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179 Cards in this Set

  • Front
  • Back
matter
- occupies space and has mass
- composed of elements
- elements are composed of atoms
nucleus
- central core of an atom
- composed of protons and neutrons
protons
have a positive charge and a mass of 1 atomic mass unit
neutrons
carry no charge and have a mass of 1 amu
atomic mass
# protons + # neutrons
isotopes
different forms of an element due to variations in atomic mass
radioactive isotopes
unstable, decay into other elements with the release of energy

ex: carbon 14 decays to nitrogen 14
half-life
measurement of radioactive decay

amnt of time for 1/2 of a given amnt of a radioactive isotope to decay
electrons
- one negative charge
- mass of 1/1860 amu
-"orbit" around nucleus in defined patterns
# of electrons = # of
protons in an uncharged atom
Atomic bond
connecting atoms together
formation of compounds
2 or more atoms connected together to form a chemically discreet entity
molecule
single grouping of atoms
ionic bond
- gain/loss of electrons between atoms
ions
gain or lose electrons
gain an electron
net negative charge
lose an electron
net positive charge
+ and - ions ______ each other in proportion of charges
attract
covalent bond
sharing of electrons between atoms

shared in pairs, one electron from each atom

ex: water- H electron-sharing-0-electron-sharing-electron-H
hydrogen bonds
in water and other molecules, slight charges attract
Water
50-95% of organisms
75% of earth's surface
biological importance of water
-bathing
-raw material for metabolism
-carries substances in and out of cells
-internal medium for cells
solvent properties
- polar and other ionic substances dissolve best in water
hydrophilic
polar substances that dissolve well in water
hydrophobic
nonpolar substances that do not dissolve well inw ater
cohesion
hydrogen bonds hold water molecules together to act as a unit
adhesion
attraction of polar water molecules to other substances
suface tension
pull of water molecules of surface molecules creates a coherent surface
caillary action
water is drawn into a small tube due to water being attracted to the tube (adhesion) , and the film of water on the tube in turn attracts other water molecules (cohesion)
high heat retention
-hard to evaporate because the hydrogen bonds must be broken to separate molecule

= requires more heat energy than other substances

-retains lots of heat

-sweating = excess heat is carried away by water evaporating fromthe sweat
acid
gives up a proton easily in water

weak acid does not give up H+ as readily as a strong acid

hydrophilic

0-<7
base
gives up an OH- group easily in water

hydrophilic

7-14
pH=
-log(H+) = negative log of the hydrogen ion concentration
the numbers show a difference in acidity/basicity by a factor of ___
ten
chemical reactions
involve breaking and re-forming bonding patterns
breaking of bonds ____ energy
releases

ex: things on stove- energy is released as light and heat
formation of bonds _________ of energy
requires input of energy
oxidation
reactions that release energy

loss of an electron

ex: burning

***oxidation and reduction are coupled, i. e., occur simultaneously -when a substance is oxidized, another substance in the overall reaction is reduced
reduction
reactions that require/store energy

gain of an electron

***oxidation and reduction are coupled, i. e., occur simultaneously -when a substance is oxidized, another substance in the overall reaction is reduced
ex: photosynthesis
reduced compounds
higher energy stored
oxidized compounds
lower energy stored
polymer
large molecule composed of many repeating subunits called monomers

ex: starch
synthesis
building

-monomers have an H on one side of the molecule and an OH on the other

-synthesis involves removing a hydrogen from one monomer and an -OH from the other monomer unit, then the H and OH are combined to form water and the two monomers are joined together.

also called dehydration synthesis
hydrolosis
breakdown of a polymer, using water

-a water molecule is broken down and as the monomers are separated, the H from the water is attached to one monomer and the OH from the water is attached to the other monomer unit
energy
ability to do work
kinetic energy
energy of motion
potential energy
stored energy
first law of thermodynamics
cannot create or destroy energy
second law of thermodynamics
Some useful energy is lost to a system when a conversion takes place. [No energy conversion is ever 100% efficient.]

order -------- > disorder ===>energy lost as heat and possibly some useful energy is released

disorder ------> order =requires a useful energy input from outside system

Example: Whe you eat a piece of bread, you break down the oder of the starch molecules to release their energy. You can never absorb all of the energy released from the starch, and some of it is used to increase order in (buildup) your body, and some is lost as heat. Thus the starch order goes to disorder, and within your body, disorder goes to order.
organic
compounds containing carbon
carbohydrates
sugars
monosaccarides
simple sugars
3-7 carbon atoms
straight chain or ring form
disaccharides
two covalently bonded monosaccarides
polysaccharde
polymer of monosaccharides
functions of carbohydrates
energy source
energy storage
structure
lipids
fats, waxes, oils, sterols
strongly hydrophobic
neutral fats
subunits: glycerol and fatty acids

-3 fatty acids join 1 glycerol by synthesis to form a neutral fat
glycerol
3-carbon unit with an -OH attached to each carbon
fatty acid
long chain of C's and H's

-number of carbons always an even number

-saturated fatty acid - all C's joined by single bonds

-unsaturated fatty acid - some C's joined by double bonds

-different fatty acids have different chain lengths and differing number of of double bonds (12 to more than 40 carbons long)
unsaturated fatty acids
neutral fat that is liquid a room temp. => oils

-derived from plants (some animal sources)
saturated fatty acids
neutral fat that is solid at room temperature => fats

-derived from animals (some plant sources)
soap
fatty acid + base
sterols/steroids
-four ring backbone -side groups determine the exact compound steroid. examples of steroids: cholesterol, testosterone, estrogen
functions of lipids
1. energy source

2. energy storage

3. structure

4. hormones
proteins
basic unit: amino acids

20 amino acids in living things

various proteins differ in the number, kind, and linear arrangement of constituent amino acids
peptide
short chain of amino acids protein: long chain of amino acids - may be thousands long
primary protein structure
linear arrangement of amino acids in the polymer

amino acids join by synthesis

-covalent bond between amino acids = peptide bond
secondary protein structure
primary chain coils like a spring (alpha-helix) or folds in a pleated sheet arrangement

-held in place by hydrogen bonds between amino acids
tertiary structure
coiled chain folds and forms bonds between R- groups of the aa's ===> globular or sheetlike appearance

-sulfur-containing amino acids form -S-S- (disulfide) bridges
quaternary structure
interactions of protein units to form a functioning unit

-not all proteins have quaternary structure
denaturation
-usually changes or destroys function

-heat, chemicals, radiation can cause denaturation

-frying an egg; hair perm
functions of protien
1. structural

2. energy source

3. enzymes

4. other: hormones; antibodies; carriers
functions of nucleic acids
-heredity and cellular/organismal control

-information storage and processing
Types of nucleic acids
dna and rna
enzymes
virgually all reactions in an organism

protiens
organic caalyst
speeds a reaction without being altered overall

E + S ---> ES complex ---> E + P
active site
place on the enzyme where catalysis occurs

-substrate binds at active site for reaction
specifity
enzymes are very specific - each does only one kind of reaction

ex: lock and key
catalase
catalyses the breakdown of toxic hydrogen peroxide to water. This is all that this enzymes does!
amylase
an enzyme in saliva that breaks starch down into glucose monomer units. This is the only substrate on which this enzyme works. Cellulose is also a polymer of glucose but amylase will not break down cellulose.
mechanism for catalyzing reactions
enzymes lower the activation energy of a reaction
activation energy
"prime" of energy to begin a reaction
stopping enzyme activity
1. competitive inhibiation
2. denaturation
competitive inhibition
ubstance similar in size and shape to the substrate "fools" the enzyme and gets into the active site

-binds up the enzyme because the reaction does not occur and enzyme cannot release the inhibitor

-destroys the activity of the enzyme

-analogy: getting the wrong key stuck in a lock
denaturation
- change in tertiary structure of protein changes the configuration (shape) of the active site and the substrate cannot bind which means that catalysis cannot occur

-causes of denaturation: anything that will alter the chemistry or destroy proteins

-pH - for most enzymes extremes of acidity or basicity will change the tertiary structure

-temperature - for example, cooking

-heavy metals - mercury, arsenic, lead, etc.

-radiation - UV light, radioactivity, etc. destroy protein structure by breaking the molecule apart
conditions for enzyme activity
optimum temperature and pH
cofactors
1. activators
2. coenzymes
activators
inorganic substances that bind w/ the protien to create a functioning enzyme
coenzymes
- change in tertiary structure of protein changes the configuration (shape) of the active site and the substrate cannot bind which means that catalysis cannot occur

-causes of denaturation: anything that will alter the chemistry or destroy proteins

-pH - for most enzymes extremes of acidity or basicity will change the tertiary structure

- temperature - for example, cooking

-heavy metals - mercury, arsenic, lead, etc.

-radiation - UV light, radioactivity, etc. destroy protein structure by breaking the molecule apart
control of enzyme activity
-control of enzyme activity is critical in regulating metabolism

-turning on enzymes when required

-turning off enzymes when not required

-regulating level of activity

mechanisms:
concentration of substrate
allosteric site
concentration of substrate
-low substrate concentration --> low enzyme activity

-presence of product may lower rate of enzyme activity

-feedback mechanism may lower rate of enzyme production, leads to lower activity
allosteric sites
-site away from the active site to which molecules bind

-changes shape of the active site, blocking catalysis
noncompetitive inhibition
the substance does not fit into the acitve site like a competitve inhibitor, but does halt enzyme activity
biochemical pathway
series of reactions within an organism that result in particular products being formed. Enzymes usually mediate each step of the reaction.

-each enzyme is specific to the step in the pathway that it catalyses

-various biochemical pathways can interconnect and these inteconnections can become quite complex within the metabolising cell
cell theory
organisms are composed of basic units called cells

1. living things are composed of cells
2. cells come from existing cells

1805

earlier idea: organisms composed of interwoven fibers, like cloth
robert hooke
1665
English
Observed "pores" in cork
named cells after monks's cells
Antonie van Leeuwanhoek
1677 Dutch
Ammature lensemaker and microscopist
single celled animas, spermatozoa
Lorenz Oken
-cell theory
- all organisms originate from and are composed of cells
Matthias Schleiden; Theodore Schwann
1839 Germans
-cell theory published, restatment of Oken
Rudolf Virchow
1855 German
-cell division
-all cells come from existing cells
-restatement of Oken
Basic Cell Structure
I. Outer Bounding Membrane
-cell membrane
II. Protoplasm
A. nucleus - if present
B. cytoplasm
1. organelles
2. ground substance
III. Cell Wall - if present
Cell types
eukaryotic and prokaryotic
Eukaryotic
* nucleus
* membrane-bound organelles
* generally larger cells
Prokaryotic
* no nucleus
* no membrane-bound organelles
* generally smaller cells
Cell membrane
completely surrounds cell
Cell membrane acts to
- control movement of substances into and out of cell
o selective
- hold cell intact
o cell dies if broken
- recognize other cells and molecules
Membrane Structure
two major components:
lipid bilayer
embedded protiens
Lipid Bilayer major components
phospholipid and cholestoral
Phospholipid structure
glycerol
"tail" of two fatty assets (hydrophobic)
phosphate head (hydrophlic)
bilayer
two layers of phospholipid.

in the membrane, tails are to the inside and head is it to the outside
embedded proteins
- interspersed in lipid bilayer
o “mozaic”
- partially or completely through lipid bilayer
- can move about within the lipid bilayer
o “fluid”
- often with complex carbohydrates attached
o glycoprotein (“glyco” = sugar)
membrane function
- acts as a barrier
- controls was crosses
protein functions
- cell-cell recog
- substance recog (only specific substances, relay a chemical message)
- carry substances across
- enzymes
- attach cells to eachother
semipermeability
- some substances pass through easily: water
- some hard: sugar
- alternate names: selectively permeable and differentially permeable
amnt of semipermeability based on
size and charge

- harder in large molecules
- small, nonpolar substances easily cross, larger polar do not
Passive Transport
transport across membranes
- does not require energy expenditure
types of passive transport
simple diffusion
osmosis
facilitated diffusion
diffusion
-based on random movement of molecules due to heat
- any temperature above absolute zero involves molecular motion
-little motion: solid, much motion: gas
-concentration gradient higher and lower concentrations of a substance

- NET movement of a substance from an area of higher to lower concentration

- In area of higher concentration, more molecules available to move in direction of lower concentration than vice versa

-eventually events out
-dynamic equilibrium- constantly balanced and unbalanced, but on average, balanced
transport by diffusion
- substance moves across membrane by simple diffusion
- solutes = dissolved substances
o diffusion across membrane = dialysis
- solvent = water
o diffusion across membrane = osmosis
Osmosis
* net movement (diffusion) of water across a semipermeable membrane
* dissolved substances lower the concentration of water in a solution
o more dissolved substance = lower water concentration
* across a membrane, this can create a concentration gradient --> diffusion
hypotonic
lower solute concentration
hyper
higher solute concentration
net movement in osmosis
hypertonic --> hypotonic
isotonic =
no net movement
cell in hypotonic solution
gains water
cell in a hypertonic solution
loses water
Facilitated Diffusion
* protein channel across
* selective
* allows diffusion of polar substances
* follows concentration gradient only
transport across membranes and types
requires energy expendature by cell

types:
-proten carriers
-vasiculation
protein carriers
* movement by change in shape in protein
* selective
* chemical energy (ATP) used
* movement against a concentration gradient
o accumulation of substances
o exclusion of substances
vasiculation
involves formation of membrane sacs
vesticles
membrane sacs
endocytosis
entry into a cell
cell membrane forms vesticle around engulfed object
exocytosis
exit from a cell
vesicle fuses with cell membrane, releases substance
cell size
20 um to ostrich egg

-as cell size increases, surface area becomes too small to serve volume -> limits on size
protoplasm
everything inside the cell membrane: nucleus and cytoplasm
nucleus
- defines eukaryotes
# surrounded by double membrane with large pores
# contains chromatin-heredity material
# often spherical and central
functions of nucleus
- regulates cellular activity
- storehouse of info
- reproduction
nucleolus
-area in nucleus of RNA synthesis
- not an organelle
endomembrane System
* interconnected and interacting membrane-bound organelles
* endoplasmic reticula
* Golgi apparatus
* lysosomes
* vacuoles and vesicles
endoplasmic reticulum
two types: rough and smooth
- interconnected network of membrane sacs
rough ER
* membrane sacs
* covered with ribosomes
o protein synthesis
o protein export
* forms vesicles
* forms new membrane
Smooth ER
* membrane tubules
* lack ribosomes
* lipid synthesis
o neutral fats
o steroids
* sugar control
* detoxification
Golgi Bodies
* stacks of membrane sacs
* packaging and secretion of substances
* receiving face-membrane from ER
* chemical modification
* vesicles form on transport side
lysosomes
* vesicles that contain digestive enzymes
* merge with food vesicles (from endocytosis) to digest food
* digest worn organelles
* “suicide sac” - if bursts, digests and kills cell => programmed cell death
o cells between developing fingers and toes
o disappearance of tadpole tail
pompe's disease
lysosome related disease
glcogen accumulates
lacks glycogen digesting enzyme
tay-sach's
affects nervous system
lacks lipid digesting enzyme
Vacuoles
* bounded by membrane
* storage
* plants: large central vacuole
o contains water - water relations
o contains wastes and pigments
+ cooking beets releases betacyanin - cooking water turns red
o stores nutrients
Peroxisome
* vesicles
* contain enzymes for breakdown of hydrogen peroxide to water and oxygen gas
mitochondrion
breakdown of substances to release energy in useful chemical form

double membrane- inner is folded, sight of enzyme activity

- cellular respiration
- all eukaryote
cholorplast
photosynthesis
* double membrane
* internal stacks of membrane sacs (grana)
* matrix (stroma)
* chlorophyll (green)
* photosynthesis
* plants and algae
flagellum/cilium
* cell extensions
* internal framework of tubes
o 9 doublets of tubes around 2 central tubes
+ 9+2 arrangement
o spokes of protein fibers
o protein arms on tubes use ATP energy to create movement
flagellum
* long and whiplike
* relatively few in number
* whiplike undulations cause movement
cilium
* short and bristlelike
* relatively numerous
* “breaststroke” movement - stroke/recovery movement
basal body
* anchors cilium or flagellum in cell
* 9 triples of tubes without central core = 9+0
centrioles
* similar to basal body - 9+0
* paired, lie at right angle nest to nucleus
* function in cell division
* not found in plants
cytoskeleton
* latticework of fibers and tubes
* not rigid - easily broken and re-formed
cell wall
* outside the cell membrane
* basketlike, very porous
* plants, fungi, algae, bacteria
* composed of:
o cellulose - plants => paper, cotton
o proteinaceous substance - bacteria
o chitin - fungi
tight functions
protein rivets, leakproof seal

*animals*
anchoring junctions
protein plates, allow substances to pass by

*animals*
communicating junctions
protein channel between cells

*animals*
middle lamella
pectic glue between cell walls
plasmodesmata
membrane-lined channels between cells
plants do not have
lysosomes centrioles
animals do not have
cholropasts
central vacuole
cell well
prokaryotic cells
no nucleus- DNA is naked in cytoplasm (nucleoid)
no membrane-bound organelles
cell wall proteinaceous
energy
ability to do work
cellular work
- metabolism
- transport
- reproduction
cellular energy
chemical energy
- readily available
- universal
ATP
bond between last 2 phosphates easily broken and releases energy

# ATP breaks down to ADP and a phosphate
- releases immediately useful energy to do work
- "energy currency" of the cell
ATP formation
ADP + Pi = ATP
stores energy for immediately cellular work
chemiosmosis
* energy used to pump H+ across membrane
* creates a charge across membrane = “battery”
* ATPase in membrane allows flow of H+
* H+ flow energy allows ATPase to form ATP
* mechanism of ATP formation
photosynthesis
* uses light energy to form energy-rich organic compounds
* reduction
* autotrophs
* cloroplasts
* grana- stacks of membrane sacs contain chlorophyll
* stroma- surrounding matrix and contains enzymes
* 6 CO2 + 12 H2O --> C6H12O6 + 6 O2 + 6 H2O
Cellular respiration
* releases stored chemical energy to form ATP
* oxidation
* autotrophs and heterotrophs
* occurs in cytopasm
* eukaryotes, continues in mitochondria
suggests a two-step process:
1) light reactions - harvest light energy
2) nonlight reactions - fix carbon into organics
* overall, carbon is reduced, storing energy
aerobic respiration
in mitochondria
requires oxygen gas
36 atp made
part of cellular respiration
all aerobic organisms
alcoholic fermentation
no ATP made (2 are made in glycolosis, available to organism)
lactic acid synthesis
no atp made
- occurs in the absence of oxygen gas
# ATP made in glycolysis
- 2 used as prime + 4 made = 2 net
role of mitochondrion
aerobic respiration
inner folded membrane site of ATP synthesis
chemiosmosis across the inner membranes
folds create pockets for H+ concetration buildup