u1 biochem Flashcards
what are covalent bonds?
covalent bonds are bonds where two atoms share electrons to have a full, satisfied outer shell
what are polar covalent bond and non-polar covalent bonds?
polar covalent bonds are bonds between two or more atoms that share the same electrons unequally because 1 atom is more electronegative than the other so it has more pull for the electrons. one side of bond is more negative and other is more positive.
non polar covalent bonds are bonds between two or more atoms that share the same electrons equally. no charges.
what bond is it where the EN difference is <0.5
non-polar covalent
what bond is it where the EN difference is 0.5<EN<1.7
polar covalent
what bond is it where the EN difference is >1.7
ionic bond
what is hydrogen bond and explain its dipoles briefly
a force of attraction between a hydrogen atom and a more electronegative atom such as O, N, F.
Has very strong dipole interactions due to their electronegative properties.
ground state
The original state of electrons/energy at rest. This is the most stable arrangement
excited state
electrons absorb energy and jump to outer orbits
isotopes
atoms that have the same # of protons but different number of neutrons (which effects mass).
anion
the atom that receives an electron (becomes more negative)
cation
the atom that gives away an electron (becomes more positive)
what is electronegativity
electronegativity measures the power of an atom to attract bonding pairs of electrons.
why do non-polar molecules not dissolve in water
non-polar doesn’t dissolve in water because it doesn’t have dipoles to interact with water. hydrogen bonds are too strong to interfere with as well.
dipole-dipole vs vander waals
dipole-dipole IMF is permanent and there are charges.
vander waals or LDF is temporary and there are no charges.
what are compounds
two or more atoms
intermolecular vs intramolecular
inter. means forces WITHIN a molecule (eg. H giving e- to Cl)
intra. means forces between two or more diff. molecules. (eg. H2O bonding with OH)
5 properties of water
- high surface tension
- high specific heat
- low density at solid
- high heat of vaporization
- adhesion/cohesion
why is water a universal solvent
water is very polar, meaning it has one negative end and another positive end which helps it dissolve things (positive and negative charges attract other pos/neg charges)
what is the strongest bond and why
hydrogen bonds are the strongest because they have high electronegative difference which allows it to attract many electrons.
bc of the EN diff. where oxygen has high EN and hydrogen has low EN, O hogs the e- which results in a polar covalent bond with a neg end and a pos end.
what are the functional groups (needed for test)
hydroxyl (OH), amino (NH2), sulfhydryl (SH), carboxyl (COOH), carbonyl (COO)
hydroxyl
OH - makes things more soluble in water
structural isomer
two or more compounds that contain the same # of atoms but differ in geometric arrangement. (Same molecular formula different arrangement).
monomer
a molecule that can combined to others of the same kind to create larger, more complex structures
polymer
made up of many joined monomers
examples of monomers that create polymers
many glucose –> glycogen
many amino acids –> protein (hair, muscle, protein)
dehydration synthesis
a water is removed when two molecules join tgt to create 1 large molecule. (monomers into polymer)
neutralization rx
reaction between acids and bases where water is removed and a salt is formed.
base + acid –> salt + water
hydrolysis
water is added when one large molecule breaks down into two molecules (polymer into monomers)
redox rx
OIL
Oxidation is LOSS of e-
RIG
Reduction is GAIN of e-
differentiate carboxyl and carbonyl
carbonyl is a carbon atom attached to two oxygen atoms.
carboxyl is a carbonyl bonded to a hydroxyl
function of carbohydrates
“fast, temporary source of energy”
energy storage, strength/support, communication
function of lipids
longterm energy, insulation, vitamin absorption, protects organs, lubricates joints.
eg. wax on leaves makes it waterproof
function of protein
makes enzymes, communication, boosts immunity (antibodies), creates structure (muscle + skin)
what are the 4 levels of structure and explain it
- primary - sequence of A.A that makes up proteins
- secondary - consists of Beta pleated sheets and alpha helix which makes structure very strong bc H bonding
- tertiary - folded structure, polypeptide chain (disulphide bridge)
- quaternary - 2 or more polypeptide chains (an arrange tertiary structure)
saturated chains have ____ bonds
No double bonds
unsaturated chains have ____ bonds
double bonds
glycerol + 3 fatty acid = ?
triglyceride
ribose and deoxyribose
ribose has 5 carbon structure
deoxyribose is ribose but remove an oxygen
prefix oligo
naming prefix for 3-10 molecules
monosacchride
monomer that makes up carbohydrates
disacchride
the sugar formed when two monosaccharides join together
difference between triglyceride and phospholipid?
triglyceride is glycerol linked to 3 fatty acids while a phospholipid is basically a triglyceride except one fatty acid is replaced with a phosphate group.
diff. between saturated and unsaturated fatty acid structure
saturated is joined by single bonds
unsaturated is joined by one or more double bond.
dipeptide
a molecule of two amino acids joined together by a peptide bond (covalent bond)
describe the fluid mosiac model
a fluid mix of phospholipids that makes up the plasma membrane
parts of the fluid mosiac model.
draw and label
hydrophilic heads, hydrophobic tails, cholesterol membrane, integral transport protein, exoskeleton, peripheral protein, glycocalyx
integral protein function
transport molecules across membrane,
cell adhesion, act as enzymes
symporter
transports many different types of molecules
secondary active transport
pumps one ion one way and another ion the other way at the same time. eg. na+ and k+
endocytosis
cell engulfs substances (brings into cell)
exocytosis
moves substances out of cell
types of endocytosis and explain
phagocytosis - engulfs a large molecule
pinocytosis - engulfs smaller molecules or liquids
receptor mediated - receptor receives specific targeted molecule
sodium potassium pump + how it works
3 na+ exported, 2 k+ imported
uses ATP (adenosine triphosphate), potassium stimulates the pump to change shape to release sodium ions and take in potassium (also released into extracellular space)
what is it called when energy from atp is put in
potassium is lost and atp –> adp (adenosine diphosphate)
diffusion
net movement down a gradient (high concentration to low concentration)
facilitated diffusion
uses transport proteins to move down gradient
active transport
uses ATP to move against concentration gradient
what does a deep purple in a lugol test mean?
it is positive meaning polysaccharides are present
what does benedicts test do?
indicated if there are monosaccharides present
benedict test
tests for monosaccharides
lugols test
tests for polysaccharides
biuret test
tests for protein
a solute has a concentration outside the cell that is greater than the solute concentration inside the cell how will it reach equilibrium
the solvent particles inside the cell will diffuse through the cell membrane to the outside of the cell until the concentrations inside and outside the cell are equalized. Because solvent particles will leave the cell, the cell will get smaller.
sudan red test
tests for lipids
what can affect rate of diffusion
temperature, particle size, concentration difference, and distance of diffusion
what are aquaporins
large family of integral proteins that are known as water channels that help maintain homeostasis
integral protein
type of protein that can partially pass through membrane. it is then embedded in the bilayer to help transport molecules
enzymes
protein based catalyst meaning it speeds up reactions (and are not used up in the process)
lock + key principle
enzyme acts as a unique lock while the substrate is the unique key. the substrate is meant to specifically fit the enzyme.
activation energy (Ea)
the amount of energy to break or make bonds
factors affect Ea
temperature, ph level, substrate concentration
gibbs free energy
the energy available to useful work
exothermic (exergonic) reaction
reactant expels light or heat energy to create product (catabolic rx - 1 reactant –> 2 products)
endothermic (endogonic) reaction
absorbs heat to create product (anabolic rx - 2 reactant, 1 product).
biochemical pathway
a specific sequence where a chain of enzymes catalyze a variety of diff. reactions
feedback inhibition
cellular control mechanism where activity of enzyme is inhibited by the end product (helps prevent cells from wasting energy)
allosteric regulation
when another particle bonds to the allosteric site of an enzyme and essentially deactivates the enzyme.
conformational change
when the shape of enzyme active site changes and substrate cannot act upon
co factors
inogranic atoms and binds to enzyme temporarily
co enzymes
organic molecule that binds to active site
competitive inhibition
substrate cannot bind to blocked active site
non competitive inhibition
active site prevents substrate binding due to conformational change so it binds to allosteric site
london dispersion forces
type of imf that exists in all molecules regardless of polarity, however it is the ONLY force in non-polar molecules. it is caused by electrons of a molecule being attracted to the nucleus of the other. this forms temporary/instantaneous dipoles
dipole dipole
occurs in all polar molecules. Caused by the attraction of the δ + end of one molecule and δ - end of a neighbouring molecule
hydrogen bond
very strong type of dipole dipole force. caused by the attraction of positive hydrogen atom bonded to an electronegative atom (only N, O, F) in a molecule
ester link/bond
bond between a carboxylic acid and an alcohol
peptide bond
(carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another
c1 linked to n2
denaturation
When a protein’s shape is altered, it can no longer function. Salt, concentration, pH, and high heat cause it.
