Chapter 1 - The Basis of Life Flashcards
Cell Theory
Proposed after dev. of microscope in 17th century
- All living things are composed of cells
- The cell is the basic functional unit of life
- Cells arise only from pre-existing cells
- Cells carry genetic information in form of DNA
- DNA passed from parent to daughter cell
Studying the Cell:
Microscopy
(types)
Most basic tool used to study cells
- Compound light microscope
- Phase contrast microscopy
- Electron microscopy
Magnification
Increase in apparent size of an object
Resolution
Differentiation of two closely situated objects
Compound Light Microscope
- two lenses or lens sytems to magnify an object
- total magnification = mag of eyepiece x mag of objective
- observe non-living specimen
- requires contrast b/w cells and cell structures
- staining = cell death
Daiphragm
(compound light microscope)
controls amount of light passing through specimen
Coarse adjustment
Fine adjustment
(compound light micr)
roughly focuses image
sharply focuses image
Phase Contrast Microscopy
- light microscope
- study of living cells
- differences in refractive index produce contrast b/w cellular structures
Electron Microscopy
- beam of electrons
- x1000 higher mag than light microscopy
- non-living
- because tissues fixed, sectioned, stained with heavy metal solutions
Centrifugation
(Studying the Cell)
- separate cells or mixtures of cells w/o destroying
- components sediment at diff. levels in test tube based on relative densities
- (nuclie, ER, mitochondria more dense, on bottom)
Cell Biology
Organelles are specialized in function
nucleus, ribosomes, ER, golgi apparatus, vesicles, vacuoles, lysosomes, mitochondria, chloroplasts, centrioles
Cell Membrane
(Plasma membrane)
- encloses cell
- exhibits cell permeability
- regulates passage of materials into and out of cell
Fluid Mosaic Model
(cell membrane)
- cell membrane consists of phospholipid bilayer
- proteins embedded throughout
- lipids and proteins can move freely within membrane
- allows membrane to be:
- permeable to small nonpolar & polar molecules
- small charged proteins cross membrane through protein channels
- larger cross membrane with help of carrier proteins
carrier proteins
- involved in movement of ions, small molecules or macromolecules across bio membrane
- exist within membrane
- assist via facilitated diffusion or acrive transport
- recognizes only one substance or small group of substances
Nucleus
- controls activities of cell, including cell division
- surrounded by nuclear membrane
- contains DNA
- contains nucleolus
DNA
- made up of structural proteins - histones; form chromosomes
nucleolus
- dense structure in nucleus
- synthesize ribosomes
- site of RNA (rRNA) synthesis
Ribosome
- sites of protein production, synthesized by nucleolus
- free ribosomes in cytoplasm
- bound ribosomes line outer membrane of ER
Endoplasmic Reticulum
- network of membrane-enclosed spaces
- transport of materials throughout cell
- esp. those to be secreted by cell
Golgi Apparatus
- Receives vesicles and contents from smooth ER
- Modifies them (glycosylation)
- repackages into vesicles
- distributes to cell surface via exocytosis
Mitochondria
- aerobic respiration
- supply energy
- bounded by outer, inner phospholipid bilayer
Cytoplasm
- Metabolic activity
- transport within via cyclosis
Cyclosis
streaming movement within cell
Vacuole
(& Vesicles)
- membrane-bound sacs
- transport and storage of materials that are ingested, secreted, processed, or digested by cell
- vacuoles larger than vesicles; more likely in plant than animal
Centrioles
- microtubule involved in spindle organization during cell division
- not bound by membrane
- in pairs; oriented in right angles
- in region called centrosome
- ONLY ANIMAL CELLS
Lysosome
vesicles containing hydrolytic enzymes –> intracellular digestion
break down material ingested by cell
Autolysis
- rupture lysosome membrane and release hydrolytic enzymes
- injured or dying tissue way to commit suicide
Cytoskeleton
- composed of microtubules and microfilaments
- gives cell mechanical support
- maintains shape
- functions in cell motility
Form follows function
- not all cells have same relative distribution of organelles
- cells requiring lots of energy for locomotion (sperm cells) - lots of mitochondria
- cells involved in secretion (pancreatic islet cells) - lots of Golgi bodies
- cells involved in transport (red blood cells) - no organelles
Transport across cell membrane
- substances move in and out of cells
- various methods
- passive (no energy) vs. active (energy expenditure - ATP)
Simple Diffusion
(transport)
- net movement of dissolved particles down concentration gradients
- higher to lower
- passive (no external energy req’d)
- e.g. osmosis
Osmosis
(Simple diffusion)
- simple diffusion of water
- low solute conc. to high solute conc.
Hypertonic Solution
- cytoplasm of cell has lower conc. of nonpenetrating solutes than extracellular medium
- medium is hypertonic to cell
- water will flow out of cell
- cell shrivels
- process is called plasmolysis
Hypotonic Solution
extracellular env. less conc. than cytoplasm
extracellular medium is hypotonic
**water will flow into cell **
cell will swell and lyse (burst)
e.g. red blood cells burst in DI water
Facilitated Diffusion
(passive transport)
- net movement of dissolved particles down conc. gradient through special channels or carrier proteins in cell membrane
- no energy req’d
Active Transport
- net movement of dissolved particles against conc. gradient
- with help of transport proteins
- requires energy
Passive Diffusion
Down gradient
No carrier
No energy req’d
Facilitated Diffusion
- Down gradient
- Carrier
- No energy req’d
Active Transport
Against gradient
Carrier
Energy req’d
Prokaryotes
- Bacteria
- Cell wall present
- Cell wall composed of peptidoglycans
- No nucleus
- Ribosomes (subunits = 30S & 50S)
- No membrane-bound organelles
Eukaryotes
- Protists, Fungi, Plants, Animals
- Cell wall in FUNGI and PLANTS only
- Nucleus
- Ribosomes (subunits = 40S & 60S)
- Membrane-boun organelles
Circulation
transportation of material within cells and throughout body of multicellular organism
Intracellular Circulation
via:
- Brownian Movement
- Cyclosis or streaming
- Endoplasmic reticulum
Brownian Movement
(Intracellular Circulation)
- movement of particles via kinetic energy
- spreads small suspended particles throughout cytoplasm
Cyclosis or streaming
(Intracellular circulation)
circular motion of cytoplasm around cell transport molecules
Endoplasmic reticulum
(intracellular circulation)
- channels throughout cytoplasm
- direct continuous passageway from plasma membrane to nuclear membrane
Extracellular Circulation
Diffusion
Circulatory System
Diffusion
(Extracellular Circulation)
- cells in direct/close contact with external environment
- sufficient means of transport for food and oxygen from env. to cells
- more complex animals - imp. for for transport of materials bw cells and interstitial fluid
Interstitial Fluid
fluid which bathes cells
Circulatory System
(Extracellular Circulation)
includes vessels to transport fluid and pump to drive circulation
req’d by complex animals - cells too far from external env. to transport materials by diffusion
Enzymes
- organic catalysts
- proteins
- many are conjugated proteins (work with non-protein coenzyme)
- affects rate of rxn w/o being changed/consumed
- crucial to life because living need continuous controlled chem. activity
- speed up for slow down rxns
- decrease activation energy
- do not affect overall dG
Enzyme Specificity
- selective
- catalyze only 1 rxn, 1 specific class of related rxns
- acts upon substrate
- substrate binds to enzyme’s active site
2 models of enzyme binding
- lock and key theory
- induced fit theory
Lock and Key theory
- spatial structure of enzyme’s active size exactly matches that of substrate
- fit together like lock and key
- largely discounted theory
Induced Fit Theory
- widely accepted
- active site has flexibilty of shape
- appropriate substrate comes in contact - active site conforms to fit substrate
Enzyme Reversibility
- product synthesized by enzyme can be decomposed by same enzyme
- e.g. enzyme synthesizes maltose from glucose; enzyme hydrolyzes glucose from maltose
Enzyme Action depends on:
- Temp
- pH
- Concentration
Effects of Temp
- as temp increases, rate of enzyme action increases
- optimum temp at 40C
- past 40C, heat alters shape of active site and deactivates it
- thus - rapid drop in rate
Effects of pH
- optimal pH for each enzyme -
- above & below enzyme activity declines
- optimal pH matches conditions under which enzyme operates
Human Enzyme Activity pH
- human max enzyme activity - 7.2 (pH of most body fluids)
- pepsin - highly acidic stomach - pH 2
- pancreatic enzymes - alkaline - pH 8.5
Effects of Concentration
Concentration of enzyme + substrate low:
- active sites unoccupied
- rxn rate low
increasing substrate concentration
- increase rxn rate until all active sites occupied, then plateus
- Michaelis-Menten Model (pg. 22)
Examples of Enzyme Activity (Rxn types)
Hydrolysis
Synthesis
Hydrolysis
(Enzyme Rxns)
- digest large molecules into smaller components
- e.g.
Lactose —-> glucose + galactose
enzyme: lactase (over arrow)
monosaccharaides: glucose + galactose
* e.g.
proteins —> amino acids
enzyme: proteases
* e.g.
lipids —> fatty acids + glyerol
enzyme: lipases
Hydrolysis in multicellular organisms
- digestion can begin outside cells, in gut
- other hydrolytic rxns within cells
Synthesis
(Enzyme Rxns)
- can be catalyzed by same enzymes as hydrolysis
- directions reversed
- occur in diff. parts of cell
- e.g. protein synthesis in ribosomes - dehydration synthesis bw amino acids
- survival depends on ability to ingest substances that cannot be synthesized
- once ingested, substanes —> useful products
Synthesis (Enzyme Rxns)
required for:
- growth
- repair
- regulation
- protection
- production of food reserves (e.g. fat, glycogen) by cell
Cofactors
many enzymes require help of nonprotein mlc to become active
can be: metal cations (Zn2+, Fe2+) or coenzymes
Coenzymes
(Cofactors)
- small organic groups
- most cannot be synthesized by body
- obtained from diet as vitamin derivatives
Prosthetic Groups
(Cofactors)
Cofactors which bind to enzyme via strong covalent bonds
Cellular Respiration
- metabolic rxns in cells: catabolic redox rxns
- convert biochemical energy from nutrients into ATP (adenosine triphosphate)
- then release waste products
- cell gains energy
Photosynthesis
converts energy of sun into chemical energy of bonds in compounds (e.g. glucose)
Respiration
conversion of chemical energy in bonds (re: photosynthesis) into usable energy needed to drive processes of living cells
(favored) Fuel molecules
- Carbohydrates
- Fats
Hydrogen
(cellular respiration)
Hydrogen removed = bond energy made available
C-H bond is energy rich
C-H bond releases largest amount of energy/mole
CO2
(cellular respiration)
contains little usable energy
stable, energy exhausted
end product of respiration
dehydrogenation
(redox; cellular respiration)
during respiration, high energy H atoms removed from organic mlc’s
oxidation reaction
reduction
(cellular respiration)
acter dehydrogenation, acceptance of H by H acceptor (Oxygen in final step)
energy released by reduction forms high energy phosphate bond in ATP
redox net energy
(cellular respiration)
- intial oxidation requires energy
- net is production
- energy released in series of step: electron transport chain
- if in one step, little could be harnessed
Glucose Catabolism
Degradative oxidation of glucose (energy production)
stages of glucose catabolism
glycolysis
cellular respiration
Glycolysis
series of rxns
rxns occur in cytoplasm
mediated by enzymes
leads to:
- 2 pyruvate
- production of ATP
- NAD+ —> NADH
pyruvate
carboxylate anion of pyruvic acid
key in metabolic pathways
made from glucose via glycolysis
converted to fatty acids through acetyl-CoA
supplies energy to living cells through citric acid cycle (krebs cycle) in presence of oxygen
no oxygen: ferments to produce lactate
glycolytic pathway
(glycolysis)
- glucose
(atp –> adp)
- glucose 6-phosphate
- fructore 6-phosphate
(atp –> adp)
- fructose 1,6-diphosphate
glycolytic pathway step 4
fructose 1,6-diphosphate split into
- dihydroxyacetone phosphate
- glyceraldehyde 3-phosphate (PGAL)
- dihydroxyacetone phosphate isomerized –> PGAL; used in subsequent rxns
- 2 mlc PGAL/1 mlc glucose
- steps 5-8 occur twice/1 mlc glucose
glycolytic pathway (cont’d)
- 1,3-Diphosphoglycerate
(ADP —> ATP)
- 3-Phosphoglycerate
- 2-Phosphoglycerate
- Phosphoenopyruvate
(ADP —> ATP)
- Pyruvate
Products of Glycolytic Pathway
1 mlc glucose yields:
2 mlc pyruvate
2 ATP used (steps 1,3)
4 ATP produced (2 in 6, 2 in 9)
2 PGAL
2 NADH (one per one PGAL)
Substrate Level Phosphorylation
- ATP synthesis occurs during degradation of glucose w/o intermediate mlc (such as NAD+)
- occurs during glycolysis + krebs cycle
- free phosphate added to ADP –> ATP
Oxidative Phosphorylation
- occurs during electron transport chain
- NADH oxidized to NAD+ –> 2.5 ATP
- electrochemical or chemiosmotic gradient of protons (H+) across the inner mitochondrial membrane to generate ATP from ADP
Net RXN Glycolysis
glucose + 2ADP + 2Pi + 2NAD+ –>
2Pyruvate + 2ATP + 2NADH + 2H+ + 2H2O
After Pyruvate
most intial energy not released once in pyruvate form (present in bonds of pyruvate)
Pyruvate Degradation
(Glycolysis)
- anaerobic - pyruvate reduced during fermentation
- aerobic - pyruvate further oxidized during cell respiration in mitochondria
Fermentation
(Glycolysis)
- def: glycolysis + steps in formation of ethanol or lactic acid
- produces 2 ATP/1 glucose mlc
- NAD+ regenerated for glycolysis to continue in absence of O2:
- reduce pyruvate into ethanol
or
- reduce pyruvate into lactic acid
Alcohol Fermentation
- only in yeast and some bacteria
- pyruvate produced in glycolysis converted to ethanol
- NAD+ regenerated and glycolysis can continue
Lactic Acid Fermentation
certain fungi, bacteria, human muscle cells during strenuous activity
oxygen supply to muscle cells lags behind rate of glucose catabolism —> pyruvate generated reduced to lactic acid
NAD+ regenerated when pyruvate is reduced
Cellular Respiration
- most efficient catabolic pathway to harvest energy from glucose
- glycolysis = 2 ATP/1 mol glucose
- cell resp = 36-38 ATP/1 mol glucose
- aerobic process - oxygen final acceptor of electrons
- rxns occur eukaryotic mitochondrion
- catalyzed by rxn-specific enzymes
stages of cellular respiration
- pyruvate decarboxylation
- citric acid cycle
- electron transport chain
LEARN CELLULAR RESPIRATION
LEARN CALVIN CYCLE
Total energy production
net amount of ATP produced per molecule of glucose
- substrate level phosphorylation
+
- oxidative phosphorylation
Substrate Level Phosphorylation
glycolysis + krebs cycle
glycolysis: 2 ATP
krebs cycle: 1 ATP/turn = 2 ATP
net = 4 ATP
Oxidative Phosphorylation
pyruvate decarboxylation: 1 NADH/turn = 2 NADH
citric cycle: 3 NADH + 1 FADH2 / turn = 6 NADH + 2 FADH2 (per glucose mlc)
1 FADH2 = 2 ATP
8 NADH = 24 ATP
2 NADH reduced during glycolysis cannot cross inner mitochondrial membrane - must transfer electrons to intermediate carrier mlc
intermediate carrier mlc transfers e to second carrier protein complex, Q
these 2 NADH generate 2 ATP / 1 glucose = 4 ATP
24 + 4 = 28 ATP from NADH
4 ATP from FADH2
=
32 ATP by oxidative phosphorylation
oxidative + substrate level phosphorylation energy
(eukaryotes)
total = 4 ATP (substrate) + 32 ATP (oxidative) = 36 ATP
oxidative + substrate level
(prokaryotes)
38 ATP
2 NADH of glycolysis do not have mitochondrial membranes to cross - do NOT lose energy!
Eukaryotic ATP Production per Glucose Molecule
Glycolysis
2 ATP invested (steps 1, 3) (substrate)
4 ATP generated (steps 6, 9) (substrate)
2 NADH x 2 ATP/NADH (step 5) (oxidative)
Eukaryotic ATP Production per Glucose Molecule
Pyruvate Decarboxylation
2 NADH x 3 ATP/NADH
Eukaryotic ATP Production per Glucose Molecule
Citric Acid Cycle
6 NADH x 3 ATP/NADH
2 FADH2 x 2 ATP/FADH2
2 GTP x 1 ATP/GTP
Eukaryotic ATP Production per Glucose Molecule
Total
36 ATP
Alternate Energy Sources
body uses other energy when glucose is low
preferential order:
- other carbs
- fats
- proteins
substances –> glucose/glucose intermediates –> degraded in glycolytic pathway & citric acid cycle
Carbohydrates
(Alternate energy sources)
- disaccharides —> monosaccharides —> glucose/glycolytic intermediates
- e.g. glycogen stored in liver can be converted into glycolytic intermediate
Fats
(Alternate energy sources)
stored in adipose tissue
form = triglyceride
lipids —> fatty acids + glycerol (enzyme: lipases)
carried by blood to other tissues for oxidation
Fats - Processes
glycerol
(Alternate energy sources)
glycerol –> PGAL
PGAL = glycolytic intermediate
Fat processes
Fatty acids
(Alternate energy sources)
fatty acid –> activated in cytoplasm - 2ATP
activated fatty acid —> mitochondrion —> undergo series of beta-oxidation cycles —> converted to acetyl CoA
acetyl CoA —> TCA cycle
each B- oxidation cycle yields 1 NADH, 1 FADH2
Fats
(Alternate energy sources)
extra info
yield greatest number of ATP/gram of all high-energy compounds used in cellular respiration
efficient energy storage mlc
glycogen storage = demands for 1 day
fat storage = demands for 1 month
Proteins
(Alternate energy sources)
amino acids —-> transamination rxn
carbon atoms —-> acetyl CoA, pyruvate, intermediates of citric acid cycle
inermediates —> respective metabolic pathways —> cells produce fatty acids, glucose or ATP
Transamination Reaction
amino acids lose an amino group to form an alpha-keto acid
oxidative deamination
removes ammonia mlc from amino acid
ammonia
toxic substance in vertebrates
fish excrete ammonia
insects and birds convert ammonia to uric acid
mammals convert ammonia to urea for excretion
autotroph
organism that manufactures its own organic molecules
e.g. glucose, amino acids, fats
from inorganic materials
e.g. CO2, H2O, mineral salts
organic molecules and energy
organic molecules contain potential energy in form of chemical bonds
photosynthesis
autotrophs harness radiant energy from sun to form chemical bonds (containing PE)
occurs in algae and multicellular green plants
Chemosynthesis
used by autotrophic bacteria to obtain energy for manufacture of organic materials
CALVIN CYCLE!!!!
