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117 Cards in this Set

  • Front
  • Back
Endomembrane system
All the membranes within the cell inside the plasma membrane... Golgi apparatus, lysosomes, ER, vesicles, endosomes, peroxisomes
-primary center for protein and lipid synthesis in eukaryotes
Protein Sorting Pathways
-Gated Transport
-Transmembrane Transport
-Vesicular Transport
Cytosolic protein- free in the cytoplasm
Gated transport
Cytosol to nucleus (through nuclear pore)
-fully folded
Transmembrane transport
Needs to pass through membrane/lipid bilayer- needs to be mediated
-Occurs in mitochondria, ER, choloroplasts peroxisomes
-Protein needs to be unfolded- energy required
Vesicular Transport
After accomplishing transmembrane transport, from ER to Golgi
Pulse-Chase experiment
Pulse cell w/ radio-labelled leucine- able to see protein synthesis occuring in the ER
Chase w/ unlabelled amino acids- after protein synthesis- where do they go?
-Immediatley- in rough ER
-after 20 min- in golgi
-after 120 min - in secretory vesicles
Rough ER
-Synthesis of membrane-bound, soluble (ER, Golgi, or lysosomal), and secretory proteins
-Rough bc of ribosomes
Lumen=newly manufactured proteins undergo folding and other types of processing
Smooth ER
-Sequestration of Ca 2+ (cell signaling)
-Synthesis of steroid horomones
-Enzymes for detoxification
-Enzymes for glucose release
No ribosomes- no protein synthesis. i.e. liver cells
ER Proteins
Any protein making its way to the ER needs to be targetted to the ER- needs signal attached to cytosolic protein
Co-translation translocation
Secretory proteins into ER lumen
-signal sequence in amino acid
-SRP (signal recognition particle) binds to signal sequence on newly translated protein in the cytosol
-Ribosome recruited
-SRP binds to receptor in ER membrane
-Protein pushed through translocon into ER-> SRP released through GTP hydrolysis
-Protein refolded in the ER
Proved w/ experiment using microsomes( cell free protein synthesis
Adding one or more carbohydrate groups to proteins- results in glycoprotein
-Starts in ER and goes to golgi
N-linked-> ER happens at nitrogen (covalent bond) (Asparagine)
-most common
O-linked-> Golgi- happens at oxygen (has OH group on sugar)
-subsequently- modification of N-linked sugars in golgi
Oligosaccharid protein transferase- present in ER membrane (peripheral or transmembrane) ALWAYS facing the lumen
*Only add sugars to proteins as oligosacchardies on the lumen side of the membrane
-Eventually the vesicle fuses w/ the membrane and the carbohydrates face the exterior of the cell
Post-translational processing
Folding and glycosylation
Membrane Asymmetry
N-terminus- out of the cell
-Starts at ER and is maintained
Golgi apparatus
Stacks of membrane bound vesicles called cisternae
CisFACE- side of Golgi facing cytosol towards ER- recieves products from the rough ER
transFACE- side of Golgi facing plasma membrane away from ER- ships products toward cell surface
-trans and cis cisterna are hard to tell apart except when using protein stains
-specific proteins are found in each type of cisterna
-Sequencial processing of sugars through the Golgi
Transport through golgi
-Vesicular transport model- smaller protein transport (bud from cisterna)
-Cisternal maturation model
-cisterna mature from cis-medial- trans
-allows cisterna to be renewed
-allows larger proteins that would not fit in the vesicle (i.e. collagen) to be transported
Vesicular Traffic
-Lipid interactions facilitate membrane transport
-donor compartment (budding)-> target compartment (fusion)
New vesicle forms w/ contents selected for transport
-protein coated vesicles-> facilitate the process of budding and deformation of membrane, recruiting
i.e. clathrin forms triskeleton- puts together 3 subunits of protein- very rigid
-Coat assembly and cargo formation
-Clathrin molecules get recruited and force deforming of membrane
-Bud formation: Clathrin bind to adaptin (binding sites for cargo receptors)- provides specificity of cargo selection
-Vesicle formation- dynamin- protein that mediates pinching off from donor compartment
group of proteins that target to different compartments
-can be re-used
Vesicle Targetting
t-SNARE/ v-SNARE (come from vesicles) bind to each other and form alpha helix
-also used for process of lipid bilayer fusion
*Used for docking of transport vesicles (first event)
-Only work in acidic envionment- pH b/w 5 and 6
-materials delivered by phagocytosis, autophagy, receptor-mediated endocytosis
Protein Sorting
Specificity of vesicular transport
-Enzymes can be activated
-Mannose-6-phosphate (M6P) enters golgi, binds to M6P receptor, enters lysosome-> removal of phosphate (dissociation at acidic pH)- acts as a safety mechanism
M6P- acts a zip code- targets proteins for vesicles that deliver their contents to lysosomes
Protein Sorting in Trans Golgi network (TGN)
Signal-mediated diverson to lysosomes (M6P)
-Signal-mediated diversion to secretory vesicles- for regulated secretion-(package cargo- high conc.- in vesicle- pH dependent)
-Constitutive secretory pathway- always occuring
-Transport vesicles bound for plasma membrane secrete their contents to the outside of the cell
-Vesicle membrane and plasma membrane make contact and fuse
-Two sets of lipid bilayers rearrange in a way that exposes the interior of the vesicle to the outside of the cell
-i.e. mast cells and horomone producing cells (insulin producing)
Pinching off of the plasma membrane that results in the uptake of material from the outside of the cell
3 mechanims:Pinocytosis, phagocytosis, receptor-mediated endocytosis
- cell drinking- uptake of fluids and small particles via tiny vesicles that form invaginations of the plasma membrane
-Cell eating- Uptake of large molecules
-very specialized- only phagocytic cells- i.e. white blood cells
Receptor-Mediated Endocytosis
Macromolecules outside the cell bind to membrane proteins that act as receptors
-Vesicle becomes coated- then uncoating occurs
-Fusion w/ endosome- sorting occurs in endosome
-dissociation of receptor from cargo
-Budding off of transport vesicles
i.e. entry of LDL into the cell from extra cellular environment
Synaptic transmission
Action potential- triggers release of neurotransmitter
-action potential arrives- triggers entry of Ca 2+
-In response to Ca 2+- synaptic vesicles fuse w/ presynaptic membrane- then release neurotransmitter
-Ion channels open when neurotransmitter binds
-ion flow causes change in postsynaptic cell potential
-Dynamin- wraps around vesicles- pinching off
-i.e Botanism-Botox- cleaves the SNARES and prevents neurotransmission
Plant ECM
-Cell Wall- Fiber composites- criss cross of cellulose and pectin fibers-> other sugars involved as well (glycan)- provides ridgity
-Cellulose- polysaccharide- main component
-Pectin- another component of plant cell wall- not as strong as cellulose-hydrophilic polysaccharides- waterproofing surface of plasma membrane- i.e. leaves
Animal ECM
Protein fibers instead of polysaccharide filaments (plant ecm)
-Collagen=most abundant protein
-3 imporant parts
1. gel- ground substance
2. structural fibers- i.e. collagen
3. Adhesive elemts- i.e. glycoproteins
Organized mixtures of many cell types
-arranged in particular patterns
Connective Tissue
Tissue type in animals made largely of ECM
-padding material- i.e. blood, bone, cartiledge
Tissues that form external and internal surfaces
-Form a layer that separates parts of the body that contain different solutions
i.e. urine vs. blood
The Gel Components of the ECM
Sugars- glycosaminoglycan (GAGS)- chain og sugars w/ amino group linked by covalent bonds-many negatively charged groups-sulfate/carboxyl groups

Core proteins- recruit GAGS-i.e. proteoglycan
Aggregates (Proteoglycan)
Very large- several proteoglycans come together. Can be the size of a bacteria
-Neg. charge-makes it osmotically actived- Na + ions drawn in so will draw in water
-ability to expand and contract- similiar to sponge- can absorb water
Space Filler- resistance to compression
-tissue morphogenesis and repair- manipulates ECM, causes swelling- forms gut in embryo
Animal specific- every cell has it- i.e. leather, gelatin
Structure: 3 chains that wind around each other to form a triple helix
-many collagen triple helixes put together form collagen fibrill- very weak bonds
-Many different types- coded by different genes (about 28)- collagen specific proteases- i.e. different for skin, bones, ear, nose- due to difference in structure
Cells that make collagen- gives strength to tissue
Collagen Synthesis
In ER/Golgi
-synthesis of pro-alpha chain- immature collagen
-Self-assembly of 3 pro-chains
-Exocytosis out of ER to golgi
-Then secretion thorough plasma membrane and pro-collagen will assemble into collagen molecule-more mature due to addition of OH groups to amino acids
-Self-assembly into fibril
-Aggregation of collagen fibrils to a form a collagen fiber
i.e. Scurvy- defects in collagen assembly- Vitamin C needed- OH groups cannot be added to amino acids
Adhesive Glycoproteins
-Fibronectin/Laminin- acts as bridging molecule b/w ECM and collagen molecule
*Multiple binding domains*- will bind to different proteoglycans, cell, collagen
-Multi-adhesive proteins- cross- linking components of the basal lamina- provides cushioning and support
Basement Membrane
Very strong- separates underlying tissue and supports cell- acts as barrier- diffusion possible
-important component of laminin
-tissue regeneration
Trans-membrane protein/ receptor
-integrates cell and ECM via fibronectin and laminin
-connected to plasma membrane by actin filaments
Integration w/ Cytoskeleton
Focal Adhesions- Uses actin filaments- concentrated area of integrins- uses actin filaments for cell crawling on substrate (components of ECM)
-always cell to anchor in environment
-uses many integrins to give strength- but like velcro- will eventually wear out
-important for migrating over a substrate- provides rigidity
Parallel array in the ECM
cells migrate into ECM and become elongated in shape and align parallel- very orderd
-weak adhesion and rolling- selectin dependent
-strong adhesion and emigration- integrin dependent
Cell-cell adhesion in leukocyte extravasation
Regulated exocytosis
-Recieves signal- puts out selectin receptor
-Binds to p-selectin-> weak interaction
-PAF activates integrin-> not all about cell ECM- also used by cell-cell adhesions (mediates)- Stronger affinity than selectins
-Firm adhesion via integrin binding
-Extravasation (makes its way outside of blood vessel)-> Integrin sends signal to change shape
Mediate cell-cell adhesions
-homophilic- only binds to another cadherin. i.e. N-cadherin to N-cadherin
-cell-cell recognition and cell sorting- by type (E-cadherin vs. N-cadherin), also by expression leveles- high vs. low
-Ca 2+ dependent
Adhesion Belt
Many cadherins together forming dense array- linked to actin filaments (cell-cell)
Function: Forms tubes- utlilizes contraction and motors w/ associated actin filaments
Uses intermediate filaments instead of actin- very similar to adhesion belts
-structural stability- allows streching
Tight Junctions (Occluding Junctions)
Essentially closes gap between cell
-commonly found in gut
-Nutrients able to go through- but barrier to toxins
-Only in epitheial cells
-Trans-cellular transport across intestinal epithelium
- one direction-> drives into blood stream
Co-transporter- transport glucose in opposite direction
-uses energy from sodium gradient (high conc outside, low inside)- used to drive glucose against its concentration gradient
Gap Junctions
Open gates within adjacent cells
-Size restriction-> up to 1000 Dalton can go through- ions, monomers, nucelotides, amino acids, proteins CANNOT
-Connexins- proteins that line gap junctions- many connexins from a channel, where communication happens
-Oocyte- support from surrounding cells- gap junctions link nurse cells to oocyte- metabolic and chemical coupling
-Closer to basal
-Plasmodesmata= gap junction in plant cells
Downstream from signals. Cause a cascade of signals- like dominos
Signal Transduction
The conversion of a signal from one form to another
Intracellular signaling proteins
Target proteins that produce altered metabolism, altered gene expression, and altered cell shape or movement
Properties of cell-cell signaling
Amplification: 1 molecule binds to receptor- produces many products
-cascade of enzymes being activated
Divergence to multiple targets: 1 signalling molecule activates many enzymes
Cell-surface receptor
Hydrophillic signal molecule on cell surface
Intracellular Receptors
Small hydrophobic signal molecule
-receptor in nucleus
Steroid Horomones
Nuclear receptors- intracellular receptors
-have DNA binding domain- like TFs
-bind to receptor protein-> conformational change- activates receptor protein
-Activated receptor- cortisol complex moves into nucleus
-Activated receptor-cortisol complex binds to regulatory region of target gene and activates transcription
-Cascade of genes to be transcribed
G-protein linked receptors
Ligand binding region- specificity
-Multipass transmembrane system
-Receptor binds to ligand- recruits G-proteins (peripheral)- can readily move within lipid bilayer
-activates G-protein by binding to GTP (switch)
-When GTP is hydrolyzed to GDP (inactive)
-Enzyme activation by G-protein- adenyly cyclase found in plasma membrane (trans-membrane protein)- activated by conformational change
-once activated can convert ATP to cAMP (intracellular messenger molecule)
Used during signal transduction
-Serine side chain- has OH group-> Phosphat group added facilitated by protein kinase (PKA) uses ATP to make ADP
Protein phosphatase- dephosphorylates- but can still be activated
Second Messengers
Non-protein signaling molecules that increase in concentration inside a cell and elicit a response to the received signal
-They are intracellular signals that spread the message carried by the extracellular signal- the horomone
Receptor Tyrosine Kinases (RTKs)
-growth factors
-Can be soluble and found in extracellular space
-Can also bind to ECM
-Must be activated
-Inactive receptor tyrosine kinase-> signal molecule in form of a dimer (receptor dimerization) -> phosphorylates itself bc tyrosine kinase domains are so close (autophosphorylation)
Activation of Ras by RTK- adaptor protein attached to activated RTK recruits proteins that activate Ras
Regulation of glucose uptake by insulin
-When glucose levels are high-insulin activated to get glucose into the cell
-Insulin-stimulated cells-more transporters- signal binds to insulin receptor and causes relocalization of glucose receptors to plasma membrane to boost glucose uptake into the cell
-Can use endocytosis to shut off signal- brings it into the cell
Amino Acids
Amino group (NH2), Carboxyl group (COOH)-> acidic due to highly electronegative oxygens, makes it easy to lose a proton, R side chain- if has OH group, S, NH2 = polar-hydrophillic
Process of linking monomers- amino acids polymerize to form proteins
-done so through condensation reactions (dehydration reactions)-loss of water molecule
Breaks polymers apart by adding a water molecule
-dominate in comparison to condensation bc it increase entropy and bc it is energentically favorable- lowers the potential energy of the electrons involved
Peptide Bond
C-N bond b/w amino acids due to condensation reactions
-stable bc electrons are partially shared bw the neighboring carbonyl functional group and the peptide bond
Series of amino acids linked by peptide bonds
Backbone- side chains stick out, it has directionality, and it is flexible
left side- amino group- N terminus
right side- carboxyl group- C terminus
Primary Structure
Unique sequence of amino acids in a protein (backbone polypeptide chain)
Secondary Structure
Folding due to hydrogen bonding that occurs bw the carboxyl oxgyen of one amino acid and the hydrogen on the amino group of another
-Not interactions among side chains but bw amino acids on backbone
types: alpha-helix: H-bonds parallel to molecular axis, B-pleated-sheet- sturdier, stronger, H-bonds perpendicular to molecular axis
-Large # of H-bonds makes these structures highly stable
Tertiary Structure
Long-range folding due to interactions b/w R-groups or b/w R-groups and the peptide backbone
-Disulfide bonds- covalent bonds that form b/w sulfur atoms due to redo reactions bw sulfur containing R-groups (cystein)- referred to as bridges
van der Waals interactions: water molecules interact w/ hydrophillic side chains causing the hydrophobic side chains to coalesce- once they hydrophobic side chains become close to each other they are stabilized by such electrical attractions- minute partial charge on one molecule induces an opposite partial chagrge in the nearby molecule causing an attraction - increase stability
-Ionic bonds: b/w groups that have full and opposing charges-i.e. ionized amino and carboxyl functional groups
-Hydrogen bonds:b/w hydrogen atoms and the carboxyl group in the peptide-bonded backbone and b/w hydrogen and atoms w/ partial negative charges in side chains
Quaternary Structure
Combination of polypeptides as subunits- non-covalent interactions- may be held together by bonds or other interactions among R-groups or sections of their peptide backbones
Spontaneous bc folded molecule is more energetically stable
-facilitated by molecular chaperones
-denaturation- unfolding of proteins- disulfide and hydrogen bonds are broken
Different types of proteins
Movement-motor and contractile proteins
Catalysis-enzymes-speed up chemical reactions
Signaling-Peptide horomones-bind to receptor proteins
Structure-Fingernails, hair
Other molecules that bind to enzyme to make them more active- i.e. Zn+, Mg 2+, other organic molecules (coenzymes)
Competitive Inhibition
Molecular that is similar in size and shape to the substrate binds to the active site preventing binding of substrate
Allosteric Reulation
A regulatory molecule binds at a location other than the active site- binding changes shape of the enzyme in a way that makes the active site accessible or inacessible- conformational change
A phosphate group (neg charged) covalently linked to 5-carbon sugar arranged in a ring (ribose or deoxyribose)- covalently linked to a nitrogenous base (C,U,T,A,G) w/ the 1' carbon
Phosphodiester bond
B/w nucleotides- formed by condensation reaction- joins the 5' carbon on the ribose of one nucleotide to the 3' carbon on the ribose of the other
-Polar- free 5' and 3' phosphate group and sugar on the end
Single-ringed base, C,U,T
- no mechanism for pre-biotic synthesis
Double-ringed base, G,A
-Pre-biotic synthesis possible
single-stranded-> secondary structure similar to protein- can be hairpin structure- stems and loops- stems- neighboring base-pairing (intra-molecular)
RNA world
Autocatlysis: ribozymes-> base-pairing w/ substrate
-Central role of different RNA molecules in protein synthesis
-Protein synthesis takes place in the absence of DNA, but not RNA
-Replicating biological system- such as viroids and RNA viruses
-Catalytic and Autocatylic responses of RNA
-DNA must be created from enzymes- hard to produce in the cell
Polymers that form when monosaccharides are linked together- i.e. glucose
-may be used to store energy in the form of starch or glycogen
Simple sugar- carbonyl group and hydroxyl groups
Glycosidic Bond
Bond b/w sugar units- always b/w hydroxyl groups-> reactive bond in dissacharide
-formed by condensation reaction
-analgous to peptide bonds (proteins) and phosphodiester bonds (nucleotides)
-location and geometry can vary widely among polysaccharides unlike the other two which always form at the same location in their monomer
Alpha-glucose monomers that are joine by glycosidic linkages- branched and unbranched molecules
-used as storage in plants
-storage role in animals- similar to starch in plants
-nearly identical to branched form of starch
major component of the cell wall
-each glucose monomer in the chain is flipped in relation to the adjacent monomer- increase the stability of cellulose strands- due to increased H-bonds
Cell recogniton and signaling- protein w/ sugar attached
Carbon-containing compound that are found in all organism and are largely nonpolar and hydrophobic
3 major classes: steroid, phospholipds, fats
Fatty Acid
Hydrocarbon chain bonded to a carboxyl functional group (hydrophillic head)
Amphipathic- hydrophilic and hydrophobic components
3 carbon molecule called glycerol that is linked to a phosphate group- gives to polarity w/ a neg charge
4-ring structure- hydrocarbon chain w/ OH groups- makes it polar
i.e. cholesterol
Plasma membrane
composed primarily of phospholipids and cholesterol
Phospolipid Bilayer
-Hydrophilic heads interact w/ water
-Hydrophobic tails interact w/ each other
-Thus, nonpolar on inside, polar on outside
-sealed compartment
-Carbohydrate groups-provide aqueous surface on top of cell
-Selective permeability:
High permeability- small, non polar molecules
Low permeability- large, polar molecules and ions
The Fluid Mosaic Model
-Amphipathic lipids/proteins and membrane structure- peripheral membrane protein
Integral membrane protein (transmembrane)- tightly embedded in bilayer
-Dynamic and Fluid
Membrane Fluidity
Unsaturated chain- double bond exists b/w to carbon atoms- cause kinks in phospholipid tails- more fluid bc kinks produce spaces among tightly packed tails- reduce the strength of hydrophobic interactions among the tails
-Saturated fatty acid- more bonding opportunity- less fluid
-Length: Longer hydrocarbon chain- less fluid bc hydrophobic interactions become stronger
Cholesterol: increase ridgity-goes in between phospholipids- however- can also create disorder providing fluidity
Membrane proteins
anchor- allow cell-cell interaction
-recieves external stimulus-senses environment
Membrane Transport
Combination of size and charge that affect permeability- need transport proteins to facilitate
Passive movemet along an electrochemical gradient, through a membrane or a channel- no help needed- high to low concentration
Facilitated Diffusion
Passive movement- but facilitated by proteins to make an opening- but still high to low concentration
Active Transport
Low concentration to high concentration-> NEEDS ENERGY- thus active movement
-uses phosphate groups from ATP
Carrier Protein
Like a gate-> used for facilitated diffusion + active transport- binds specifically to solute-> conformational change- then opens to other side- VERY SPECIFIC
Channel Protein
Open gate w/ aqueous pore- much faster than carrier protein
-also called ion transport bc usually ions that transfer- HIGHLY SELECTIVE
Great deal of potential energy
- 3 phosphate groups in ATP contain a total of 4 negative charges confined to a small area- thus charges repel each other so large potential energy
-When ATP reacts w/ water during a hydrolysis reaction- the bond bw ATP's outermost phosphate group and its neighbor is broken resulting in the formation of ADP and inorganic phosphate- highly exergonic
Activated carrier molecule
Has high energy bond that is readily broken to give off energy, small molecules, able to diffuse and move quickly throughout cell, nucelotide derivatives
i.e. FAD+ 2H++ 2e-->FADH2
NADP+->NADPH- reduced- highest level of energy
-ATP gives phosphate group to glucose
-Isomerization-> glucose-6-phosphate to fructose-6-phosphate
-Phosphorylated again- from ATP molecule-catylzed by enzyme
-Allosteric inhibiton by ATP
-Splitting of 6 carbon sugar into 2 3-carbon sugars
-4 ATP molecules made-> but 2 used- so net of 2 ATP and 2 molecules of pyruvate, 2 NADH
In the absence of electron acceptor- used to produce ATP- uses pyruvate- accepts electrons from NADH and produces lactate
-also pyruvate to make ethanol
-ensures glycolysis continues
-Recycles NADH to make NAD+
MANY-#s depend on need
-Many membranes- increase surface area- double membrane organelle- infolding (cristae) in matrix
Pre-Krebs Cycle
Pyruvate is converted to an acetyl CoA intermediate by pyruvate dehydrogenase
-mediated by 3 enzymes that come together as a large complex- coenzymes-bind to enzyme's active site and stabilize the reaction's transition state
-pyruvate- carboxyl group comes off->oxidized to CO2
-Acetyl CoA reacts w/ oxaloacetate to produce citrate
Krebs Cycle
Goal: To oxidize Acetyl CoA to CO2-> 8 steps
-very efficient- can continue to reuse molecules as long as pyruvate is present
Net Result: 3 NADH, 1 GTP, 1 FADH2, 2 CO2
Chemiosmotic Theory
The connection b/w electron transport and ATP generation is indirect- no high energy intermeidate- two seperate steps
Electron Transport Chain
Inner membrane of mitochondria
-proteins pump protons (H+) into intermembrane space
-strict membrane requirement-H+ pumped from matrix to intermembrane space in 2 different steps
-Electrons from NADH and FADH pass through molecules (proteins and Q) with lower electronegativity to one w/ high electronegativity via redox reactions- oxygen= final electron acceptor
-proteins are pumped by 3 complexes- Q and cytochome C act as shuttles that transfer electrons between complexes
Chemisosmotic Coupling
Protons pumped into intermembrane space- pH changes from 8-7, creates proton gradient
-ATP synthase acts as a moter- stationary w/ moving parts
-H+ travel b/w arm and base on ATP synthase causes conformational change causing the head to rotate producing ATP from ADP
-also electrochemical gradient caused by movement of H+- drives ATP synthase
Outer/Inner membrane
-Thylakoids-vesicle like structures- often occur in interconnected stacks called grana. Space inside a thylakoid is its lumen
-Fluid filled space between the thylakoids and the inner membrane is the stroma
The most abundant pigment found in the thylakoid membrane
-absorbs blue and red light and reflects green light
-two types: a and b