Bio Unit 2

Cytoskeleton

dynamic network of fibrous proteins throughout the cytoplasm (three major fiber types: microtubules, microfilaments/actin, intermediate filaments)

functions: provide cell with shape and rigidity and help attach cell to neighboring cells and surroundings

movement of vesicles, organelles, chromosomes during mitosis, cells, and muscles

Microtubules

Provide Support and Enable Movement

• Hollow tubes assembled of tubulin (protein)

• Dynamic - grow and shrink with the addition or removal of individual proteins

• Maintain cell shape (compression-resistant beams)

• Functions: movement of chromosomes during cell division, vesicles/organelles move on MT tracks like trains, cell: cilia, flagella

• Form the mitotic spindle that pull chromosomes apart during cell division

• Motor proteins use microtubules as tracks

Microfilaments

• solid rods, actin (protein) polymers, form linear and branched structures

• dynamic - grow and shrink with the addition or removal of individual proteins

• functions: maintain cell shape, movement (skeleton-muscle, cell-amoeboid movement)

• The motor protein myosin pulls actin filaments together to contract muscles

Connective Tissue

mostly structural, includes bones, cartilage and fat

Epithelial Tissue

forms barriers between different spaces

Muscle Tissue

movement

Nervous Tissue

communication and coordination

Gap Junction

pathway: protein pore connecting cytoplasm of neighbors

Desmosome

rivet: transmembrane proteins anchor cells together

Tight Junction

liquid seal: transmembrane proteins pull cell membranes together, often making a water-tight barrier between cells

Reactants/Substrates

the starting materials in a chemical reaction, it is the specific reactant that binds to the active site of an enzyme to be transformed in to a product

Products

the final molecule created after the chemical reaction is complete

Transition State

the highest-energy, most unstable point of a chemical reaction where old bonds are half-broken and new bonds are half-formed

Activation Energy

energy required to get from reactants to transition state

Enzymes

proteins which speed up chemical reactions, shaped to stabilize the structure of the transition state, enzyme not only recognized substrate but also induces the formation of transition state, by stabilizing transition state enzymes reduce activation energy to speed up reactions, enzymes only affect reaction kinetics (speed) not energy absorbed or released by reactions, can be reused over and over, its structure includes an active site, amino acids found at the active site might not be next to each other in primary structure of polypeptide

Active Site

where substrates/reactants bind and the reaction can be catalyzed

Metabolism

the sum total of chemical reactions in an organism

Anabolic

small to big

biosynthetic, join small to get larger molecules, consumes energy

Catabolic

big to small

degradative, break down large to smaller, releases energy

Competitive Modulator

• similar shape to substrate, compete for active site

• always inhibit enzyme because takes space of substrate

• overcome by increased substrate

Allosteric Modulator (noncompetitive)

noncompetitive

• bind away from active site (no competition), alter protein shape

• can increase or decrease enzyme activity depending on how it changes enzyme shape

• unaffected by substrate

Negative Feedback

products of a reaction or pathway inhibit an enzyme in the pathway, reducing production of the product

Positive Feedback

products of a reaction or pathway activate an enzyme in the pathway, increasing production of the product

ATP

adenosine triphosphate, the cell’s useable energy

ATP Hydrolysis

catabolic reaction where ATP reacts with water to break a phosphate group off, producing ADP and a phosphate group, releases energy

Phosphorylation

addition of a phosphate group

Autotroph

“self feeders”

• producers: generate food from non-living sources (ex: CO2)

• -photoautotroph: use light energy to synthesize organic compounds

Heterotroph

“other feeders”

• consumers: live on compounds produced by other organisms

Photosynthesis

captures light energy, stores in stable forms (light to carbohydrates)

6CO2 + 12H2O + Light → C6H12O6 + 6O2 + 6H2O

Cellular Respiration

converts energy from stable to versatile forms (carbohydrates to ATP)

Endosymbiosis

one organism living inside another, eukaryotic ancestors engulfed prokaryotes (evidence: double membrane, own DNA, ribosomes, and proteins, autonomous growth/replication, energy production)

Chloroplasts

sites of photosynthesis, three membrane bound compartments:

• inter-membrane space

• stroma

• thylakoid space

Light Reactions

“Photo”

-where: thylakoid

-what: convert solar energy to chemical energy

Calvin Cycle/Dark Reactions

“synthesis”

• where: stroma

• what: transform chemical energy into storable forms

Pigments

plants use pigments to absorb light, pigments absorb specific wavelengths of light and reflect others, pigments can send high energy electrons to NADPH, water is the source of new electrons for photosynthesis

Flow of Electrons during Light Reactions

water → PSII → ETC → PSI → NADPH

Electrons flow from water to NADPH

ATP Synthase

A spinning turbine that uses hydrogen ion flow to power ATP production (ADP + P → ATP)

Cyclic Electron Flow

• electrons cycle within PSI

• generates additional ATP, provides photo protection (light can’t harm molecule if it were to be absorbed else where)

What are the tenets of cell theory?

1. Cells are the simplest unit that can carry out all functions of life

2. All living things are composed of one or more cells (organismal functions have basis in cell functions)

3. New cells are created by previous cells (all family)

What characteristics do prokaryotic and eukaryotic cells/organisms have in common? How are they different?

Prokaryotic and Eukaryotic cells/organisms have a cell(plasma) membrane composed of a phospholipid bilayer, a selective barrier, and encloses cytoplasm, they also both have biological molecules such as carbohydrates, lipids, proteins, and nucleic acids (DNA and RNA)

Prokaryotic and Eukaryotic cells/organisms differ because:

prokaryotic is “before nucleus”, domains: archaea and eubacteria, smaller, DNA stored in cytoplasm, only single-celled organisms

eukaryotic is “true nucleus”, domain: eukarya, DNA stored in nucleus (surrounded by membrane), Organelles (“little organs”) surrounded by membranes with specialized jobs, larger, single and multi-called organisms

Why don’t larger organisms have larger cells?

Larger organisms don’t have larger cells, just more cells. This is because metabolism imposed theoretical limits on cell size, the need to exchange things with the environment limits the size of cells. This is due to the constraint of metabolism on the surface area to volume ratio of cells. Smaller cells have a higher surface area to volume ratio.

What is a vesicle?

small sack surrounded by membrane used to move things between organelles

Explain the functions of the following structures:

a) Mitochondria

b) Lysosome

c) Rough Endoplasmic Reticulum (RER) and Golgi Apparatus

d) Vesicles

a) site of most energy production in Cell Respiration, found in all eukaryotic cells but cells with higher energy demand have more

b) digest objects brought into the cell by endocytosis, found in most animal cells but more found in endocytic cells like immune cells

c) rough because covered in protein-making factories called ribosomes, site of protein synthesis for proteins that will be released to outside of cell

Golgi sorts, modifies, and ships proteins meant for release to outside of cell

d) small sack surrounded by membrane used to move things between organelles

What is the cytoskeleton made of and why is it described as “dynamic”?

made of fibrous proteins throughout the cytoplasm (three major fiber types: microtubules, microfilaments/actin, intermediate filaments), described as dynamic because the protein subunits are constantly assembling and disassembling

What effects can cytoskeletal fibers have on other structures when the fibers get longer or shorter? Provide two examples from class.

They can exert physical forces that directly manipulate other cellular structures. Examples would be movement of chromosomes during cell division and the movement of vesicles/organelles on MT tracks like trains.

What are the types of tissues found in animals and what are their functions?

-Connective Tissue: mostly structural, includes bones, cartilage, and fat

-Epithelial Tissue: forms barriers between different spaces

-Muscle Tissue: movement

-Nervous Tissue: communication and coordination

How do enzymes increase the speed of a chemical reaction?

by stabilizing transition state, enzymes reduce activation energy to speed up reactions

How does an enzyme’s environment dictate its evolution and activity?

• enzyme and substrate concentrations influence reaction rate

• temperature increases reaction rate to an optimum (can denature enzyme or alter active site if above optimum)

• enzymes function best at a specific pH (alters acidic/basic amino acids, prevents ionic bonds, binding and catalytic amino acids affected)

What is negative feedback?

products of a reaction or pathway inhibit an enzyme in the pathway, reducing production of the product

In the above pathway, which enzymes would have to be active, inactive, or would not matter to maximize the concentration of: F? B? C?

F: active: 1, 3, 6 inactive: 2, 4, 5, 7

B: active: 1 inactive: 2, 3, 4, 5, 6, 7

C: active: 2 inactive: 1, 3, 4, 5, 6, 7

Define biosynthetic, anabolic, and catabolic.

• biosynthetic: the multi-step, enzyme-catalyzed process where living cells convert simple nutrients into complex molecule

• anabolic: join small to get larger molecule, consumes energy

• catabolic: breaks down large to get smaller molecules, releases energy

What is the role of ATP in the cell?

the cell’s useable energy, ATP powers most cellular work such as chemical work, transport work, and mechanical work

How does phosphorylation provide energy for proteins to carry out work?

phosphorylation of a protein adds a phosphate group that temporally changes its structure, allowing it to do work

What are the relationships between photosynthesis and cell respiration? What happens to the atoms and energy that move through these processes?

They are reciprocal processes, the products of photosynthesis are the inputs for cellular respiration and vice versa. Photosynthesis: light → carbohydrates. Cellular Respiration: carbohydrates → ATP. Energy flows through ecosystems and is used up, chemical elements are recycled.

How did the mitochondria and chloroplast evolve? What is the evidence for this?

They evolved through endosymbiosis (one organism living inside another). Eukaryotic ancestors engulfed prokaryotes, with oxygen-using mitochondrion and photosynthetic chloroplast. Evidence is a double membrane, own DNA like ribosomes and proteins, autonomous growth/replication and energy production

What is the source of carbon for photosynthesis and where does it come from?

The source of carbon is carbon dioxide that comes from the surrounding atmosphere.

What role do each of the following play in photosynthesis:

1. Water

2. Pigments

3. NADPH

1. electrons are transferred from water to NADPH, water is the source of new electrons of Photosynthesis, releases oxygen as a byproduct into the atmosphere, the breaking of water realizes hydrogen ions that help build a proton gradient to drive ATP synthesis and reduce NADP+

2. plants use pigments to absorb light, pigment electrons absorb photon energy and fluoresce, pigments can send high energy electrons to NADPH, excite electrons to drive the ETC

3. high energy electron carrier, powers the Calvin cycle, helps build sugars (G3P)

What are the products of the Light Reactions?

O2 (oxygen), ATP, NADPH

What are the products of the Calvin Cycle?

G3P, ADP, P, NADP+

What molecules are needed for the Calvin Cycle? Where do they each come from?

• CO2 (carbon dioxide): from the atmosphere

• ATP: from the light reactions

• NADPH: from the light reactions

What molecules are needed for the light reactions? Where do they each come from?

• H2O: absorbed from the soil by plant roots

• light: sunlight

• ADP:

• P

• NADP+

What are pigments and what happens with them during photosynthesis?

Pigments light absorbing molecules, used by plants. In photosynthesis they help the plant absorb light, exciting the electrons and sending them to high energy electron carriers

What molecule is the source of new electrons for photosynthesis?

water

How is ATP generated in the light reactions?

the flow of electrons pulls hydrogen ions into the thylakoid space, creating a concentration gradient across the thylakoid membrane, ATP synthase uses this gradient to power ATP production

What is the useful product of the Calvin Cycle? Why is it important?

G3P, it goes towards making glucose

What is the source of energy for cell respiration?

glucose

Where will you find:

A. Glycolysis Enzymes?

B. Citric Acid Cycle Enzymes?

C. Electron Transport Chain Proteins?

D. High concentration of hydrogen ions?

What is the source of electrons in glycolysis? How are those electrons transferred to the Electron Transport Chain (ETC)?

What are the products of glycolysis?

What is the function of the ETC?

How does ATP Synthase work? What does it need and how does it relate to other processes in respiration?

What is the role of oxygen in respiration?

What processes in cell respiration won’t work under anaerobic conditions and why?

What processes in cell respiration will work under anaerobic conditions and why?

What is accomplished in fermentation reactions?

Transpiration

CAM Pathway

C₄ Pathway

Thylakoid

Stroma

Glycolysis

Pyruvic Acid/Pyruvate

Citric Acid Cycle

Substrate-level Phosphorylation

acetyl-CoA

Anaerobic Respiration

Lactic Acid Fermentation

Alcoholic Fermentation

3 Tenets of Cell Theory

Prokaryotic Cell

Eukaryotic Cell

Mitochondria

• site of most energy production in cell respiration

• found in all eukaryotic cells, but cells with higher energy demand have more

Vacuole

Lysosome

• digests objects brought into the cell by endocytosis

• found in most animal cells, but more found in endocytic cells like immune cells

Smooth Endoplasmic Reticulum (SER)

• contains enzymes for destroying toxins

• where phospholipids are made

Peroxisome

• manages hydrogen peroxide levels

• regulates fat metabolism

Rough Endoplasmic Reticulum (RER)

• rough because covered in protein-making factories called ribosomes

• site of protein synthesis for proteins that will be releases to outside of cell

Golgi apparatus

sorts, modifies, and ships proteins meant for release to outside of cell

Vesicle

a small sack surrounded by membrane used to move things between organelles