chp 1 biological chem DAT Flashcards
CHP 1 - foundations of bio
what is matter ?
anything that takes up space and has mass
what is an element ?
a pure substance that takes up space and has mass
what is an atom ?
the smallest unit of matter
what is a molecule ?
2 or more atoms join together
what are the 2 forces for molecule attraction ?
intermolecular and intramolecular
what is intermolecular ?
the force BETWEEN molecules
what is intramolecular ?
the force WITHIN a molecule
what are monomers ?
a single molecule with ability to polymerize
what is polymerization ?
a process where monomers chemically combine to make a chain which the chain is then called polymers.
what are polymers ?
substances made of many monomers linked together
what 2 reactions govern polymerization ?
dehydration and hydrolysis
what is dehydration?
also called CONDENSATION - it takes a small monomers subunits , puts them together while releasing water molecule.
what is hydrolysis ?
also called DEPOLYMERIZATION- uses water to break bonds. so water is used
CARBS -
what are carbs ?
carbohydrates are used for both fuel and structural support
what are carbs composed of ?
carbon , hydrogen, oxygen
what are the types of carbs ?
mono , di , poly
shape for carbs ?
rings
what is a monosaccharide ?
the simplest type of carb
what are common mono carbs ?
glucose, fructose , ribose
what are disaccharides ?
made of 2 monosaccharides that are joined by a glycosidic bond.
what is reaction is required for glycosidic bond ?
dehydration reaction.
what are common disaccharides?
glucose and fructose = sucrose
what group forms a glycosidic bond ?
hydroxyl groups- they are main elements in carb composition therefore making them ready to be linked = glycosidic bond
what are polysaccharides ?
multiple monosaccharides together in a long polymer held by a glycolic bond
what are types of polysaccharides ?
-starch ; energy storage in plants and help with cell wall.
-glycogen ; energy storage in animals ( this can be hydrolyzed, resulting in glucose and then used as energy.
-cellulose ; structural support , made of many glucose monomers. ( cell wall )
PROTEINS-
what are proteins?
the building blocks of proteins are amino acids
what are amino acids composed of ?
carbon, hydrogen, oxygen and nitrogen
what is the basic structure of amino acids?
R group, carboxyl group ( COOH) and Amino group (NH2)
what are polypeptides ?
a polymer that is made of amino acids
what holds together polypeptides ?
peptide bonds
how are peptide bonds created ?
by dehydration reactions, and broken down by hydrolysis.
what are the protein levels ?
primary, secondary , tertiary, quaternary
what is the primary Level?
the simplest sequence of amino acids that is resulted from mRNA translation.
what Is the secondary level?
this is where alpha helices and beta sheets are formed.
what is the tertiary level?
this is the 3D structure that is formed by the R group interactions.
what interactions are used to hold these structures ?
3 types - hydrophobic, disulfide and additional tertiary interactions.
what is hydrophobic interactions?
afraid of water - so these interactions will be counting on non polar R groups
what are disulfide bonds ?
covalent bonds between 3 sulfide atoms
what are additional tertiary interactions?
hydro and ionic interactions between R groups.
what is the quaternary structure ?
multiple tertiary structures together
what are conjugated proteins?
they are protein made of amino acids and non protein components
what are metalloproteins?
proteins that contain a metal cofactor
example of metalloprotein ?
hemoglobin ; this is a molecule responsible for carrying oxygen throughout the blood within RBCs- the iron in Hg is the cofactor , its bound to the Hg protein that allows for interaction in the oxygen.
what are glycoproteins?
these are protons that have a carb group
what is protein denaturing ?
when a protein has loss its function and higher order structure
what are factors of protein denaturing ?
temp , Ph , salt concentrations
what are some functions of proteins?
storage
hormones - signaling molecule
receptos - binding to signaling molecule
structure - strength
immunity- anitbody
enzymes - regulating rate of chem reaction
ENZYMES -
what Is a catalyst ?
it is a substance that INCREASES the reaction rate by DECREASING activation energy
how do catalyst work ?
you can reach the transition state WITHOUT a catalyst but it will require HIGH amount of energy, WITH a catalyst you can reach transition state with less energy
what does a catalyst not do ?
it DOES NOT shift the equilibrium or alter spontaneity
what do catalyst do ?
increase reaction rate and decrease activation energy
how do enzymes facilitate catalytic activity ?
by having an active site
what is an active site ?
it is where and enzyme can receive material (substrate) and start reaction
what is specificity constant?
measuring enzyme binding efficiency for substrate
what are some theories for enzymes ?
induced fit theory - this expresses that the active site molds to favor the substrate binding
lock and key theory - this is outdated , this is where the active site of enzyme fits perfectly ( indicating that is is very selective)
can enzymes denature ?
yes , due to temp and ph
what are some common enzymes ?
phosphatase - cleavage of phosphate groups ( dephosporylate by using water to remove P )
phosphorylase - directly ADDS P group ti substrate
kinase - indirectly adds a phospho group to sub. this is because kinase doesn’t have a P group attached instead it will use a molecule that has a P
what are some NON PROTEIN enzymes ?
ribozymes - RNA molecules that are able to act as enzymes.
cofactor - non protein molecules that help enzyme function.
coenzymes - organic and inorganic molecule (vitamin, metals ..)
what is a holoenzyme ?
complex formed when enzyme binds to cofactor
what Is apoenzyme ?
enzyme without a cofactor
prosthetic groups ?
tightly/covanlent bond to enzyme
what affects a enzyme reaction rates ?
if a molecule either than the desired one bind to the active site or allosteric site
what is an active site ?
it is a receipt region that is specific for desired reaction
what is an allosteric site ?
separate region on the enzyme that is not the active site but substrate is still able to bind
what are types of enzyme inhibition ?
competitive and non competitive
what is competitive ?
it is when there is direct competition for the active site - this is inhibitor vs sub. This can cause the reaction rate to decrease due to the inhibitor using the active site.
- this can be solved by increasing the substrate concentration. This way the inhibitor will be diluted and overcome.
what is non competitive ?
this is where the inhibitor bind to the allosteric site. They are giving the sub to the active site. ThIs leads to a change in the active site which results in decreased rate reaction. this cant be solved
what is uninhibited ?
enzyme and sub at active site = success
what is Michaelis constant ?
this is the sub concentration required to reach half of the Max velocity
how does this relate to affinity ?
km has an inversely relationship to the enzyme sub biting strength
what is the desired result for km ?
if an enzyme can get to 1/2 V max with the smallest amount go sub available = affinity would be strong
HIGH km -
more sub is required to get to 1/2 v max
LOW km -
less sub is required to get to 1/2 v max
Km in a competitive inhibitor -
km will increase but vmax has no change (km increases because we need more sub but since we can dilute inhibitor Vmax is the same)
Km in a non com inhibitor -
vmax is decreased but km doesnt change (if less enzymes available vmax will decrease - km is the same because affinity is not manipulated )
what is feedback ?
feedback describes how the product of reaction affects the rate of reaction
neg feedback -
reaction products will slow/ inhibit reaction
pos feedback -
reaction products will activate/ increase reaction
LIPIDS -
what are lipids ?
Lipids are fatty, waxy, or oily compounds that are soluble in organic solvents and insoluble in polar solvents such as water
what are the components of lipids ?
carbon, hydrogen, oxygen
what are fatty acids ?
Fatty acids can be defined as carboxylic acids with long aliphatic chains
what are saturated fatty acids ?
hydrocarbon chains WITHOUT double bonds ( all carbons in the can are full with hydrogens ) = TIGHT
what are unsaturated fatty acids ?
hydrocarbon chain with a double bond. = LESS TIGHT
what are triglycerides ?
triglycerides or triaglycerol is a lipid containing glycerol backbone and 3 fatty acids (most triglycerides are hydrophobic and nonpolar )
what is glycerol backbone?
has 3 carbons that serve as anchors for the fatty acid chains.
what are phospholipids?
composed of a glycerol backbone , 1 phosphate group, and 2 fatty act tails.
amphiphatic
has both hydrophilic and hydrophobic regions
Lipid subtypes
waxes, carotenoid , lipoproteins and cholesterol
what factors affect the fluidity of the membrane?
temp, cholesterol, degree of fatty acid unsaturation
cholesterol
its an amphipathic lipid. it maintains stability in both low and high temps. precursor to steroid hormones, vitamin D and bile acids.
lipoproteins
complex of lipids and proteins that caryry lipophilic (hydrophobic) molecules through the blood. Their coat is composed of phospholipids, cholesterol and proteins
waxes and carotenoids
-waxes are simple lipids with long fatty acids chains connected to alcohols.
-carotenoids are lipid derivatives containing long carbon chains and conjugated double bonds that function ad pigment ( yellow , red and orange )
-sphingolipid are lipids with backbone containing aliphatic amino acids,
-glycolipids are lipids found in plasma membranes w carbs groups rather than phospho.
NUCLEIC ACIDS-
what are nucleic acids ?
they are composed of sugar monomers. they store genetic information, transfer molecules and gene silencing.
what are the 2 main types of nucleic acids?
DNA and RNA
what is a nucleoside ?
made of 1 ribose or deoxy sugar and 1 nitro base
what is a nucleotide ?
made of 1 ribose or deoxy , 1 nitro base and a phospho group.
RNA composition ?
ribose sugar with OH groups on 2’ and 3’
DNA composition ?
ANTIPARALLEL double helix, has deoxyribose and OH on 3’ and H on 2’
what is the sugar phosphate bone ?
it is how nucleic acids support themselves. it is a structural chain of alternating sugar and phosphates held together by phosphodiester bonds.
what are the terminal ends ?
3’ OH and 2’ p group
what is nucleic acid polymerization ?
it is when nucleic acids elongate as nucleoside triphosphate continue to be added to the 3’ OH group
what are the types of RNA ?
mRNA-messenger
tRNA-transfer
rRNA-ribosomal
miRNA-micro
dsRNA -double strand
mRNA-messenger
these result from DNA transcription. contains info to create proteins
tRNA-transfer
protein synthesis by carrying AA to ribosomes
rRNA-ribosomal
protein synthesis by complexing with proteins ti make ribosomes that read mRNA
miRNA-micro
silencing gene expression. they go the opposite direction. disrupts info passage and shuts down expression
dsRNA -double strand
genetic info reservoir , used by viruses
