mod 2 chap 2 Flashcards
Elements
Pure substances that cannot be further broken down by methods of chem
Atom
Each eleemnt contains only one type of atom, the basic unit of matter
Atom contains dense central nucelus made up of protons and neutrons
Electrons move around nucelus at some distance from it
Protons is = atomic number - speciies an atom as particular element
protons + neutrons give atomic mass, mass of atom
isotopes - atoms of the same element that have diff number of neutrons
some chem processes cause atom to gain or lose e-
losing e- gives pos charge and gaining is neg charge
electrically charged atoms are called ion
electrons in orbital
Exact path of e- is unknonw but region of space called an orbital where an e- is present most of the tiem can be found
max e- in orbital is two
e- in orbitals close to nuceulus have less energy than e- in orbitals further away
e- gives up energy when it moves to closer orbital which is why e- fill up orbitals close to nucelus beofre occupying ones further away
Several orbitals can exist at an energy level or shell
Periodic table
In the first three rows, elements in same row have same number of shell so they have same number and types of orbitals - e- will fill the shell until a full compleent of e- is reached
elements in verticalc olumn are called group or family - same number of e- in outershell - number of e- here dtermnes how elements interact with other elements
Molecules and Cehmical bonds
Atoms can combine with other atoms to form molecules which are groups of two or more atoms attached together that act as a single unit
When two atoms form a molecule, the indidual atoms interact through a chemical bond, a form of attraction between atoms that hold them together
Covalent bonds
ability of atoms to combine with other atoms depend on valence e- which are e- in outermost shell
When atoms combine, the atoms share valence e-
The two atomic orbitals will merge whcih is called a molecular orbital and the shared pair of e- consitutes a covalent bond that holds the atoms together
two adjacent atoms can share two pairs of e- forming a double bond - four orbitals merge to form two molecular orbitals
molecules tend to be most stable when the two atoms forming the bond share enough e- to fill the outermost shell
octet rule doesnt apply to all elemnts
polar covalent
in many bonds the e- arent shared equally
part of molecule has slight pos charge and other has slight neg charge - ex. water
in water, the e- more likley to be near oxygen
the unequal sharing of e- reuslts form a diffeence in ability of atoms to attract e- known as property of electonegtaibty - inc across a row
when e- are shared unequally between two atoms the resulting interaction is a polar covalent bond
covalent bond between atoms of same or nearly same electronegtaivty are nonpolar covaelnt bond which means the atoms share bonding e- pair almost equally - these bonds do not mix well with water
ionic bonds
When atom of high EN is paired with atom of low EN, the difference is so great that the electriengatbe atom steals the e- form its less electronegtive partner - there is atom if neg chareg and one with pos - this opp charges attarct and so they ascoiate with each other in an ionic bond
ionic compounds disolve in water (ionize)
chemical rxn
chemical bonds that link atoms in molecules can change in a chem rxn
inchem rxn, atoms keep identity but atoms to whcih they are bonded to change
start subsatnce are reactants and ends are products
in biological systems, chem rxns provide way to build and break down moelcules for use by cell and to harness energy which can be held in chem bonds
Water
medium in which the molecules of life interact
polar covalent bonds
polar molecule - regions of pos and neg charge
polar interact with polar (non polar doesnt)
hydrophilic
Hydrophobic
hydrphilic usually polar - disvolve in water
hydrophobic compounds usually nonpolar - arrange themsleves to miminize contact with water
hydrophobic effect - polar molecules like water exlcude nonpolar ones which drives such biological proccesses as the formation of cell membrane and folding of proteins
hydrogen bond - interactions between an H atom with slight pos charge and electronegtive atom of another molecule - weaker than colavent but presence of many can stablize biolical moelcules
Hbonds in water cause features - in liquid, water will form H bonds with eachother, when frozen the molecules become hydrogen bonded to foruth other molecules forming crystaline structure called ice - molecules pack less close so ice is less dense than water - hbonds also give proeprty of cohesion, emaning water sticks to one another which can provide high surface tension - hbonds also allow water to have high heat absorbance meaning the hbonds must break before water rises in temp
pH
small portion of water exists as protons and hdyroixde ions
pH of solution measures proton conc
pH infleunces many chem rxns and biological processes
pH = -log[H+]
high proton conc is acidic and pH lower than 7 but high hydroxide ion conc pH greater than 7 and basic
Carbon
hydrogen and helium most absundant elements in universe
in cell, C,O,H and N account for 90% of total dry mass and most abundant is carbon
Organic molecuels are moelcules containg carbon
Carbon has ability to combine with many other elemts to form variety of molecules, each specilzied for the fucntion it carries out in teh cell
Carbon behvaes as if 4 unpair e- - occurs because one of e- in valence shell spehrical orbital moves into dumbell shaped orbital - the single large spehrcial orbital and three dumbell shaped orbitals change becoming 4 hybrid orbiatls
ability of C to form 4 covalent bonds, the spatial orientation of bonds in tetrhedron and ability of bond to rotate freely contribuet to ways to the strcutures diversty of c based moelcules
carbons can linke to other c, forming chain which can be branched or they can form rings
double bonds can form - double bond is shorter than single and isnt free to rotate so all covalent bonds formed by C connected by double bond are in same geometrical plane
moelcuels with same chem formula but diff strcutures are isomers
Organic molecules
proteins provide structral support and act as catalysts that facilatte chem rxns
nucleic acids encode and transmit gentic info
carbs provide a soure of enegry and make up cell wall in bacteria, plants and algae
lipids makeup cell mebrane, store enegry and act as signallig moelcules
these moelcules are large and many are polymers, complex molecules made up of repeated simpler units connected by covalent bonds
proteins are polyemrs of amino acids, nucelic acids are polymers of nuelcotdes and carbs are polymers of sugars
lipids are not defined by chem strcuture but because they are hydrphobic
buidling blcoks of pokymers are subunits or monomers
functional groups
simple repeating units of polyemrs are often based on nonpolar core of c atoms - attached to them are functional groups, groups of one or more atoms that have particular chem properties
functional groups with n, o, p and s are electroneg so they are polar
proteins and aa
Proetins do mcuh fo cells work
some proteisn are catalysts that accelerate rates of chem rxns (enyzmes), others can act as strural components necessary for cell shape and moveemt
proteins conisst of aa linked covalently to form a chain
each aa contains central carbon atom called alpha carbon, covalentlt linked to four groups: an amino group, carboxyl group, h atom and r group or side chain whcih differs from one aa to the next
at pH in cell, amino and carboxyl group are ionixed (charged) owing to interactions with the surrounding medium - amino gains proton (NH3+) and carboxyl group loses proton (COO-)
aa linekd in chain to form proteins - carbon in carbxyl joins to n in amino by covalent linkage called peptide bond - invoves loss of water molecules to form the CN bonds- dehydration reaction
aa classified accoridng to the R group
sequence of aa in protein determines how it folds - 3d strcyture in turn dtermines proteins function
nucelic acids
informational moelcules - large moelcuels that carry info in seqencue of nucelotides that make them up
deoxyriboncuelic acid is genetic material in all cellular organisms - trasnmited to offspring, contains info needed to specify amino acid seuqence of all prteins syntehsized in organsim
ribonucelic acid - key player in protein synthesis and regulation of gene expression
nucleic acids made up of nucelotides - nucelotide composed of 5c sugar, nitrogen base, and one or more phosphate groups
sugar can be ribose or deoxyribe - ribose has oh on 2ā carbon
bases built from nitroegn containg rings - pyrmidine have single ring and icnlude cytosine, thymine and uracil - purines are double ring and made up of adenine and guanine
sequence of nucelotides detrmines info in DNa and RNA
in DNA and RNA adjecent pair of nucleotides is connected by phosphodiester bond, which forms hwne phpsphate group of one nucelotide is covalently linked to sugar unit in another ncuelotide - also releases water
DNA made up of two strands which form double helix - sugar phasphate backbones and bases inward
pureine and prymidine pairs are complementary - reuslts form H bonding
genetic ifno in DNa is contaiend in sequence or order of nuelotides
carbohydrates
sugars belonge to carbs, distinctive molecules composed of C, H and O atoms usually in 1:2:1 ration
carbs are major source fo energy for metablosim
sugars or saccharides are simplest carbs - simple sugars are linear or cyclic containg 5-6 c
6c suagrs have same chem formula but diff configuration
smple sugar called monosaccharide and linking two is disccharide
simple sugars combine in many ways to form polysaccharide that provides long term energy storage and strcutral support
long branched chains of monosaccharides are complex carbs
monosachcarides are unbranched c chains with either aldehyde or ketone group
monosaccharide with aldehyde are aldoses and those with ketones are ketoses - in both types the other Cās cary OH and H atoms
almost all monosacchardies are in rings form - one end of chain bonds with anotehr part of the chain: the carbon in aldyhe or ketone forms covalent bond with odygen of hydroxyl group of another C atom
presence of polar hydroxyl groups makes them highly soluble water
monosacharides are building blocks of complex carbs - attached to eachother by glycosidic bonds - release water molecule - happens between C1 of one monosachride and hydroxyl group carried by a c atom in diff monocaschidd
some carbs made up of one monosacharide type while others are mix
lipids
these share a similar property - are all hydrophobic
divsere groups - include fats that makeup diet, componets of cell memrbane and signalling molecules
triaclyglycerol is example of lipid used for energy storage - made up of three fattu acids joined to glycerol - fatty acid is long chain of c atoms attached to carbyxl at one end - glycerol is 3c moelcule with OH attached to each c - the cabryxl end of fatty acid hcains attached to glycerol at the OH groups, realsing water
fatty acids differ in lengths - usually even number because synthszed in 2carbon units
fatty acids with no double bonds are saturated so saturated with H atoms
fattya cids with double bonds are unsatured - wil have kink triacylglycerols are nonpolar - e- are distrubted evenly - hydrophobic - effecient form of energy storage because by exlcuding water, a larger number can be packed into a small volume
althoug. fatty acids are uncharged, the cosntant motion of e- leads to slight pos and neg regions - these charged euther attract or repel e- in neighbouring molecules creating more charged regions - the temporaliy polaied moelcules weakly bind to one another because of attarctions fo opp charge - van der wal forces - because of these forces melting pount of fattya cids depend on length and saturation - as length inc, van der wall interactions inc so higher energy needed to break inetraction - kinks in double bonds recues tightness of packing and number of interactions so melting point lower
steroids like cholesterol are secnd type of lipid - core composed of c atoms bonded to form four fused rings and is hydrophbic
cholesterol is compoent of cell membrane and serves as precursor for synthesis of steroid hroomes like estrogen or testosterone
phospholipids are thrid type of lipid - they makeup the cell memrbane
first molecules of life
Life likely originated on Earth by a set of chemical reactions that gave rise to the molecules of life. In 1953, Stanley Miller and Harold Urey demonstrated that amino acids can be generated in the laboratory in conditions that mimic those found on the early Earth. Other experiments have shown that sugars, bases, and lipids can be generated in the laboratory. Once the building blocks were synthesized, they could join together in the presence of clay minerals to form polymers.
