Midterm Flashcards
Do Kings Play Chess Or Family Games Sometimes
domain- archaea, bacteria, eukarya kingdom- eukarya splits to plantae, amnimalia, fungi, protista eubacteria and archaebacteria phylum class order family genus species- most specific level, organisms are so similar they can mate and reproduce
what elements make up >96% of living matter
C H O P S N
covalent bond
sharing a pair of valence electrons by two atoms
two or more atoms held together by covalent bonds=molecule
ionic bond
2 atoms with a very different affinity for valence electrons combine, the electron is transferred from one to the other leaving 2 atoms with a net change in their charge. the oppositely charged cations and anions form an ionic bond
change in charge forms the bonds
compounds formed by ionic bonds are salts not molecules
weak
hydrogen bond
when hydrogen forms a covalent bond with an electronegative atom. it will have a positive charge allowing it to interact with another negatively charged atom
van der waals interactions
because of random positioning of electrons in the orbitals, net displacement can occur, creating brief charge differences. the dynamic charge distribution allows the molecules to stick to each other if they are very close.
dipole-dipole interaction
gecko foot and wall, the geckos feet contain millions of little hairs which stick to many surfaces through van der waals interactions
water
polar molecule with unique properties
- cohesion of water molecules-allows water molecules to stick (h-bonds)
- moderation of temperature by water- water has high heat of vaporization, water contributes to evaporative cooling
- water solid is more dense than water liquid, crystalline lattice structure makes ice about 10% less dense than liquid
- water is an important solvent- salts dissolve in water, polar molecules are soluble in water (hydrophilic) and non-polar molecules are insoluble in water (hydrophobic)
hydrocarbons
organic molecules consisting of only H and C
isomers
- structural (or constitutional) isomers can have a different bond order of atoms, atoms are connected in a different way
- geometric isomers e.g. cis vs. trans isomers, a double bond restricts rotation of the two atoms with respect to each other; trans=different side, cis=same side
- enantiomers, when 4 different atoms (or group of atoms) bind to carbon, an asymmetric arrangement occurs. if the 2 molecules are mirror images, and cannot be superimposed on each other, they are enantiomers
Pharmacological Importance of Enantiomers
Ibuprofen: S-ibuprofen is effective but R-ibuprofen is not
7 functional groups important for biological molecules
hydroxyl: OH
carbonyl: C=O
carboxyl: COOH
amino: NH2
sulfhydryl: SH
phosphate: PO4 2-
methyl: CH3
macromolecules
large molecules that make up living cells, many form by the addition of small monomeric subunits, to make polymers
carbohydrates, proteins, and nucleic acids add nucleotides to form macromolecules, they are polymers
lipids are macromolecules
formation of polymers
polymers form through dehydration reactions, monomers are attached through the formation of a covalent bond and the simultaneous removal of a water molecule= dehydration reaction
dehydration removes a water molecule and forms a new bond
disassembling of polymers
polymers are disassembled into monomers by the reverse reaction, or hydrolysis
hydrolysis adds a water molecule, breaking a bond
carbohydrates
fuel and building material
monosaccharides added to build polysaccharides and disaccharides
most common biological monosaccharides contain either 3, 5, or 6 carbon atoms
molecular monosaccharides are usually multiples of CH2O
e.g. C3H6O3 (glyceraldehyde)
C5H10O5 (ribose)
C6H12O6 (glucose, galactose, and fructose)-structural isomers
monosaccharides
monosaccharide names end with -ose and can be grouped into general categories based on the number of carbons e.g. trioses, pentoses, hexoses
simple monosaccharides have a linear structure with a carbonyl group (C=O) and multiple hydroxyl groups
glucose is a hexose and it prefers a circular shape
many monosaccharides change dynamically between linear molecules and rings
monosaccharides like glucose are a major nutrient for cells, cells extract glucose via cellular respiration (breaking them down into a series of reactions)
disaccharides
forms when a dehydration reaction joins two monosaccharides, can form polysaccharides
ex. two glucose molecules joined by an alpha 1-4 glycosidic linkage=maltose
glycosidic linkage is with 2 sugar molecules
storage polysaccharides
- starch: glucose polymers, each monomer is joined by 1-4 glycosidic linkages with all monomers in the alpha configuration. a simple starch, amylose, is unbranched and helical. amylopectin is a branched starch it uses alpha 1-6 linkages, it is not helical because of the branches.
- glycogen: how we store glucose. animals store glucose in this polysaccharide form and it is structurally similar to amylopectin but with more frequent alpha 1-6 linkages=more branching.
structural polysaccharides
- cellulose: like starch it is a polymer of glucose but with covalent 1-4 linkages which involve beta form of glucose. cellulose forms straight polymers that never branch it is very strong because of the h-bonds between different polymers lying parallel -this forms in microfibrils. most animals cant digest cellulose but cows and other ruminants can because they have special cellulose-digesting bacteria and/or protists that we dont
- chitin: a structural polysaccharide used in arthropods to build their exoskeleton. chitin contains N-acetylglucosamine monomers which are a derivative of glucose. it as an acetyl amine group instead of OH which allows for increased h-bonding between adjacent polymers giving chitin increased strength
starch
- made of glucose monomers
- used by plants to store surplus glucose
glycogen
- made of glucose monomers
- more highly branched structure than starch
- used by animals to store glucose
cellulose
- made of glucose monomers, but different anomeric form of glucose than in starch
- major component of plant cell walls
chitin
- made of N-acetylglucosamine monomers
- component of arthropod exoskeletons
lipids
lipids are hydrophobic because they consist mostly of hydrocarbons which are non-polar
classes: fats, phospholipids, steroids
dont form by polymerization because they dont make long chains
fats
fats are not polymers but they are built from monomers that are added by dehydration reactions
a fatty acid has a long chain of 16-18 carbons with a carboxyl group on the end, hence why its and acid
in a fat, 3 fatty acids are joined to glycerol by an ester linkage creating a triacylglycerol or a triglyceride
fatty acids vary in length and the number and location of double bonds
major function is energy storage
humans and other mammals store their fat in adipose cells
adipose tissue cushions vital organs and insulate body
saturated fat
saturated fatty acids do not have double bonds
all carbons have the maximum amount of hydrogens, making it saturated with hydrogen
the tail of a saturated fatty acid is straight which allows them to be packed tightly therefore making it solid at room temperature
unsaturated fat
have one or more double bonds
plant and fish fats are usually unsaturated
carbons do not contain the max amount of hydrogens
the cis double bonds prevent rotation, causes a bend and doesn’t allow close packing therefore it is liquid at room temperature
fats are essential but,
a diet rich in saturated fats may contribute to cardiovascular disease
trans fats may contribute more than saturated fats
cause arteries to be less flexible and clog
trans fats are found in fried food
trans fats
trans fats are a biproduct of a reaction
they are unsaturated fats
the kinks found in the structures of unsaturated fats is removed so it will be solid at room temperature
the double bonds are saturated by adding H atoms
makes plant oil solid at rt, increases shelf life, and can be used as butter substitute
the process creates a lot of trans fat as a by-product i.e. some cis 2 bonds in the plant oil become rearranged rather than saturated, our bodies aren’t used to this
phospholipids
two fatty acids and a phosphate group attached to glycerol
phosphate group is hydrophilic the 2 fatty acid tails are hydrophobic
phospholipids are amphipathic molecules, having both a hydrophilic polar end and a hydrophobic non polar end
because of their amphipathic nature, when phospholipids are added to water, they can rearranged into various structures
phospholipids are the major component of all cell membranes
liposome
=spherical lipid bilayer with aqueous middle
hydrophilic heads interact with H2O and hydrophobic tails interact with each other, away from water
steroids
steroids are amphipathic
lipids with a carbon skeleton consisting of 4 fused rings
cholesterol is an important component of animal cell membranes it provides strength and flexibility
too much cholesterol leads to cardiovascular disease
some steroids include cortisol and testosterone
proteins
form by addition of amino acids
lots of variability
proteins are involved in every biological task
polymers of amino acids (there are 20 biologically relevant amino acids)
vary extensively in structure
e.g. enzymes, antibodies, storage proteins, hormones, transporters, structural cytoskeletal proteins, intracellular machines
amino acid
amino acids can exist as different enantiomers but all proteins use L-enantiomers
side chains are what make them different
amino with carboxyl
linked by peptide bonds
can be put together to form macromolecules, a polymer
ribosomes make peptide bonds
3-main categories of amino acids
- non-polar side chains (hydrophobic)
- polar side chains (not charged) (hydrophilic)
- electrically charged side chains (+ or -) (hydrophilic)
polypeptide
a polymer of amino acids
polypeptides have an NH3+ (amino) end and a COO- (carboxyl) end and they can be composed of a few to more than a thousand monomers
each polypeptide can have a unique linear sequence of amino acids with an amino end (N-terminus) and a carboxyl end (C-terminus)
primary level of protein structure
linear sequence of amino acids
primary structure is determined by the inherited genetic information
amino terminus in the start and carboxyl terminus is the end
change in primary structure can affect a proteins function
secondary structure
the formation of alpha helices or beta pleated sheets due to hydrogen bonding between the O of a carboxyl group and the H of the amino group
h-bonds make the structure stable
depending on how the amino acids line up different structures will form
beta pleated sheet forms when peptide sequences lie next to each other in antiparallel orientation or parallel orientation
beta strand is shown as a flat arrow pointing towards the carboxyl end
tertiary structure
the arrangement of the peptide chain due to interactions between R groups that gives the protein its distinctive shape
involves reactive groups
hydrophobic “pockets” that exclude water and push other amino acids to the outside
van der waal interactions
ionic bonds
h-bonds
disulphide bonds
quaternary structure
results from the aggregation of 2 or more polypeptide subunits
not all proteins exhibit quaternary structure
denaturation
loss of a protein’s native structure
denatured protein is biologically inactive
protein folding
chaperonins are proteins that assist proper folding of other proteins
a specific protein may or may not require a chaperonin to assist its folding.
proteins aren’t functional until they’re completely folded
nucleic acids
contain code for a species
coded information that cells transmit to future generations and the messages that determine protein production
2 types: DNA and RNA
DNA stores hereditary info and transmits information to cell descendants
mRNA transmits information within the cell
amino acid sequence of a polypeptide is programmed by a region of DNA called a gene
nucleotide
consists of 3 different molecules joined together, phosphate, 5-carbon sugar, and nitrogenous base
(nucleoSide is without the phosphate and nucleoTide has a phosphate)
5-carbon sugar
in ribonucleic acid (RNA) the sugar is ribose
in deoxyribonucleic acid (DNA) the sugar is deoxyribose and there is no oxygen hence the deoxy-
features of a nucleotide
5’C - attaches to phosphate group “five-prime phosphate”
3’C - OH important for polymer formation “three-prime OH”
2’C - OH in RNA “two-prime OH”
2’C - H in DNA
1’C - attaches to the base
prime indicates its in the sugar ring not the nitrogenous base ring
nitrogenous base
2 types:
- Pyrimidines (single 6-sided ring), cytosine, thymine, uracil
- Purines (6- and 5-sided rings fused), adenine, guanine
structure of DNA
2 polynucleotides spiralling around an imaginary axis, forms a double helix
DNA double helix: 2 backbones run in opposite 5’->3’ directions from each other in an antiparallel arrangement
nitrogenous bases for H-bonds
complementary base pairing
A-T and G-C
structure of RNA
usually a single nucleotide chain
complementary base paring can occur between RNA and DNA, other RNAs, or itself
A-U and G-C
plasma membrane
a boundary that separates the living cell from its surroundings
exhibits selective permeability allowing some substances to cross more easily that others
integral membrane proteins
embedded in the bilayer at least one portion of the protein is hydrophobic
peripheral membrane proteins
attached loosely to the surface of the membrane (usually interacting with an integral protein)
glycoproteins
membrane proteins that have a sugar attached
important function in cell recognition
glycolipids
membrane lipids that have a sugar attached
cholesterol
inserts between phospholipid molecules
influences membrane permeability and fluidity
membranes
fluid at physiological temperature
like an oil, is flexible, moves, is dynamic
phospholipids and some proteins in the membrane can move
high temperature increases fluidity, gaps form if the temperature is too high
cholesterol has an effect on membrane fluidity
6 major functions for membrane proteins
- transport of molecules into or out of the cell
- enzymatic reactions near the membrane
- signalling via receptors
- cell-cell recognition
- intercellular attachment
- attachment of the cell to extracellular matrix proteins
Diffusion (passive transport)
occurs best with small hydrophobic molecules like O2
these are soluble in the bilayer and can pass through quickly
when a molecule is more concentrated on one side of a membrane, diffusion occurs until equilibrium is reached
i.e. molecules diffuse down their concentration gradient
called passive transport because no energy is required
Osmosis (special case of passive transport)
diffusion of water across a selectively permeable membrane
water moves from high to low free water concentration (or lower to higher solute concentration)
tonicity
the relative concentration of a solute in two solutions separated by a membrane that it cannot cross
if water can pass freely, the solute [ ] difference determines whether cells gain or lose water
hypotonic
= less [solute] outside cell
animal cells: lysed, the cell bursts, too much water
plant cells: turgid(normal) plant cell prefers the pressure of the water
isotonic
= equal [solute]
animal cells: normal
plant cells: flaccid, starts to lose some pressure, less strength so plants start to wilt
hypertonic
=more [solute] outside cell
animal cell: shrivelled
plant cell: plasmolyzed, plasma membrane pulls away from cell wall and can tear membrane, cell also shrinks (plasmolysis)
facilitated diffusion (passive transport aided by proteins)
specific molecules that are impeded by the membrane diffuse passively with the aid of a transport protein
channel proteins
- a specific channel protein usually allows only one type of molecule or ion to pass through
cellular conditions determine if the channel is open or closed
e.g. aquaporins are a type of channel protein that facilitates osmosis. water moves across the membrane faster if it goes through a channel
e.g. ion channels allow specific ions through (usually a different protein for each ion)
channel proteins can be “gated”, turned on or off by different stimuli
carrier proteins
these undergo a subtle change in shape (conformational change) to translocate a solute across the membrane
specific for the molecule being transported
solute also diffuses down its [ ] gradient
protein has the same affinity for target molecule on both sides of the membrane i.e. movement can occur in any direction
active transport
used to move a substance against the concentration gradient
requires energy usually in the form of ATP
why do cells do this?
-to concentrate nutrients in the cell
-to expel waste
-to establish voltage/chemical gradients
proteins involved in this type of transport are all carrier proteins, specific protein for each substance
sodium-potassium pump is one type of active transport system
active transport allows cells to establish and maintain concentration gradients that might not occur naturally
sodium potassium pump
- cytoplasmic Na+ binds to the pump
- Na+ binding stimulates phosphorylation by ATP, ATP is hydrolyzed energy so it causes a change in shape
- phosphorylation causes the protein to change its shape Na+ is expelled to the outside
- K+ binds to extracellular side and triggers release of the phosphate group
- loss of phosphate restores the protein’s original shape
- K+ is released and the cycle repeats
cotransporters
couple the “downhill” transport of a solute to the “uphill” transport of a second substance against its own concentration gradient
bulk transport
big molecules like polysaccharides must be transported using a bulk transport mechanism
involves formation of vesicles
membrane is flexible and can bend into different shapes including pinching off into vesicles, this requires energy
exocytosis (secretion)
exporting substances out of the cell
endocytosis
3 main types:
- phagocytosis (cell eating)
- pinocytosis (cell drinking)
- receptor-mediated - a mechanism involving receptors to import specific things
lipoproteins
transport fats to cells via the blood stream
LDL
low density lipoprotein, low in density, but high in cholesterol
LDL cholesterol is often referred to as bad cholesterol
HDL
high density lipoprotein, highest density due to high protein/lipid ratio
these particles can remove excess cholesterol from blood vessels (for transport to the liver)
HDL cholesterol is often referred to as good cholesterol
uniporters
those that transport only one type of molecule
symporters
transport two different molecules in the same direction
antiporters
transport two different molecules in the opposite direction
membranes and transport
- cellular membranes are fluid mosaics of lipids and proteins
- membrane structure results in selective permeability
- passive transport is diffusion of a substance across a membrane with no energy
- active transport uses energy to move solutes against gradients
- bulk transport across plasma membranes uses exocytosis and endocytosis
cell membrane
fluid barrier that separates cell interior from the exterior but it is not very strong so cells typically have additional structures that reinforce the membrane