwater (trout) and saltwater (salmon)

 High in good fats

 Consider farm raised fish and overfishing

 Meat (land animals)

 High protein, bad fat

 Nutrition

o What element makes up most of your body weight?  

 Oxygen 

o What molecules are most prevalent in the human body? Oxygen,  carbon, hydrogen, nitrogen 

o Chemical building blocks of life

 Fats

 Phospholipids

 Triglycerides (aka cellulite, what we think of as “fat”)

o Three fatty acid molecules bonded to a glycerol

molecule

o Built from saturated fatty acids

o Fat tissue can be brown (converts chemical  

energy  heat) or white (storage)

o Lipolysis: fat cells break down triglycerides to  

release individual fats to produce ATP

 Cholesterol

o Both cholesterol and fats are hydrophobic

o Sterols

 Fats that have the same structure with  

different ingredients attached to them

 Contain four hydrocarbon rings fused  

together

o Hormones

o Anabolic steroid (resembles testosterone o Examples

 Eggs, shellfish

 Trans fat is the worst fat found in food, because it  affects blood cholesterol and consistently increases  bad cholesterol

 Saturated fats/fatty acids

o All carbon atoms in the hydrocarbon chain are  linked with a single covalent bond

o Solid at room temp

o You can stack them

o Examples

 Tropical fruits

 Animal products (meat)

 Unsaturated fats/fatty acid

o The beneficial form of fats that mainly come  from vegetables and fish 

o One or more atoms have a double bond, so  there is a kink preventing them from being able to lay flat

 Natural peanut butter with the oil on top  is due to the kinks, whereas  

hydrogenation of peanut butter makes it  

consistently smooth

o Examples

 Veggies

 fish

 Functions:

o Make up membranes of cells

o Signals within cells

 Can act as hormones

o Provide body heat

o Provide insulation and cushioning

 Problems with food labels:

o If a product has less than 0.5g trans  

fat/serving, it is allowed to be listed as “0”

o So a reduced serving size allows companies to  put 0g trans fat

o Look at ingredients to determine if there is  transfat

 Sodium

 It is an ion with a charge, usually found as an  additive

 Carbohydrates

 Monomers, individual units of a macromolecule  Polymers, chains of monomers bonded together o Include carbohydrates, proteins, and nucleic  acids

o How to build:

 Dehydration synthesis:

 Remove water molecules so  

monomers can bond

o How to break:

 Hydrolysis

 Add water, breaking apart  

polymers

 Cellulose is the most common carbohydrate on earth  Food label: Listed as sugars and fibers

o 15g sugars, 5g fiber, but total carbs = 25 g

 5g that are missing = starch  glucose

o Not all carbs are sugars but all sugars are carbs  Monosaccharides

 Glucose and fructose

 Love water

 Disaccharides

 Sucrose formed through  

dehydration synthesis

 Glucose and fructose are bonded

 Polysaccharides

 On food label is listed as fiber

 Monomers are linked together in  

different ways

o Glycogen is a storage molecule

o Chitin is produced in fungi and invertebrates  for structure

 Proteins

 Built from amino acids— there are 20 different ones  Make you who you are

 Storage

o Energy (contribute 4cal/g)

 Structure

o Cytoskeleton = scaffolding of cells

o Defines function

o The sequence of amino acids is their structure

 This is 3-D

o The folding determines their function

 Transport:

o Blood cholesterol

 High density lipoproteins (HDL)

 Bring fats home to the liver while  

LDL does its job

 Low density lipoproteins (LDL)

 Brings fats to cells

 Contain a lot of cholesterol,  

phospholipids, and a lot of fat

 Saturated fats keep both of these high,  

while unsaturated fats keep HDL high  

and LDL low

o Channel proteins: tunnels in cells that allow  specific substances in and out

o Carrier proteins: move to bring a substance in  or out of cell

 Catalysis

o Speed up reactions, by way of enzymes

 Defense

o Antibodies are produced to defend against  specific invaders

 Communication

o Insulin and glucagon regulate blood sugar

o Leptin and grelin regulate appetite

 Gene regulation

o Transcription factors turn the gene on or off o Can be influenced by diet

 Denaturation

o Destruction of the 3D shape by heating them  up, changing the pH or making it very acidic,  

increasing the salt concentration

 Nucleic acids

 Nucleotides are the building blocks of hereditary  material

 DNA is turned on and  RNA produces proteins  Vitamins

 Take vitamins after a meal so that you can break  down the substance 

 Needed in tiny amounts

 Organic molecules

o Fat soluble

 Can get locked up in fat stores

o Water soluble

 Can consume at high rates and is okay in

short term

 Most common vitamin deficiency in US: B6 

 Vitamin D is the only one that human can synthesize  but people still don’t get enough

 Minerals

 Highest mineral deficiency is iron 

 We need trace minerals

 The ones we need come in the form of ions

 Iodine is critical for metabolism

o From salt and seafood

 Fluoride for teeth

 Cobalt

 Digestion

o GMOs

 We don’t have to label GMOs

 Drug production

 Food production

 Curing genetic disease

 Sugar Beets have the highest percentage of genetically  engineered crops in the US 

 Roundup prevents plants from making an essential amino  acid

 A gene inserted into a plant makes it produce its own insecticide, and doesn’t really effect farmers as much

because they produce more crop

o We have to break food down in order to digest it and utilize the  nutrients

o Ingestion, digestion, absorption, elimination

 Ingestion

 Animals are consumers, so we eat other organisms in some way or another

 Digestion

 We break down the consumed organism

 Absorption

 Outside the cell we consume monosacharides,  

disaccharides, etc.

o As we consume proteins we must degrade  

them

 We absorb the vitamins and minerals

 Enzymatic reactions

o Reactant undergoes some sort of change that makes it become a product (and produces ATP as well)

 This process or change requires activation energy o Enzymes are biological catalysts

 Without them, reaction time would be way too slow—  enzymes lower the activation energy needed and therefore increase the speed of the reaction

 This could be one million times the actual rate of the  reaction

o Structure of enzymes:

 3D shape determines the function

 There is an active site within the enzyme

 A substrate binds to this site

o Substrate ~ reactant in a typical chemical  

reaction

o If you require a substrate, this means that an  

enzyme is involved

o Anabolic Reaction

 Enzyme has an induced fit and it can store energy for later  use

o Catabolic Reaction

 There is a big substrate that docks into a different type of  enzyme, which causes it to change shape through different processes

 Involves breaking down energy for current use

o Metabolism:

 A  (enzyme 1)  B  (enzyme 2)  C  (enzyme 3)  D  If enzyme 2 isn’t formed properly, what is the result? o Increase in Product B 

 A  (enzyme 1)  B  (enzyme 2)  C  (enzyme 3)  D  What is enzyme 3’s substrate? 

o C 

 A  (enzyme 1)  B  (enzyme 2)  C  (enzyme 3)  D  What enzyme is directly responsible for the  

production of D? 

o Enzyme 3 

 CO2 + H2O  glucose

 Glucose  glycogen

o Endergonic reaction series (storing energy)

 Anabolic: building up something big,  

happens during photosynthesis

 Makes monomers into polymers  

during dehydration synthesis

 Break down glycogen by adding water through hydrolysis  This makes it a catabolic reaction  cellular  

respiration

o AKA exergonic reaction

 Metabolic pathways in the body involve several reactions  and there are several intermediates, each one of which has its own enzyme

 Food Processing

o Enhancing colors

 For example, farm-raised salmon has food coloring added  to it

 It naturally is not pink because it is not eating the  

natural things that make it turn pink

o Augment the flavors

 Hydrogenated oils are trans fats

 Hydrolyzed food products are added to foods to make them tasty

 Sweet, sour, bitter, salty, umami

o ***Smell is essential for taste!***

o Extend shelf life by using preservatives

 GRAS substances: “generally recognized as safe  

compounds”

 Old techniques include smoking, salting, drying, freezing,  sugaring

o Improve texture by adding trans fats

o Reduce calories by removing trans fat

o High Fructose Corn Syrup

 Naturally occurring carbohydrates are digested to create  fructose

 You need less, so it ends up being cheaper

 Food Labels

o Organic vs. natural

 You can have an organic product that isn’t natural

 Organic:

 Grown and processed using organic farming methods that recycle resources and promote biodiversity

 Crops grown without synthetic pesticides,  

bioengineered genes, petroleum based fertilizers,  

and sewage sludge based fertilizers

 Natural:

 Can’t be highly processed

 More regulated in poultry and meat industry

 Adding heat to a system

o Denatures proteins

o The vitamins can also degrade

o Burning (ie. Grilling) causes carcinogens to form

 Which structure does not digest to absorb nutrients?

o Esophagus 

 Mouth:

o Chemical: salivary amylase, mucus

o Physical: smell/taste, tongue, teeth, hard/soft palate o Digestion: starch

o Absorption: glucose

 Esophagus:

o Chemical: no enzymes, mucus

o Physical: smooth muscle peristalsis

 Sphincters (upper and lower)

 Epiglottis: shuts off respiratory system from throat to  prevent food from going into respiratory system

o Digestion: none

o Absorption: none

 Stomach:

o Chemical: HCL (acid), denatures protein

 Pepsin (enzyme in stomach) can chew it up, mucus  

(protects stomach lining)

o Physical: rugae— folds that churn the food, allowing for more  efficient digestion, phonic sphincter

o Digestion: breaking down proteins

o Absorption: amino acids and alcohol

 You only get about 10% of nutrients here

 Pancreas:

o Chemical: enzymes lipases, carbohydrates, proteases  These all get sent to the small intestine

o Physical: n/a

o Digestion: n/a

o Absorption: about 80%

 Small Intestine:

o Which of the following reasons explains why starch molecules  must be broken down before they can be absorbed by the small  intestine? 

 They are too large to pass through the plasma membrane  of the intestinal cells 

o All ingredients from pancreas as well as mucus

o Chemical: n/a

o Physical: n/a

o Digestion: fats, proteins, carbs

o Absorption: amino acids, fatty acids, cholesterol,  

monosaccharides, minerals, vitamins

 Liver/Gall Bladder:

o Makes bile

o Goes around food and pulls apart fats, allows lipases to “get in  there and chew them out”

o Chemical: n/a

o Physical: n/a

o Digestion: n/a

o Absorption: n/a

 Large Intestine:

o Chemical: mucus

o Physical: villi, microvilli

o Digestion: not much

o Absorption: water, vitamins, minerals (due to mutualistic bacteria that live there)

 Fiber-rich food: will absorb more sacccharides

 An organism who can create organic substances from carbon dioxide  by chemical energy is considered: 

o A chemoautotroph