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Dr. V at Tulane's Biology
142
Biology
Undergraduate 1
06/22/2011

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Term
Light Reactions
Definition
Light Dependent

Light energy is captured and converted into chemical energy (ATP and NADPH).

Take place at thylakoid membrane.
Term
Calvin Cycle
Definition
Light Independent

ATP and NADPH are used to drive synthesis of carbohydrates.

Take place in stroma.
Term
Heterotroph
Definition
Must eat food, organic molecules from their environment to sustain life
Term
Autotroph
Definition
Make organic molecules from inorganic sources
Term
Phototroph
Definition
Autotrophs that use light as a source of energy to make organic molecules
Term
Chloroplasts
Definition
Semiautonomous organelles found in plant and algal cells that carry out photosynthesis. Contain large quantities of chlorophyll.

Outer, Inner, & Thylakoid membrane
Intermembrane Space
Stroma
Term
The majority of photosynthesis occurs in the ___________.
Definition
leaves (the internal part of the leaf is called mesophyll)
Term
Carbon dioxide enters and oxygen exits the leaf via pores called ______.
Definition
stomata
Term
Chlorophyll contained in ______________.
Definition
thylakoid membrane
Term
3 chemical products of light reactions
Definition
ATP, NADPH, O2
Term
NADPH
Definition
An energy intermediate
nicotinamide adenine dinucleotide phosphate
can accept 2 electrons
presence of additional phosphate grp (difference from NADH)
Term
Visible light detected by human eye
Definition
380-740nm
Term
In photosynthesis, ATP is regenerated by _________.
Definition
photophophorylation
Term
Biosphere
Definition
regions of earth and atmosphere where living organisms exist
Term
Reason for Speciation
Definition
Plants production of O2
Term
Light Energy
Definition
type of electromagnetic radiation
travels as waves (shorter= more energy)
photons
Term
Fate of Photons
Definition
1. pass through object (no change)
2. change path of light (no change)
3. object may absorb light (change)
Term
Pigment
Definition
A molecule that can absorb light energy
Term
Light energy may be absorbed by _________________________________________.
Definition
boosting electrons to higher energy levels
Term
Excited State
Definition
An electron that has absorbed energy
Term
Chlorophyll
Definition
2 types: a & b
Both are bound to integral membrane proteins in the thylakoid membrane.

Porphyrin ring
Mg is bound to porphyrin ring
Delocalized electron (can absorb light energy)

Phytol tail
Long hydrocarbon structure, hydrophobic
Anchors pigment to the surface of proteins within the thylakoid membrane.
Term
Carotenoids
Definition
Type of pigment found in chloroplasts
Yellow -> Orange -> Red
Term
Absorption Spectrun
Definition
Range & Efficiency

wavelengths are absorbed by different pigments
Term
Action Spectrum
Definition
Effectiveness to promote photosynthesis
Term
Pigment with maximum absorption spectrum?
Definition
Chlorophyll a (additional methyl grp than Chlorophyll b)
Term
PSI and PSII
Definition
Two distinct complexes of proteins and pigment molecules that capture light located in the thylakoid membrane.
Term
Light Dependent Reaction stages
Definition
1. Primary Photoevent
2. Charge Separation
3. Electron Transport
4. Chemiosmosis
Term
Excited electrons are moved out of PSII by?
Definition
QB
Term
PSI makes:
Definition
NADPH
Term
PSII makes:
Definition
O2, ATP
Term
PSI
Definition
13 proteins
130 chlorophyll pigments
P700nm
functions 2nd
Term
PSII
Definition
functions first
19 proteins
250 chlorophyll
P680 nm (more energy than 700)
P680->pheophytin->QA->QB
Term
Cyclic Electron flow
Definition
aka Cyclic Photophosphortylation
18ATP & 12 NADPH

electron cycling releases energy to transport H+ into lumen during synthesis of ATP. Ferrodoxin will not make NADPH because it has enough NADPH but not enough ATP. Takes electrons to QB. Never use PSII, no O2, no breakdown of H2O
Term
Noncyclic electron flow
Definition
electron begins at PSII and eventually transfers to NADPH

linear process produces ATP and NADPH equally (18ATP & 12 NADPH)
Term
Prokaryotic vs. Eukaryotic (Photosynthesis)
Definition
Prokaryotes only use PSI, only produce ATP (no O or NADPH), not as efficient
Term
Calvin Cycle
Definition
ATP and NADPH are used to make carbohydrates

inorganic C-> organic compound
direct production: glyceraldehyde-3-phosphate (NOT glucose)
Term
3 Phases of Calvin Cycle
Definition
1. Carbon Fixation
2. Reduction and Carbohydrate production
3. Regeneragtion of RuBP
Term
For every 6CO2 incorporated, ___ ATP and ___ NADPH are used.
Definition
18 ATP and 12 NADPH
Term
Actual Calvin Cycle
Definition
6X RuBP-- +6X CO2--> 12X 3PG --> 12X 1,3-BPG --> 12X G3P (repeat)

10 G3P- regenerate Rubisco
2 G3P- make glucose by reverse glycolysis
Term
C3
Definition
90% of plants species on Earth
named because 3PG is a 3 carbon molecule
Term
Photorespiration
Definition
active site of Rubisco can also function as an oxygenase (but affinity for CO2 is 10fold than for O2)

when O2 is high and CO2 low, Rubisco adds O2 to RuBP

RuBP+O2--> 1X 3PG + Phosphoglycolate (2C)
Term
C4
Definition
minimizes photorespiration
mesophyll cells & bundle sheath cells

(3C)Phosphoenolpyruvate (PEP)--+CO2--> 4C Oxaloacetate by PEP Carboxylase (does not recognize O2=> minimizes photorespiration)

eventually enters Calvin cylcle
Term
CAM plants
Definition
some C4 plants separate processes using time
Crassulacean Acid Metabolism
Stomata close at nigh
ex. cactus
Term
2 reasons why cells need to respond to signals
Definition
1. Need to respond to a changing environment
2. Cells need to communicate with each other
Term
Phototropism
Definition
Property (investigated by Darwin and son) that allows a plant to move towards light
Term
Auxin
Definition
a signaling molecule transmitted from cell to cell and inhibited by the light
Term
Direct Intercellular Signaling
Definition
Cell junctions allow signaling molecules to pass from one cell to another
Directly connected tissue
Term
Contact Dependent Signaling
Definition
Some molecules are BOUND to the surface of cells and serve as signals to cell coming in contact with them.
No energy to move
Term
Autocrine Signaling
Definition
Cells secrete signaling molecules that bind to their OWN cell surface or neighboring cells of the same type.
Term
Paracrine Signaling
Definition
Signal does not affect cell secreting the signal but does influence cells in close proximity (SYNAPTIC signaling)
LOCALIZED & SHORT-LIVED
Term
Endocrine Signaling
Definition
Signals (hormones) travel LONG distances and are usually LONGER-LASTING
Term
3 stages of Cell Signaling
Definition
1. Receptor Activation
2. Signal Transduction
3. Cellular Response
Term
Possible Cellular Responses
Definition
Alter activity of 1 or more enzymes
Alter structural protein function
Change gene expression (transcription)
*NEVER Change gene EXPRESSION*
Term
Ligand
Definition
=signaling molecule
binds noncovalently to receptor
very specific
very rapid
causes conformational change
Term
Types of Cell Surface Receptors
Definition
1. Enzyme-linked receptors
2. G-protein couples receptors (GPCR)
3. Ligand-gated ion channels
Term
Enzyme-linked receptor
Definition
A cell surface receptor
Found in ALL living species.
Extracellular domain binds signal.
Present on plasma membrane.
Causes intracellular domain to become functional catalyst.
Most are protein KINASES (add or take Pi).
Has aa: serine, theorine, TYROSINE.
Term
G-protein couples receptors (GPCR)
Definition
A cell surface receptor
Common in EUKARYOTES.
Protein has 7 TRANSMEMBRANE (pass/multipass) segments.
Activated receptor binds to G-protein.
Releases GDP (inactive) and binds GTP (active) instead.
GTP causes G-protein to disassociate.
a-subunit and B/y-dimer interact with other proteins in a signaling pathway.
Term
What happens when GPCR's signal is gone?
Definition
a-subunit recognizes loss and hydrolyzes GTP -> GDP + Pi which then breaks into a-GDP & B/y (inactive state)
Term
Is G-protein a transmembrane protein?
Definition
No, the receptor is a transmembrane protein.
Term
Ligand-gated ion channels
Definition
A cell surface receptor
Found in plant AND animal cells
Ligand binding causes ion channels to open and ions to flow through membrane.
In animals: signals btwn nerve & muscle cells, btwn 2 nerve cells, Ca2+ uptake
Term
Intracellular Receptors
Definition
More rare compared to cell surface receptors.
ex) Estrogen Rs are in nucleus. Estrogen-R dimer complexes bind to DNA to activate transcription
ex2) Auxin
Term
Auxin
Definition
An indirect transcription factor
1. Auxin binds to TIR1 in cytosol
2. Activated TIR1 enters nucleus and causes breakdown of a protein that inhibits several genes that are needed for cell division. These genes are then transcribed into mRNA, and the mRNA is translated into proteins that promote cell division.
Term
Transcription factors regulate _________________.
Definition
transcription of specific genes
Term
Tyrosine Kinases
Definition
A category of enzyme-linked receptors found in animals.

Recognizes various types of signaling molecules (ex. Growth factor).

EGF (Epidermal Growth Factor) stimulates epidermal cells to divide.
Term
Second Messengers
Definition
Signals binding to cell surface are 1st messenger.
Many signal transduction pathways lead to production of 2nd messengers.
RELAY information.

ex. cAMP, Ca2+, Diacyglycerol (DAG) , & inositol triphosphate (IP3)
Term
cAMP
Definition
cyclic adenosine monophosphate
adenylyl cyclase stimulate synthesis
can activate protein kinase A (PKA)
2 advantages: Signal Amplification & Speed
Term
ECM
Definition
Extra Cellular Matrix
=proteins (strength) and polysaccharides (gel-like)secreted by exocytosis from ER form a complex meshwork outside of cells.

ex. bone, cartilage, woody part of plants
Term
Proteins of ECM
Definition
1. Adhesive
help cells adhere to ECM
ex. Fibronectin & Caminin
2. Structural
ex. Collagen & Elastin
Term
Fibronectin
Definition
Adhesive protein of ECM
connects
Term
Caminin
Definition
Adhesive protein of ECM
skin
Term
Collagen
Definition
Structual protein of ECM
provides tensile strength
found in bone, cartilage, tendon, skin
Term
Elastin
Definition
Structural protein of ECM
needed in ares taht expand and return to original shape
covalent cross links
ex. blood vessels
Term
Most abundant polysaccharide in animal ECM?
Definition
glycosaminoglycans (GAGs)
-long, unbranched with repeating disaccharide unit
-highly negative charge attracts ions and water
-majority linked to core proteins to form proteoglycans
Term
Primary cell wall
Definition
in plant cell walls
-develops btwn newly made cells
-flexible and allows for size increase
-main macromolecules:
1. cellulose (thick microfiber)
2. hemi-cellulose (think microfibers, any sugar BUT glucose)
3. glycans (branched polysaccharide)
4. pectins (charged polysaccharide, highly negative)
Term
Secondary Cell Wall
Definition
in plant cell walls
-layers of cellulose, lignin & other components
-more variable structure than primary cell wall
Term
Cell Junctions
Definition
Proteins that allow cells of a certain tissue to be associated with each other.

adhere cells to each other and ECM

animal cells are more varied

plants' cellular organization is diff bc of rigid cell wall
Term
_____ activates PKA (protein kinase A).
Definition
cAMP (by binding to the regulatory subunits of PKA which release the catalytic subunits)
Term
Activate PKA phosphorlyzes ________ & ____________.
Definition
phosphorlyase kinase (inactive) & glycogen synthase (active) (both involved in metabolism of glycogen)
Term
________ converts cAMP to AMP
Definition
Phosphodiesterase
Term
DAG & IP3 pathway
Definition
Signaling molecule binds to GPCR, then activates G-protein. Instead of activating adenylate cyclase (to make cAMP), the a subunit activates PHOSPHOLIPASE C. This breaks a covalent bond in a plasma membrane phopholipid with an inositol head group, producing DAG and IP3.
Term
IP3 binds a ligand-gated Ca2+ channel in ER membrane and causes?
Definition
the channel to open, releasing Ca2+ into the cytosol. Ca ions act as 2nd messengers now. Ca2+ can bind to PKC(which in combo with DAG, activates PKC) or bind to calmodulin
Term
Open Ca channels cause?
Definition
plants-phototropism, opening and closing of stomata, gravitropism

animals- nerve transmission, muscle contraction, secretion of digestive enzymes
Term
Epinephrine
Definition
heart muscle cells contraction
Ca store in sarcoplasmic reticulum
ca binds to troponin leading to muscle contraction
dropping ca causes muscle to relax
PHOSPHOLAMBAN activates Ca pump
activates adenylyl cyclase (prod. cAMP)
Term
cAMP activates PKA to phosphoylate _______ & ________.
Definition
troponin & phospholamban
Term
Ca concentrations in SER, cytosol, and outside of cell?
Definition
high, low, high
Term
Troponin has a lot of _______ receptors.
Definition
Ca2+
Term
Formation of Structural Proteins of ECM
Definition
usually made in ER lumen in form of a-fibers (3a-fibers=pro-collagen, has extensions that prevent lengthening and increase thickness)

Pro-collagen secreted in vesicles, extensions dissolve, and pro-collagens combine.
Term
Anchoring Junctions (4 types & function?)
Definition
-connect, hold, attach cells to each other and to ECM
-rely on Cell Adhesion Molecules (CAM) (cadherin & integrin)

1. adherins junctions
2. desmosomes
3. local adhesions
4. hemidesmosomes
Term
Adherens
Definition
A type of Anchoring Junction
CAM: Cadherin
Type of Adhesion: Cell to Cell
Cytoskeletal Protein: Actin
Term
Desmosomes
Definition
A type of Anchoring Junction
CAM: Cadherin
Type of Adhesion: Cell to Cell
Cytoskeletal Protein: Intermediate fibers
Term
Focal Adhesion
Definition
A type of Anchoring Junction
CAM: Integrin
Type of Adhesion: Cell to ECM
Cytoskeletal Protein: Actin
Term
Hemidesmosomes
Definition
A type of Anchoring Junction
CAM: Integrin
Type of Adhesion: Cell to ECM
Cytoskeletal Protein: Intermediate fibers
Term
Cadherin
Definition
-Cell to Cell junctions
-Major CAMs of vertebrates
-Dimer of identical subunits
-Extracellular domain of 2 cadherin dimers in adjacent cells bind to each other to promote cell-to-cell adhesion
-Inside cell, linker proteins connect cadherins to the cytoskeleton
Term
Integrins
Definition
-Transmembrane proteins
-group of cell surface receptor proteins
-extracellular domain for binding cell to ECM
-intracellular domain for binding to cytoskeleton
Term
Tight Junctions
Definition
-or occluding junctions
-forms tight seal btwn adjacent cells
-prevents ECM from leaking btwn cells
-made by occludin & claudin (bind to each other to form tight seal, not mechanically strong, not bound to cytoskeleton)
Term
Signals Outside Affect?
Definition
cell adhesion
cell migration
cell growth
Term
Signals Inside affect?
Definition
alter ability to bind to components in ECM
lowering/increasing affinity
cell adhesion
migration
Term
Gap Junctions
Definition
aka communicating
-sm gap btwn plasma membrane of cells at junction
-6 connexin proteins in 1 cell align with 6 in an adjacent cell to form a connexon
-connexon allows passage of ions and sm molecules, sharing of metabolites & directly signal on each other
Term
Middle Lamella
Definition
In plant cells
-Dont form cell-to-cell connections
-An additional component of ECM
-1st layer forms when cells dividing
-cement cell walls of adjacent cells together
-rich in PECTIN (ripening fruit secrete pectinases so that ripe fruit is less firm)
Term
Plasmodesmata
Definition
-functionally similar to gap junctions
-allow passage of ions, water, signaling molecules btwn cells
-diff bc they are open channels where the cell membrane of 1 cell is continuous with adjacent cell membrane
-desmotubule connects ER membrane of adj. cells
Term
Infections in plant cells move easily because of _________.
Definition
the desmotuble (plasmodesmata).
Term
_______ contain the genetic material.
Definition
Chromosomes
Term
Chromosomes are composed of _________ & ________.
Definition
DNA & proteins
Term
Primary function of genetic material?
Definition
To store needed information
Term
__________ is the DNA-protein complex making up chromosomes.
Definition
Chromatin
Term
The longest chromosome?
Definition
chromosome 1
Term
the shortest choromosome?
Definition
chromosome 22
Term
DNA wraps itself around _________.
Definition
histone proteins
Term
Nucleosome
Definition
11nm in diameter
A repeating unit of DNA wrapped around an octamer of histone proteins.

The negative charges of DNA are attracted to the positive charges of histones.

200 nucleotide base pairs
Term
Octamer
Definition
8 histone proteins + 146 nucleotide base pairs

H2- 2 copies
H2- 2 copies
H3- 2 copies
H4- 2 copies
Term
What brings nucleosomes closer together?
Definition
Linker proteins
Term
DNA length would be ____.
Definition
1 meter!
Term
Histone proteins
Definition
very basic proteins
large number of positively charged lysine & arginine aa. (negative charge of DNA is attracted to this positive charge)
Term
MAR/ SAR
Definition
Matrix Attachment Region/ Scaffold Attachment Region

associated with histone linker protein that brings nucleosomes together to form 30 nm fibers.
Term
30 nm fibers
Definition
Made when nucleosomes are organized into a more compact structure (shortens nucleosome structure by 7fold)

interact/anchored with the nuclear matrix

compacts 30nm fiber by formation of RADIAL LOOP domains
Term
Is compaction uniform?
Definition
No
Term
Do chromosomes overlap?
Definition
No they are located in discrete non-overlapping chromosome territory. Different chromosomes are not substantially intertwined even when non-compacted.
Term
Heterochromatin
Definition
-HIGHLY compacted
-transcriptionally INACTIVE
-some localized regions in non-dividing cells
-radial loops (30 nm in range of 700nm)
Term
Euchromatin
Definition
-LESS condensed
-capable of GENE TRANSCRIPTION
-Most chromosomal regions in non-dividing cells
-radial loops (30nm in range of 300nm)
-LIGHTLY stained
-ALL euchromatin converted to heterochromatin when preparing to divide (most transcriptional activites cease during cell division)
Term
Metaphase chromosomes
Definition
-MAXIMUM compaction
-1400nm by condensin and cohesin (proteins)
-highly compacted radial loops remain anchored to a scaffold formed from proteins in the nuclear matrix
-when all euchromatin are converted to heterochromatin
Term
Mitosis
Definition
=cell division in eukaryotes that requires a replication & sorting process that is more complicated
- cell divides to produce 2 new cells (daughters) genetically identical to the original (mother)
-plants: asexual reproduction
-animals:production & maintenance of multicellularity
Term
Diploid
Definition
2n (humans n=23)
Term
Haploid
Definition
1n (gametes have 1 member of each pair)
Term
Homologous
Definition
genetically similar 99%
Term
5 Stages of Mitosis
Definition
1. G1
2. S
3. G2
4. M
5. C
AKA cell cycle
Term
Interphase
Definition
Phase G1, S, & G2
Term
Go (zero) phase
Definition
A cell in this phase has either postponed dividing or decided to never divide again
ex. nerve cells
Term
G1 phase
Definition
1st gap
-cell prepares to divide
-accumulating nutrients to grow, etc
-reaches restriction point (can only go forward)
-maximum density
-takes the longest
Term
S phase
Definition
synthetic
-chromosomes are replicated. the double strands unwind & copy
-at end of S, cell has twice as many chromatids as chromosomes in G1
ex. 46 chromosomes in G1-> 46 pairs of sister chromatids, 92 sister chromatin, 46 centromeres in S phase
Term
___________ tell you how many chromosomes there were to begin with.
Definition
Centromeres
Term
G2 phase
Definition
-Organelles DIVIDE
- cell prepares for genomic separation
-deposition of KINECTOCHORE around centromere
-microtubules begin to assemble
-chromosomes CONDENSE
Term
M phase
Definition
-where mitosis occurs
-distributes the replicated chromosomes to the two daughter cells
(1. Interphase)
2. Prophase
3. Prometaphase
4. Metaphase
5. Anaphase
6. Telophase
(7. Cytokinesis)
Term
Prophase
Definition
1st phase of mitosis
-chromosomes start condensing
-nuclear membrane broken into vesicles
-nucleolus disappears
-microtubules formed by rapid polymerization of tubulin protein (3 types)
-mitotic spindle forms
-kinetochores begin to mature & attach to spindle
Term
3 types of spindle microtubles
Definition
formed in prophase but not functional until prometaphase
1. Aster (astral)
-imp for positioning of spindle apparatus
2. Polar
-help to push the poles away from each other
3. Kinetochore
-attach to the kinetochore, which is bound to centromere of each individual chromosome
Term
Prometaphase
Definition
-mitotic spindle completely formed
-centrosomes move apart
-spindle fibers interact with sisters
-2 kinetochores on each pair of sisters are attached to kinetochore microtubules from opposite poles
Term
Metaphase
Definition
pairs of sister chormatids ALIGN in a single row
Term
Anaphase
Definition
sister chromatids are pulled towards poles
-poles move apart
-centromeres move toward poles
Term
Telophase
Definition
aka reverse prophase
-spindle disassembled
-nuclear envelope forms around each set of sisters
Term
Cytokinesis
Definition
-cleavage of cell into 2 halves
animal cells: constriction belt of actin filaments, cleavage furrow, constricts like drawstring
plants: cell plate grows outward, space between cells get pectin (middle lamella)
Term
Cyclins/Cyclin-dependent kinases (cdks)
Definition
-responsible for advancing a cell through the phases of the cell cycle
-3 checkpoints (G1/restriction point, G2, & Metaphase)
Term
Meiosis
Definition
=sexual reproduction requires a fertilization event in which two haploid gametes unite to create a diploid cell called a zygote
-process by which haploid cells are produced from a cell that was originally diploid
-begins after interphase
Term
3 key differences between Meiosis and Mitosis
Definition
1. Homologous pairs form a bivalent/tetrad (synapsis)
2. crossing over
3. reduction division
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