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MU / Biology / BIO 203 / Are cells diverse?

Are cells diverse?

Are cells diverse?

Description

School: Miami University
Department: Biology
Course: Cell Biology
Professor: James
Term: Fall 2018
Tags: Cell and Biology
Cost: 50
Name: BIO 203 Exam One
Description: intro to the cell, cell structure, macromolecules, cell membrane
Uploaded: 09/20/2018
16 Pages 49 Views 4 Unlocks
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Leeann Tran


Are cells diverse?



Miami University

BIO 203 JAMES Exam One Notes (Ch. 1, 2, 4 11) CHAPTER 1: THE FUNDAMENTAL UNITS OF LIFE A. Cell theory (Schleiden, Schwann, Virchow)

-Every living organism composed of one or more cells

-Functional units of life

-cells are simplest basic most fundamental structural unit of life (anything  less than a cell is not alive)

-all cells arise from pre-existing cells

B. Cells are diverse

-Size (<1 micrometer to <200 micrometers)

-Shape

-example: nerve cell (central cell body with long extensions called  axons and dendrites)

-example: paramecium (covered in cilia to help it move, hairy looking  appearance)

-nucleus


How do cells move?



-scientists say 200 types of cells in human body but actually more than that: classification of different types of cells lie on a spectrum  -cell wall (all cells have plasma membrane but not a cell wall which lies  outside of a cell membrane) If you want to learn more check out How did the form of writing evolve during the middle ages?

-cell wall exists for extra protection and support

-many bacteria have cells walls, plant cells have cell walls

-member of community or independent

-motility (how they move)

-flagellum

-cilia

-chemical requirements If you want to learn more check out What are the disadvantages of population growth?

-some require oxygen (aerobic), some are killed by oxygen (anaerobic), some need sunlight, some need complex macromolecules made by  other organisms

-function

-example: nerve cells generate electrical signals

-example: muscle cells generate signals to result in mechanical force  and movement


What is the function of golgi apparatus in cell structure?



C. Cell Unity (cells are the same in some fundamental ways) -central dogma: DNA-RNAprotein

-store genetic info as DNA

-replicates DNA by templated polymerization requiring sugar  (deoxyribose), phosphate group, and nucleotides (A with T, G with C) -transcribe genetic info to RNA

- are typically single stranded, instead of deoxyribose as sugar RNA  has ribose

-translate RNA into proteins which dictate function of cell -proteins made of monomers called amino acids, there are 20 amino  acids

Leeann Tran

Miami University

-use protein catalysis (most enzymes are proteins which speed up  reactions) We also discuss several other topics like What is the difference between patrilocal and matrilocal residences?

-regulate genes (regulation is essential for establishing different  functions between cells)

-require free energy  

-synthesize biological macromolecules from subunits (monomers make up polymer)

-are enclosed in a plasma membrane

D. Review of Cell Structure

1. Prokaryotic (before nucleus) include bacteria and archaea -ex. Eubacterium (surrounded by cell membrane and cell wall,  have DNA but NOT enclosed in a membrane aka nucleus)

- small (a few microns)

-reproduce quickly (ex. every 20 mins)

-spherical, cylindrical, or spiral

-unicellular but can exist in clusters or chains

-tough cell wall

-no INTERNAL membranes that exist inside cell membrane so NO  ORGANELLES

-DNA in nucleoid, NOT membrane bound

-limited cytoskeleton

2. Eukaryotic (true nucleus)

-usually larger than prokaryotes

-multicellular and unicellular We also discuss several other topics like What are the various functions of tissue as cell groups?

-organelles:

1. nucleus: contains DNA

-nuclear envelope made of TWO concentric membranes

2. mitochondria: make chemical energy from oxidation of food  molecules

-produce ATP

-cellular respiration: uses oxygen and produces CO2

-have their own DNA and binary fission (evidence of  

evolution from bacteria)

-also two membranes

-folding of inner membrane is called cristae (lots of surface  area)

3. endoplasmic reticulum: system of membrane bound  

compartments

-where cell membrane products are assembled

4. Golgi apparatus: modifies and packages products from ER for  “shipping”

5. lysosomes- intracellular digestion

6. peroxisomes- vesicles where H2O2 inactivates toxic molecules -endocytosis: vesicles form at cell membrane to bring material  into cell

Leeann Tran We also discuss several other topics like What are the symbols for frequency and wavelength?
Don't forget about the age old question of What are the three aspects observed in burdens at trial?

Miami University

-exocytosis: vesicles from inside cell fuse with cell membrane  and release contents to outside

7. cytosol: part of cytoplasm not located in intracellular  

membranes

-cytoskeleton: THREE types of protein filaments that support cell  shape

1. actin filaments (thinnest, responsible for muscle  

contraction)  

2. microtubules (thickest, like hollow tubes, aids cell  

division, made of tubulin)

3. intermediate filaments (provide strength to cell support) -cytoplasm: interior of the cell, always moving and dynamic -motor proteins: use energy to carry organelles and proteins in  cytoplasm

PLANTS ONLY

8. plastid: two membranes, manufacture and storage  

-storage plastids (store fats, oil, or starch)

-chromoplasts (store pigments)

-chloroplasts (photosynthesis)

9. chloroplast: photosynthesis creates sugars

-release energy by oxidizing sugars in mitochondria

-have their own DNA and binary fission (evidence of  

evolution from bacteria)

-two membranes

10. vacuoles: storage and turgidity for cell

11. cell wall- structure and support

E. Eukaryotic cells may have been predatory in the past

- early anaerobic eukaryotic cells may have ingested bacteria that  eventually came to become the mitochondria and exist in the  symbiotic relationship

CHAPTER 2: CHEMICAL COMPONENTS OF CELLS - Organic chemistry is chemistry based on carbon compounds o Depends on almost only aqueous solutions

o Extremely complex, chemistry of cells is more complex than any  chemical system

o Dominated by “polymeric molecules” which are collections and  chains of subunits

- Life is carbon based

A. Chemical Bonds

- elements: substances that cannot be broken down by chemical  means

- atom: smallest part of element that retains distinct characteristics  1. dense, positively charged nucleus (contains protons and  neutrons) at center surrounded by electron cloud

Leeann Tran

Miami University

2. neutrons have almost same mass as protons

- isotopes: atoms that are same element so same # of protons but diff  # of neutrons

-atomic number: equal to # of protons and unique to each element - atomic weight/molecular weight: mass relative to H atom, mass of  protons + neutrons

-chemical bonds occur using electrons in the valence (outermost) shell 1. ionic bond: electrons transferred from one atom to another 2. covalent bond: two atoms share pair of electrons

+

+

+

+

Covalent ionic

-8 electrons make up a “stable” and full outer shell

1. # of electrons an atom must lose or gain to achieve a full shell determines how many bonds it can make

-molecule: cluster of atoms joined by covalent bonds

1. shared electrons between atoms opposes repulsion of  

positively charge nuclei

2. attraction and repulsion are balanced when nuclei are  

separated by a known distance, aka bond length

- covalent bonds are characterized by bond angles, bond lengths, and  bond energies

1. single bonds, double bond, and triple bond (triple is shortest  and strongest)

2. polar covalent bonds: electrons shared unequally and creates  a positive and negative end

-electronegativity: tendency of an element to attract an electron 1. increases as you move up and to the right of the periodic table - ionic bonds formed usually between atoms that easily give up or  accept electrons

1. ions held together only by ionic bonds are “salts”

2. example: NaCl

- noncovalent bonds: weak, temporary bonds between atoms 1. electrostatic attraction: forms between fully charged atoms -weaker kinds can also form between molecules with polar  covalent bonds

-polarity allows for electrostatic attraction

2. HYDROGEN BONDS

- oxygen is highly electronegative so it attracts e-

Leeann Tran

Miami University

- in H2O, O end is negative and H ends are positive

-weak and lasts very short time between two water  

molecules

-can also form between H in one molecule with a  

negatively charged atom (usually O or N), or water with  

polar molecules  

-hydrophobic molecules: “phobia” hate water

uncharged, few hydrogen bonds, don’t dissolve in  

water

ex. hydrocarbons

-hydrophilic molecules: water “loving”

Usually have polarity, carry charge, dissolve in water

Leeann Tran

Miami University

BIO 203 JAMES Week TWO Notes (Ch. 2 & 4)

Covalent bonds

Nonpolar: O2

-electrons shared equally between atoms

Polar covalent:  

-molecules with partial positive and partial negative charges Example: H2O

Oxygen is highly electronegative, so electrons are attracted to O, making the molecule polar

B. Hydrogen bonds:

- noncovalent

-H covalently bonded to electronegative O or N interacting with O or N Example H2O and NH3, partial positive H is attracted to partial  negative N

-a weak, but important bond  

 Each water molecule can form up to four bonds with:

-other water molecules

-other polar molecules

-other atoms in same molecule (affecting shape, such as secondary  structure of proteins)

-atoms in two different large molecules  

-multimeric protein subunits (multimeric meaning two or more  polypeptides)

 Water

-Biological systems are aqueous systems (exist in water)

-Most of living tissue is water (70-90%)

-Universal solvent for charged and polar molecules

-Hydrophilic molecules DO INTERACT with water

(ie sugar because of OH ends)

-hydrophobic molecules DO NOT interact with water

-oil and water separate spontaneously  

-minimize interaction between n water molecules

-hydrophobic molecules aggregate together, so water molecules  must become disordered to reorient around the collection of  hydrophobic molecules

-decreases “order”, water population less ordered, higher  

entropy, MORE ENERGETICALLY FAVORABLE

C. Carbon

-Four valence electrons= can share 4 e- pairs= form up to 4 single  covalent bonds

-can form chains, branches, or rings

-hydrocarbons: molecules comprised ONLY of C and H

Leeann Tran

Miami University

-organic and nonpolar (HYDROPHOBIC)

-not all organic molecules are hydrophobic (because of functional  groups)

D. Functional groups

-impart specific chemical properties to molecules

-different groups have different properties

1. hydroxyl- OH

2. carbonyl- C=O

Aldehyde- O is on outside

Ketone- O on inside

3. carboxyl- COOH

4. amine- NH2

5. methane- CH3

6. sulfhydryl- S-H

7. phosphates- PO3

-Often bond to free hydroxyl group

-Kinases add phosphates to molecules

-Dephosphorylation: removing phosphate groups

-anhydride: phosphate with carboxyl or two or more  

phosphate groups

-ATP!!!! High energy phospho-anhydride bond

CHAPTER 4: FOUR BIOLOGICAL MACROMOLECULES

1. Carbohydrates (Polysaccharides, glycogen, starch)

2. Fats and lipids

3. Proteins

4. Nucleic acids

-macromolecules (polymers) are created by putting together subunits  (monomers)

Subunits of macromolecules:

1. Sugar carbs

2. Fatty acids (most abundant) fats and lipids

3. Amino acids proteins

4. Nucleotides nucleic acids

Cells are 70% water, 30% nonwatery

o 4% inorganic ions and small molecules

o 2% phospholipid

o 1% DNA

o 6% RNA

o 15% protein

o 2% polysaccharide

- How are monomers linked together?

o Condensation/dehydration reaction= synthesis

 OH from one monomer and H from another monomer  

removed to produce H2O and link two monomers

o Hydrolysis= breakdown

Leeann Tran

Miami University

 H2O split up and OH and H attached to respective ends of  split molecules

A. Carbohydrates (all the sugars, monosaccharides + polysaccharides) -Some multiple of (CH2O)n

-energy storage

-structural

-Monosaccharides: simple sugars/subunits, short term  

energy storage

-Polysaccharides: macromolecules, long term energy  

storage, structure

1. Monosaccharides  

-Subunit (building block)

-Short term energy storage

-3 (trioses), 4, 5 (pentoses), or 6 (hexoses) carbons

-Every C has OH or =O

Aldoses (=O at end)

Ketoses (=O in middle)

-OH makes them hydrophilic and polar

DIFFERENT STRUCTURES OF MONOSACCHARIDES

-form rings in solution  

-isomers (same chemical structure but different spatial  

arrangement)

(EX. glucose, mannose, and galactose are all C6H12O6)

-Beta v alpha (beta has OH above plane, alpha has OH  

below plane)

-sugar derivatives: hydroxyl (OH) group replaced by other  groups

-link two monosaccharides= disaccharide, three=  

trisaccharide

2. Polysaccharides

-biological macromolecule

-long chains of monosaccharides, branched or straight

-long term energy storage

-glycogen (animals, fungi)

-starch (plants)

-structural

-cellulose (plants)

-we cannot digest cellulose

- starch has 1-4 linkage of alpha glucose

-cellulose has 1-4 linkage of beta glucose

-some polysaccharides are nonrepeating subunits  

with sugar derivatives

-glycoproteins and glycolipids (cell  

membranes)

Leeann Tran

Miami University

-extracellular matrix

-also make up peptidoglycan in bacteria

-lipopolysaccharides (gram negative bacteria)

-chitin (arthropods and fungi)

B. Lipids

-macromolecules but NOT POLYMERS

- insoluble in water = HYDROPHOBIC

-fats, oils, waxes

-important in membranes, hormones, vitamins

-VERY long-term energy storage, insulation

-TWO TYPES

-fatty acids: carbon chain (usually 16-18 Cs) with carboxyl  (COOH) group on one end  

- differences between fatty acids can be length, degree of  saturation

-Can be unsaturated (one or more double bonds create  

kinks, less H atoms) so fatty acids cannot pack as  

tightly together

-can be saturated (no double bonds, as many H atoms as  

possible are present)

a. lipids with fatty acids

1. Triacylglycerol

-very long-term energy storage

-insulation

-three fatty acids attached to three C alcohol  

(glycerol)

-aggregate in aqueous solution  

1. fats and oils

-energy storage

-efficient

-9,300 cal/g

-very long term

-insulation

-fats: saturated fatty acids, solid at room temp,

most animals and some plants

-oils: unsaturated fatty acids, liquid at room  

temp, in plants and fish

2. waxes

-long chain fatty acids linked to long chain  

alcohols or carbon rings

-soft, solid masses

-waterproof coatings on leaves, bark, fruits,  

feathers

-structural material in beehives

-Protective coating in ear canal

2. phospholipids

Leeann Tran

Miami University

-glycerol, two fatty acids, one polar group,  

phosphate, nitrogen

-membranes (phospholipid bilayer)

-amphipathic: both hydrophobic (fatty acids) and  

hydrophilic (phosphate group) properties

-when in aqueous solution, phospholipid  

spontaneously orient hydrophobic tails away from  

water and hydrophilic heads on outside toward water

-unsaturated fatty acids help keep the membrane  

flexible  

b. lipids WITHOUT fatty acids

1. sterols

-four rings and various functional groups

-inserts into biological membrane (ie cholesterol in  

animal cells)

-hormones (ie testosterone)

-vitamins

C. Proteins

-enzyme, structural, transport, motor, storage, signal, receptor, gene  regulatory, special purpose

-unbranched chain of amino acids linked by peptide bonds -variable in size

1. amino acids (monomers of proteins)

-made of central C, amino group (NH2), carboxyl group (COOH),  H, side chain (R)

-20 different kinds

-can be nonpolar or polar and charged (acidic or basic)

-Linked by peptide bonds (carboxyl group of one amino acid  linked to amino group of another amino acid

2. polypeptide: unbranched chain of amino acids but NOT necessarily  final 3D structure

3. protein: folded, functional unit (may be one or more polypeptides) -protein structure: STRUCTURE DRIVES FUNCTION  

-unique, stable structure for each protein, unique due to  

chemical properties of R groups

-noncovalent interactions maintain 3D shape

-electrostatic attractions

-hydrogen bonding

1. Between atoms of two peptide bonds

2. Between peptide bond and amino acid side chain

3. Between two side chains

-hydrophobic interactions

-Van de Waals  

-disulfide bonds stabilize some extracellular protein structure -interchain (diff polypeptide) or intrachain (same  

polypeptide)

Leeann Tran

Miami University

-hierarchy of protein structure

1. primary structure: linear sequence of amino acids

2. secondary structure: localized regions of folding within  

polypeptide

-driven by hydrogen bonding between backbone  

structure

-alpha helix can form coils and cross lipid bilayers

-beta sheet

3. tertiary structure 

-3D shape forms

-of protein contains only ONE polypeptide, this is  

FINAL structure

4. quaternary structure- final 3D shape for proteins with  

more than one polypeptide

-homodimer- two identical polypeptide chains

-heterodimer

-homotetramer- four identical polypeptide chains

-heterotrimer

-heterotrimic

-most proteins are globular: polypeptide chains fold up into  irregular, compact ball

-some proteins are fibrous: elongated 3D structure to span large distance

-ie alpha keratin, keratin, collagen

-extracellular matrix

-many proteins consist of multiple domains: any part of  

polypeptide chain that pack together into stable, independently  folding elements

-some domains shuffled during evolution and some are  

conserved

-protein families: groups of proteins that has amino acid  

sequence and 3D conformation similar to each other  

-binding site: any region on protein that interacted with  

another molecule through noncovalent bonds

-dimer: symmetrical structure of two subunits (subunit is each  polypeptide chain in a protein)

-proteins can form  

-filament: helix of molecules extended indefinitely in either  direction

-sheets

-spheres

-tubes

-protein folding happens during synthesis, transport across membrane, and can fold afterward

-sometimes denatured proteins can refold spontaneously, others  require “HELP”

Leeann Tran

Miami University

-chaperone proteins “guide” parts of proteins along pathways and  prevent aggregation and help it fold back together

-protein quality is monitored

-proteasome degrades misfolded proteins

What proteins help other proteins fold?

-two family of chaperones

1. hsp 70: during and after synthesis or during passage through  membrane

Hsp60: polypeptide isolated in central chamber and correctly  folded, will usually happen after synthesis DURING transport  through endoplasmic reticulum

-chaperones prevent aggregation of misfolded proteins by fixing them  -how are misfolded proteins marked for destruction  

-polyubiquitin chain added

-ubiquitin (76 amino acid chain)

-ubiquitin activating enzyme (primes ubiquitin ligase)

-ubiquitin ligase (adds ubiquitin to misfolded protein)

-most signals recognized will be exposed hydrophobic regions Proteins can be properly folded initially but became worn out, or  exposed to some stressor

D. Nucleic Acids

-nucleotides- subunits that consist of base (A, G, T, C , sugar (ribose or  deoxyribose), 1, 2, or 3 phosphates

-RNA and DNA

-in ribose, 2’ C is bonded to hydroxy  

In deoxyribose, 2’C has one less oxygen, bonded to H

-5’ C is attached to phosphate

-3’ C is attached to hydroxy

-Nucleoside: ONLY BASE AND SUGAR, NO phosphate

-Bases: adenine, guanine, cytosine, uracil, thymine

-when bases connected to sugar to form nucleoside= adenosine,  guanosine, cytidine, uridine, thymidine

-nucleotides: four roles

1. energy (ATP) very short term

-phosphoanhydride bonds (phosphate group to carboxyl)  

hold a lot of energy so when those bonds are broken  

energy is released by hydrolysis

-cells generate energy by glycolysis and aerobic  

respiration

-glycolysis: glycogen broken down into glucose with  

goes through glycolysis to produce a couple ATP  

molecules and pyruvate

-aerobic respiration: fats and oils are hydrolyzed to  

fatty acids which are oxidized for aerobic respiration,  

also use pyruvate from glycolysis

2. coenzymes (NADH, coenzyme A) (energy currency)

Leeann Tran

Miami University

3. intracellular messengers (cAMP, GTP)

4. components of nucleic acids (monomers or subunits)

-Nucleic acid= unbranched chain of nucleotides

-single stranded or double stranded

-sugar phosphate backbone

-phosphodiester bonds

-5’ (phosphate group) and 3’ ends (carboxyl group)

RNA

-single stranded

-A, G, C, U

-informational (mRNA from DNA to ribosome)

-enzymatic, structural, regulatory

CHAPTER 11: MEMBRANE STRUCTURE

-plasma membrane: two ply sheet of lipid molecules (lipid bilayer) with  proteins

-has highly selective channels and transporters that allow specific  molecules to be imported and exported

-simplest bacteria have only one membrane

-eukaryotes have internal membranes that make up organelles -plasma membrane:

1. has proteins to receive signals from environment

2. transport proteins import and export small molecules

3. flexibility allows for expansion for growth, storage, and more LIPID BILAYER

-each lipid has both hydrophobic and hydrophilic ends (amphipathic  characteristic)

-most abundant type are phospholipids (phosphate containing  hydrophilic head linked to pair of hydrophobic tails)

-hydrophobic tails face toward each other and hydrophilic heads  face aqueous environment, creating lipid bilayer

-if any “tears” occur membrane will spontaneously rearrange to  seal or seal inward on itself

-exposed edges are not energetically favorable

-membrane acts like a fluid where molecules can move around  and switch places

Flip flop: phospholipid molecules flip from one half of  

bilayer to the other (VERY RARE)

Often switch places with neighbors (lateral diffusion)

Can flex hydrocarbon tails (flexion) and rotate along long  axis (rotation)

Fluidity of Lipid Bilayer Depends on Composition

-nature of hydrocarbon tails affect how tightly they pack

1. length

-shorter reduces interaction between tails and  

increases fluidity

Leeann Tran

Miami University

-usually between 14-24 C atoms, most common 18-

20

2. number of double bonds

-double bonds means LESS than max possible # H  

atoms

-saturated: no double bonds and fully filled  

with H

-unsaturated: double bond creates kink in tail  

so more difficult for tails to pack tightly  

Cholesterol (in animal cells) are short and rigid to fill in spaces between phospholipids= STIFFEN BILAYER

*Membrane fluidity important for:

-allowing membrane proteins to diffuse quickly and interact (cell  signaling)

-distribute molecules like lipids and proteins evenly throughout  membrane

-allow membranes to fuse with each other and mix molecules MEMBRANE ASSEMBLY BEGINS IN ER

-ER enzymes manufacture new phospholipids which are  

deposited in cytosolic side of membrane

-scramblases move randomly selected phospholipids from one  half of lipid bilayer to the other for equal distribution

ASSYMETRICAL SIDES OF MEMBRANE- why????

-although phospholipids are evenly scrambled, flippases from  Golgi body flip certain phospholipids from exterior side to  

cytosolic side

-floppases moves phospholipids from cytosolic side to exterior  side

-to switch from one side to the other ATP is required

-glycolipids only on exterior side

-certain phospholipids on the cytosolic side are cleaved into IP3  and other inner cell signaling molecules (that’s why they’re on  the inside)

Plasmalogen phosphoglycerides

-one fatty acyl chain and one fatty alkyl chain (ether linked to sn 1 position of glycerol)

-20% of phosphoglycerides in humans

-high in heart and brain

-can contain double bond between C1 and C2

-may protect cells from oxidative stress

Sphingolipid

-derived from sphingosine

-amino alcohol with long hydrocarbon chain

-sphingosine + fatty acid= ceramide

-long chain fatty acid attached to amino

Leeann Tran

Miami University

HOW LIPIDS GET TO OTHER COMPARTMENTS

-everything in endomembrane system is connected

-nuclear envelope, ER, Golgi, transport vesicles, vacuoles,  lysosomes

-if not part of endomembrane system:

-mitochondria, plastids (chloroplasts)

MEMBRANE PROTEINS

-can be transporters, channels, anchors, receptors, enzymes -types:

Integral: embedded in at least one layer of lipid bilayer

-transmembrane: from one side to the other, all the way through  (one part interacts with hydrophobic side, other interacts with  hydrophilic side)

-monolayer: associated alpha helix (part of protein that is alpha  helix is embedded in one layer or one leaflet of cell membrane  (usually cytosolic)

-lipid-linked: attached directly to lipid membrane via covalent  attachment

(part that is embedded is lipid)

-most common membrane spanning secondary structure is  alpha helix

Peripheral: none of polypeptide enters hydrophobic core of membrane -protein attached

-more about alpha helix structure

-protein is folded so hydrophobic side chains are facing out,  that’s how it interacts with hydrophobic core of membrane -SOME membrane proteins can diffuse laterally  

-mouse cell and human cell creates hybrid cell with evenly mixed proteins from each

-FRAP (fluorescence recovery after photobleaching)- protein  labeled with fluorescent dye, then bleached so it never becomes  fluorescent again. Then unbleached proteins move into bleached  area (REPLACEMENT) and recover fluorescence  

-movement of some membrane proteins is restricted

-could be linked to extracellular protein, or intracellular protein,  proteins on other cells, or something blocks the way

-examples of barriers:

1. Tight junction

Apical membrane: facing lumen side

Basal membrane: facing tissues

FINAL POINTS

Lateral plasma membrane: facing other cells

1. Detergents and membrane solubilization

a. Has hydrophobic end and hydrophilic end

b. Surround particle to create micelle

2. Cell cortex provides support

Leeann Tran

Miami University

3. Cell surface covered with carbohydrates

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