Quiz 1 Chap 2&3 Flashcards
Atoms, Bonds, and Water, and Biological Molecules
primordial soup
water in oceans many years ago, where life originated
matter
made up of elements, containing mass
elements
substance that cannot be broken down to other substances by chemical reactions
compounds
substance consisting of 2 or more elements in a fixed ratio
- different from the individual elements in its characteristics
how many elements are essential to life? which elements are essential to life?
25 elements total, although some are trace elements (minute quantities)
- 96% of human body. weight is oxygen, carbon, hydrogen, and nitrogen
- then calcium, phosphorus, potassium, and sulfur
atom
smallest unit of an element
composed of subatomic particles (protons, neutrons, electrons)
electrons move around nucleus in orbitals
what does the chemical behavior of an element depend on?
the number of UNPAIRED valence elections in the valence shell
molecule
atoms that stay close together by chemical bonds (can be 2 of the same atom)
intramolecular forces
bonds that hold molecules together (ionic bonds, covalent bonds, polar covalent bonds)
intermolecular forces
bonds that hold different molecules together (hydrogen bonds, Van der Waal bonds)
bonding capacity of an element
of covalent bonds that each element can form (# of unpaired electrons in the valence shell)
ionic bonds
- give away or steal an electron
- formed by attraction of two oppositely-charged ions
- strong in dry environment
- weak in aqueous environment (water is polar, it splits apart ions)
- formed by a metal and a non-metal
salts
compounds formed by ionic bonds, typically crystals containing huge numbers of cations and anions
covalent bonds
- share valence electrons so that both atoms can fill their valence shells
- can from between atoms of the same or different elements
- very strong bonds
- bonds made and broken from chemical reactions
nonpolar covalent bonds
no charges on molecule, atoms share electron(s) equally
polar covalent bonds
partial positive and negative charges on each molecule due to the electron not being shared equally (one atom is more electronegative)
hydrogen bonds
result of attraction between a partially positive hydrogen (covalently bonded to a more electronegative atom like oxygen) and another electronegative atom
- what causes water to adhere to itself
- hydrogen typically bonded to oxygen or nitrogen in living cells
- weak individually, but many can be strong
role of hydrogen bonds in biological systems
- bonds between nitrogenous bases in DNA, able to be unzipped
- factor in protein structure
why do substances dissolve in water??
water is the universal solvent because of its polarity (oxygen has partial negative, hydrogens have partial positive)
- ionic bonds broken as ions are attracted to these partial charges
- large proteins have polar regions on their surfaces which attract water molecules
hydration
ionic bonds break and ions attach/come close to polar water molecules
Van der Waals bond
- intermolecular force
- electrons accumulate randomly in nonpolar molecules (temporary and by chance)
- individually weak, powerful if occurring simultaneously
which type of bond is strongest?
covalent bonds
role of weak bonds (ionic, hydrogen)
- reinforce shape of large molecules
- help molecules adhere to each other
what determines molecular shape?
the position of valence orbitals
- orbitals may hybridize in covalent bonds
what is the importance of molecular shape?
biological molecules recognize and interact with each other based on shape, so molecules with similar shape can have similar biological effects
- i.e. morphine and endorphins
significance of water in organisms
most cells surrounded by water and are made up of 70-95% water
what 4 properties of water facilitate life processes
- cohesive behavior
- ability to moderate temperature
- expansion upon freezing
- versatility as a solvent
cohesion
hydrogen bonds hold water molecules together
- causes surface tension
- helps transport of water against gravity in plants
adhesion
attraction between water and other substances
- notably, plant cell walls (again allows for transport up plants)
what is the significance of water’s high specific heat capacity?
- can absorb/release large amounts of heat without changing its own temperature much, which helps maintain HOMEOSTASIS
- **heat is absorbed when hydrogen bonds break (ice crystals breaking) and released when bonds form
why does water expand when it freezes?
hydrogen bonds are more ordered, causing molecules to be farther apart (less dense)
at what temp is water the most dense?
4 celsius
why is water a versatile solvent?
- polarity (hydrogen bonds) allow for even large molecules (e.g. proteins) to be dissolved if they have ionic/polar regions
hydration shell
when each ion in an ionic compound is dissolved in water
primary molecules that make up cells
carbon-based (organic) compounds
why is carbon so important in organic chemistry?
it’s tetravalent (4 unpaired valence electrons)
hydrocarbons and example of a hydrocarbon
organic molecules made up of carbon and hydrogen only (e.g. fats)
macromolecule and the 4 classes
large organic molecules made up of thousands of covalently connected atoms
- carbohydrates, lipids, proteins, nucleic acids
monomer
small organic molecule, “building block” of polymers
polymer and 3 types of polymers
long molecule made up of many similar, smaller units (monomers)
- carbohydrates, proteins, nucleic acids
isomers
compounds with the same numbers of each atom, but a different configuration
***different structure means different function!!
dehydration reaction
2 monomers bond together through the loss of a H2O molecule
hydrolysis reaction
polymer disassembled into monomers, reverse of a dehydration reaction (requires water)
main functions of carbohydrates
fuel, building material
what are monosaccharides and how are they classified?
simple sugars–molecular formulas in multiples of CH2O
- glucose is most common
- classified by location of carbonyl group (C=O) and # of carbons in skeleton
aldoses vs ketoses
aldoses have double bonded O on end of carbon chain
ketoses have double bonded O on a middle carbon
examples and roles of storage polysaccharides
starch
- plants: granules in chloroplasts and plastids
- beneficial form of storage compared to lipids because it doesn’t go bad
glycogen
- animals: stored in liver and muscle cells of vertebrates
examples and roles of structural polysaccharaides
cellulose
- component of tough cell wall in plants, allow them to grow tall
chitin
- found in insect exoskeletons and fungi cell walls
difference between cellulose and starch in digestion
***both are glucose polymers with different linkages
- humans can digest alpha linkages of starch, but don’t have enzymes to digest beta linkages of cellulose
- cellulose passes through digestive tract as insoluble fiber
- microbes in some herbivores digest cellulose
characteristics of lipids and the 3 types
- do not form polymers
- mostly hydrocarbons that form nonpolar covalent bonds –> hydrophobic
- generally lighter than water
- fats, phospholipids, and steroids
fats
made up of glycerol (3 carbon alcohol with 3 hydroxyl groups) and fatty acids (carboxyl group attached to long carbon skeleton) attached with ester linkage
triglyceride
3 fatty acids joined to a glycerol by an ester linkage
where is fat stored in animals, and what is its role?
stored in adipose cells
- energy storage
- cushions organs
- insulates body (warmth)
saturated vs unsaturated fatty acids
saturated (most animals)
- max # of hydrogen atoms possible on each carbon
- no double bonds
- solid at room temp (with exceptions)
unsaturated (fish, plants)
- double bonds
- liquid at room temp
what is the danger of excess saturated fats?
it can form plaques blocking things like arteries
hydrogenation
unsaturated fats turned into saturated fats by adding hydrogen to create trans fats
- hydrogen atoms on opposite sides before/after double bonded carbon
- even more unhealthy than saturated fats
phospholipid structure and purpose
2 fatty acids and a phosphate group attached to glycerol
- fatty acids are hydrophobic, phosphate forms a hydrophilic head
- major component of all cell membranes
what happens when phospholipids are added to water?
they self-assemble into a bilayer, with hydrophobic heads pointing interior and phosphate group on the outside
(both interior and exterior of cells are aqueous)
structure and function of steroids
carbon skeleton consisting of 4 fused rings
- hormones, metabolism, inflammation, immune functions, salt & water balance, development of sexual characteristics
danger of steroids
important component of animal cell membranes, but high levels in blood can cause cardiovascular disease
protein
one or more polypeptides
function and importance of proteins
- more than 50% of dry mass of cells
- structurally diverse (structure determines function)
- structural support, storage, transport, movement, cellular communications, defense against foreign substances
enzymes
protein that acts as a catalyst (speeds up chemical reactions)
- perform functions repeatedly
polypeptide
polymers built from the same set of 20 amino acids
amino acid
organic molecules with a central carbon, a hydrogen, an amino group, a carboxyl group, and a variable group
peptide bonds
bonds that link amino acids to form polypeptides
- formed by a dehydration reaction to connect the carboxyl group of one amino acid with the amino group of another
primary protein structure
unique sequence of amino acids
secondary protein structure
(in most proteins) by inherited genetic info, coils and folds in the chain as a result of hydrogen bonds between animo acids
*alpha helices and beta pleated sheets
alpha helices vs beta pleated sheets
alpha helices are coils, beta pleated sheets have folded structure
tertiary protein structure
determined by interactions among various side chains (R groups)
- hydrogen bonds, van de waals bonds, ionic bonds, hydrophobic interactions, disulfide bridges (covalent)
quaternary protein structure
protein consisting of multiple polypeptide chains (i.e. collagen, hemoglobin)
what causes sickle cell anemia?
a single amino acid substitution (passed on genetically) completely changes the shape
other factors determining protein structure
alterations in pH, salt concentration, temperature, and environmental factors
denaturation
protein unravels, losing its native structure
- becomes biologically inactive!
how do we determine protein structure (historically and now)?
- x-ray crystallography
- nuclear magnetic resonance spectroscopy
- now: bioinformatics (computer programs)
what were the two types of bacteria in lab and what were their features?
micrococcus luteus - round, gram positive (violet)
E. coli - rod shaped, gram negative (pink)
If an antibiotic is effective, the bacteria is _______ to the antibiotic.
If an antibiotic is ineffective, the bacteria is _______ to the antibiotic.
susceptible, resistant
two types of antibiotics used
- classes
- mode of action
- effective on
penicillin
- B lactam
- inhibits peptidoglycan layer
- effective on gram + (micrococcus luteus)
streptomyosin
- aminoglycocide
- inhibits protein formation on ribosomal level
- effective on gram - (E. coli)
what techniques did we use in lab?
zone of inhibition bioassay and a gram stain
why were antibiotics effective/not effective on Gram +/- bacteria?
Penicillin targets peptidoglycan layer, so it’s only effective on the gram + cells with a thick peptidoglycan layer.
Streptomyosin targets ribosomal functions but is large in size, so it’s only effective on gram - cells with thinner peptidoglycan layers that it can pass through.
