biochem ch4 amino acids and peptide bonds

amino acids have what kinds of carbon

central tetrahedral carbon

what are the bonds between amino acids

peptide bonds

how many common AA are there

20

are all amino acids found in proteins

no

what structure do most amino acids pocess , except for proline

most amino acids are (referring to central carbon)

chiral

what does it mean for a carbon to be chiral

has 4 different substituents and it is tetrahedral

all amino acids have what 3 groups and have what shape

• an acidic carboxyl group

• a basic amino group

•  an a-hydrogen connected to the a-carbon

tetrahedral shape

which amino acid is exception for last flashcard

proline

what is the R group

unique 4th substituent of an amino acid that

glycine (chirality, R group)

not chiral as R group is H

-so has central carbon has 2 H groups

how do amino acids form peptide bonds

by dehydration to form covalent bond

what are the 5 classes of an amino acid

nonpolar, aliphatic

aromatic

polar neutral

acidic

basic

what are nonpolar AA’s (characteristics)

nonpolar so love fat

they are aliphatic so sidechain has open structure

what are the nonpolar AA’s

Glycine

alanine

valine

leucine

isoleucine

methionine

proline

glycine (1 letter, 3 letter)

G, Gly

alanine (1 letter, 3 letter)

A, Ala

valine (1 letter, 3 letter)

V, Val

proline (1 letter, 3 letter)

P, Pro

Leucine (1 letter, 3 letter)

L, Leu

Isoleucine (1 letter, 3 letter)

I, Ile

Methionine (1 letter, 3 letter)

M, Met

aromatic AA’s polarity

mostly nonpolar, except for tyrosine which has slight polarity due to OH group

aromatic AA UV

270-280nm,  Allows us to quantify protein concentrations (Spectrophotometry)

what are the aromatic AAs

Phenylalanine

Tyrosine

Tryptophan

Phenylalanine (1 letter, 3 letter)

F, Phe

tyrosine (1 letter, 3 letter)

Y, Tyr

Tryptophan (1 letter, 3 letter)

W, Trp

polar uncharged AAs can form what bond? what about cys?

hydrogen bonds and cysteine forms disulfide bonds

what are the polar uncharged AAs

Serine

Cysteine

Threonine

glutamine

asparagine

Serine (1 letter, 3 letter)

S, Ser

Cysteine (1 letter, 3 letter)

C, Cys

Threonine (1 letter, 3 letter)

T, Thr

Glutamine (1 letter, 3 letter)

Q, Gln

Asparganine (1 letter, 3 letter)

N, Asn

acidic amino acids have what charge

polar with negative charge (carboxyl is negative)

what are the acidic amino acids

glutamate

aspartate

aspartate (1 letter, 3 letter)

D, Asp

Glutamate (1 letter, 3 letter)

E, Glu

basic amino acids have what charge

polar with positive charge (amine is positive)

what are the polar basic amino acids

lysine, arginine, histidine

lysine (1 letter, 3 letter)

K ,Lys

Arganine (1 letter, 3 letter)

R, Arg

Histidine (1 letter, 3 letter)

H, His

what are uncommon amino acids

Not incorporated by ribosomes

how do uncommon amino acids come to be (how are they made (4), what is the most common)

 Arise by post-translational modifications of proteins

• phosphorylation

• hydroxylation

• methylation

• acetylation

Reversible modifications, especially phosphorylation (kinases/phosphatases), are important in regulation and signaling (MOST COMMON)

selenocysteine is found in, made by, why is it important?

• Selenocysteine has been found in many organisms

  •  Half of eukaryotes and most bacteria contain selenoproteins

•  Selenocysteine is the only common amino acid that humans can make but higher plants cannot

•  Replacement of sulfur with selenium creates molecules more resistant to oxidation

human selenoenzymes are involved in

• peroxide removal,

•  reduction of thioredoxins (The thioredoxin ((Trx) system is one of the central antioxidant systems in mammal cells)

•  selenophosphate synthesis,

•  activation and inactivation of thyroid hormones,

•  Repair of oxidized Met in protein

pyrrolysine found in

several archeal species

Hydroxylysine, hydroxyproline are found in

collagen

carboxygltamate is a ______________ protein

blood clotting

pyroglutamate is found in

 in bacteriorhodopsin (is a archeal protein in halobacteria that acts as a protein pump)

phosphorylated amino acids act as a

signaling device

what role do amino acid derivatives play (2)

act as neurotransmitters and hormones

acidic PH means

Basic pH means

Neutral pH means

acidic =  (↑H+)

basic = (↑OH-)

neutral = pH 7

at acidic pH, what happens to amino acids

• the carboxyl group becomes pronated since it was either neutral or negative before

• this turns the amino acid into a cation (positive charged) since the amine group is already positive or neutral

at neutral pH, what happens to amino acid

the carboxyl group becomes deprotonated (negative) and the amine group becomes pronated (+) so the net charge is 0 (neutral)

when a amino acid has a net charge of 0, it is called

zwitterions

-also can be called amphoteric or ampholyte

what are zwitterions (&function)

when in pI

can act as a acid OR a base

in a alkaline pH, what happens to amino acids

the amine group becomes neutral (NH2) (as it was positive before and lost a H+)

-the amino acid is now in anionic form (because the carboxyl group is negative, so that makes an overall negative charge)

what is the isoelectric point

is the pH at which the average charge on the molecule is zero

when at zwitterion

for a simple amino molecule, the pI is found how

• average of the two pKa values surrounding the isoelectric species

  • Since amino acids has 2 or more groups that can be pronated (the carboxyl and amine group), it has 2 pka (or more)

pK is what

the tendency to give up a proton

isoelectric point of glycine

what is a tritation curve

• a graphical representation of the pH of a solution in a tritration

  • To the left of the pI, we have added H+, to the right of the pI we have taken away H+. So this means that the more left the more positive, the more right, the more negative

  • when having to figure out the titration curve, look for when the amino acid is at 0, and that is the pI

ionizable side chains can also be

tritiated (because they can be pronated or deprotonated)

when an amino acid has a ionizable side chain, how does this affect the titration curve

• Titration curves are now more complex

  • Three pKa values

  • Because of R groups that can also be pronated or depronated

•  pKa values are discernable if two pKa values are more than two pH units apart

if given a titration curve of a ionizable amino acid, how do you find the pI

find the pk1 and pk2 and add those, then divide by 2

OR

just find when the amino acid charge is 0

what makes something chiral and aka’s (2)

has 4 different groups attached to it

aka - stereocenter, or asymmetrical carbon

Fischer projection vs perspective projection

• Fischer Projections:

  •  Horizontal bonds: out of plane;

  • Vertical bonds: behind plane

•  Perspective formulas:

  •  Dashed bonds – behind plane

  •  Solid bonds – out of the plane

what are the 4 types of isomers

stereoisomer

geometric isomers

enantiomers

diastereomers

stereoisomers have (same/dif in what properties )

different physical properties

• these then break down into more specific types of stereoisomers

geometric isomers are also called? differ or same in what properties ?

aka cis and trans

different physical and chemical properties

enantiomers are what? same or different in what properties ?

mirror images

SAME chemical properties BUT differ in CERTAIN physical and biological properties

diastereomers are what and differ or same in what properties

not mirror images

DIFF physical and chemical and biological properties

all amino acids are chiral except for

glycine (has H as R group)

what are the 2 strutures of amino acids (think letters)

L and D

D,L nomenclature (what is what, what groups go where)

based on glyceraldehyde

COO- group is on top

R group on bottom

Is D is amine group is on right side

is L if amine group is on left side

which type of D,L nomenclature in amino acids is mainly seen in nature

L-amino acids

what 2 amino acids have 2 chiral centers

Ile and Thr

how do we name using R,S system (what is the main focus)

• by viewing the molecule from the chiral center to the atom with the lowest priority.

  • r,s system is used to identify the absolute configuration of enantiomers (r stands for right and S for left- way the arrows go)

  • The priorities of the functional groups are:

    •  SH > OH > NH2 > COOH > CHO > CH2OH > CH3

      • Thiol> alcohol> amine> carboxyl> aldehyde>  hydroxymethyl> methyl> hydrogen

• So we first assign priority to all groups except the chiral carbon. We use the top 3 priorities.  We write the one with highest priority, then you place the other group in order based on priority, but if it is L, you do it counterclockwise and it is an S system. If it is D, then you write them clockwise and it is a R system. You write arrow starting at highest priority in the order it goes.

what are the priorities of the functional groups

• SH > OH > NH2 > COOH > CHO > CH2OH > CH3

  • Thiol> alcohol> amine> carboxyl> aldehyde>  hydroxymethyl> methyl> hydrogen

all amino acids absorb what kinds of light

infrared

what amino acid absorb UV ligth

• Only Phe, Tyr, and Trp absorb UV

•  Absorbance at 280 nm is a good diagnostic test for amino acids

  • Rmb how nucleotides absorb at 250-270nm)

what does chromatography do (really basic function)

separation of amino acid mixtures

proteins are ___________ polymers

unbranched

how do amino acids bond together

N terminal to C terminal using peptide bonds h

how do we read an amino acid sequence

N terminus to C terminus

how is the peptide bond formed

dehydration

the peptide backbone of a protein consist of repeated sequences of : (hint, not amino acids but like parts of them)

•  –N-Cα -Co -

  •  “N” is the amide nitrogen of the amino acid

  •  “Cα ” is the alpha-C of the amino acid

  •  “Co ” is the carbonyl carbon of the amino acid

when amino acids link up to a chain, they are called a

peptide

each amino acid unit is called a

residue

dipeptide

tripeptide

oligopeptide

polypeptide

(number wise; each one )

dipeptide- 2 residues

tripeptide- 3 residues

oligopeptide- 12 to 20 residues

polypeptide- >15-20 residues

what is a polypeptide (MW)

10,000

a protein (MW to make it one)

> 10,000

peptide are usually in what conformation

trans conformation

peptide bond has a large (type of force)

dipole moment

why does peptide have a large dipole moment

 N partially positive; O partially negative

length of peptide bond

Has a length of about 0.133 nm - shorter than a typical single bond but longer than a double bond

what do we mean by peptide bond having a resonance hybrid

Resonance hybrid- the electron within a structure change constantly due to movement of bonds, so molecule represented by more than one Lewis structures, these combined give a resonance hybrid

SOOOOOOO

this means that in the peptide bond, the carboxyl and Nitrogen atom (within the peptide bond) kinda go back and forth where the C=O bond then become C=N bond and vice versa. This gives the peptide bond a partial double bond character and an amide plane (limiting rotation between the C (of carbonyl) and N bond