Biology Test 1 Study Guide

Chapters 2-5: The Chemistry of Life

Atom

Human Body is mainly made up of Oxygen, Carbon,

Hydrogen, Nitrogen
Emergent Properties: property that is not found on the
previous level (each level has properties that previous did not)

Atoms
Molecules
Macromolecule

In pure state, # of protons and # and electrons are equal and their charges cancel
1st shell: max of 2 electrons; all others: max of 8
elements like to fill outer shell to 8 by sharing eelectrons have more potential energy (potential to
do work) further away from the nucleus
o they move through energy input.
Elements join together to form molecules by
forming chemical bonds
Covalent and Ionic bonds are strong; hydrogen
bonds are weak
Covalent Bonds (shared charge) sharing of
electrons in outer shell
o Sharing 2 electrons=single bond
o Sharing 4 electrons=double bond
o Some electrons pull the elements (H2O)
Electronegativity: measurement of how strongly
and element pulls electrons towards itself
Non-polar = even sharing of electrons (H2, O2)
Polar = uneven sharing (H2O, CH4)
Ionic Bonds (electronegativity is different between
elements)
Stealing/donating of electrons
Anion: gains electron, - charge
Cation: loses electron, + charge

Water: very polar molecule, held together by covalent bonds; bonds to itself
(cohesion) and other molecules (adhesion) through hydrogen bonds.
Water is the universal solvent.
Forms hydration shell around other molecules
Cells are mostly composed of water on the inside
Influences the shape and structure of large molecules
pH and osmolarity of the cell
Large molecules are hydrophilic and hydrophobic
pH

Water dissociates by forming hydrogen bons and forms an equilibrium

H+ = Hydronium ion (or proton) decrease OH- (hydroxide ion)

Acids: H+ > OH- (below 7 on pH scale)

Neutral H+ = OH- (7)
Bases: H+ <
OH- (above
7)
pH

influences
the rate of
chemical
reactions

Functional Groups: play a key role in functionality

Metabolism: sum of chemical reactions of the cell

Catabolism (hydrolysis rxn): reactions that are breaking things down water
molecule added
Anabolism (dehydration): reactions that are building new bonds water molecule
removed0-i

Carbs polymers of sugars

Simple sugar: monosaccharide (monomer)
Hydroxyl groups and 1 carbonyl (CnH2nOn)
Aldose carbonyl is first; Ketose carbonyl in the middle of chain
Glucose (C6H12O6) is an important building block
o Can fold itself 2 diff ways
o Alpha = starch, glycogen = storage
o Beta = cellulose, chitin = structural, nondigestable
Held together by bonds
Proteins
Monomers: amino acids (amino acids > peptides > polypeptides > proteins)

Functions: structure, cellular communication, catalyze chem rxns (ENZYMES)

Structure: Alpha carbon, amino group (base/H+ acceptor), carboxyl group
(base/H+ donor), R group (shape/function)
Peptide bonds like amino acids together through the carboxyl and amino groups
(through dehydration synthesis)
Structures
o Primary: linear chain of amino acids
o Secondary: 2D of amino acid, via hydrogen bonding (alpha helix, beta
pleated sheet)
o Tertiary: 3D shape stabilized by side chain reactions (dependent on R
group
o Quaternary: 2/+ separate (could be identical) polypeptides interact

Nucleic Acids
Monomer: nucleic acids (DNA or RNA)
Function: store and transmit hereditary information
Structure: Pentose sugar, Phosphate group, Nitrogenous base
Phosphodiester Bond
Flow of information usually goes from DNA-RNA-protein
Lipids not polymers
Function: in storage of carbs and NRG, insulation, padding
Structure: Glycerol and 3 fatty acids
Bonded by Ester Linkage
Fats
o Saturated: single-bonded carbons, saturated in hydrogen
o Unsaturated: atleast one double bond, kinks molecules
Phospholipids
o Hydrophilic head
Glycerol
Phosphate group
Choline
o Hydrophobic tail
Fatty and chains (sat/unsat)
o Self assemble into bi-layer in water
Steriods Cholesterol
Ch. 6 Tour of the Cell
Prokaryotes
No nucleus
No membrane-bound organelles
Plasma membrane
Both have:
Cytosol
Chromosomes
Ribosomes
Evolution of Eukaryotes
Infolding of plasma membrane

Eukaryotes
Nucleus
Membrane-bound organelles

 Nucleus
Endomembrane system
Engulfing prokaryotes (endosymbiosis)
Organic carbon feeding bacterium
Mitochondria
Photosynthetic bacterium
Chloroplast
Nucleus
Chromosomes
o Chromatin
o Genes: all info that the cell needs for life
Nuclear Envelope
o Double Membrane: nuclear lamina on the inside (protein filaments)
Nuclear Matrix
o Fiber framework
Nuclear pores
Nucleolus
Ribosome factory (rRNA + protein)
Ribosomes
Free in cytosol
Bound to nuclear envelope and ER
Endomembrane System (nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles,
plasma membrane)
Endoplasmic Reticulum- little net within the cytoplasm
Continuous with the nuclear envelope
Tubules and cisternae(folds in ER)
ER lumen: outermost part of the walls that wind around

Smooth
o Lipid synthesis
Membranes
Steroid hormones
o Ca2+ storage in muscle
o Detoxification of drugs/poison
Rough
o Synthesis of proteins and glycoproteins(protein w/ carb)
For export, membranes, lysosomes
o Membrane synthesis
Transitional ER (vesicles Golgi)
Golgi: finishing school & post office
Cis: receives transport vesicles from Rough ER (vesicles fuse to cis)
Trans: generates new transport vesicles
Proteins and glycoproteins are modified/mature
Lysosomes: Garbage men
Sacs of hydrolytic enzymes (very acidic)
Phagocytosis (cell will engulf something and deliver to proteins) & digestion
Recycle old parts of the cell
Digest proteins, lysosomes convert old proteins into amino acids, recycle for
protein translation
Autophagy: self-eating, digests damaged cell
Vacuoles
Thought to have
Plant & Fungal
evolved via
central vacuole (storage)
endosymbiosis
Animal cells (some)
Have
food vacuole & contractile vacuole
prokaryote-like
DNA
Mitochondria: powerhouse of cell/structure &

Have
function
prokaryote-like
makes ATP
ribosomes
has a lot of membranes = allows + surface area
Divide
own ribosomes = self production of most proteins
independent of
own DNA (maternal)
cristae: folds in mitochondria
matrix: space between cristae and inner membrane
Chloroplasts
2 membranes (inner and outer)
produce glucose from sunlight
contain chlorophyll contained by thylakoids (stack = granum)
stroma = stroma inside
have their own DNA
Cytoskeleton: cell shape and support
movement of cells and organisms; as well as materials within cells
Microtubules, microfilaments, intermediate filaments all function to maintain cell
shape
Microtubulues: movement of chromosomes (cilia, flagella) during cell division
o Hollow tubes; Subunits of tubulin

o Highway system of organelle movement

o Centrosomes, centrioles
Intermediate Filaments: coils of fibrous proteins (keratin_
o Maintain cell shape
o Anchorage of nucleus and other organisms
o Formation of nuclear lamina
Microfilaments: two intertwined strands of actin
o Maintain cell shape, muscle contraction, cell division

Extracellular Structure
Plant - Cell Wall (mainly cellulose)
Structure and support
Barrier to infection
Animal cells Extracellular Matrix
Holds cell together
Contributes to physical properties & plays a role in chemical signaling
Intercellular junctions
Plants: plasmodesmata
Animals: intercellular junction (desosomes like an anchor)

Ch. 7 Cell Membranes Structure and Function

Composition: Phospholipids, lipids, proteins, carbs

Fluid mosaic model describes phospholipid bilayer
Membrane Lipids
Phospholipids are amphipathic influences how phospholipids aggregate
Cholesterol is hydrophobic
Phospholipids spontaneously form bilayers (hydrophobic/philic domain)
Membrane fluidity
o Factors affecting fluidity
Hydrocarbon tails
Saturated
Unsaturated
Cholesterol
Reduces fluidity at moderate temps (body temp - 37 C)
Reduces solidification at lower temperatures
Lateral movement frequent; flip-flop movement rare

Peripheral proteins are

hydrophilic

Noncovalently attached
to integral proteins

Form bridges to
Cytoskelton & Extracellular
Integral proteins are
amphipathic

Transmembrane
domains

Hydrophobic helix
(nonpolar amino acids)

1.

Membranes Carbs
Glycolipids (CHO and lipid)
Glycoproteins (CHO and protein) cell recognition
On exoplasmic surfaces only (outside of cell)
Membrane Proteins - Functions

Sidedness: Membranes are asymmetrical

Phospholipid, protein and CHO distribution is asymmetrical
Orientation of proteins is also asymmetrical
Carbohydrates on exoplasmic side
Note sides from ER to Golgi to cell membrane
Membranes are selectively permeable to ions and molecules.
Passive Transport
Simple Diffusion

Large molecules do NOT enter this way

(glucose, amino acids)
Small, uncharged enter easily (CO2, O2, H2O)
Lipid solubility often diffuse easily (ie: steroid
hormones)
2. Facilitated Diffusion through Channel
Protein (Provide corridors that allow a specific
molecule
or ion to cross the membrane)
Channel proteins do NOT change shape
Ions (Na+, K+, Cl-) diffuse thru channel
proteins
Some are gated ion channels (open or close in
response to conditions)
3. Facilitated Diffusion through Channel
Protein (Undergo a subtle change in shape
that translocates the solute-binding site across
the membrane)
Solute binds to transporter
Transporter changes shape to deliver the solute to
the inside of the cell
Glucose transporter
Active Transport
4. Active transport (Na+/K+ Pump)
Moves solutes AGAINST concentration gradients
Requires NRG input
Ion gradients are maintained by active transport
Solute(s) binds to active transporter
One example: Na+/K+ pump

Na+/K+ Pump

+
+
-3 Na out, 2 K in, 1 ATP used

for each cycle

-Animal cell uses up to 50% of its

energy on this!

Electrogenic pumps create membrane potentials

3 + charges out for every 2 +s in. Therefore, net
o Voltage formation (An electrogenic pump)
Also form a Na+ gradient

The charge difference is called a membrane potential (remember this!)

A membrane potential is also POTENTIAL ENERGY - a potential to do WORK!

NA+/K+ pump is known as an electrogenic pump (animal cells)
Proton pump (plants, fungi, bacteria)
The membrane potential is often used in COTRANSPORT
Uses potential energy in ion gradients
H+/sucrose cotransporter in plants
Bulk transport also moves materials across membranes: Exocytosis
Bulk transport also moves materials across membranes: Endocytosis

Endocytosis
Phagocytosis:
engulding large
piece of material
(food/particle)
Pinocytosis: taking
in fluid

Osmosis:
Diffusion of water
through a lipid
bilayer
water diffused
through lipid bilayer
also aided by aquaporins (facilitated diffusion)
Hyptonic (Lysed): [solution] < [cell] water moves into cell
o Plant: Turgid but this is normal
Isotonic (Normal)
o Plant: Flaccid
Hypertonic (Shriveled): [solution] > [cell] water moves out of cell
o Plant: Plasmolyzed

 Ch. 8 Intro to Metabolism

First Law of Thermodynamics - Energy can neither be created nor destroyed

(ie: the amount of energy is constant)
o BUT, energy can be transformed from one form to another.
Second Law of Thermodynamics - Every energy transfer or transformation
increases the entropy (disorder) of the universe.
o Ie: The first law is not perfect!
Kinetic NRG: Energy of movement
Energy
(heat)
Released
Potential NRG: energy at rest
& Harvested!
(chemical)
Metabolism: sum of all chemical
reactions
Catabolism: sum of all reactions that
break things down (starch >>>
glucose)
Anabolism: sum of all reactions that
build things up (glucose >>> starch)
G = Free energy change; tells us whether a metabolic reaction occurs
spontaneously
G = G final state - G initial state
-G = Loss of free energy during
the reaction (SPONTANEOUS, catabolic
Energy
or exergonic) **downhill**
Required
+G = Gain of free energy during
the reaction (Non-spontaneous,
anabolic, endergonic)
**uphill**
Equilibrium and metabolism
Flow of NRG
o Closed vs. Open systems
o Single step vs multi-step systems
o Metabolism is a flow of energy via multi-step chemical reactions
o NET flow is exergonic makes overall G negative
Exergoni
o Only reach equilib when you die
c
ATP powers cellular work by coupling exergonic
reactions
to endergonic reactions
o Can be recycled
o Overall, powers cellular work by
phosphorylating other molecules which Endergoni
become
more reactive (less stable)
c
Look at free NRG (G) of
o Reactants
o Products
o Transition state
EA = Activation Energy
Enzymes (proteins) role in chemical rxns
Specific enzymes act on specific substrates, usually ending in ase

Catalyze chemical reactionCatalysts increase rate of rxn, not direction & are not
consumed in reaction

Enzyme-substrate complex
Active site
o Determines specificity
o Induced fit
o Shape change
Enzymes lower activation energy and
speed up reaction but G is unaffected
Why do reactions have Activation
energy in the first place?
o 2nd law of thermodynamics: what
would quickly happen to proteins
that are rich in free energy
without the Ea requirement?
Factors affecting enzyme activity
o Temp and pH
o Cofactors inorganic ions: iron, zinc
o Coenzymes (protein) organic molecules: riboflavin, B12
o External inhibitors from outside of the body (toxin/posion)
o Allosteric regulators - need to regulate enzyme production b/c you dont want
to produce to many/waste NRG
External Enzyme Inhibitors
o Normal Binding substrate binds with active site (allosteric site is separate)
o Competitive binding substrate competes with competitive inhibitor
If you have more substrate than inhibitor, the substrate can overcome
This is reversible if the substrate isnt tightly bonded
o Non-competitive non-comp. inhibitor bonds to allosteric site, this changes
the shape of the active site and prohibits enzyme from bondng to active site
Purposeful regulation of enzyme active helps control metabolism