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notes for biology 1201 final, Study notes of Biology

Louisiana State University at Alexandria Biology

study notes for biology 1201 final exam

Typology: Study notes

2019/2020

Uploaded on 02/22/2022

ashton-porche 🇺🇸

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Biology 1201 Final

Chapter 1

• Qualifications of LIFE:

• order

• reproduction

• energy use

• growth and development

• response to environment

• homeostasis (internal response to the environment)

• evolutionary adaptation (longterm responses to the environment)

•

system: combination of components working together

•

to know how a system works requires understanding of interaction of its parts

•

examples: cells, ecosystem, etc

•

systems are usually complex to study in full

•

Reductionism (small picture) vs. Systems Biology (big picture)

•

there are 2 types of Biology :

•

Discovery Sciences: descriptive or comparative biology

•

uses inductive based logic and reasoning (drawing generalizations from observations

with no prior knowledge)

•

Hypothesis-Based Sciences: forms a testable hypothesis based on observations

•

uses deductive logic and reasoning (drawing specific conclusion from generalizations; if

then logic)

•

observations, hypothesis, experimentation, data analysis, conclusion (scientific method)

•

hypothesis: an untested assertion

•

theory: in broad scope, and often complex.

•

supported by a large body of evidence

•

ex: Theory of Relativity, Germ Theory, Theory of Evolution

•

Law: fact that can be proven mathematically

•

generally simple, straightforward concept

•

ex: Law of Conservation of Mass and Energy, Boyle’s Law of Gases

Chapter 2

•

elements: consist of a certain atom and molecule, and cannot be broken down into any

other substance

•

molecule: two or more atoms held together by a covalent bond

•

compounds: consist of two or more elements combined by a fixed ratio

•

25 elements essential to life (need to know: O, C, H, N, Ca, P, K, S, Na, Cl, Mg)

The Structure of Atoms:

•

atomic number: number of protons (and electrons) in an atom

•

atomic mass (mass number): sum of protons and neutrons in an atom

•

isotopes: the same atom with a different number of neutrons (different atomic mass)

Partial preview of the text

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Biology 1201 Final

Chapter 1

Qualifications^ of^ LIFE:
- order
- reproduction
- energy^ use
- growth^ and^ development
- response^ to^ environment
- homeostasis^ (internal^ response^ to^ the^ environment)
- evolutionary^ adaptation^ (longterm^ responses^ to^ the^ environment)
system:^ combination^ of^ components^ working^ together
- to^ know^ how^ a^ system^ works^ requires^ understanding^ of^ interaction^ of^ its^ parts
- examples:^ cells,^ ecosystem,^ etc
systems^ are^ usually^ complex^ to^ study^ in^ full
Reductionism^ (small^ picture)^ vs.^ Systems^ Biology^ (big^ picture)
there^ are^2 types^ of^ Biology^ :
- Discovery^ Sciences:^ descriptive^ or^ comparative^ biology
  - uses^ inductive^ based^ logic^ and^ reasoning^ (drawing^ generalizations^ from^ observations with no prior knowledge)
- Hypothesis-Based^ Sciences:^ forms^ a^ testable^ hypothesis^ based^ on^ observations
  - uses^ deductive^ logic^ and^ reasoning^ (drawing^ specific^ conclusion^ from^ generalizations;^ if then logic)
  - observations,^ hypothesis,^ experimentation,^ data^ analysis,^ conclusion^ (scientific^ method)
hypothesis:^ an^ untested^ assertion
theory:^ in^ broad^ scope,^ and^ often^ complex.
- supported^ by^ a^ large^ body^ of^ evidence
- ex:^ Theory^ of^ Relativity,^ Germ^ Theory,^ Theory^ of^ Evolution
Law: fact that can be proven mathematically
- generally^ simple,^ straightforward^ concept
- ex: Law of Conservation of Mass and Energy, Boyle’s Law of Gases

Chapter 2

elements:^ consist^ of^ a^ certain^ atom^ and^ molecule,^ and^ cannot^ be^ broken^ down^ into^ any other substance
molecule:^ two^ or^ more^ atoms^ held^ together^ by^ a^ covalent^ bond
compounds:^ consist^ of^ two^ or^ more^ elements^ combined^ by^ a^ fixed^ ratio
25 elements^ essential^ to^ life^ (need^ to^ know:^ O,^ C,^ H,^ N,^ Ca,^ P,^ K,^ S,^ Na,^ Cl,^ Mg) The Structure of Atoms:
atomic^ number:^ number^ of^ protons^ (and^ electrons)^ in^ an^ atom
atomic^ mass^ (mass^ number):^ sum^ of^ protons^ and^ neutrons^ in^ an^ atom
isotopes:^ the^ same^ atom^ with^ a^ different^ number^ of^ neutrons^ (different^ atomic^ mass)

electron^ shells:^ different^ levels^ (layers)^ for^ electrons^ in^ an^ atom
oxygen has 6 valence electrons
a^ water^ molecule^ is^ polar^ with^ a^ bent^ molecular^ geometry
- oxygen's high electronegativity makes the molecule polar
energy^ is^ defined^ as^ a^ capacity^ to^ cause^ change
potential energy: energy that matter has because of its location or structure
electrons^ of^ an^ atom^ differ^ in^ the^ amount^ of^ potential^ energy^ they^ possess
an ionic bond is an attraction between cations and anions (ex: NaCl)
- ionic^ compounds^ form^ crystals
a hydrogen bond forms when hydrogen covalently bonds to electronegative atom is attracted to another electronegative atom
Vander^ Waals^ Interactions
- occur^ when^ transiently^ positive^ and^ negative^ regions^ of^ molecules^ attract
- reinforce^ large^ molecules
- help^ molecules^ adhere^ to^ each^ other^ and^ are^ easy^ to^ break
shape^ is^ very^ important^ to^ a^ molecule’s^ function
- bonds^ are^ key^ to^ determining^ its^ shape
- determines^ how^ biological^ molecules^ recognize^ and^ respond^ to^ one^ another^ with specificity
Chemical^ Reaction:
- making/breaking^ chemical^ bonds
- changes^ in^ composition^ of^ matter
- convert^ reactants^ to^ products

Chapter 3 : Water is Key to Life on Earth

life^ evolved^ and^ stayed^ in^ water^ for^ billions^ of^ years
70%^ of^ the^ Earth’s^ surface^ is^ water
cells^ are^70 - 95%^ water
water^ is^ polar
- O^ is^ more^ electronegative^ than^ H,^ and^ pulls^ the^ shared^ electrons^ from^ them
- hydrogen^ bonding:^ the^ electrical^ attraction^ resulting^ in^ structural^ organization^ of^ water molecules
  - weak:^ 1/20^ strength^ of^ a^ covalent^ bond;^ but^ lots^ together^ create^ strength
  - ephemeral:^ constantly^ forming,^ breaking^ and^ reforming
- water^ molecules^ have^ positive^ and^ negative^ poles
- cohesion:^ attraction^ between^ water^ molecules
- adhesion:^ sticking^ of^ water^ to^ other^ surfaces:^ adheres^ to^ other^ things
- because^ of^ cohesion^ and^ adhesion,^ the^ transport^ of^ water^ against^ gravity^ is^ possible Heat Retention of Water
- in^ the^ world^ there^ are^ huge^ bodies^ of^ water;^ needs^ to^ have^ high^ specific^ heat
- kinetic^ energy:^ energy^ of^ motion;^ the^ faster^ particles^ move,^ the^ greater^ the^ kinetic^ energy
- heat:^ measure^ of^ kinetic^ energy^ (related^ to^ volume)

• DNA

lipids
steroids
sugars
there^ is^ lots^ of^ diversity^ from^ carbon^ skeleton^ variations
carbon chains form the skeletons of most organic molecules, and vary in length and shape
hydrocarbons: only contain Carbon and Hydrogen (no oxygen or nitrogen)
consist of straight carbon chains, branched chains, ringed chains, etc.
Isomer: a compound with the same molecular formula but a different structure
structural: varies in covalent partners
geometric:^ varies^ in^ arrangement^ about^ a^ double^ bond
enantiomers:^ varies^ in^ spatial^ arrangement^ around^ asymmetric^ Carbons^ resulting^ in molecules that are mirror images of each other Functional Groups: define an organic molecule
Hydroxyl:^ —-OH
provide^ polarity,^ making^ alcohols
soluble^ in^ water
Carbonyl:^ —-CO
make^ ketones^ and^ aldehydes
provide^ polarity,^ meaning^ some^ of^ the^ molecule^ is^ hydrophilic
Carboxyl:^ —-COOH
make^ Carboxylic^ Acids
both^ polar^ and^ ionic
highly^ hydrophilic
Amino:^ —NH
make^ amines
basic^ in^ water
ionic^ and^ highly^ hydrophilic
Sulfhydril:^ —SH
make^ thiols
Phosphate:^ —PO4-^3
polar^ and^ ionic,^ highly^ hydrophilic
nucleotides:^ adenine,^ thymine,^ uracil,^ guanine,^ cytosine

Chapter 5: Macromolecules

polymer: long molecule consisting of many identical or similar building blocks called monomers
- proteins are strings of amino acids, and DNA is a string of nucleotides
polymerization:^ condensation^ reaction^ that^ forms^ bonds^ between^ polymers^ (dehydration)
depolymerization: hydrolysis reaction that breaks bonds between polymers
- releases^ water^ in^ the^ process Carbohydrates:

Carbohydrates:^ strings^ of^ sugar^ monomers^ ranging^ from^ one^ to^ thousands^ of^ sugars^ strung together
- common^ sugars^ have^ both^ hydroxyl^ and^ carbonyl^ groups
- glucose is the most common carbohydrate monomer
- monosaccharide:^ carbohydrate^ made^ up^ of^ one^ sugar
- disaccharide: carbohydrate consisting of two sugars
- carbohydrates (sugars) are joined by glycosidic linkages caused by a condensation reaction
- polysaccharides are composed of glucose connected by glycosidic bonds
- starch and cellulose in plants and glycogen and chitin in animals function for storage and structure Lipids:
NOT polymers
fats^ and^ steroids
fats^ consist^ of^ three^ fatty^ acids^ joined^ to^ glycerol^ by^ ester^ bonds
plants^ don’t^ have^ fats^ except^ in^ seeds
unsaturated^ fats^ consist^ of^ double^ bonds,^ while^ saturated^ fats^ consist^ of^ single^ bonds
unsaturated^ are^ usually^ liquid,^ saturated^ are^ usually^ solid
phospholipids^ are^ key^ to^ membrane^ structure
- phosphate^ joined^ with^ lipid,^ so^ both^ hydrophobic^ and^ hydrophilic^ (phosphate^ head,^ philic, tail, phobic)
steroids^ and^ some^ hormones^ consist^ of^ four^ fused^ rings
- lipids^ involved^ in^ cellular^ communication^ and^ cell^ membranes
- functional^ groups^ are^ key^ to^ steroid^ and^ hormone^ operation Proteins:
proteins^ are^ polymers^ made^ of^ strings^ of^ amino^ acids
polypeptides^ are^ protein^ polymers^ formed^ by^ condensation^ reactions
there^ are^ four^ structures^ of^ proteins:
- primary^ structure:^ the^ order^ in^ which^ amino^ acids^ are^ strung^ together
- secondary^ structure:^ spontaneous^ folding^ or^ twisting^ of^ the^ polypeptide^ backbone
  - formed^ by^ interaction^ of^ the^ molecule’s^ backbone^ to^ itself^ by^ hydrogen^ bonds
  - formed^ between^ carbonyl^ and^ amino^ groups^ in^ the^ backbone
  - alpha^ helices^ or^ pleated^ sheets^ are^ formed
- tertiary^ structure:^ interactions^ between^ the^ side^ chains^ of^ proteins
  - four^ kinds^ of^ side-group^ interactions
  - hydrogen^ bonds,^ ionic^ bonds,^ Vander^ Waals^ interactions,^ Disulfide^ Bridge
- quaternary^ structure:^ interactions^ between^ peptide^ chains
  - denaturation^ is^ the^ loss^ of^ 3D^ structure^ and^ renaturation^ is^ the^ re-establishment^ of^ 3D structure in proteins
enzymes^ are^ types^ of^ proteins Nucleic Acids (DNA, RNA):
nucleotides^ consist^ of^ nitrogenous^ bases^ (pyrimidines^ and^ purines),^ pentose^ sugars (deoxyribose or ribose), and phosphate backbone

Ribosomes

ribosomes are synthesized from rRNA in the nucleus
they^ function^ to^ translate^ proteins^ from^ mRNA^ in^ the^ cytoplasm
there are two types of ribosomes:
- free^ ribosomes^ are^ in^ the^ cytosol^ that^ function^ to^ make^ enzymes^ and^ other^ proteins^ for cellular use
- ribosomes bound in the ER membrane function to make proteins for membrane construction and proteins for export Endoplasmic Reticulum
there are two types of ER
- Smooth ER has no ribosomes, and synthesizes lipids and detoxifies things imported into the cell
- Rough ER is embedded with ribosomes and produces mainly proteins that will be secreted from the cell
  - packaged^ in^ transport^ vesicles
  - Rough^ ER^ also^ a^ membrane^ factory Golgi Apparatus
the^ “warehouse”^ of^ the^ cell
functions^ for^ storage,^ modification^ and^ export^ of^ material^ that^ arrives^ in^ transpor^ vesicles from the ER
manufactures^ macromolecules^ (polysaccharides) Lysosomes
membrane-enclosed^ digesting^ organelles
contain^ hydrolytic^ enzymes
lysosomes^ are^ in^ charge^ of^ phagocytosis^ and^ autophagy Vacuoles and Vesicles
the^ central^ vacuole^ is^ a^ membrane^ bound^ organelle^ in^ plants^ that^ functions^ for^ storage^ of seed proteins, ions, waste, and water Chloroplasts and Mitochondria
chloroplasts^ and^ mitochondria^ are^ the^ “powerhouses”^ of^ the^ cell
once^ believed^ to^ be^ separate^ organisms^ completely,^ because^ they^ both^ contain^ their^ own DNA

Chapter 7: Membranes

the cell membrane consists of a phospholipid bilayer
- phospholipids^ are^ amphipathic,^ both^ hydrophobic^ and^ hydrophilic
membranes contain proteins, which are also amphipathic (like the membrane itself)
cell^ membranes^ make^ up^ a^ Fluid-Mosaic^ Model
- phospholipid^ membranes^ have^ the^ consistency^ of^ a^ fluid,^ allowing^ phospholipids^ to^ move laterally
  - fluidity^ influenced^ by^ temperature^ and^ hydrocarbon^ structure
  - unsaturated^ fatty^ acid^ tails^ kink,^ minimizing^ packing^ and^ maximizing^ fluidity

the^ proteins^ drift^ with^ the^ phospholipid^ bilayer,^ but^ they^ make^ up^ the^ mosaic^ part^ of^ the model
- carbohydrates^ attached^ to^ proteins^ are^ on^ the^ outside^ only
- integral proteins that are amphipathic include those that connect to non polar amino acids that form helical structures
the function of membrane proteins are diverse
for^ transport^ in^ and^ out^ of^ the^ cell^ (passive^ and^ active)
as enzymes, mediating chemical reactions
as^ signal^ transducers,^ aiding^ communication^ from^ outside^ to^ inside^ the^ membrane
as connectors for intercellular joining
for^ cell^ to^ cell^ recognition
for^ the^ cytoskeleton^ attachment Diffusion and Transport
diffusion^ is^ the^ tendency^ to^ fill^ available^ space^ of^ a^ fluid
molecules^ diffuse^ naturally^ from^ areas^ of^ greater^ to^ lesser^ concentration^ (down^ the concentration gradient)
movement^ caused^ by^ thermal^ motion^ of^ molecules
dynamic^ equilibrium:^ when^ equal^ rates^ of^ movement^ occur^ in^ both^ directions^ across^ a membrane
facilitated^ diffusion:^ molecules^ pass^ through^ a^ membrane^ protein^ down^ the^ concentration gradient
use^ enzyme-like^ transport^ proteins
active^ transport:^ molecules^ pass^ through^ a^ membrane^ protein^ against^ the^ concentration gradient with energy input from ATP
ex:^ Na+-K+^ pump
ATP^ consists^ of^ three^ phosphates
the^ addition^ of^ a^ phosphate^ to^ a^ protein^ can^ change^ the^ shape^ of^ the^ protein,^ allowing^ ions or polar molecules to pass through a membrane
active^ transport^ results^ in^ the^ electrochemical^ gradient
proton^ pumps^ also^ generate^ an^ electrochemical^ gradient
H+^ and^ Na+^ are^ pumped^ outside^ of^ a^ cell,^ and^ return^ passively^ via^ membrane^ proteins for 2 reasons:
concentration^ gradient
electrochemical^ gradient
membranes^ are^ both^ “barriers^ and^ gateways”^ and^ can^ be^ selectively^ permeable
passive^ transport^ works^ for^ hydrophobic^ molecules^ and^ small^ polar^ molecules^ (H20^ and ethanol)
active^ transport^ is^ required^ for^ large^ polar^ molecules^ and^ ions
cotransport^ is^ the^ ATP^ investment^ in^ pumping^ H+^ out^ of^ cells^ that^ sets^ up^ an electrochemical gradient Osmosis
osmosis:^ diffusion^ of^ water^ molecules
water diffuses across a membrane to equilibrate its relative concentration

Exergonic,^ negative^ ∆G,^ gives^ off^ energy
hydrolysis of ATP is exergonic, gives off energy ATP and Enzyme Activity
when ATP energy is given off through a phosphate, energy not lost, but transferred to objective molecule
a reactive phosphorylated intermediate is produced
the key to effective use of energy in metabolism is to harness as much energy as possible at every step of the reaction
Activation energy: energy required to break bonds in reactants for a reaction o occur
because large molecules are unstable, they must be protected against spontaneous breakdown
without^ activation^ energy,^ all^ reactions^ would^ spontaneously^ occur^ at^ once
cells use enzymes to lower activation energies of reactions
they^ speed^ spontaneous^ reactions^ without^ being^ consumed^ in^ the^ process
substrate:^ reactant^ molecule
active^ site:^ area^ of^ enzyme^ where^ substrate^ attaches
an^ enzyme^ may:
stress^ key^ bonds
orient^ the^ substrate^ with^ other^ reactants
provide^ an^ environment^ likable^ to^ reaction
react^ briefly^ with^ the^ substrate^ to^ form^ a^ reactive^ intermediate
factors^ influencing^ enzyme^ activity:
temperature^ (heat^ speeds^ up^ enzyme^ activity)
change^ in^ pH
cofactors^ (non^ protein^ enzyme^ helpers)
enzyme^ inhibition^ controls^ enzyme^ expression
allows^ reaction^ to^ be^ turned^ off^ when^ undesirable
a^ competitive^ inhibitor^ mimics^ substrate^ and^ competes^ for^ the^ active^ site
a^ noncompetitive^ inhibitor^ binds^ to^ the^ enzyme^ at^ a^ location^ away^ from^ active^ site,^ but changes shape of active site in the process so substrate cannot enter
allosteric^ regulation^ causes^ changes^ in^ the^ active^ site^ by^ binding^ molecules^ at^ a^ different location

Chapter 9: Cellular Respiration

cellular respiration: consumption of oxygen and organic fuel to produce energy to do bodily work
respiration occurs in cells, where organic fuel is broken down and energy moved from glucose to ATP
the^ larger^ the^ organic^ molecule,^ the^ greater^ the^ stored^ energy^ by^ virtue^ of^ number^ of chemical bonds and imposition of order on the electrons
- starches^ and^ glycogen^ consist^ of^ long^ strings^ of^ glucose^ monomers
- fats have lots of energy stored in hydrocarbons of the fatty acids

cellular^ respiration^ is^ catabolic
the transfer of energy in cellular respiration is based on the flow of electrons caused by oxidation and reduction reactions
- oxidation: loss of electrons
- reduction:^ gain^ of^ electrons
- O2 is strongly electronegative, and is the classic “oxidizing agent” meaning what is reduced
- reducing agent is what is oxidized
in respiration, H2O and CO2 are the “waste products” which have no potential energy because of how electronegative oxygen is
There are three parts to cellular respiration
- Glycolysis:^ initial^ breakdown^ of^ glucose^ in^ the^ cytoplasm
- Kreb’s (Citric Acid) Cycle: completes the breakdown of glucose to CO2 in the mitochondria
- Electron^ Transport^ Chain:^ receives^ electrons^ from^ NADH^ and^ FADH2^ produced^ by glycolysis and the Kreb’s Cycle and uses redox reactions to produce ATP OverView of Cellular Respiration
in^ Glycolysis:
- glucose,^6 carbons,^ is^ oxidized^ into^2 pyruvate^ (3^ carbons^ each)
- 2 ATP^ and^2 NADH^ are^ produced^ by^ substrate^ level^ phosphorylation
Before^ entering^ the^ Kreb’s^ Cycle,^ the^2 pyruvates^ diffuse^ into^ a^ mitochondria^ via^ an^ integral protein
- the^ two^ pyruvates^ are^ oxidized^ to^2 Acetyl-CoA^ (2^ Carbons)^ and^ 2CO2^ and^ 2NADH
in^ the^ Kreb’s^ Cycle:
- the^ breakdown^ of^ glucose^ is^ completed
- the^2 Acetyl-CoA^ enter^ the^ cycle
- 2ATP,^6 NADH,^ 2FADH2,^ and^ 4CO2^ are^ produced
the^ Electron^ Transport^ Chain:
- receives^ electrons^ from^ NADH^ and^ FADH
- uses^ these^ electrons^ to^ produce^34 ATP^ through^ oxidative^ phosphorylation Glycolysis:
two^ ATP^ invested^ to^ make^ the^ glucose^ reactive
the^ glucose^ is^ split^ into^ two^3 carbon^ molecules,^ pyruvate
2NADH^ are^ produced
- NAD+/^ NADH^ is^ a^ coenzyme^ that^ works^ with^ enzymes^ that^ breakdown^ glucose
- acts^ as^ electron^ transferring^ molecule
4 ATP^ produced^ by^ substrate-level^ phosphorylation,^ but^ only^2 net^ because^ of^ the^ originally invested
NET:
- 2 ATP
- 2NADH
- 2 3 - carbon^ Pyruvate

Oxidation^ of^ Pyruvate:
- 2 Acetyl-CoA
- 2CO
- 2NADH
Kreb’s^ cycle:
- 6NADH
- 2FADH
- 2ATP
- 4CO
ETC:
- 34 ATP
- O Fermentation
glucose^ can^ break^ down^ under^ aerobic^ and^ anaerobic^ conditions
glycolysis^ can^ proceed^ without^ O2^ ,^ because^ ATP^ is^ produced^ by^ substrate^ level phosphorylation
without^ Oxygen^ there^ is^ no^ ETC,^ and^ NADH^ has^ nowhere^ to^ go,^ so,^ the^ cells^ need^ an alternative oxidizer to O2 so more glucose can be oxidized to make more ATP
in^ Alcohol^ Fermentation:
- CO2^ released^ to^ make^2 carbon^ Acetaldehyde,^ which^ oxidizes^ NADH,^ producing^ Ethanol and NAD+
in^ Lactic^ Acid^ Fermentation:
- pyruvate^ is^ reduced^ with^ electrons^ from^ NADH^ directly^ to^ form^ lactate
- this^ frees^ up^ NAD+^ to^ re-enter^ glycolysis
facultative^ anaerobes^ are^ organisms^ that^ can^ both^ ferment^ and^ respire^ depending^ on^ Ox availability Other Sources for Glycolysis
fats^ can^ go^ to^ glycolysis
- glycerol^ to^3 carbon^ Glyceraldehyde
- fatty^ acids^ catabolized^ to^2 carbon^ fragments^ that^ enter^ Kreb’s^ Cycle^ as^ Acetyl-CoA
Proteins^ can^ also^ be^ used^ as^ fuel,^ but^ must^ first^ be^ hydrolyzed^ and^ deaminated^ (take^ the^ N off) Feedback Control
feedback^ control^ determines^ if^ metabolism^ is^ catabolic^ or^ anabolic
- if^ there^ is^ plenty^ of^ ATP,^ then^ glycolysis^ is^ inhibited
- ATP^ or^ AMP^ can^ bind^ to^ an^ allosteric^ enzyme
- if^ ATP^ binds,^ the^ enzyme^ is^ turned^ off^ and^ glycolysis^ stops
- if^ AMP^ binds,^ the^ enzyme^ is^ turned^ on^ and^ glycolysis^ resumes
if^ there^ is^ lots^ of^ ATP^ and^ a^ shortage^ of^ macromolecules,^ cells^ divert^ intermediates^ from glycolysis and the Kreb’s Cycle to build needed compounds
- no^ fat^ diets^ don’t^ necessarily^ work

Chapter 10: Photosynthesis

Photosynthesis is the harvesting of sun’s energy as chemical energy (opposite of Respiration)
plants^ photosynthesize^ to^ make^ sugar^ and^ other^ organic^ chemical^ building^ blocks
Green Plant Photosynthesis:
- occurs^ mainly^ in^ the^ leaves
- stoma are pores for gas exchange in leaves and stems
- chloroplasts^ are^ the^ sites^ of^ photosynthesis
- mesophyll is the type of cell that contains most of the chloroplasts
Chloroplast^ Structure:
- use^ membranes^ in^ a^ way^ analogous^ to^ mitochondria,^ to^ establish^ a^ proton^ gradient^ (proton motive force)
- thylakoids:^ hollow^ membrane^ chambers
- thylakoid^ space:^ inside^ thylakoid^ (key^ for^ establishing^ H+^ gradient)
- stroma:^ space^ outside^ the^ thylakoid^ (also^ key^ for^ H+^ gradient) Overview of Photosynthesis
Photosynthesis^ occurs^ in^ two^ phases:
Light^ Reactions:^ the^ “photo”^ part^ of^ photosynthesis
- occurs^ in^ the^ thylakoids^ converting^ light^ energy^ to^ ATP^ and^ transferring^ energized electrons from water to NADP+, an electron carrier analogous to NAD+ in respiration
Calvin^ Cycle^ (Dark^ Reactions)^ :^ the^ “synthesis”^ part^ of^ photosynthesis
- occurs^ in^ the^ stroma,^ producing^ sugar^ using^ the^ ATP^ and^ electrons^ from^ NADPH^ from^ the light reaction Phase 1: Light Reactions:
in^ this^ phase,^ solar^ energy^ is^ converted^ into^ chemical^ energy
in^ a^ summary:^ water^ splits,^ O2^ is^ a^ byproduct^ released^ as^ gas,^ ADP^ and^ P^ form^ ATP,^ and NADP+ forms NADPH
- NADP+^ is^ a^ close^ cousin^ of^ NAD+^ from^ respiration^ but^ with^ an^ extra^ P
- no^ sugar^ produced^ in^ the^ light^ phase
light^ energy^ is^ electromagnetic^ energy^ that^ travels^ in^ waves
- chloroplasts^ have^ pigments^ that^ absorb^ light
  - chlorophyll^ a:^ violet^ and^ red
  - chlorophyll^ b:^ blue^ and^ yellow
  - cartenoids:^ blue
  - only^ chlorophyll^ a^ converts^ energy^ directly^ to^ light^ reaction
the^ sun’s^ photons^ excite^ electrons,^ and^ raise^ them^ to^ a^ higher^ orbit
- electrons^ in^ higher^ orbits^ are^ unstable^ with^ more^ potential^ energy
photosystems^ are^ clusters^ of^ pigment^ molecules
- photosystems^ are^ light-harvesting^ units
- photon^ energy^ excites^ electrons^ in^ pigment^ molecules
- when^ chlorophyll^ a^ is^ oxidized,^ its^ excited^ electron^ is^ trapped^ by^ a^ primary^ electron acceptor (PEA)
The^ Light^ Reactions^ of^ photosynthesis^ take^ place^ in^ two^ Photosystems

O2^ begins^ to^ be^ fixed^ in^ the^ Calvin^ Cycle^ instead^ of^ CO2,^ and^ G3P^ isn’t^ produced
There are a few solutions: Keep O2 away from Calvin Cycle (C4 Plants) or increase amount of CO2 in the stroma (CAM plants) Solutions
C4^ plants:^ spatial^ solution
- the light reaction and Calvin Cycle are performed in different cells (mesophyll and bundle- sheath)
CAM plants: temporal solution
- at^ night,^ stomata^ are^ opened,^ allowing^ CO2^ to^ enter^ the^ cell^ and^ O2^ be^ released
- CO2 is fixed at night into organic acids and stored in the vacuole of the plant cells
- during^ the^ day,^ it^ is^ retrieved

Chapter 11: Cell Communication

cellular^ communication^ is^ essential^ for^ cells^ to^ survive;^ they^ send^ and^ receive^ environmental clues
yeast^ cells^ identify^ matching^ mating^ types^ by^ exchanging^ specific^ proteins,^ if^ they^ match, they fuse together
cells^ have^ different^ ways^ of^ communicating^ with^ one^ another,^ long^ and^ short^ distance
local^ signaling:
- paracrine^ signaling:^ the^ secreting^ cell^ discharges^ a^ regulator^ that^ reaches^ to^ adjacent^ cells; “shotgun method”
  - no^ particular^ directionality
- synaptic^ signaling:^ a^ nerve^ cell^ transmits^ a^ neurotransmitter^ into^ a^ synapse,^ the^ space leading to the next cell
  - this^ is^ highly^ directional
long^ distance^ signaling:
- hormones^ released^ from^ a^ cell^ travel^ through^ the^ circulatory^ system^ to^ communicate^ with distant cells
cells can also communicate via direct contact
- animal^ cells^ use^ gap^ junctions
- plant cells use plasmodesmata
- in^ these^ case,^ signal^ molecules^ move^ between^ the^ cells^ without^ crossing^ a^ plasma membrane
- cells^ can^ also^ communicate^ via^ surface^ contact
there are Three Stages of Cellular Communication
1. Reception: an outside signal detected by the receiving cell
2. Transduction: the signal is transmitted to the inside of the cell
3. Response: the cell takes action
- a^ signal^ molecule^ is^ a^ ligand,^ a^ small^ molecule^ that^ binds^ to^ a^ larger^ one,^ causing^ a^ change in shape of the larger molecule
  - this^ change^ in^ shape^ causes^ a^ reaction^ inside^ of^ the^ cell
Epinephrine^ (Adrenaline)^ Example:

glycogen^ is^ a^ large^ polymer^ of^ glucose^ used^ for^ storage^ often^ in^ the^ liver
glucose is an energy source for cellular respiration
a^ signal^ molecule^ is^ epinephrine,^ a^ hormone^ and^ neurotransmitter^ from^ the^ adrenal^ gland in the kidney
the^ receptor^ would^ be^ a^ protein^ on^ the^ surface^ of^ liver^ cells
transduction would be a series of steps to the activation of glycogen phosphorylase, which breaks down glycogen to glucose
the response would be in the liver, the breakdown of glycogen and the release of glucose for cellular respiration Membrane Receptors
there are three main types of membrane receptors: G-Protein linked receptors, tyrosine- kinase receptors, and ion-channel receptors
these are a large family of receptors all featuring a polypeptide with 7 helices embedded in the plasma membrane
G-Protein^ Linked^ Receptor:^ a^ cell^ surface^ receptor
a^ G^ Protein^ is^ attached^ to^ the^ receptor
the^ G^ protein^ is^ inactive^ in^ the^ absence^ of^ a^ signal^ from^ the^ receptor,^ and^ inactive^ until bound to GTP (Guanasine Triphosphate)
signal^ received^ by^ the^ receptor^ stimulates^ binding^ of^ G^ protein^ to^ the^ receptor,^ and^ then GTP displaces GDP, activating the G protein
the^ G^ protein^ dissociates^ from^ the^ receptor^ and^ activates^ an^ enzyme
after^ activating^ the^ enzyme,^ the^ G^ protein^ hydrolyzes^ GTP^ to^ GDP^ and^ returns^ to^ an inactive state
Tyrosine-Kinase^ Receptor:
these^ receive^ signals^ such^ as^ growth^ factors^ from^ outside^ the^ cell
signal^ binding^ causes^ the^ Tyrosine-Kinase^ Receptors^ separate^ polypeptides^ to^ coalesce into a dimer whose tyrosines become phosphorylated by ATP
the^ receptor^ can^ activate^ many^ proteins^ at^ once,^ the^ “kinase”^ part^ of^ its^ function
kinases^ are^ enzymes^ that^ use^ phosphate^ groups^ to^ activate^ other^ enzymes
Ion-Channel^ Receptor:
signal^ molecules^ are^ ligands^ (ligand-gated^ ion^ channel)
the^ channel^ consists^ of^ a^ protein^ embedded^ in^ the^ plasma^ membrane,^ which^ when^ opened lets ions flow through diffusion
the^ ligand^ attaches^ and^ opens^ the^ membrane^ channel
ion^ flow^ causes^ electrical^ changes^ inside^ the^ cell^ that^ activates^ chemicals^ in^ the^ cell
most^ signal^ molecules^ are^ water^ soluble^ and^ too^ big^ or^ polar^ to^ pass^ through^ the^ plasma membrane
some^ hydrophobic^ chemical^ messengers,^ like^ steroid^ hormones,^ thyroid^ hormones,^ and nitric oxide can pass through and reach intracellular receptors (like testosterone) Transduction
signal^ transduction^ links^ a^ mechanical^ or^ chemical^ signal^ from^ outside^ a^ cell^ to^ a^ response within the cell

the^ transcription^ response^ is^ similar^ to^ testosterone^ activation^ via^ intracellular^ reception
amplification effect: one signal molecule causes a huge response
Specificity:
- epinephrine as a signal molecule affects liver cells differently than heart cells
  - liver^ breaks^ down^ glycogen^ to^ produce^ glucose
  - heart cells contract
- single response
- dual response
- cross-talk
- single response, but different receptor
Speed:
- molecules^ must^ diffuse^ through^ the^ cytoplasm^ to^ interact
- proteins move slowly because of their size (slower than second messengers)
- to^ improve^ speed,^ signaling-pathway^ enzymes^ may^ be^ attached^ to^ scaffolds^ that^ hold^ them in adjacent positions so they can easily activate the next protein more rapidly

Chapter 12: The Cell Cycle

during^ the^ cell^ cycle,^ an^ exact^ copy^ of^ the^ original^ cell^ is^ produced:^ mitosis
cells^ create^ packets^ of^ DNA^ for^ duplication^ called^ chromosomes
chromatin^ is^ a^ complex^ of^ DNA^ and^ proteins
- each^ chromosome^ consists^ of^1 DNA^ molecule^ and^ various^ proteins
- chromosomes^ are^ condensed^ chromatin
- chromatids^ are^ replicated^ chromosomes^ attached^ together
- sister^ chromatids^ are^ joined^ by^ a^ centromere
- chromosome^ number^ “N”^ refers^ to^ number^ of^ unique^ chromosomes
somatic^ cells:^ body^ cells^ that^ have^ two^ copies^ of^ every^ chromosome
gametes:^ sex^ or^ reproductive^ cells,^ each^ containing^ one^ copy^ of^ a^ chromosome
genome:^ total^ DNA^ content^ of^ a^ cell^ or^ an^ organelle
in Mitosis the division of a somatic cell results in two somatic cells each with 2N chromosomes The Cell Reproductive Cycle
G1:^ Growth^ after^ Cytokinesis:^ occurs^ after^ cells^ divide^ in^ cytokinesis
- cytoplasm and organelle content increases
- cell grows
S: chromosome duplication; DNA replication occurs
G2: Growth after S before Mitosis
- cell adds cytoplasm in preparation for division
- centrosomes (microtubule organizing centers) duplicate
- microtubules^ extend^ out^ from^ centrosomes
- chromosomes are relaxed chromatin
Mitotic^ Phase^ is^ the^ separation^ of^ chromosomes^ into^ daughter^ cells
- five sub phases

Cytokinesis:^ the^ actual^ splitting^ of^ the^ cell Mitosis
there^ are^5 sub^ phases^ of^ Mitosis^ (and^ Cytokinesis)
- prophase, prometaphase, metaphase, anaphase, telophase, cytokinesis
Prophase:
- nucleoli disappear within nucleus
- chromatin^ condense^ into^ chromosomes
- microtubules elongate to mitotic spindle
Prometaphase:
- nuclear membrane breaks down
- kinetochore^ microtubules^ near^ the^ centromeres^ of^ chromosomes
Metaphase:
- mitotic spindle fully formed
- chromosomes^ line^ up^ along^ “metaphase^ plate”
- each^ chromatid^ connected^ to^ separate^ microtubule^ via^ kinetochore
Anaphase:
- centromeres^ come^ apart,^ chromatids^ separate^ forming^ chromosomes
- kinetochores^ shorten
- chromatids^ considered^ distinct^ chromosomes
Telophase:
- nuclear^ membranes^ reform^ in^ new^ daughter^ cells
- chromosomes^ relax
- nucleoli^ reappear
- cytokinesis^ underway
Cytokinesis:
- division^ of^ cytoplasm^ into^ two^ separate^ daughter^ cells
- cleavage^ furrow^ develops
- actin^ participates^ to^ separate^ cells
- in^ plant^ cells^ vesicles^ from^ Golgi^ Body^ fuse^ to^ form^ cell^ plate,^ forming^ cell^ wall Prokaryotic Cell Cycle
method^ of^ replicated^ chromosome^ movement^ in^ prokaryotes^ unknown
chromosomes^ attach^ to^ plasma^ membrane
binary^ fission

Chapter 13: Meiosis

heredity: transmission of traits from one generation to the next
- information stored in DNA in order of nucleotides
- transmitted to somatic cell to somatic cell via DNA replication
genetics:^ study^ of^ heredity
mitosis occurs for asexual reproduction of somatic cells or single-celled organisms, and results in daughter cells that are clones of the parent
sexual reproduction creates variation

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Biology 1201 Final

Chapter 1

Chapter 2

Chapter 3 : Water is Key to Life on Earth

• DNA

Chapter 5: Macromolecules

Chapter 7: Membranes

Chapter 9: Cellular Respiration

Chapter 10: Photosynthesis

Chapter 11: Cell Communication

Chapter 12: The Cell Cycle

Chapter 13: Meiosis