Chem test 3 Flashcards
if a zwitter ion is in a basic solution…
(ph 12) it will lose an H from NH3 to become NH2
if a zwitter ion is in an acidic solution…
pH 1, it will gain an H, to become NH3 - OH
peptide bond is just…(amino acid)
the C and the NH joining - the OH and the other H from the N form a + H20
ex. of primary structure
Asp-Arg-Val-Tyr
secondary structure is also the…(second loop-d-loop)
loops and coils
Tertiary structure held together by…
noncovalent bonds - primarily amino acid side chains, sometimes disulfide bonds between thiol groups
Quaternary structure - held together by what bonds?
held together by noncovalent interactions
how to tell if it’s quaternary? (quarterback has more than one leg)
if there is more than one polypeptide chain
if there are bends, twists, or a compact structure, it’s (tt twist)
tertierary
5 interactions in tertiary and quatranery structures (SHHHD the tert and quat)
hydrophilic and hydrophobic interactions, salt bridges, hydrogen bonds, and disulfide bonds
motifs of secondary structures - this is just what secondary structures are
alpha, beta, loops and coils
Polypeptides are primarily held together by
noncovalent forces, but covalent bonds and non–amino acid portions may also be incorporated
Cofactors can be…(co can be uptight or loose)
tightly held or loosely bound, so that they can enter and leave the active site
coenzyme is an…
organic molecule that acts as an enzyme cofactor
By combining with cofactors, enzymes acquire…
chemically reactive groups not available in side chains, ie metal ions and trace minerals
are enzymes soluble or not?
most are soluble, globular, with a few exceptions
The catalytic activity of an enzyme is measured by…
its turnover number
enzymes - Because oxidation and reduction must occur together, these enzymes…(always need a co)
require coenzymes that are reduced or oxidized as the substrate is oxidized or reduced
Oxidoreductases Subclasses - this is an enzyme subclass (just dehydrate the oxi, but keep the ases)
Oxidoses
Reductases
Dehydrogenases
Oxidoses (oxidize me)
catalyze oxidation by addition of O2 to a substrate
Reductases (reduct the oxygen)
removing oxygen
Dehydrogenases (not what you think)
catalyze the removal or addition of 2 H atoms and require a coenzyme
enzyme classification (enzymes, TO HILL! all ase ending - they’re enzymes)
Oxidoreductases, Transferases, Hydrolases, Isomerases, Lyases, Ligases
Transferases catalyzes…
transfer of a group from one molecule to another.
types of Transferases (kin is transferring to tran)
Transaminases and Kinases
Transaminases
transfer an amino group between substrates
Kinases
transfer a phosphate group from adenosine triphosphate (ATP) to produce adenosine diphosphate (ADP) and a phosphorylated product.
Hydrolases
catalyze the hydrolysis of substrates, the breaking of bonds with addition of water. These enzymes are particularly important during digestion, and provide amino acids for protein synthesis and glucose for use in energy- generating pathways.
Hydrolases Subclasses (PLAN to split the water) think digestion
lipases, proteases, amylases, nucleases
Lipases (fatty lips) type of hydrolases
break glycerides (fats) into glycerol and fatty acids
Proteases (tease protein into amino acids) type of hydrolases
break proteins into peptides and amino acids
Nucleases - type of hydrolases (nuclear DNA)
break deoxyribonucleic acid (DNA) and RNA into nucleic acids
Lyases (type of hydrolases) (liase-on makes a double bond - client and boss)
catalyze the addition of a molecule such as H2O, CO2, or NH3 to a double bond or the reverse reaction in which a molecule is eliminated to create a double bond
Lyases Subclasses (as a liase-on I hid - HDDD) think De - removal
Decarboxylases
Deaminases
Dehydratases
Hydratases
Decarboxylases
catalyze the removal of CO2
Deaminases
catalyze the removal of NH3
Ligases (2 substrates need a lig up for ATP and DNA)
catalyze the bonding together of two substrate molecules. Because such reactions are generally not favorable, they require the simultaneous release of energy by a hydrolysis reaction, usually by the conversion of ATP to ADP. Ligases are involved in synthesis of biological polymers, such as proteins and DNA
Ligases Subclasses (lig up in SoCal)
Synthetases and Carboxylases
Synthetases (synthetic ATP)
catalyze the formation between two
substrates using ATP energy
Carboxylases
catalyze the formation of a bond between CO2 and a substrate using ATP energy
Enzymes act as catalysts because of their ability to: (COPE)
proximity, orientation, catalytic, and energy effect
Enzymes denature when
Enzymes denature when noncovalent attractions between protein side chains are disrupted, destroying the active site
Water-soluble vitamins contain
Water-soluble vitamins contain –OH, –COOH, or other polar groups that impart water solubility
types of vitamins
water soluble and fat soluble
water soluble vitamins found in what foods? (BMMP)
milk, meat, bread, potatoes
fat soluble vitamins (KADE is…)
A, D, E, and K
no fat soluble vitamins are…(fat can’t be co)
coenzymes
antioxidants - (not anti free radicals)
defuse free radicals - prevent oxidation by reacting w/ oxidizing agent
mutarotation (mutate god position)
alpha and beta switch due to change in equalibrium
As the open-chain aldehyde is oxidized,
the equalibrium is thrown off and it continues to reproduce as open chain
Carbohydrates that react with mild oxidizing agents are…(mild sugar)
classified as reducing sugars
tautomerism (the H taught the double bond to switch)
equilibrium that results from a shift in position of a hydrogen atom and a double bond
can easily be converted to sugar alcohol
monosaccharides. This is done by exposing sugar to H2 in presence of catalyst Pt. Basically H-C=O becomes CH2OH
hemiacetals plus alcohols makes..
acetals. Bi-product is H2O
glycosides
glucose and other monosaccharides are cyclic hemiacetals, they also react with alcohols to form acetals called glycosides
Glycosidic bond
A bond between the anomeric carbon atom of a monosaccharide and an –OR group
the reverse of glycosidic bond formation
hydrolysis - takes place during digestion of all carbohydrates
common monosaccharides (mono mi fgg)
fructose, galactose and glucose
common disaccharides (SML disacchrides)
lactose, maltose, sucrose
reducing sugar
Sugars that can freely interconvert between the cyclic structure and the straight chain form with an available aldehyde or ketone
how to calculate the number of possible stereoisomers in sugars
it’s just 2 (n), n = number of chiral carbons, so if it’s 3, then it’s 2 x 2 x 2.
cellulose structure (to get rid of it, start up! )
3 is up, 2 is down, O is up, 3 is down, 2 is up
amylose, amylopectin and glycogen (the same) structure (amy start up, but then goes down in the middle)
up, down, down, up, down
common use of fructose
to make high fructose corn syrup
common use of maltose
in beer, used to sweeten foods
common use of lactose
milk sugar
common use of sucrose
table sugar, made from sugar beets
common use of amylose (amy loves potatoes)
20% starch, beans, grains, potatoes
amylopectin (amy hangs out with amy)
found in seeds, plants, 80% of starch
glycogen
stored as glucose
glyceraldehyde
only 3 carbons, and it’s an aldehyde of course
Catalase (heme enzyme) is almost completely specific for one reaction:
the decomposition of hydrogen peroxide
Thrombin
catalyzes hydrolysis of a peptide bond following an arginine, and primarily acts on fibrinogen, a protein essential to blood clotting.
Carboxypeptidase A (A to C)
removes many different C-terminal amino acid residues from protein chains during digestion
Papain
catalyzes the hydrolysis of peptide bonds in many locations
in lyases subclasses, only Hydratases is..
addition, decarboxylases, Deaminases, and Dehydratases are all removal
if a double bond is created or removed in a reaction, it’s (the bond is the liase -on)
lyases
acids…
donate protons
bases
accept
The rate when the enzyme is saturated is determined by (PET rate)
the efficiency of the enzyme, the pH, and the temperature
Rates of enzyme-catalyzed reactions do not increase…
continuously with rising temperature. They reach a plateau and then drop
example of nonpolar and neutral amino acid AND it’s structure
glycine - no side chain, just an H
example of polar and neutral amino acid AND it’s structure
cysteine - side chain is just CH2 with an SH hanging off it
example of acidic amino acid AND it’s structure
asparatic acid, side chain is just one CH2 with a C-O- attached.
||
O
example of basic amino acid AND it’s structure
lysine - 4 CH2s and the last one is NH3+
ribose structure (down w/ ribs)
5 carbon circle - all OHs are down
deoxyribose structure (missing one rib)
5 carbon sugar circle - only 2 OHs, both down - just 2 Hs in the middle
all simple sugars, including all aldehyde and ketose (in basic solution) are…
reducing sugars - any sugar than can be turned into carboxylate
to identify chiral carbons in cyclic molecules…
go in a circle clockwise and counterclockwise. In glucose circle, there are 5 chiral carbons. In straight chain, there are 4.
galactose structure (galactose and glucose are in the same neighborhood)
galactose the same but 2 houses on the left
dextrose is just…
glucose
when 2 monosaccharides join, both hemiacetals, it forms…
disaccharides, they become acetals. The alcohol is from the OH on carbon 4 of the hemiacetal on the right
maltose is made of (malt on gg bridge)
2 glucoses
one polysaccharide humans can use is…
starch. Remember - polysaccharides are made only of glucose.
which is soluble, amylose or amylospectine?
only amylose
glycogen link is…(god needs glycogen)
alpha 1,4 (a few 1,6)
if an amino acid has an OH in the side chain, it’s always going to be…
polar neutral
dipolar ions are…
zwitter ions. They have one + charge and one - charge
wool, hair and fingernails are alpha or beta?
ALPHA
trace minerals join with enyzme by…
coordinate covalent bonds (just means one is providing 2 electrons) and they act as a lewis acids - BECAUSE they are positive ions and they need electrons - ie Mg2+
important co-enzymes (B an important FAN of co-enzymes)
FAD, A, B12, NAD
naming enzymes ex.
pyruvate carboxylate (this is ligase) adding a carboxyl group to pyruvate
active site is…(the shape is active)
a pocket in an enzyme with the specific shape and chemical makeup necessary to bind a substrate
Specificity of the enzyme is…(specificity is the STR of the show)
the limitation of the activity of an enzyme to a specific substrate, specific reaction, or specific type of reaction
a co-enzyme is a type of…
cofactor
what vitamins are water soluble?
all B and C and biotin AND they act as co-enyzmes
vitamin B1 does what?
lowers blood pressure
