Unit 1: Chemistry of Life Flashcards
Covalent Bond
when electrons in atoms are shared between 2 atoms in bond
nonmetals do this = CHNOPS
Polar Covalent Bond
OPPOSITE CHARGES (H2O WATER)
Electrons are shared UNEQUALLY meaning one atom attracts more electrons (is NEGATIVE) & other atom is positive
EX: hydrogen has a polar covalent bond w/ OXYGEN bc oxygen is partial NEG (polar) due to it attracting the electrons, making HYDROGEN POSITIVE (nonpolar)
Nonpolar Covalent Bond
EQUALLY CHARGED CH4 METHANE
Electrons are shared equally between 2 atoms in bond (NO PARTIAL CHARGES)
ex: carbon-hydrogen no partial charges (CH4 methane)
Hydrogen bond
Intermolecular interaction occurs when the partial pos of H (bonded to O,N,F ex: H2O) interacts w/ the partial neg charge on a high electro neg. element = O,N,F
MADE by POLAR molecules
Ex: The partial pos charges of H in H2O create hydrogen bonds w/ the partial neg of O in another H2O molecule
Ionic Bonds
complete transfer of valence electron(s) between 2 atoms, generates two oppositely charged ions (cation & anion)
Ionic: 2 ions (+/-) bond (givers/takers) Na+Cl- Affected by environment (eg. water)
weaker than covalent
metal loses electrons to become a cation/nonmetal accepts those electrons anion
Water H2O
Polar molecule
polar covalent bonds
oxygen end = partial neg, hydrogen = partial pos
cohesive
can form up to 4 hydrogen bonds (bc O has 2 neg lone pairs & 2 pos Hydrogen atoms)
Methane CH4
Nonpolar molecule
nonpolar covalent bonds
equal sharing of electrons w/ 4 hydrogens
Strongest Bonds
- Covalent Bond (polar & nonpolar)
- Ionic Bond (2 atoms share valence e- (ions) givers(metals) & takers(nonmetals) can be affected by pos/neg environ )
- Hydrogen bonds (polar covalent molecule) attraction only in partial charged molecules
- when the partial pos of h is attracted to any close neg charge, bonds broken easily (temporary/weak interaction)
ex: Ammonia NH3 dissolves in water bc hydrogen bonds made when N- attracts H+ of H20
Nonpolar substances
Hydrophobic:
oyxgen (O2), nitrogen (N2), ozone (O3), lipids, wax
Polar substances
Hydrophilic:
water, salt, ammonia (NH3), sugar, hydrogen chloride (HCL)
Isotopes
atoms of same elements w/ SAME # of protons but DIFF # of neutrons = diff masses
radioactive, tracers follow molecules, med diagnosis
uncontrolled exposure = harm
pH
power of Hydrogen
-how ACIDIC (H+) / BASIC(OH-) a solution is
-water = neutral pH 7 out of 0-14
How to calculate pH
If H+ = 10^-7, then pH = 7 & OH-=10^-7
If OH- = 10^-4 then H+ = 10^-10 & pH= 10
Acidic Solution
Lots of H+ (hydrogen ions) & only a few OH-(hydroxide ions)
H+ > OH-
Neutral Solution
Equal amounts of H+ ions & OH- ions
ex: water
H+ = OH-
Basic Solution
Lots of OH- ions & only a few H+ ions
H+ < OH-
Buffers
Minimizes changes in concentration of H+ & OH- in solution
ABSORBS H+ ions if TOO ACIDIC & ADDS H+ ions if TOO BASIC
keeps blood at pH 7.4 slightly basic to survive
Carbonic Acid Bicarbonate System
important buffers in blood plasma
too much O2, CO2 absorbs that bc breathing gets rid of carbonic acid (H2CO3)
Properties of Water
Cohesion
Surface tension
Adhesion
Transpiration
Moderation of Temp. (high specific heat, thermal energy(heat)
Evaporative Cooling
Expansion Upon Freezing
Solvent of Life
Cohesion
H-bonding between LIKE (H2O) molecules (LIKES/Works well together)
Water LIKES Water
helps plants transport water from roots, contributes to waters high boiling point which helps regulate animal temp
Adhesion
H-bonding between UNLIKE molecules (STICKY)
H2O molecules form bonds w/ other POLAR substances or CHARGED molecules
adhesion of water (H2O) to vessel walls (attraction between H20 & walls of small tubes, force helps hold the water in xylem against the pull of gravity
helps transport water from roots to leaf of plant
ex: shirt sticks to u bc ur skin has polar molecules
Surface Tension
Measure of how difficult it is to break/stretch surface of liquid (Ex: bugs walking on water)
H-bonds of molecules right below surface of water
helps insects such as water striders walk on water
Transpiration
Movement of H2O up plants
H2O clings to each other by Cohesion (like each other) cling to xylem tubes by Adhesion (sticky)
High Specific Heat
Water takes a lot of energy to break hydrogen bonds so more kinetic energy = ++heat
changes temp less when absorbs/loses heat
large bodies of water absorbs more heat = cooler coastal areas
create stable marine/land environ
Evaporation (evaporative cooling)
water = high heat of vaporization so can absorb lots of heat before it becomes steam
molecules w/ greatest KE leaves as gas
stable temp in lakes/ponds
cooler plants (mostly water)
human sweat (water molecules released to absorb KE & heat from body to cool down) HOMEOSTASIS
Solvent of Life (like dissolves like)
solution = liquid, homeostasis mix of 2+ substances (Ex: salt water or Ocean water)
Solvent: dissolving agent liquid (WATERRR)
Solute: dissolved substance (ex: polar: salt)
helps cells transport and use substances like oxygen or nutrients ex: our blood bc it has water in it
Water Floats
-less dense when solid, water floats
-forms crystal lattice structure
-important bc oceans & lakes do not freeze solid
~insulates water below & helps marine life
~seasonal turnover of lakes
Hydrophilic
Affinity (LIKES) for H20 polar, ions, cellulose, sugar, salt, blood (rly likes water), paper
Hydrophobic
Repel H20 (SCARED of it) non-polar oils, lipids (fats), cell membrane, wax
Carbon
major element of life: CHNOPS (carbon, hydrogen, nitrogen, phosphorus, sulfur)
important due to its electron configuration
bc able to make 4 stable covalent bonds (TETRA VALENCE) most frequent bonding partners = (H, O, N)
bonds can be single, double, triple covalent bonds
Tetra-valence allows them to be strung together in chains
Example of carbon & 4 bonds
Methane!!! CH4 = 4 covalent bonds, nonpolar & perfectly balanced/shared e-
Ethane
alkane - single bond (2e-)
Ethene
alkene - double bond (4e-)
Ethyne
alkyne - triple bond (6e-)
hydrocarbons
-combinations of C and H (methane)
-nonpolar
~not soluble in water
~hydrophobic
-stable
-very little attraction between molecules
-gas at room temp
Macromolecules
carbon forms large molecules w/ other elements
4 classes: Carbohydrates, Proteins, Lipids (fats), Nucleic Acids (mRNA, DNA)
**molecules can be chains, ring-shaped, branched = lots of diff SHAPES = lots of DIFF FUNCTIONS
Isomers (formed by carbon)
molecules have same molecular formula, but differ in atom arrangement ex: same atoms but one= branch & other = ring
diff structures/shapes = diff properties/functions
Structural (Isomer)
Varies in covalent arrangement
Cis-Trans (Isomer)
Varies in spatial arrangement (sides are diff)
Enantiomers (Isomer)
Mirror images of molecules (like ur hands)
Thalidomide
Originally enantiomer
good enantiomer = reduce morning sickness can convert to bad thru enzyme converting it to weird shape = diff function
bc BAD enantiomer = causes birth defects
Functional Groups
patterns of atoms, that display consistent “function” (properties and reactivity) regardless of the exact molecule they are found in
behavior of organic molecules depends on these
substitute other elements for hydrogen
involved in chemical reactions
give organic molecules distinctive properties
affect reactivity
make hydrocarbons hydrophilic
increase solubility in water
Hydroxyl (F Group)
(OH-)
hydrogen & oxygen = BASIC
POLAR-like water structure
POLAR
Alcohols
Ex: Ethanol
Carbonyl (F Group)
(>CO) C double bonded to O w/ 2 lone pairs
Ketones (inside skeleton) & aldehydes (at ends)
Ex:Acetone, Propane
Carboxyl (F Group)
(-COOH)
POLAR
Carboxylic acids, organic acids
Ex: Acetic acid
Amino Group (F Group)
(-NH2)
Amines
Ex: Glycine
SUPER POLAR
Sulfhydryl (F Group)
(-SH)
POLAR
Thiols
Ex: Ethanethiol
Phosphate (F Group)
(-OPO_3^2-/ -OPO_3H_2)
Organic Phosphates
POLARRR (neg charge)
Ex: Glycerol Phosphate
Methyl (F Group)
-CH3
Methylated Compounds
NON POLARRRR + HYDROPHOBIC
wont be able to dissolve in H2O
Ex: methyl cytidine
Peptide Bonds
Bonds that make Amino Acids
Monomers
Small, Organic
Used for building blocks of Polymers
Connections w/ condensation RXN (DEHYDRATION SYNTHESIS)
Polymers
Long molecules of Monomers
w/ many identical/similar blocks linked by COVALENT BONDS
Macromolecules
BIGGGG
Giant molecules
2/2+ polymers bonded together
Amino acid to protein
amino acid -> peptide -> polypeptide -> protein
Dehydration Synthesis
creates larger organic compound/molecule by joining smaller monomers (by releasing water)
Condensation RXN (takes water away, makes protein)
1 monomer donates -OH, other donates H+ together forms H2O
A+B = AB
__ + __ = ____ + H2O
Synthesis RXN
Hydrolysis
Digestion of organic compounds, Breaks down polymers to monomers using water
opposite of dehydration syn, releases energy
split off one monomer at a time
H2O split into H+ & OH-
AB = A + B
____ + H2O = __ + __
Amino Acid
compounds that make up proteins & polypeptide chains
MADE OF AMINO/AMINE GROUP (-NH2) & CARBOXYL GROUP/CARBOXYLIC ACID (-COOH)
properties: hydrophobic, hydrophilic, ionic (acids & bases)
R Group (AA)
each AA has a specific side chain attached to the alpha carbon
Peptide Bond
covalent bonds that hold together amino acids
formed when the carboxylic acid of one amino acids reacts with the amino group of another amino acid/molecule
Monomers
small, organic
used for building blocks of polymers
connects w/ condensation RXN (dehydration synthesis)
Polymers
(multiple) long molecules of monomers
w/ many identical/similar blocks linked by covalent bonds
Macromolecules
BIGG molecules
2 or more polymers bonded together
Proteins
large, complex molecules that play many critical roles in the body
required for the structure, function, and regulation of the body’s tissues and organs
50% dry weight of cells
has CHNOPS
Primary Level of Protein Structure
linear sequence of Amino Acids
abt 20 diff AAs (peptide bonds = link)
Secondary Level of Protein Structure
Gains 3-D shape (FOLDS, COILS) by H-BONDING
alpha helix. beta pleated sheet
pleated sheets = rly strong
if real positive attracts O-, breaks hydrogen bond between barely pos H
+ HEAT breaks hydrogen bond, causing protein structure to shake bc molecules get rly hot & falls apart (wrong shape = wrong function) ALSO CHEMICAL EXPOSURE can change protein shape TOO
Basic Principles of Protein Folding
Hydrophobic AA buried in interior of protein (hydrophobic
interactions)
Hydrophilic AA exposed on surface of protein (hydrogen
bonds)
Acidic + Basic AA form salt bridges (ionic bonds).
Cysteines can form disulfide bonds (2 SULFURS)
Tertiary Level of Protein Structure
Final 3D protein shape (makes bean side groups/ stacking + bends)
Bonding between R groups(side chains) of amino acids
hydrophobic interactions = amino acids w/ nonpolar hydrophobic R groups cluster together on the inside of the protein
hydrophilic amino acids on the outside to interact w/ surrounding water molecules
H bonds, ionic bonds, disulfide bonds, hydrophobic
interactions, van der Waals interactions
More info on Tertiary Structure
polar & nonpolar dont mix in proteinc -> causes bonds & diff shapes/functions
sulfur likes bonding w/ sulfur (S-S covalent bond) = disulfide bond
adding kinetic energy can break bonds causing changes in shape/function (curly/straight hair)
Disulfide bonds
covalent linkages between sulfur-containing side chains of cysteines much stronger than the other types of bonds that contribute to tertiary structure
act like molecular “safety pins,” keeping parts of the polypeptide firmly attached to one another
Quaternary Level of Protein Structure
2+ polypeptides bond together
(Stack beans together)
spirals & bonds = made & can meet other protein spirals/bonds & proteins interact w/ each other
peptide
multiple amino acids are linked together by peptide bonds, thereby forming a long chain
polypeptide
a polymer of amino acids joined together by peptide bonds
Chaperonins
assist in proper folding of proteins
(ex: chaperonin =folding matt & t-shirt = protein)
Protein Structure & function is sensitive to…?
Chemical & Physical conditions like heat
protein unfolds/denatures if pH & temperature are not optimal (falls apart)
ex: cooking egg, egg proteins denatures clear->white
Nucleic Acids
Function: store hereditary info
RNA & DNA
DNA
Double-stranded helix
N-bases: A, G, C, Thymine
Stores hereditary info
Longer/larger
Sugar: deoxyribose
RNA
Single-stranded
N-bases: A, G, C, Uracil
Carry info from DNA to
ribosomes
tRNA, rRNA, mRNA,
RNAi
Sugar: ribose
Nucleotides
monomer of DNA/RNA
Sugar + Phosphate + Nitrogen Base
Purines
Adenine, Guanine
Double RIng
Pyrimidines
Cytosine, Thymine (DNA)
Uracil (RNA)
Single ring
Carbohydrates
Fuel & Building material
Include simple sugars (fructose) & polymers (starch)
Ratio of 1 carbon: 2 hydrogen: 1 Oxygen / CH2O
monosaccharide 🡪 disaccharide 🡪 polysaccharide
Monosaccharides
simple one monomer sugars (ex: glucose, ribose)
Polysaccharides
large polymer sugars
Storage (plants-starch, animals-glycogen)
Structure (plant-cellulose, arthropod-chitin)
(Differ in position & orientation of
glycosidic linkage)
2 forms of Glucose
alpha glucose & beta glucose
Starch
links 1-4 alpha glucose monomers
Cellulose
links 1-4 Beta glucose monomers
Denature
Protein breakdown/unfolding, (polypeptide chains disordered) CHANGING its 3D structure/shape & FUNCTION
can happen bc of heat/chemicals (changes in pH)
acid H+ & bases OH-(chemicals/ph change ruins protein)
Conformation
How proteins reach final state
Nucleic acids
store hereditary info
DNA & RNA
DNA
Double stranded helix
N-bases: A, G, C, Thymine
Longer, Larger
Sugar: Deoxyribose (nonpolar)
pass onto children
RNA
Single strand
N-bases: A,G,C, Uracil
Shorter, diff uses
HRNA, rRNA, mRNA, RNAi
Sugar: Ribose (more polar)
dont pass down to children, they make their own
Nucleotide
Monomer of DNA & RNA, held together by hydrogen bonds has phosphates
A-T G-C (DNA), U-T, G-C (RNA) held together by hydrogen bonds
BUT phosphate (P bonded to 4 O’s = covalent bond)
sugar + phosphate + nitrogenous base (A,T,G,C,U)
DNA cells/DNA strands are held together by? why?
HYDROGEN BONDS bc needs to be able to split (every once in a while) to make more, makes them more easily accessible, & hydrogen bonds = somewhat stable
two strands are held together by hydrogen bonds between pairs of nitrogenous bases
DNA, RNA, Proteins
DNA makes RNA, RNA makes proteins!!
Change DNA, changes RNA, changes Proteins, changes functions!!
mutations = crazy changes (cancer, defects)
Carbohydrates
carbon hydrated by water
fuel & building material
simple sugars (fructose) & polymers (Starch)
ratio of 1 carbon: 2 hydrogens: 1 oxygen or CH2O
monoSaccharide(Sugar), dissacharide, polysacharide
monosaccharide
monomers (ex: glucose, ribose)
polysaccharide
immediate fuel and energy
(storage) plants make starch, animals make glycogen
(structure) plants make cellulose, arthropod makes chitin
Isomer
same chemistry makeup/formula but is connected/shaped diff
long sugars make rings structure (stable, diff functions, soluble in water)
Glucose Bonded w/ Glucose (important)
Dehydration reaction in the synthesis of maltose
take away h2o (dehydration synthesis - condensation RXN) = C12, H22, O11
bc it wouldve been C6H12O6 * 2 but take away 2 H’s & 1 O
= Maltose
Glucose Bonded w/ Fructose (important)
Dehydration reaction in the synthesis of sucrose
take away h2o (dehydration synthesis - condensation RXN) =
(C6H12O6 + C6H12O6) - H2O = C12, H22, O11
Sucrose
Maltose & Sucrose
Fructose & Glucose
Isomers
2 Forms of Glucose
Alpha Glucose & Beta Glucose
Isomers & reversible js diff shape (OH) = diff function
Starch
Alpha glucose monomers
uneven, POLAR, ex: binders stacked = chemical arrangement same spine side stacked = slides off
Cellulose
Beta glucose monomers
even, LESS Polar
Binders: arranged = chemical arrangement oppositely so binder to end and stays put = diff, diff functions)
Lipids (fats)
triglyceride = store energy (nonpolar) water doesn’t mess w/ it
body stores extra energy as fat bc water doesn’t mess w/ it (hard to make into energy but sugar = easy)
saturated, unsaturated, polyunsaturated
Steroids
cholesterol & hormones (chemical messengers travel thru blood) so bc fat = nonpolar, doesnt dissolve in blood (mostly water)
Phospholipids
lipid bilayer of cell membrane (so cells have stable structure & bc body made up of water)
hydrophilic head + hydrophobic tail
are fat molecules polar or nonpolar? methyl group?
NONPOLAR methyl groups binded together & build up doesnt like blood (polar) but binds together bc nonpolar likes nonpolar
Van der Wall Interactions/Forces
nonpolar, long, = stable
driven by induced electrical interactions between 2 or more atoms or molecules that are very close to each other
weakest of all intermolecular attractions between molecules
Saturated fats
flat & more stable
bonded w/ H
solid at room temp = butter, lard
unsaturated fats
curves & cant stack vanderwall interactions = weak & unstable in room temp (liquid)
phospholipid
hydrophobic/hydrophilic interactions make phospholipid layer
The backbones/sides of DNA are made up of alternating ?
sugar & phosphate molecules which are held together by strong covalent bonds
The steps/rungs of DNA are made up of ?
Pairs of Nitrogenous bases held together by weaker hydrogen bonds that allow for splitting to make more DNA, more accessible
What is stronger G-C or A-T?
G-C bc they have 3 hydrogen bonds holding them together
A-T only has 2 hydrogen bonds holding them together
What bond is most strongly affected by water?
Ionic bond
What would happen if we add methyl group to CH4 or non polar groups in proteins?
The protein will be less soluble, & change shape bc linear sequence (primary structure changes so function changes badly = blood clots & sickle cell anemia (dents)
what happens when theres a variant in protein where amino acid in primary sequence is changed to something non polar?
when oxygen levels = low, altered hemoglobin molecules bond together & distort shape of red blood cells, creating abnormal (dented) sickle cells,
hydrophobic interactions between protein -> clump together (oxygen carrying capacity reduced), deforms red blood cell & function changes bc no longer can transport oxygen w/ weird shape thru blood stream
Phosphorus in?
nucleic acids & lipids
