BIO TEST UNIT 1 (not finished)

Reductionism

Reduces complex systems into simpler components that are more manageable.

Ex] Studying molecular structure of DNA that were extracted from cells. (James Watson and Francis Crick)

Emergent Properties

Unique things that a complex system develops when indivudial parts interact.

Ex] photosynthesis, bicycle.

Describe how structure is related to function, with examples

structure determines function. The shape, form, and composition dictate what job it can preform. Natural selection acts on these structure over generations, favoring variations that work best and helping the organism live.

Ex]Humming bird to flower→

• The wings allows it to rotate

• extend their beaks

• tubular flower shapes

• mutual benefit

Prokaryotic Cells

• Nucleoid

• Plasma Membrane

• cytoplasm

• ribosomes

• cell wall

• single celled

• bacteria and archaea

• smaller

Eukaryotic cell

• Nucleus

• Organelles

• bigger

• cholorplast

DNA is…

• the genetic material and directs cell process

• Library of genetic → genomes

• mRNA→ transcription→ amino acids→ translation → protein → protein folding

• Double helix

• A C T G

• Nucleus with DNA + Sperm cell → egg cell→ fertilization→ egg with both parents DNA→ Embryo cells with copies of DNA→ offspring

  

Energy and matter…..

• are transferred and transformed in the ecosystem

  Chemical (CYCLE)	Energy (FLOW)
  Plants take up chemical elements from the soil and air (molecules and ions)	Light energy comes from the sun
  Matter in plants is passed to organisms that eat the plants.	Plants convert sunlight to chemical energy
  Decomposers like fungi and bacteria break down until it return to the soil.	Organisms use chemical energy to do work
  	Heat is lost from the ecosystem

Organisms interact with… (list examples)

one another

• Mutualism (+/+)

• Commensalism (+/o)

• Parasitism (+/-)

• Predation (+/-)

• Herbivory (+/-)

• Competition (-/-)

• Amensalism (-/o)

• Neutralism (o/o)

Evolution accounts for….

uList an example of the unity of life:

uWhat, specifically, accounts for the unity of life?

uList an example of the diversity of life:

uWhat mechanism of evolution accounts for the diversity of life?

for the unity and diversity of life

UNITY OF LIFE:

• Example: All organism, use DNA and RNA to store genetic information and the same 20 amino acids to build proteins.

• Cause: Common Ancestry

DIVERSITY OF LIFE:

• Example: Million of distinct species exist today, such as cacti that survive in dry deserts and whales swimming in cold oceans.

• Cause: Natural selection acts on random genetic changes over long period of time, helping organisms adapt to their environments.

  

Three Domains of life

Bacteria

• Single-celled and lack a nucleus (prokaryotic).

• Most diverse and widespread group of prokaryotes

• Examples: Escherichia coli, Streptococcus, and cyanobacteria

Archaea

• Prokaryotic cells

• Live in extreme environments on Earth

• Examples: Thermophiles, Halophiles, Methanogens

Eukarya

• Kingdom Plantae, Fungi, Animalia, Protists

• Can be single-celled or multi-celled.

• Examples: Humans, oak trees, yeast, and amoebas.

  

why is life classified into 3 domains?

• Because of deep genetic and structural differences.

• Different evolutionary paths

• Core Differences

  • Bacteria: Single-celled prokaryotes with unique cell walls made of peptidoglycan and ester-linked membrane lipids.

  • Archaea: Single-celled prokaryotes that lack peptidoglycan, featuring distinct branched hydrocarbon cell membranes that often let them survive extreme environments.

  • Eukarya: Organisms with complex cells that store DNA inside a distinct membrane-bound nucleus, including plants, animals, and fungi.

Why aren’t protists grouped together in their own kingdom of life?

Protists are not grouped into a single true kingdom because they do not share a single common ancestor.

How does water react with everything else?

Experiment	What you see	Concept
penny	Lots of drops stick toghther	cohesion/ surface tension
balloon	water stream bends	polarity
wax paper	water form droplets	cohesion + hydrophobic interactions
soap	Droplet change	soap disrupts water interactions
ethanol	Different than water	different molecular interactions

water is polar because?

uneven distribution of charge (O-/H+)

water molecules interact with eachother forming?

Hydrogen bonds BE ABLE TO DRAW

Why does the water stay on the penny?

• the water attracts to each other due to hydrogen bonding. (cohesion and surface tension)

• CHAIN: polar→ hydrogen bonds→ attraction→ cohesion→ surface tension → dome on penny

Why does the water bend against the balloon?

• the positive side of the water is attracted to the negativly charged balloon.

• Causes stream to bend towards the balloon.

• CHAIN: polar→ +/- → interactions→ reorient → water bends

• BE ABLE TO DRAW

How does the wax paper resist the water?

• water is strongly attracted to itself.

• wax paper doesn’t interact favorably with water because it’s hydrophobic

• so instead of spreading out it form droplets

• BE ABLE TO DRAW

How does soap interact with water?

Soap has two regions

• a hydrophillic head and a hydrophobic tail.

• the water molecules form tightly through hydrogen bonds to create surface tension.

• soap slips between and weaken grip.

• Lower tension → water spreads

H20 —- H20—- H20

H20—- SOAP —-H20

• Soap molecules feature a hydrophilic (water-loving) head and a hydrophobic (water-fearing) tail. The tails push to the surface, breaking water cohesion. This allows water to spread, wet surfaces, and trap oils.

Why does ethanol react so different compared to water?

• Ethanol has a non-polar carbon portion

• very different from water

• weaker overall cohesion and behave different on wax paper (spreads)

water map!

Cohesion? Surface tension?

• Cohesion is the binding force between identical molecules caused by intermolecular attractions like hydrogen bonds.

• Surface tension is the result of these inward cohesive forces at a liquid's surface, creating a tight boundary layer that resists external force.

• EX] basilisk lizard running across water, water strider

What are 4 properties of water?

1. Cohesion and Adhesion

2. Resists temperture change

3. expands when it freezes

4. acts as solvent to life

All of these properties stem from the fact that the water molecule is polar.

Adhesion?

• clinging of one substance to another

• water molecules can clip to polar or charged surfaces

Transpiration?

Loss of water from a plant from the leaves as water vapor

LABELING COVALENT AND HYDROGEN BONDS

🙂

Be able to describe transpiration and the role adhesion and cohesion plays in the process of trees!

WATER must MOVE →

soil → roots → stem → leaves → outside air

1. WATER ENTERS THROUGHT THE SOIL: water is taken up from the soil through root hairs

2. WATER ENTERS THE XYLEM: the xylem contain xylem sap, which carries water through the plant

3. COHESION: Water molecules stick to one another through hydrogen bonds, which maintain the continous water movement.

4. ADHESION: stick to the walls of the xylem. This helps water remain attracted to the xylem walls as it moves upward.

5. TRAINPIRATION: This loss helps pull more. The water eventually reaches the leaf and is lost through the stoma. The stoma are pore on the leaf surface. The guard cells open and shrink.

Stomata and Guard cells?

• Stomata are microscopic pores on plant leaves and stems, and guard cells are the specialized cells that surround each pore.

• They control water loss and let carbon dioxide in for food making.

• Opening (Swelling): Water follows through osmosis. The cells swell up, bend apart, and open the pore.

• Closing (Shrinking): Water leaves the guard cells. The cells go limp and the pore squeezes shut.

• Light, water shortage, and carbon dioxide can trigger it.

What is a hormone?

A hormone is a chemical messenger made by glands in the body. It travels through the blood to target organs and cells to control and coordinate important functions like growth, metabolism, and mood.

Plant hormone?

• Plant hormone called abscisic acid (ABA) is produced in roots and leaves in response to water deficiency and signals guard cells to close.

• CHAIN: when a plant has a water defienciecy → ABA → guard cells close → stomata close → less water loss

Explain why water rises higher by capillary action in a tube of smaller diameter that one of a wider diameter.

• Capillary action: Movement of water through a narrow space due to cohesion and adhesion.

Smaller tube:

• Greater proportion of water molecules touching the walls.

• Adhesion: Water molecules stick to the walls of the glass tube and climb up.

• Cohesion and Surface Tension: Water molecules pull each other upward as a group.

Why does water resist temperature change? Explain.

—Specific heat: the amount of heat that must be absorbed or lost for 1 gram of a substance to change its temperature by 1 degree C

• average kinetic energy is not contributing to movement

Why does water have a higher specific heat capacity than most liquids?

• Because of hydrogen bonding

• Heat energy → breakers hydrogen bonds → some of the energy used in disrupting instead increase the temperature

• EX] when you touch a hot pan on the stove but the water is still just warm.

How does water’s high specific heat help the temperature of the environment?

• Because water resists temperature change, water helps to moderate climates.

• high specfic heat → temp stability → stable environment

High Heat of Vaporization?

• Heat of vaporization: the quantity of heat a liquid must absorb for 1 gram of it to be changed into  a gas.

• Because water must absorb a relatively large amount of heat before it evaporates, the evaporation of water from our bodies is an efficient way to cool off → Evaporative cooling

• ex] dog panting/human sweating

Explain water expanding when it freezes and its benefits.

• when water freezes, hydrogen bonds arrange the molecules into a more pen structure.

• expand→ becomes less dense → ice floats

• floating ice makes a layer while liquid water remain underneath.

• important for aquatic environment

• water expands → ice floats → liquid water remain → no freeze over

Solvent of life?

Water dissolves: (POLAR)

• polar molecules

• charged molecules

• ionic substances

—Ionic and polar substances that dissolve in water are said to hydrophilic or “water loving.”

—Non-polar substances that will not interact and dissolve in water are said to be hydrophobic or “water fearing.”

EX] fabrics can be water repellant by coating them with substances that cause water to form beads.

Name a water-soluble protein?

Human lysozyme

• helps biological molecules exist and function.

Which would have a higher boiling point- dimethyl ether (C₂H₆O) or ethanol (C₂H₆O) ?  Explain!

Ethanol

• can form hydrogen bonds

• stronger intermolecular forces

• more energy

• high boiling point

Surfactants reduce surface tension of a liquid. Which of the following would result if water was treated with surfactants?

A.Surfactant-treated water droplets will form a thin film instead of beading on a waxed surface.

B.Surfactant-treated water will form smaller droplets when dripping from a sink.

C.Water striders will sink.

D.All of the above will occur.

E.Only A and C will occur.

d.

Acid and Bases? Define

Acids and bases are chemical opposites. Acids give away hydrogen ions and taste sour, while bases accept hydrogen ions and taste bitter with a slippery feel.

Measured on a pH scale from 0 to 14,

• acids score below 7,

• bases score above 7,

• neutral level is 7.

  

Buffers?

—Substances that minimize changes in pH

h+ is protons

—Accept H+ when it is in excess

—Donate H+ when it is depleted

—Example: carbonic acid/bicarbonate ion

Carbonic Acid/bicarbonate ion Buffer System

—If pH increases (and hydrogen ions are depleted), carbonic acid acts a hydrogen donor:

  H₂CO₃ → HCO₃^-  + H⁺

—If pH decreases (and hydrogen ions are in excess), the bicarbonate ion acts as a hydrogen ion acceptor:

  H₂CO₃ ← HCO₃^-  + H⁺

• pH goes down → H+ increases → HCO3 accepts H+ → H2CO3 forms→ excess H+ decreases → pH moves towards normal

why do we care about buffers?

—Carbonic acid is a buffer that contributes to pH stability in human blood

• ocean acidification → 25% of carbon dioxide is absorbed by the ocean.

CHAIN:

Human made CO2 → CO2 absorbed by ocean → ocean chemistry change → fewer carbonate ions → coral have more difficulty building coral reefs → coral reefs affected

• coral reefs are important ecosystems!

Fill in the blanks:

Buffers…

________  H+ when pH becomes more acidic

________  H+ when pH becomes more basic

accept

donate

more maps

What are the 7 functional groups?

• hydroxyl O-H

• Carbonyl C=O

• carboxyl C=OOH

• amino NH2

• sulfhydryl SH

• phosphate PO-24

• methyl CO3

How many covalent bonds do carbons have?

4

Isomers?

•Have the same number of atoms of the same elements but different structures

•Different structures means different properties!

Ex]

a) structural isomers

b) cis isomer- the two x are on the same side

c) trans isomers- the two x are on opposite sides

d) enantiomers- mirror images

7 Functional groups?

*Be able to draw!

1. Hydroxyl -OH

2. Carbonyl C=O

3. Carboxyl COOH

4. Amino -NH₂

5. Sulfhydryl -SH

6. Phosphate -PO₄^2-

7. Methyl -CH3

What are the 4 major biological molecules?

´Carbohydrates

´Lipids

´Proteins

´Nucleic Acids

polymer

• a larger molecule made by joining many smaller units

• ex] In carbohydrates: glucose + glucose + glucose= polysaccharide

monomer

• a small molecular unit that can be joined to other monomers to make a larger molecule (building block)

• for carbohydrates, individual sugar molecules can act as building blocks.

• Ex] glucose → one sugar unit

dehydration synthesis

• Dehydration synthesis is a reaction that joins molecules toghther while removing water

• the molecules are being built toghther

• small molecules called monomers, join toghther to form larger molecules called polymers, by releasing a molecule of water.

• connect simple sugar molecules

hydrolysis?

• breaks a larger molecule apart by adding water

• during the process, water splits into a hydrogen ion and a hydroxyl group while attach a new seperated parts of the original molecule

• (water enters molecule breaks)

• breaks glucose bonds holding complex CH together

Monosaccharide?

• a carbohydrate made of 1 sugar unit

• major nutrients of cells used for energy and building blocks for other molecules

• Glucose breaks down during cellular respiration to make ATP

• Ex] glucose and fructose

Disaccharides?

• 2 sugars joined together

• Sucrose: plants transport carbohydrates from leaves to roots

• Lactose: (milk sugar)

• Sucrose: One glucose unit plus one fructose unit (table sugar).

• Lactose: One glucose unit plus one galactose unit (milk sugar).

• Energy Source: The body breaks them down into single sugars to power cells.

• Nutrient Supply: Milk sugar gives vital food and energy to baby mammals.

• Plant Transport: Plants move food energy through their stems using double sugars

Oligosaccharides?

• a few sugars

• Cell surface glycan

• Human milk oligosaccharides:

Cell-surface glycans

• a molecular identification label

• Cell-surface glycans are sugar groups attached to molecules on the surface of the cells

• CSG ARE IMPORTANT FOR: cell to cell recongniton and communication

• Sugar groups attached to molecules on the cell surface

HMOs?

• found in human breast milk

• evolved to feed beneficial bacteria

• humans don’t make an enzyme to recognize them

• supports beneficial microbes

What is a Polysaccharides?

Polysaccharides are complex carbohydrates made of long chains of simple sugar molecules linked together.

4 examples and functions of polysaccharides.

1. Starch: energy storage in plants

´Polymer of glucose

´How plants store sugar reserves

´Stored in plastids of plant cells

2, Glycogen: energy storage in animals

•Polymer of glucose

•How animals store sugar reserves

•In vertebrates, found mainly in liver cells and muscle cell

3. Cellulose: structural support in cell wall plants´Polymer of glucose

´Major structural component of the plant cell wall

´Part of “insoluble fiber” in human diet

´Cow solution?

´Termite solution?

4. Chitin: strutural support in fungi and arthropods

´Used to build exoskeletons of arthropods

´Fungi use to build their cell wall

Give two examples of symbiotic relationships involving carbohydrates, animals, and microbes

1. Humans + beneficial bacteria

• microbes use HMO as food source

2. Cows + microbes

• plants have lots of cellulose

• cellulose i hard for animals to digest

• microbes in the cows digestive system help break down plant material

• cows obtain nutrients

3. Termites + Microbes

• consume wood, which has cellulose

• animal gets help by obtained nutrients

ALL MUTUALISM

Molecular structure of a carbohydrate

To recognize a carbohydrate by its molecular structure, look for a carbon chain bound to hydrogen and oxygen in a 1:2:1 ratio,(C_n(H₂O)_n), containing multiple hydroxyl groups (-OH) and an internal carbonyl group (C=O) that forms either an open chain or a ring.

Name all 8 important proteins!

1. Enzyme

2. Storage proteins

3. hormonal proteins

4. contractile and motor proteins

5. defensive proteins

6. transport proteins

7. receptor protein

8. structural protein

Enzymatic protein?

function: selective acceleration of chemical reactions

example: digestive enzyme catalyze the hydrolysis of bonds in food molecules.

Storage proteins?

Function: Storage of amino acids

Examples: Casein, the protein oof milk, is a major source of amino acids for baby mammals. Plants have a storage protein in their seeds.

• Ovalbumin is the protein of egg while, used as an amino acid source for the developing embryo

Why are things for baby plants and animals so rich in storage proteins?

• Baby plants (seeds) and animals (eggs and milk) need a dense and easy-to-use source of food and building blocks to grow before they can find or make their own food. Storage proteins hold large amounts of nitrogen, carbon, and amino acids in a small space.

Hormonal Proteins?

Function: Coordination of an organism’s activities

Example: Insulin, a hormone secreted by the pancreas, causesother tissues to take up glucose thus regulating blood sugar concentration.

contractile and motor proteins

Function: Movement

Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles

What do the actin and myosin do?

• Actin and myosin are the two main protein filaments that work together to make muscles contract and move.

• Thick myosin filaments pull on thin actin filaments, sliding past each other to shorten the muscle cell in a process powered by energy from ATP

• Tears in muscles causes soreness after new exercise.

Defensive proteins?

Function: Protection against disease

Example: Antibodies inactivate and help destroy viruses and bacteria

what is an antigen?

An antigen is any substance, such as a protein or sugar, that makes your body start an immune response

transport proteins

Function: Transport of substances

Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes

Receptor Proteins?

Type of Cells

• Neurons: The cells shown in the diagrams are nerve cells (neurons).

• Presynaptic Cell: The neuron transmitting the signal.

• Postsynaptic Cell: The neuron receiving the signal.

Name of Signaling Molecules

• Neurotransmitters: The chemical signaling molecules released into the synaptic cleft.

Relation to "Mouse Party"

• Both the diagrams and the "Mouse Party" animation depict how neurons communicate at a synapse.

• The signaling molecules cross the gap and bind to specific receptor proteins on the postsynaptic membrane.

• The "Mouse Party" animation specifically shows how different drugs (like THC, ecstasy, or cocaine) alter this exact mechanism by blocking, mimicking, or overstimulating these receptor proteins and neurotransmitters (such as dopamine and serotonin).

Structural proteins?

Amino Acids?

• Monomers that build proteins

• 20 different amino acids make up all living things

• BE ABLE TO DRAW

The properties of R groups….

Properties of R groups give amino acids and their proteins different properties.

answer?

• The images demonstrate that changing a single amino acid's R-group can drastically alter a protein's structure and function, leading to physiological diseases like sickle cell anemia.

• Glutamic Acid: Possesses a hydrophilic (polar/charged) R-group. It interacts favorably with water on the exterior of normal hemoglobin molecules. This keeps red blood cells flexible and disc-shaped.

• Valine: Possesses a hydrophobic (nonpolar) R-group. When it replaces glutamic acid, it avoids water and seeks out other hydrophobic regions.

Be able to identify a peptide bond!

Primary Structure of a Polypeptide?

• The amino acid sequence

• DNA (genes) tell the cell what order to put the amino acids in

• The primary structure helps to dictate the secondary and tertiary structure

• Chemical nature of backbone and R-groups

Secondary Structure of a Polypeptide?

• Coils and folds

• Result of hydrogen bonding within the backbone of the chain

}C=O and H-N

• Alpha helix

• Beta pleated sheet

Tertiary Structure of a Polypeptide?

• Overall shape that results from interactions between R groups

}Hydrogen bonds

}Disulfide bridges

}Ionic bonds

}Hydrophobic interactions

Quaternary Structure of a Polypeptide?

• The interaction of two or more polypeptide chains

• Not all proteins have a 4^th level of structure

Why doe shape matter in a protein?

• Functions of proteins depend on recognition and binding to other molecules

• Antibodies bind to antigens on viruses/bacteria and mark them for destruction

• Morphine, heroin, and other opiates mimic shape of naturally occurring endorphins

Endorphins are neuropeptides.

• Fit into protein receptors and trigger a cellular, then physiological response

Why correct protein folding is important?

Correct protein folding is vital because a protein's specific three-dimensional shape determines its biological function. Without the proper shape, a protein cannot bind to its target molecules, catalyze chemical reactions, or support cellular life. Misfolded proteins lose their normal activity and can form harmful clumps linked to serious illnesses.

Central dogma?

The central dogma of molecular biology, proposed by Francis Crick in 1958, is the foundational concept explaining the unidirectional flow of genetic information within a biological system: from DNA to RNA to protein. It dictates that genetic instructions are stored, copied, and translated to build the functional molecules of life

Denaturation?

• The loss of the native shape of a protein

• Structure à function

} loss of shape means loss of function

• Caused by any environmental factor that disrupts the interactions

}Change in pH (why buffers are important)

}Change in salt concentration

}Increase in temperature (egg white)

Be able to example WHY these things cause denaturation using what you know about the bonds responsible for each level or protein interaction.

}Change in pH (why buffers are important)

}Change in salt concentration

}Increase in temperature (egg white)

🧪 Change in pH

• Bonds disrupted: Ionic bonds (salt bridges) and hydrogen bonds.

• Why it happens: Altering H+ ion concentration changes the charges on amino acid side chains (R-groups).

• The result: Repulsions occur or attractive ionic pairs are destroyed, breaking the tertiary structure.

🧂 Change in Salt Concentration

• Bonds disrupted: Ionic bonds and hydrogen bonds.

• Why it happens: Excess salt ions shield and compete with the charged R-groups of the protein.

• The result: Normal attractive interactions between amino acids are blocked by the salt ions, causing the protein to unfold.

🔥 Increase in Temperature

• Bonds disrupted: Hydrogen bonds and hydrophobic interactions.

• Why it happens: Added heat increases the kinetic energy and molecular vibrations of the protein atoms.

• The result: The rapid movement overcomes and breaks weak heat-sensitive bonds, though covalent peptide bonds remain intact.

Buffers minimize changes in pH by________ hydrogen ions when pH increases and _____________ hydrogen ions when pH decreases

1. release

2. accept

  What kind of molecules are antibodies?

The category of molecules that antibodies fall under would be proteins, specifically defensive proteins.

    Where are antibodies normally produced/ found?

Antibodies are normally produced and found in the vertebrate immune system. They are also especially found in blood and other bodily fluids.

How are antibodies used as tools in ELISA?

Antibiotics are used because they bind to an antigen. In ELISA, a primary antibody binds to a substance being tested for. A secondary antibody combined to the primary one and then carried an enzyme that produces the color change when a substrate is added.

What characteristics of antibodies make them good tools in this way?

Antibodies are useful because they are very specific. They bind to antigens and they recognize these antigens. They also make it possible to see whether a specific substance is present. The second antibody also has the enzyme that can make a color change.

What are the four levels of protein structure? How many levels do antibodies have?

The four levels of protein structure include primary, secondary, tertiary, and quaternary. Antibodies have all 4 levels.

What kind of molecule are enzymes?

Enzymes are proteins that act as biological catalysts.

   What was the enzyme at ached to in this lab?

The enzyme was attached to the secondary antibody

How are enzymes used as tools in ELISA?

The enzyme caused a chemical reaction with the substrate, making a color change. The color told during the lab whether the substance that we were testing was there or not.

   What substrate was used? Why?

The substrate was TMB (tetramethylbenzidine). It was used because the peroxidase reacts with TMB to produce a color change making it blue, allowing the ELISA result to be seen.