CHE 476 Exam 1: Amino acids, peptides, and proteins

Proteins

1. catalysis

2. transport

3. structure

• collagen

• keratin

4. motion

• myosin

• actin

_____: main agents of biological functions

• does most of cellular work

1. ____: enzymes, speed up chemical reactions

• enolase (in the glycolytic pathway)

• DNA polymerase (in DNA replication) - connects nucelotides together

• -ase = enzyme (most of the time)

2. _____

• hemoglobin (transport O2 in the blood)

• lactose permease (transports lactose across the cell membrane) - one side of the membrane to the other

3. _____

• ___: connective tissue

• _____: hair, nails, feathers, horns

4. ____

• ____ (muscle tissue)

• ____ (muscle tissues, cell motility)

albumin

• aging

• decreases

• increases

• resumplementing

____ transports many kinds of molecules incuding fatty acids, metals, free radicals, drugs, and hormones

• a very large protein (69,000 Daltons) that is made in the liver and promptly released into the bloodstream. There, it accounts for roughly 50% of all plasma protein

• Albumin as a blood biomaker of ____

• as you get older, albium ____

• early adolescence ____, spikes down for puberty… then increases until 20s. then slolwy decreases

• _____ albumin does NOT solve aging problem… its a result of other issues like inflammation

• alpha helices; disulfide bonds

Protein: keratin

• found in rhino horn

• _____: connect through ___ bonds

• linear heteropolymers (straight chains made up of more than two different monomers)

• Alpha-carbon

• 1. capacity to polymerize

• 2. useful acid-base properties

• 3. varied physical properies

• 4. varied chemical functionality

Amino Acids: bulding blocks of protein

• proteins are _____ of alpha-amino acids

• ______: connect amino group to carboxyl group

• Amino acids have properties that are well suited to carry out a variety of biological functions

• 1. ____: attach to one another via dehydration synthesis

• 2. _____: each AA can donate or take protons

• 3. _____: BP, MP, solubility, physical properties (like light absoprtion), charges, acid/base

• 4. ____: charges… 2 witter ions… neutral overall, add up to 0

• carboxyl group (- charge), amino group (+ charge), alpha hydrogen, alpha carbon (to connect it all), and R group (changes the different types of amino acids)

• 7

BOTH tetrahedral (bc all single bonds)

Amino Acids share many features, differing only at the R substituent

• ____group, ____group, ____, ____, and ___ group

• all amino acids will be drawn at a pH of ___

VESPR:

Molecular geometry:

• alpha carbon

• 1. acidic (-)

• 2. basic (+)

• 3. hydrogen

• glycine

• chiral

• proline

Amino acids have 3 common functional groups attached to the alpha carbon:

• the ____ always has 4 subtituents and is tetrahedral

• all (except proline) have:

• 1. an ____ carboxyl group connected to the alpha carbon

• 2. a ____ amino group connected to the alpha carbon

• 3. an alpha ___ connected to the alpha carbon

• the 4th subtituent (R) is unique.

• In ____, the simpliest amino acid, the 4th substituent is also a hydrogen

• ***all AA are ____ (have chiral center) except for 1… glycine (R group is H… not C)

• ___: 5 member ring that connects R group to NH3+ (amino) making it a secondary amine, not a primary amine

• L

• carboxyl

• amine

• D

• L

L

bacteria; drug

Proteins ONLY contain ___ amino acids

• eaarly life when we had exposure to both L and D…. we somehow favored L at somepoint and its VERY unfavorable to switch back and foth

• ****Initial evolutionary prefernece and we stuck with it!!

To determine L/D:

• ____on top

• ____towards you

If amino is on right = ____

if amino group is on left = _____

Our proteins are only going to use ___ amino acid confiiguration… not D

See D amino acids in cell wall of ____ (for resistance) or if you want a ____ to last longer… you can put D-AA on it

1. nonpolar, aliphatic (7) - chains of carbons, hydrophobic

2. aromatic (3) - ring groups… good at absorbing light

3. polar, uncharged (5) - pH 7

4. positively charged (3)

5. Negatively charged (2)

9

amino acid classification:

• 20 common amino acids can be placed in 5 basic groups depending on their R substituents:

____essential amino acids - consume at least in diet since our bodies cannot make them

glycine, alanine, proline, valine, leucine, isoleucine, methionine

nonpolar amino acids

phenylalanine, tyrosine, tryptophan

aromatic amino acids

serine, threonine, cysteine, asparagine, glutamine

polar, uncharged group amino acids

lysine, arginine, and histidine

positively charged amino acids

aspartate (aspartic acid)

glutamate (glutamic acid)

negatievly charged amino acids

pKa

lower

acidic

basic

Ionization of amino acids:

amino acids contain at least two ionizable protons, each with its own pKa

• stronger acid = ___ pKa

____: at what pH does the molecule dissociate

• the carboxyilic acid has an ___ pK and will be protonated at an acidic (low) pH

• the amino group has a ___ pKA and will be protonated until basic pH (high) is achieved

• positive

• negative

• Zwitterion form

Ionization of amino acids:

• at low pH, the amiino acid exists in a _____ charged form (cation)

• at high pH, the amino acid exists in a ______ charged form (anion)

• between the pKa for each group, the amino acid exists in a ______, in which a single moelcule has both a positive and negative charge (total charge = 0) - predominate at pH values BETWEEN the pKa values of amino and carboxyl groups

PI (isoelectric point)

• zero

• soluble

• migrate

_____: average of pka’s to find when its neutral

• At this point, the net charge is ___

• Amino acid is least ___ in water

• AA does not ____ in electric field (bc of net charge of 0)

• 2.34

• 9.6

buffers

Amino acids can act as buffers:

• Amino acids with uncharged side chains, such as glycine, have two pKa values

The pKa of the alpha-carboxyl group is ___

the pKa of the alpha-amino group is ___

As ____ prevent chanage in pH close to the pKa, glycine can act as a buffer in two pH ranges

• most effective within 1

• pH does not change a lot in this region

• all amino acids act as a buffer in this region and make water

read and comprehend

Ionizable side chains also have pKa and act as buffers:

• ionizable side chains (R groups) influence the pl of the amino acid

• ionizable side chains can also be titrated

• titration curves are now more complex, as each pKa has a buffering zone of 2 pH units

• (the overlal titration curves have a less sleep slope)

Carboxylic acid - R group - amino group (sometimes its C - A - R… but mostly C - R - A)

• R groups that lose it after amine group: tyrosine, lysine, and arginine

Order of what loses H first:

small

hydrolysis reaction

condensation/dehydration

Amino acids polymerize to form peptides:

• peptides are ___ condenstation products of amino acids

• they are “small” compared with proteins

_______: breaks amino acids bonds via proteases

________: makes amino acid bonds

• amino (N)

Peptide ends are NOT the same:

• numbering and naming starts from the _____ terminus

____ configuration: to inhbit steric clashing… alternate being on top and bottom

• N

• full

• 3

• 1

Naming peptides:

• start at the ____ terminal

• use ___ amino acid names

• use ___ abbreviation

• for longer peptides like proteins… the ____ can be used

1.5

alpha C

peptide bond

Peptide bond order ___

• cannot freely rotate like a traditional single bond, which governs structure

• genomic isomers (cis-trans)

_____ is the only bond that can freely rotate

____ - between nitrogen and carboxyl C

cofactors

coenzymes

prosthetic groups

posttranslational modifications

Proteins are comprised of:

polypeptides (covalently linked alpha amino acids) and possibly:

______

• functional non-amino acid component

• metal ions or organic molecules (steroids)

• Extra non-AA component

______

• organic cofactors

• NAD+ in lactate dehydrogenase

• binds to protein and takes protons and leaves

_______

• covalently attached cofactors

• heme in myogolbin

• permanently attached cofactors

**Other modications (_______) ex. phosphate, ubiqutin, etc.

• ribosomes

• posttranslational modifications

• reversible

OH

phosphate

Uncommon amino acids in proteins:

• not incorporated by ____ (expect slenocysteine)

• arise by ______ of proteins

• ____modifications, especially phosprylation, are important in regulation and signaling

Modified - like adding an ___

reversible - ______ group

proteome

_____:

• refers to the complete set of proteins that are expressed by a cell, tissue, or organism at a certain time

• all the protein that gets made in a system

• like genome to DNA

• lipoproteins

• glycoproteins

• phosphoproteins

• hemoproteins

• flavoproteins

• metalloproteins

Conjugated proteins are covalently bound to a nonprotein entity:

Prothethic groups:

• lipids

• carbohydrates

• phosphate groups

• heme

• flavin nucelotides

• metals (iron, zinc, calcium, molybdenum, copper)

specific prothetic groups CONJUGATE proteins

• different categorization when you add different things!

• characteristics

• binding

Studying proteins and peptides sometimes requires purification from a mixture:

• polypeptides contain differing amino acid sequences

• the sequence and arragement of amino acids gives the polypeptide a chemical character (changed, polar, hydrophobic, etc.) - have their own _____

• Some polypeptides bind specific targets, which can be used to “fish them out” of a complex mixture - utilize ___ partners to get it out!

separation

chromatography

A mixture of proteins can be separated:

____ relies on differences in physical and chemical properties

• charge

• size

• affinity for a ligand

• solubility

• hydrophobicity

• thermal stability (protein that is stable in high temp… increase temp and al lother proteins wil ldegrade)

______: commonly used for preparative separation in which the protein is often able to remain fully folded

columb chromatography

________

• allows separation of a mixture of proteins over a solid phase (porous matrix) using a liquid phase to mobilize the proteins

• Proteins with a lower affinity for the solid phase will wash off first; proteins with higher affinity will retain on the column longer and wash off later

negative charged beads (cation exchange)

positive charged beads (anion exchange)

negatively

positively

Separation by charge: ion exchnage

________

______

• - charged beads are attracted to + charged prtoeins

• negative charges run through the column more quickly… since its not attarcted to it

• can be vice versa if the beads were + charged

Cation exchange:

• proteins with less than 7 pH will be ____ charged and not bind strongly to the column

• Proteins with higher than 7 pH will be ____ charged and will bind strongly to the column

• larger, smaller

Separation by Size: Size Exlcusion

• bc they have to move through channels, bigger ones don’t fit. Smaller ones have a longer way to go bc they are in the channels

• ____first, ___ last

• first

• ligand

• interest

Separation by binding: affinity

• proteins not bound to ligand (ex. insluin) will sort out ____

• then, swap buffer with higher concentration of _____. Protein detached from column and attaches to new free ligand

• Then, you can collect protein of ____

electrophoresis

• polyarcylamide

• polyarcylamide gel elctrophoresis (PAGE)

Separation in analystical scale is commonly done by _____.

• the electric field pulls proteins accoridng to their charge

• the gel matrix hinders mobility of proteins according to their size and shape

• the gel is commonly ____, so separartion of proteins via electrophoreiss is often called _______

can separate based on ______

• *****separated smaller proteins at higher resolution