Unit 2 Review The Cell (except Cell Cycle, Ch 12!)

Unit 2 Review

The Cell

(except Cell Cycle, Ch 12!)

Break down the points on this essay question:

Prokayrotic and eukaryotic cells are physiologically different in many ways, but both represent functional collections of living matter.

A.It has been theorized that the organelles of eukaryotic cells evolved from prokaryotes living symbiotically within a larger cell. Compare & contrast the structure of the prokaryotic cell with eukaryotic cell organelles, and make an argument for or against this theory.

B.Trace the path of a protein in a eukaryotic cell from its formation to its excretion from the cell.

CHAPTER 6 AN INTRODUCTION TO

METABOLISM

Section A: Metabolism, Energy, and Life

1. The chemistry of life is organized into metabolic pathways

2. Organisms transform energy

3. The energy transformations of life are subject to two laws of

thermodynamics

4. Organisms live at the expense of free energy

5. ATP powers cellular work by coupling exergonic reactions to endergonic

reactions

• Energy conversion:– child operates muscles to move limbs:

• P.E. (chemical) K.E. (muscle/body movement)

– climbing to the top of a slide: • K.E. P.E. (altitude)

– sliding down:• P.E. K.E. (movement)

– friction for slowing/stopping:• K.E. heat energy

Fig. 6.2

• Free energy (G): portion of a system’s energy able to perform work.

– “Free” is a terrible name for this, think “available” instead.

Fig. 6.5

• exergonic reaction: – releases free energy G is negative.– can be spontaneous– released energy can

perform work

Fig. 6.6a

– Cellular respiration equation: • C6H12O6 + 6O2 6CO2 + 6H2O + energy

G = + or - ?– -686 kcal/mol of glucose…

• What is that 686 kcal/mol used for?

• ATP ADP + Pi

G is -7.3 kcal/mol. This is exothermic

• Each phosphate group has a neg charge.

• Their repulsion creates instability.

Fig. 6.8b

• ATP regeneration: endergonic process requiring investment of energy: G = 7.3 kcal/mol.

• In a working muscle cell the entire pool of ATP is recycled each minute (over 10 million ATP).

Fig. 6.10

CHAPTER 6 AN INTRODUCTION TO

METABOLISM

Section B: Enzymes

1. Enzymes speed up metabolic reactions by lowering energy barriers

2. Enzymes are substrate specific

3. The active site in an enzyme’s catalytic center

4. A cell’s physical and chemical environment affects enzyme activity

• Active site: a pocket or groove on the surface of the protein into which the substrate fits.

• induced fit definition? causes?• conformation change to “hug” & stress substrates• bonding with enzyme R-groups • H-bonding with enzymes N-C-C backbone

Fig. 6.14

• Enzymes speed reactions by lowering EA.

Fig. 6.13

3. Red

2. Black

4. Enzyme names end in ???

Fig. 6.15

5.Bonus

• What determines the rate of an enzyme catalyzed reaction?– Substrate concentrations: sufficient for

enzyme saturation?– Enzyme Concentration– Temp effects?– Anything that

fouls up the shape!

Denaturation?Causes?

-excessive temp-wrong pH-wrong salinity…

– Competitive inhibition: inhibitor binds to the active site.

– Noncompetitive inhibition: • binds somewhere other than active site, but

alters the active site.

• Most allosterically regulated enzymes are…– constructed of two or more polypeptide chains.– have an active site on each subunit– allosteric sites are often located where

subunits join.

• Red line represents?– negative

feedback… – inhibits synthesis

when product is in good supply!

• Bonus!! What are threonine & isoleucine?– Amino Acids

Fig. 6.19

• cooperativity: when substrate binding at one site activates other active sites. – amplifies the response of enzymes to

substrates

Fig. 6.20

CHAPTER 7A TOUR OF THE CELL

Section A: How We Study Cells

1. Microscopes provide windows to the world of the cell

2. Cell biologists can isolate organelles to study their function

• characteristics of ALL cells:– plasma membrane: surrounds ALL cells– cytosol: semifluid substance within the

membrane – chromosomes: long DNA molecules containing

genes.– ribosomes: tiny organelles that make proteins.

Fig. 7.4 The prokaryotic cell is much simpler in structure, lacking a nucleus and the other membrane-enclosed organelles of the eukaryotic cell.Who am I, and how am I special?

Fig. 7.7

1-5 are parts of the ______ assembly line

Fig. 7.8

What’s new here?

Fig. 7.12

nucleus & ER

cis face

trans face

cell membrane

• During transit from cis trans, products from the ER are modified to reach their final state.

• ex: modification of oligosaccharide portion of glycoproteins.

Golgi Apparatus:

Fig. 7.16

Now, can you explain the roles of each part of the endomembrane system in the synthesis & processing of membrane & proteins in the cell?

• motor proteins pull protein fibers past each other, causing:

• undulations of cilia & flagella; • muscle cell contraction.• movement of vesicles/organelles along microtubule

“monorails”

Fig. 7.21

Fig. 7.24

• Microfilaments:– thinnest class of the cytoskeletal fibers– two chains of actin subunits twisted together.– resist tension.– form a 3-D network inside the plasma

membrane.– help cause cell contractions.

Fig. 7.21a

• amoeboid movement: actin-myosin contractions squeeze cytosol into expanding pseudopodia.

Fig. 7.21b

• muscle cell contraction: myosin motor molecules “walk” past actin microfilaments.

ECM: extracellular

matrix

Fig. 7.29

What is this called?

CHAPTER 8MEMBRANE STUCTURE AND

FUNCTION

Section A: Membrane Structure

1. Membrane models have evolved to fit new data

2. Membranes are fluid

3. Membranes are mosaics of structure and function

4. Membrane carbohydrates are important for cell-cell recognition

• fluid mosaic model: proteins “float”– hydrophobic region

stays “buried” in the membrane

– hydrophilic regions protrude

Fig. 8.2b

• Why are flip flops rare?

1. Membranes are fluid

Fig. 8.4a

• Which is more fluid?

• What causes the kinks?

• When would you need “kinky H-C tails”?

Fig. 8.4b

• cholesterol molecules (steroids) can do what TWO things?– dampen effects of warming and cooling on

membrane fluidity• reduce fluidity at warm temperatures by restraining

movement of phospholipids.• maintain fluidity at cool temperatures by preventing

tight packing.

Fig. 8.4c

• Differences between inner/outer surface of cell membrane?– may differ in lipid

composition– proteins have a clear

direction.– outer surface has carbs

attached.

• This begins during synthesis of new membrane in the …– ER.

Fig. 8.8

Fig. 8.9

Purposes of Membrane proteins??

• Ability of molecules to pass the membrane depends on?– Hydrophobic molecules (hydrocarbons, CO2, O2)

dissolve in the lipid bilayer and cross easily.– Large molecules, ions (Na+, Cl-, Ca+2) and polar

molecules (H2O, glucose) pass through with difficulty, Who can help?• transport proteins can assist these molecules.

4. Cell survival depends on balancing water uptake and loss

3. 4. 5.

6. What’s best for animal cells?

7. What’s best for plant cells?

• H2O will movetowards lowest ψ until dynamic equilibrium is reached.

• What causes High ψ? Low ψ?– High [H2O] or high pressure cause high ψw

– Solutes and/or low pressure can cause low ψw

ψw = ψs + ψp

ψp = 0 or positive.ψs = 0 or negative.

• Facilitated Diffusion via gated channels: open or close due to a physical or chemical stimulus.– Where would this

example occur?

• at a synapse!

• Facilitated Diffusion via “translocation” – transport proteins change shape to help a

solute diffuse.– What solutes need this pathway?

Fig. 8.14b

Fig. 8.16 Both diffusion and facilitated diffusion are forms of passive transport of molecules down their concentration gradient, while active transport requires an investment of energy to move molecules against their concentration gradient.

• Cotransport – drives active transport of amino acids, sugars,

and other nutrients.

Fig. 8.18

• Endocytosis (ex: phagocytosis): – cell ingests macromolecules/particles by

forming vesicles from its plasma membrane.

• What is needed to digest the “prey”?– fuses with lysosome

Section A: The Principles of Energy Harvest

1. Cellular respiration and fermentation are catabolic, energy-yielding

pathways

2. Cells recycle the ATP they use for work

3. Redox reactions release energy when electrons move closer to

electronegative atoms

4. Electrons “fall” from organic molecules to oxygen during cellular

respiration

5. The “fall” of electrons during respiration is stepwise, via NAD+ and an

electron transport chain

CHAPTER 9CELLULAR RESPIRATION:

HARVESTING CHEMICAL ENERGY

• Two main catabolic processes for sugar metabolism?– fermentation – yields PARTIAL breakdown.– cellular respiration: uses oxygen to complete the

breakdown of many organic molecules.• more efficient and widespread • Most steps occur in mitochondria.

• Photosynthetic organisms store energy in organic molecules. – These are available to…

• themselves, and …• others that eat them.

Really Big Picture:

Fig. 9.1

• Redox rxns often produce change in electron sharing:– Contrast high and low energy electron positions.

Fig. 9.3

low energy e- positions

high energy e- positions

Section B: The Process of Cellular Respiration1. Respiration involves glycolysis, the Krebs cycle, and electron transport: an

overview

2. Glycolysis harvests chemical energy by oxidizing glucose to pyruvate: a

closer look

3. The Krebs cycle completes the energy-yielding oxidation of organic

molecules: a closer look

4. The inner mitochondrial membrane couples electron transport to ATP

synthesis: a closer look

5. Cellular respiration generates many ATP molecules for each sugar

molecule it oxidizes: a review

CHAPTER 9CELLULAR RESPIRATION:

HARVESTING CHEMICAL ENERGY

1. Respiration involves glycolysis, the Krebs cycle, and electron transport:

an overview

Fig. 9.6

1. 2. 3.

• A little ATP is generated in glycolysis and the Krebs cycle by substrate-level phosphorylation.– How is this different

from oxidative phosphorylation?• no e- transport

chain.

Fig. 9.7

Glycolysis:

• Net Production?– 2 ATP + 2 NADH – 2 pyruvate

• NOT used?– O2

Fig. 9.8

For each pyruvate that goes in...

• What high energy electron carriers are produced?– Net of 2 NADH

– 1 FADH2

• How much ATP?– one

• Where next??

Fig. 9.15

+ 2 H+

Where is this happening?

Who’s the final electron accepter?

• ATP synthase – What kind of

molecule is it?– What does it do?– What powers it?

• Push of H+ gradient powers ATP synthase

• Chemiosmosis: using a chemical’s “push”

• lactic acid fermentation: – Lactic acid fermentation by some fungi and bacteria is

used to make cheese and yogurt.– Muscle cells switch from aerobic respiration to lactic

acid fermentation to generate ATP if O2 is scarce.• lactate is converted

back to pyruvate in the liver.

Fig. 9.17b

CHAPTER 10 PHOTOSYNTHESIS

Section A: Photosynthesis in Nature1. Plants and other autotrophs are the producers of the biosphere

2. Chloroplasts are the site of photosynthesis in plants

Formula for photosynthesis?

6CO2 +6H2O C6H12O6 + 6O2

What was left out?

• Water is split – electrons & H+ from water reduce CO2 to sugar.

• polar covalent bonds are converted to nonpolar bonds.–this boosts the potential energy of electrons

Fig. 10.3

• What’s this about?

Fig. 10.8b

• What’s a photosystem?– chlorophyll a, chlorophyll b, and carotenoid molecules.– acts like a light-gathering “antenna complex”

• Lost electrons are replaced by: – H2O 2H+ + O + 2e-

Fig. 10.11

2. What comes out?1.

Where to with these?

Fig. 10.4

Fig. 10.16

With the pieces in place, can you explain each step?

Fig. 10.14

• Mitochondria generate ATP from food…

• Chloroplasts generate ATP from light

Fig. 10.17.3

enzyme

• C3 plants (most plants) suffer photorespiration on hot, dry days. Here’s how:

1. stomata close to conserve H2O

2. Calvin cycle drops CO2 levels.

3. O2 levels rise as light reaction cracks H2O molecules.

4. rubiscos start adding O2 instead of CO2 (BAD)

5. RuBP splits into a 3-C piece and a 2-C piece.

6. 2-C piece leaves the chloroplast & is degraded to CO2

7. no ATP or additional organics are produced

Fig. 10.18

Fig. 10.19

• carbon fixation and the Calvin cycle are:– spatially

separated in C4 plants.

– temporally separated in CAM plants.

Here’s a quick review of chapters 9 and 10, KNOW IT:

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