biochem test

who was the scientist who disproved vitalism

Friedrich Wohler

explain the yeast experiment

the yeast cells were ground up and killed. when the sugar cane juice was added active yeast still occurred thus showing that enzymes can carry out the bio reactions

what 6 elements make up 97% of most living organisms

Carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur (CHNOPS)

what functional group is represented in -SH

sulfhydryl (thiol)

what is an ester linkage ?

found in lipids/fats and is a carbonyl carbon bonded to an oxygen

this is what kind of linkage (-C(=O)-O-C

ester linkage

what is a ether linkage

oxygen bonded to 2 carbon

(-C-O-C) is what kind of linkage

ether linkage

what is an amide linkage

found in proteins and connects amino acids

(-C(=O)-N) is what kind of linkage

amide linkage

T or F to link all monomers condensation reaction is done (water is lose)

True

when does an amino group on an amino acid become an amide

when it is bonded to another amino acid

how can u estimate the number of amino acids in a protein when given the molecular mass in Dalton (Da)

u divide by 120 Da which is the average mass of 1 amino acid

purines are

A and G

pyrimidines are

C, U T ( CUT the pie)

what type of tail do lipids have that make them hydrophobic

they have a hydrocarbon tail

autotroph

self feeders, make their own nutrients

heterotroph

other feeders, need to consume to gain nutrients

this tells us if a reaction can happen

thermodynamics

this tells us how fast a reaction can happen

kinetics

negative G means

spontaneous

positive G means

non spontaneous

what is the molecular shape and OH bond angle of water

V shaped and 104.5 degree

which bond in a water molecule is the donor ( O or H bond)

the H

why is the H bond the donor

bc O is electronegative and so the H pulls the electrons towards it to create a partial positive charge, and therefore, when making another bond, it’s donating its electron to the molecule

which bond in a water molecule is the acceptor (O or H)

The O

interactions that are between 2 fully charged groups and make the strongest noncovalent interactions

charge to charge

interaction between H donor and a electronegative acceptor

hydrogen bond

interaction between nonpolar molecules that bunch up in water and can be organized in cages

hydrophobic interactions

interactions that occur in a crammed space when molecules bump into each other and have permanent or temporary dipole moments

van de waals

which of the weak non covalent bonds is the weakest

van der waals

what is the numerical value of the Kw

1 × 10^-14

what is the conc of the H+ and the OH based on the Kw

1 × 10^-14 /2 = 1 × 10^-7

why is 7 the neutral pH

bc of the conc of the OH and H are both 1 × 10^-7

what is formula for pH, what is the pH if H+ = 10^-4

pH = -log(H+) if H+ as 10^-4 pH is 4 (just look at exponent)

what does the henderson-hasselbach equation refer to ( acid and base)

weak acid and con base

what does the henderson hasselbach equation tell us about pH when the base and acid are equal

tells us that pH =pKa

at which point in titration is the pH =pKa

midpoint

what does a buffer solution contains to stop the pH from changing

weak acid and con base

what is the best buffering range when having the pKa

pKa ±1

when is a buffer most effective and at its maximum capacity

when the midpoint is reached (50% base and 50% acid)

in mammalian blood plasma what is the weak acid that is that is used to help maintain the buffer system

carbonic acid (H2CO3)

in mammalian blood plasma what is the con base that is that is used to help maintain the buffer system

bicarbonate (HCO3-)

how do the lungs help to maintain the buffer system

u exhale CO2 to reduce acidity and you keep CO2 to increase activity

acid is a

proton donor

base is a

proton acceptor

strong acid dissociate completely why ?

it wants to give a hydrogen and therefore can break apart to give that

weak acid dissociate partially why ?

it doesn’t want to give a proton and therefore will only partially give a hydrogen if it needs to, but will reverse to get that H back and keep its stability

what makes proline so unique

It locks the amino group and therefore stops geometric flexibility, which creates the kink or bend in proteins

what is the name of the ring that is created in proline

pyrrolidine ring

what reaction is used to make disulfide bonds

oxidation

what reaction is used to break disulfide bonds

reduction

what is a cystine

2 cysteine residues that are linked

what kind of ring does phenylalnine have

a benzene ring

what type of ring does tyrosine have

a phenol

what is a phenol

a benzene ring with an OH

what type of ring does tryptophan have

bicyclic indole

when a benzene and pyrrole ring fuse together, it is called

bicyclic indole

a ring that contains carbon and one nitrogen atom is called

a pyrrole

the positive part of an amino acid

NH3+

the negative side of a amino acid

COO-

isoelectric point definition

the specific pH where the molecule is a zwitterion

what is the range of pKa for the carboxyl group on amino acid

1.8-2.5

what is the range of pKa for the amino group

8.7-10.7

what reaction allows polypeptides to form

condensation reaction

what makes a peptide bond a rigid planar configuration

a partial double bond that occurs when the C on the carboxyl group binds with an NH3+ causing it to act as a double bond (little movement)

this reagent is called edman reagent (also used in acid hydrolysis) that binds to N-terminus to tell TFA where to start. it also tags protein like ID badge

PITC

this reagent is used to cleave (cut) a peptide bond while leaving the peptide chain unbothered (used for Edman degradation)

TFA

This process breaks down all peptide bonds to determine how many types are in the polypeptide chain

acid hydrolysis

What chemical is used to break all peptide bonds at once when doing acid hydrolysis

HCL

this reagent is used in edman and acid hydrolysis to identify the proteins after they are cleaved and tagged with PITC

HPLC (high-performance liquid chromatography)

Lys and Arg are cut by

Trypsin

Phe, Tyr, Trp, and Leu are cut by

Chymotrypsin

Met gets cut by

Cyanogen Bromide (BrCN)

This type of chromatography separates the overall charge of proteins

ion- exchange chromatography

This type of chromatography is used to separate proteins by their size and shape

gel filtration chromatography

this type of chromatography is used to separate proteins based on their specific binding interactions

affinity chromatography

this is the relative hydrophobicity of each amino acid

hydropathy

why is the hydropathy of a protein important

bc it shows if a protien likes to be in a hydrophobic environment, interior proteins are going to be hydrophobic and exterior proteins are going to be hydrophilic

what are the 4 aliphatic amino acid structures

glycine, alanine, valine, and leucine

which amino acids have sulfur

Met and Cys

which amino acids have alcohol side chains

Ser and Thr

which amino acids have basic r groups

His, Lys, Arg

which amino acids have acidic r groups

Asp, Glu

what is the amide derivatives of the acidic groups

Asn and Gln

what bond is used to create secondary structures and on what molecule

Hydrogen bonds and they connect between amide hydrogens and carbonyl oxygens

what type of interaction is used to create the tertiary structure

hydrophobic effect

each carbonyl oxygen forms a h bond with the amide hydrogen on the __ residue ahead toward C terminus

4th residue (i+4)

how many residues per turn in a alpha helix

3.6 amino acid residues

which amino acid is the helix breaker and why

proline bc its rigid pyrrolidine locks and standard hydrogen bonding cannot occur

which amino acid can destabilize the helices and why

glycine because its small side chain (H) allows for too much flexibility

what types of bonds are formed in parllell b sheets

longer slanted bonds

what type of bonds are formed in antiparallel b sheets

straight linear bods

which is more stable parallel or anti b sheets

anti bc the bonds are shorter and stronger

What occurred in the Anfinsen ribonuclease A experiment

urea and 2ME was used to denature a polypeptide. when the polypeptide was denatured they tried different ways to put it back but found the only way that was possible was to create the peptide chain back again so that the disulfide bonds can go back to normal

what was urea used for in Anfinsen experiment

used to break non-covalent interactions (hydrophobic + hydrogen bonds)

what was the 2 ME used for in the Anfinsen experiment

used to break disulfide bonds

why was reoxidation used in Anfinsen experiment

to glue the protein back

what was the first pathway to try to get the polypeptide back to normal

2 ME was removed, reoxidation and then urea was removed

what was the result of the first pathway in Anfinsen’s experiment (reoxidation +urea)

in urea, the disulfide bond were not able to go back to its original state, therefore causing the a different shape to occur