AP Bio Unit 3, AP Bio Unit 1, AP Bio unit 2

UNIT 3

Cellular Energetics

What are enzymes?

1. Proteins that catalyze (speed up) reactions.

2. The enzyme is not used up in the reaction, they can be used again and again.

The names of enzymes usually end in "ase"

ex: lactase, amylase, sucrase, ATP synthase

How do an enzymes work?

1. Enzymes have a sort of mouth called the active site where a substrate goes.

2. The substrate is something that is reacting. The substrate IS used up in the reaction.

3. Each enzyme is designed for a specific substrate, the substrate fits into the specific enzymes active site.

sucrase example on back of card

What is induced fit?

The enzyme gives the substrate a hug. I.e. the enzyme changes its shape a little so the substrate fits

what is competitive inhibition?

if something has a similar shape to the substrate, it might fit into the active site and block substrates from getting in, making the enzyme not function anymore.

What is noncompetitive inhibition?

A noncompetitive inhibitor will bind to the enzyme's allosteric site and the active site will change shape, so the enzyme will not function anymore

What is a cofactor/coenzyme?

Something that goes into the active site to help the substrate fit

How do enzymes catalyze reactions?

Enzymes lower activation energy

remember that phrase for the AP

What factors can affect enzyme function?

1. Temperature: to high or to low of a temperature can denature the enzyme

2. PH: To high or to low PH can also denature the enzyme.

recall that denatured proteins go back to primary folding structure.

3. Amount of substrate: if there is a lot of substrate, there won't be enough enzymes to break all of it down.

ex: lactose intolerant people often still have some lactase, just not enough to break down all the lactose.

4. inhibitors

What happens when a cell is using more energy than it makes?

it dies.

what is a metabolic pathway?

A series of reactions that form a final product. The product of one reaction goes on to be a reactant in another reaction and so on until the final product is made.

Equation for photosynthesis

6 water and 6 carbon dioxide make a glucose and 6 dioxygens

6CO2 + 6H2O ------> C6H12O6 + 6O2

the 6O2s are "breathed" out

What is the goal of photosynthesis?

capture energy from the sun to make sugars (glucose)

Where did photosynthesis first evolve?

Cyanobacteria

First phase of photosynthesis:

Light dependent reactions (electron transport chain)

First step of electron transport chain:

1. Photosystem 2 is energized by light, which splits an H2O

2. water splitting provides an electron (e-) and pumps an H+ ion through the transport protein

Second step of electron transport chain:

The highly energized e- goes to the next transport protein, supplying the energy to pump another H+ ion through

Third step of electron transport chain:

1. The electron moves to Photosystem 1 and is energized by light again

2. Another H+ is pumped through a transport protein.

Fourth step of electron transport chain:

The electron can't just float around after this wreaking havoc, so NADP+ accepts the e-, turning it into NADPH

Fifth and final step of electron transport chain:

1. Because there is now a bunch of H+s at the top, they want to flow down via diffusion because of the concentration gradient.

2. The 3 H+s flow through the enzyme ATP synthase, which adds a phosphate to ADP (adenosine diphosphate) to make ATP (adenosine triphosphate).

ATP synthase is both an enzyme and a transport protein. Remember ions need to diffuse through proteins, and things that end in "ase" are enzymes.

Second phase of photosynthesis:

Light independent reactions (Calvin cycle)

What happens in the Calvin cycle?

1. 3 CO2 molecules are taken in

2. 6 ATP and 6 NADPH are spent (came from e- transport chain. ATP turns to ADP and NADPH turns to NADP+)

3. the oxygen and 3 carbons from 3 CO2 and the 6 Hydrogens from 6NADPH come together to make half of a glucose

4. The Calvin cycle goes around again providing more oxygen, 3 more carbons and 6 more hydrogens to make the other half of glucose (C6 H12 O6)

Glucose is the final product

Chemical equation for cellular respiration

glucose and 6 dioxygens make 6 water and 6 carbon dioxide and a bunch of ATP

C6H12O6 + 6O2 --> 6CO2 + 6H2O + ATP

Opposite of photosynthesis equation

Step 1 of cellular respiration (CR):

Glycolysis (occurs in cytoplasm):

1. 2 ATP is used to split 1 glucose (C6H12O6) into 2 C-C-C-P

(the phosphorus comes from the ATP)

2. To get rid of the phosphorus, 2 ATP is made for each, turning them into C-C-C (Pyruvate).

3. NAD+ accepts the electrons created from this turning it into NADH

Produced in this step:

2 ATP spent, 4 ATP made

2 NADH made

2 Pyruvate made

Net produced: 2 ATP, 2 NADH

Step 2 of CR:

Pyruvate oxidation (occurs in mitochondria):

Two CO2 molecules are made from each of the pyruvate, turning them from C-C-C into C-C (acetyl-coA). NAD+ accepts electrons again making more NADH.

Produced this step:

2 CO2 made (gets breathed out)

2 NADH made

Net produced: 2 ATP, 4 NADH

step 3 of CR:

Krebs cycle/citric acid cycle (in mitochondria):

1. the acetyl-coA (C-C) go through the Krebs cycle. Details aren't important, but know what this makes

2. makes 3 NADH, 1 ATP, FADH2, and 2CO2 (breathed out)

3. this happens twice to use both the acetyl-coA

Produced this step:

2 ATP made

6 NADH made

2 FADH2 made

Net produced: 4 ATP, 10 NADH, 2 FADH2

Step 4 of CR

Electron transport chain/oxidative phosphorylation (in mitochondria):

1. NADH gets made back into NAD+, supplying 2 electrons (the whole purpose of them was to carry the e-s to this step.) This pumps an H+ ion through a transport protein.

2. FADH2 splits into FAD, supplying 2 more e-s, pumping more H+ through

3. electrons pump more H+ through another protein.

4. Because e-s can't just float around, the e-s combine with 1/2 O2 and 2H to make water.

5. Because of the concentration gradient, all the H+s (there is a lot, varies by organism) flow through ATP synthase to make ADP into ATP

TOTAL CREATED:

Electron transport chain:

About 30 ATP from the NADH electrons

About 4 ATP from the FADH2 electrons

First three steps:

4 ATP

TOTAL: about 38 ATP! (varies per organism, can be as low as 30)

This all was made from one glucose

Why is it better for different chloroplasts in different cells to be different colors/different shades of green?

They will be able to absorb different wavelengths of light, which means more energy, the plants will be more fit.

UNIT 1

Chemistry of Life

What are ionic bonds?

A bond that takes/gives electrons (e-)s

What are covalent bonds?

shares electrons

Why is water polar?

unequal electron sharing.

Oxygen is more electronegative

What is the main ability that water's polarity gives it?

Hydrogen bonding

What are some important properties water has due to hydrogen bonding?

1. Cohesion: water likes water

2. Adhesion: water likes other polar things, ex. glass.

3. Surface tension: surface is hard to break, allows bugs/some lizards to walk on water

4. High specific heat: takes of energy to heat up

5. expands when frozen: doesn't sink, important for marine life

Living systems depend on these properties.

ex: both cohesion and adhesion are needed for water to travel up the stem of a plant.

What type of molecules make up most of life?

biological macromolecules (bio molecules)

What is the primary element of bio molecules? Why is it special?

1. Carbon!

2. Because it had 4 valence e-s, it can bond in many different ways, making it versatile for many structures/functions.

3. used in storage compounds

4. used in all bio molecules

5. 4th most abundant element

what are the four types of biological macromolecules?

1. Carbohydrates (sugars)- carbon, hydrogen, oxygen (cho)

2. Lipids (fats)- carbon, hydrogen, oxygen (cho)

3. Proteins (amino acids)- carbon, hydrogen, oxygen, nitrogen (chon)

4. Nucleic acids (DNA/RNA)- carbon, hydrogen, oxygen, nitrogen, phosphorus (chonp)

Single unit of a bio molecule

monomer

multiple monomers make a...

polymer

Common way to combine two monomers:

Dehydration synthesis

Common way to split a polymer:

Hydrolysis (digestion)

Monomer of a carbohydrate:

monosaccharide.

ex: glucose (C6 H12 O6), galactose, fructose

polymer = polysaccharide

Structure/storage of carbohydrates in plants:

1. Structure: cellulose

2. storage: starch

Structure/storage of carbohydrates in animals:

1. Structure: chitin

2. storage: glycogen

Types of lipids:

1. Saturated fatty acids: no double bonds, solid at room temp (ex: butter)

2. Unsaturated fatty acids: has double bonds, liquid at room temp

3. steroids (ex: cholesterol, testosterone, estrogen)

4. triglycerides; ester bonds, looks like:

\/\/\/\

\/\/\/\

\/\/\/\

5. Phospholipids

Amino acid structure (components of a monomer):

1. Amine group

2. Carboxyl

3. R-group: varies, determines properties

amino acids are the building blocks of a protein

levels of protein folding:

1. primary: sequence of amino acids

2. secondary: hydrogen bonds between amino and carboxyl groups (beta pleated sheet \/\/\ or alpha helix ()()()

3. tertiary: R-groups interact to form a globular structure

4. quaternary: more than one protein. Globs.

what is it called when a protein is ruined? What does this do?

1. the protein denatures

2. When a protein denatures, it loses it's structure, and therefore it's function because structure=function

3. does back to primary structure

types of nucleic acids:

1. Deoxyribonucleic acid: DNA, double stranded

2. Ribonucleic acid: RNA, single stranded

What are the nucleic acid bases? Which one do they pair with

DNA:

Adenine -> thymine (two bonds)

Guanine -> cytosine (three bonds)

RNA:

Adenine -> Uracil (two bonds)

Guanine -> Cytosine (three bonds)

to remember that A goes with T and C goes with G:

Apples in the tree, car in the garage

For RNA:

Apples are under

components of nucleotides (monomers of nucleic acid):

1. Phosphate

2. 5 carbon sugar

3. nitrogenous base

Describe DNA structure:

1. Double helix

2. Strands have a 5 prime and 3 prime end

3. strands run antiparallel

4. strands are connected with hydrogen bonds

UNIT 2

Cell Structure and Function

Organelles to remember

1. plasma membrane

2. cell wall

3. nucleus

4. nuclear envelope

5. chromatin

6. ribosomes

7. smooth endoplasmic reticulum (ER)

8. rough endoplasmic reticulum

9. golgi apparatus

10. lysosomes

11. vacuoles

12. mitochondria

13. chloroplasts

14. peroxisomes

15. cytoskeleton

16. microtubules

17. centrosomes & centrioles

18. Cilia & flagella

19. nucleolus

what does the plasma membrane do?

controls what goes in/out of the cell

Cell wall (plants)

maintains structure. usually made of cellulose

nucleus

contains DNA

nuclear envelope

surrounds DNA

nucleolus

makes DNA

Chromatin

the actual thread of DNA

ribosomes

make protein

Smooth ER

makes lipids

Rough ER

folds proteins

golgi apparatus

packages and transports materials (typically proteins)

lysosomes

splits things apart/breaks things down

vacuoles

storage (ex: stores water in plants)

mitochondria

makes ATP (energy currency) by breaking down glucose

chloroplasts

makes sugar, they're only in plants

peroxisomes

detoxify alcahol

cytoskeleton

internal structure

microtubules

smaller component of cytoskeleton

centrosomes

helps with cell division (mitosis/meiosis)

cilia/flagella

movement of cell

What is the process in which energy is made in the mitochondria?

cellular respiration

What are the steps of cellular respiration?

1. Glycolysis: glucose is broken down in the cytoplasm

2. Krebs cycle: more detail later

3. electron transport chain: more later

4.Formula: C6H12O6 (glucose) + 6O2 --> 6CO2 +6H2O

Energy = ATP

What is the process in which chloroplasts capture light to make sugars?

photosynthesis

What are the two phases of photosynthesis?

1. light dependent reactions. (electron transport chain)

2. Light independent reactions (Calvin cycle)

3. Formula: 6CO2 + 6H2O --> C6H12O6 + 6O2 (opposite of cellular respiration)

The endosymbiotic theory states...

Mitochondria and chloroplasts were once free living bacteria. they were engulfed by another cell and evolved to stay that way.

What organelles are involved in making proteins?

1. Nucleus: DNA --> RNA

2. Ribosomes: RNA --> protein

3. Rough ER: Folds proteins (structure/function)

4. golgi apparatus: packages proteins

What are the two types of cells?

1. Prokaryotes: have no organelles except for ribosomes and membrane. smaller

2. Eukaryotes: have organelles

To remember which is which:

Pro rhymes with no (no organelles)

Eu rhymes with do (do have organelles)

How does size relate to the efficiency of a cell?

1. smaller cells have a higher surface area to volume ratio (look up examples if this doesn't make sense)

2. a higher SA:V ratio is better because it is less distance traveled to move things in and out of a cell

3. cells will fold, project, or elongate to increase their SA:V ratio (Ex: o --> 0)

Three things that are usually in the plasma membrane

1. Phospholipids: make up the majority of the cell membrane. A hydrophilic head with two hydrophobic tails.

2. Proteins: channel proteins and receptor proteins exist on/in the plasma membrane. Channel proteins allow big/polar things through that cannot pass through the membrane. Receptor proteins receive signals.

3. Cholesterol (mainly animal cells): A lipid steroid that regulates membrane fluidity, keeps from freezing at low temps, and keeps from melting at high temps.

What is selective permeability?

The cell lets some stuff in and keeps other stuff out.

What types of molecules can pass through the phospholipid bilayer of the plasma membrane?

1. Small non-polar molecules (O2, CO2, N2)

2. Small polar uncharged molecules: water

(water cannot efficiently go through the membrane quickly)

If a molecule cannot pass through the bilayer, what is needed?

Channel proteins or carrier proteins

What types of molecules use proteins pass the membrane

1. Polar charged molecules

2. Big molecules

Ex: glucose is big and polar

Although water (polar uncharged) can pass through the bilayer, it can go through the membrane more efficiently through proteins called aquaporins.

What is passive transport?

1. Uses no energy

2. Things are moved from an area of high concentration to an area of low concentration (diffusion)

3. usually membrane facilitated (passes through bilayer)

What is osmosis?

1. Water with a solute (something dissolved into the water, like salt) will move across the membrane if the other side of the membrane has more solute.

2. This will occur until the water on both sides of the membrane has the same concentration of solute.

3. This is a form of passive transport

The solute does not pass through the membrane, the water does

A good way to think about it:

If there is more solute in the water, the water molecules have more stuff blocking them from moving through the membrane. If there is less solute in the water, more water molecules will pass through because there is less stuff blocking them. This balances out so the sides have the same solute per water.

What is active transport?

1. uses energy (ATP)

2. Stuff goes from an area of low concentration to high concentration

3. Proteins are used usually

what is endocytosis?

A cell engulfs something big, active transport.

What is exocytosis

A cell expels a something big, active transport.

Facilitated diffusion vs. simple diffusion

1. Facilitated diffusion uses a transport protein

2. simple diffusion goes right through the membrane

What is osmoregulation and tonicity?

1. Osmoregulation: Cells use osmosis (remember 5 cards ago?) to regulate how much water is in them

2. Tonicity: determines if water will exit or enter the cell based on how much solute is in/around the cell.

Three types of tonicity:

1. Hypotonic: more solute is in the cell, so water will enter the cell and the cell will grow. (you can remember that hypo rhymes with grow)

2. Isotonic: the solute in the cell is equal to the solute outside the cell. Size stays the same

3. Hypertonic: more solute is outside the cell, so water will exit the cell and the cell will shrivel up.

This is why saline solution is used in I.V.s; if water was used, the solute around you cells would decrease in concentration and your cells would gain water and possible burst. This is also why you shouldn't drink soy sauce, your brain cells will shrivel up because you are putting more solute around them.