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1 - Molecules
Isotopes
Isotope: SAME element but different # of neutrons
Radioisotope: unstable isotope that decays over time by emitting radiation
➢ As a result they may convert from one element to another
Half-life: half the time it takes for a radioactive sample to reach its initial amount
➢ Eg. iodine-131 (20g) has a half life of 8 days. What mass remains after 24 days?
○ = 2.5g
Radioisotope tracing: radioactive material is injected into patient and it’s movements are
traced using a PET scan
➢ Eg. injecting a radioactive glucose can be used to find a tumor bc cancerous cells will
break the glucose down faster than regular cells
Radiometric Dating: dating rocks and fossils by seeing how much of a naturally occurring
isotope is abundant in the object (how much the isotope has decayed)
intramolecular forces
➢ Ionic bonds
○ occur b/w a cation (metal) and anion (non-metal)
○ Their charges allow them to form STRONG bonds w other atoms
○ Their charges allow ions to be polar
➢ Covalent bonds
○ Occur b/w 2 non-metal atoms
○ Valence electrons are shared
○ Level of attraction b/w 2 atoms depends on their electronegativity
■ If the 2 atoms have similar electronegativities, their electrons are
dispersed/shared equally so they have no overall charge (non-polar)
■ If the 2 atoms have very different electronegativities, their electrons are
shared unequally so the molecule forms dipoles (polar)
■ A higher electronegativity = higher attraction so electrons gravitate
towards it, giving that atom the more negative charge
■ High electronegativity = O, N, Cl
■ Low electronegativity = H, C, P
Intermolecular forces
➢ 2 types:
○ Hydrogen Bonding
○ Hydrophobic Interactions
Hydrogen Bonding
➢ The slightly + hydrogen atom of one molecule attracts another slightly - atom of a
different molecule
➢ Weaker than ionic and covalent bonds but together can be very strong
➢ Represented by a dotted line bc it is a very weak type of covalent bond
➢ Help maintain proper structure and function in molecules
○ Capillary action and surface tension of water
■ Cohesion: H-bonds b/w water molecules
■ Adhesion: H-bonds b/w water and other molecules
○ Secondary, tertiary, and quaternary structures of proteins, and nucleic acids
Hydrophobic Interaction/Effect
➢ Nonpolar molecules cannot form bonds with hydrogen in H2O so instead they clump
together in the presence of water
○ Considered hydrophobic ( “water-fearing”)
○ Polar molecules are hydrophilic (“water-loving”)
Hydrocarbons
➢ Organic molecules made of only C and H
➢ Non polar (C-C is also non-polar, but CO and HO are polar)
➢ Low boiling point
➢ Flammable (used in combustion reactions)
➢ Their covalent bonds are energy-rich and release that energy when the bonds
are broken (eg. combustion)
Functional Groups
Functional group: a group of atoms that always behaves in a certain way, thus
determining the chemical and
physical properties of the organic
molecule its attached to
➢ Functional groups form the
reactive part of molecules
Isomers
Isomer: same molecular formula but different structural formula
➢ Results in different properties unless they have the same functional groups
➢ Cells know which isomers they can recognize and need to synthesize
➢ 2 types:
○ Structural Isomers
■ Positional
■ Chain
■ Functional
○ Stereoisomers
■ Geometric
■ Enantiomers
Structural Isomers
➢ Chain - C backbone is in a different order
➢ Positional - carbon backbone stays the same but but functional groups are moved
around/connected in different areas
➢ Functional - different functional groups are present
Stereoisomers
Geometric: same functional groups but arrangement of atoms on each side of the double C
bond is different
➢ Cis: when like groups are on the same sid/symmetrical about the double C bond
➢ Trans: when like groups are on opposite sides of the double C bond
Enantiomers: same molecular and structural formula but they cannot be
overlapped/superimposed (think about right and left hands overlapping)
➢ Usually due to an asymmetrical carbon
Lipids
➢ Composed of CHO, but there are a lot less oxygens than CH’s
➢ Non polar/hydrophobic
➢ Compared t o carbohydrates, lipids:
○ Store more energy
■ Yield more than double energy/gram
○ Since energy is stored in hydrocarbons, their energy is less accessible to cells
than that of carbs
■ This therefore provides longer-term energy and are broken down after
carbs are used up
➢ Other functions:
○ Insulate against heat lost (recall that lipids are fats)
○ Protective cushion around organs
○ Major component of cell membranes
○ Water-repelling coatings for fur, feathers, and leaves
○ Steroid hormones (estrogen, progesterone, testosterone)
○ Electrical insulation of nerves
➢ 4 types:
○ Triglycerides
○ Fatty acids
○ Steroids
○ waxes
Triglycerides
➢ Glycerol molecule + 3 fatty acid chains
➢ Join together through dehydration synthesis
➢ Hydroxyl on glycerol and carboxyl on fatty acid bond through an e ster linkage
○ Forms 3 H2O’s bc there are 3 tails
Fatty acid: a hydrocarbon chain that ends with an acidic carboxyl group
➢ Can either be saturated or unsaturated
Properties Saturated Unsaturated
Straight or Bent tails? straight Bent bc of double bond
State @ room temp Solid bc they are easily Liquid bc kinks push tails
stackable apart
Hydrogenation
➢ bubbling hydrogen through bent tails (unsaturated) to make them saturated and straight
➢ Unsaturated fatty acids are normally cis but get converted to a trans configuration,
making them structurally similar to a saturated fatty acid
➢ Companies use them bc they are cheap and last long but
are harmful to your health
Phospholipids
➢ R group + phosphate group + glycerol + 2 fatty acids
➢ Main component of cell membrane
➢ Phospholipid head = polar, fatty acid tail = non-polar
Phospholipid bilayer
➢ In aqueous, extracellular environments phospholipids
naturally form a bilayer
➢ phospholipids arrange themselves so the polar head faces the outward environment
and the tails form hydrophobic interiors
➢ Cholesterol molecules help maintain fluidity
○ Grab onto fatty acid tails and hold them together
when they get too warm and pull them apart
when they get too cold
Steroids
Steroid: lipid composed of 4 carbon based rings
➢ Different steroids have different arrangements and functions
➢ General functions:
○ Reduces inflammation
○ Anabolic steroids mimic male sex hormones - used for cancer and aids
treatment, and to build muscle mass
➢ Examples:
○ Cholesterol
■ Found in cell membrane & blood of animals
■ Precursor to other steroids
○ Testosterone
■ Regulates sexual function
■ Helps build bone and muscle mass
○ Estrogen
■ Regulates FEMALE sexual function
■ Increases fat storage
Waxes
waxes: lipids made of long carbon-based chains that are solid at room temp
➢ Produced in both animals and plants
➢ Functions:
○ Coats leaf surfaces
■ Prevents water and solutes from escaping
○ Repels insects
○ Coats skin, fur, leather, exoskeleton to keep surface dry
○ Forms barrier from infection
Proteins
Protein: polypeptides (polymer) made of repeating amino acid units (monomers) linked by
peptide bonds (covalent)
➢ Peptide bond forms b/w carboxyl and amino group
➢ Function depends on structure/shape
➢ Classified into groups based on function:
○ Catalyzing chemical reactions (eg. enzymes)
○ Structural support
○ Transport
○ Enabling organisms to move
○ Regulating cellular process
○ Providing defense against disease (eg. antibodies)
Amino Acids
➢ Central carbon bonded to:
○ Hydrogen (H)
○ Amino group (NH4) (basic)
○ Carboxyl group (COOH) (acidic)
○ R group
➢ N-C-C Backbone
➢ Somewhat polar bc of carboxyl and amino group
➢ Synthesized in ribosomes
➢ 20 amino acids exist, 8 are essential (must be obtained through diet)
○ Combinations of the 20 amino acids are infinite
Levels of protein organization
➢ 4 levels
○ Primary structure
■ Linear order of amino acids bonded together through peptide bonds
■ Only one that does not involve protein folding/3d shape
○ Secondary structure
■ 2 shapes
● Alpha helix - coil
● Beta-pleated sheet - folded
■ Occur due to H-bonds b/w polar groups
○ Tertiary structure
■ Responsible for folding of proteins, affected by:
● How different r-groups interact
● Mostly affected by hydrophobic effect
● Also affected by H-bonding
● ionic/electrostatic bonding b/w different r-groups
○ Quaternary structure
■ How multiple polypeptides fold together to form
a protein
■ Also affected by H-bonds
Protein Denaturation
➢ Occurs when r-group bonds are disturbed (intermolecular
forces break), so the protein starts to unfold
➢ Affects 2, 3, and 4, structures
➢ Can cause protein to lose function and can be irreversible
➢ Caused by:
○ Extreme temps
○ Exposure to chemicals
○ extreme pH
○ Agitation
Nucleic Acids
Nucleic acid: macromolecule composed of repeating nucleotides
(monomer)
➢ 2 types of nucleic acids:
○ DNA (deoxyribonucleic acid)
■ More stable than RNA
○ RNA (ribonucleic acid)
DNA RNA
Endomembrane System
➢ Composed of endoplasmic reticulum, golgi apparatus, vesicles, and cell membrane
➢ All work together to process and transport proteins
Ribosomes
➢ Composed of RNA and proteins
➢ Ribosomes found in cytosol (free ribosomes) synthesize polypeptides
Endoplasmic Reticulum
➢ Membrane-bound tubules & sacs
➢ Connected to nuclear envelope
➢ 2 types:
○ Rough ER
■ Covered in ribosomes
● Synthesize proteins (eg. polypeptides)
○ Smooth ER
■ No ribosomes
■ synthesizes lipids (eg. phospholipids in membranes)
■ Can also perform other functions depending on cell
1. Ribosomes on Rough ER surface produce proteins and then push them to Smooth ER
(through lumen) where they are stored and processed
2. Smooth ER forms vesicles around lipids and proteins to get sent to cis face of golgi
apparatus
Golgi Apparatus
➢ Stack of curved membrane sacs
➢ Cis face - longer tubed side
➢ Trans face - more circular tubed side
➢ “Post-office” of the cell
○ Packages, sorts, and distributes substances to be sent around the cell
➢ Produces lysosomes and carbohydrates
3. Vesicles release proteins and lipids into golgi apparatus where they are modified and stored,
then packaged into vesicles to be sent to their destination via the trans face
Cell Membrane
➢ Acts as a boundary from extracellular fluid and the cell itself
➢ Regulates movement of ions and molecules into and out of the cell
➢ Semi-permeable (only allows some substances through)
○ Small uncharged polar and/or lipid soluble (hydrophobic) molecules can pass
thru the phospholipid bilayer easily
■ water, oxygen, carbon dioxide, & small fatty acids
○ Ions, Large Polar and/or water-soluble molecules have a hard time passing
through bc of hydrophobic interior
■ Have to pass through protein channels that are inserted throughout the
membrane
■ Eg. Ions, amino acids, triglycerides, glucose, & nucleic acids
Facilitated Diffusion
➢ Since large polar molecules and ions cannot diffuse through the membrane, regularly,
they can diffuse using either a:
○ transmembrane/channel protein
○ Carrier protein
➢ Works as long as [ ] outside cell > [ ] inside cell
Channel proteins/transmembrane
➢ Tubular shape made of proteins
➢ Exterior is made up of amino acids with non-polar chains
○ non-polar allows it to interact with the phospholipid’s non-polar interior
➢ Tunnel in the channel protein is very specifically shaped so only certain molecules/ions
can pass through
○ Generally passes smaller polar molecules/ions
➢ Some channels are always open but some can open/close in response to:
○ Hormones
○ Electric discharge
○ Pressure
○ Light
Cystic Fibrosis
➢ Fatal genetic disorder when channel proteins that move chloride ions is defective
➢ Causes improper water movement in and out of cells which builds up thick mucus in
respiratory passages and organs
Carrier Proteins
➢ Generally passes bigger polar molecules/ions
➢ Difference is that carrier proteins must BIND to the molecules/ions that pass through
➢ Carrier proteins change shape while they transport molecules/ions
Since they can only bind to a few molecules at a time, this type of transport takes
○
longer than channel proteins (i.e. lower diffusion rate)
➢ Exterior is also made of amino acids with non-polar side chains
○ Non-polar side chains allow it to interact with the phospholipid’s non-polar interior
➢ Interior is lined with amino acids that form intermolecular bonds with the molecule of
transport
Cystinuria
➢ Genetic disorder
➢ Inability to remove cystine and other amino acids from urine
○ If cystine isn’t removed then it can cause them to crystalize into stones called
calculi which block the urinary tract
Active Transport
➢ Since the molecules are going against the [ ] gradient they require energy called ATP
○ ATP (adenosine triphosphate) is made of an adenine nucleotide with 3
phosphate groups)
○ goes through hydrolysis to create ADP and 1 phosphate, with the release of
energy