Chem ch 18 Flashcards
nylon 6.6 (nylon for diane)
hexanedioc acid. Nylon 6.6 is a polyamide
CH2 also known as…
methylene
polyester is made of what? (polyester must DI from acid and alcohol)
diacid and dialcohol
nylon 6.6 has…(carbons)
6 carbons in the acid and 6 carbons in the amine
because nylon 6.6 has 2 functional groups…
it can go on and on on each end
polyamide is made of
diacid and diamine
1,4 benzene carboxylic acid is also called…(benz is treppin)
terephthalic acid
terephthalic acid can do____formation with…
ester formation with ethylene glycol
terephthalic and ester polymer is called…(pet trep and ester)
polyethyleneterephthalate or PET or Dacron
how many naturally occurring amino acids?
20
proteins are made up of…
amino acids
class of protein based on their job in our body (protein’s job is PC Sshet)
1) structural proteins
2) contractile proteins
3) transport protein
4) storage proteins
5) hormone proteins
6) enzymes
7) protection proteins
structural protein ex
provides structural compounds, mechanical shape, support ex. collagen (tendons and cartilage) and keratin (skin and hair)
contractile proteins
make muscles moves, do mechanical work, ex - myosin and actin
transport protein
transports, carries essential substances throughout body ex. hemoglobin
types of transport proteins (2 of them)
hemoglobin - globular, transports oxygen
lipoprotein - transports lipids, ex. serum albumin (transports fatty acids)
lipoproteins
storage proteins
store nutrients and make them available when needed ex. casein - in milk, ferritin - stores iron, myoglobin - stores oxygen and releases when we need it
hormone proteins
regulates body metabolism ex. - insulin, growth hormone
enzymes
catalyze biochemical reaction in the cell
naming enzymes
most end with “ase” ie - sucrase: catalyzes hydrolysis of sucrose. Not all have this naming - trypsin - catalyzes the hydrolysis of protein. ie - amylase - begins catalyzing digestion of carbohydrates
protection proteins
recognize and destroy foreign substances, ie - immunoglobulins - stimulates immune response
amino acids
have amino and acid group - all have this basic structure
H
|
H2N _ C _ COOH
|
R (this is the side chain, 20 of them)
how many side chains?
20 different, give unique identity to amino acids
it determines it’s function
amino acids have…
name, 3 letter code, one letter code and number
has an acid and a base in the same molecule
amino acid
zwitter ion
has equal positive and negative charges. depends on the ph of the solution
only zwitter ions are found…
in our body. the full amino acid formula is not in our body, it changes to zwitter
you can tell if it’s a zwitter ion if..
there is a + and - charge on the compound
if you have a zwitter ion in acidic solution (H+)
the H+ will turn the COO- to positive, making it COOH.
amino acids in acidic solutions are positive or negative?
positively charged
amino acid in basic solution (you don’t want to be basic)
H2N - C - COO-. The OH- will take a hydrogen from the N3H, making it N2H. it is negatively charged.
at any pH, the amino acid is in it’s…
zwitter form. This Ph is called PI = isoelectric point
in isoelectric form (PI), the net charge is…
zero.
the PI point for amino acids depends on the…
nature of R group
9 amino acids that are…
nonpolar - neutral
ie H, CH3, CH(CH3)2, benzene, gylcine, alanine, valine, phenylalanine
valine (val has a friend named iso)
neutral and nonpolar
H
|
H2N - C - COO-
|
C
/ \
CH3 CH3classes of amino acids
1) neutral and nonpolar
2) neutral and polar
3) acidic amino acids
4) basic amino acids
polar and neutral amino acids (OH c=osh Oh, coosh ball is neutral at the north pole)
it will either have an OH or SH group, OR an C=O attached to NH2 group. The NH2 in the neutral amino will be attached to a C=O-O group to balance it out.
how many amino acids are polar?
6 amino acids
how many acidic amino acids?
2 - they have an additional COO- group in the R group - Look at the side chain to identify
acidic amino acids are positively or negatively charged? (opposite acid)
negatively, bc they have 2 COO-
how many basic amino acids?
only 3, they have additional NH3+ group in the R group (look at the side chain to identify)
are basic amino acids positively or negatively charged? (basically positive)
positively
R group can be…
hydrophobic or hydrophilic
MEMORIZE
glycine structure
the number after the amino acid…
tells the pH in which the acid is in zwitter ion form
MEMORIZE
structure of cysteine
acid makes you feel…
low
how many amino acids have a chiral center?
19 - all except gylcine. The 19 are also D or L
D (Elle likes amino acids)
only L-amino acids are selected to make proteins by nature
D and L is only based on the…
amino group, H3N+. If the amino group is on the left, it’s L-amino acid, right it’s D-amino acid
D an L isomers are called…ex. L-Alanine and D-alanine
two enantiomers
intermolecular forces (the intermolecular force SHILD)
non-covalent forces - 1) H-bonding 2) vander waals forces or london dispersion 3) ionic bonding - ions in R chain 4) disulfide bond - S-S Polar 5) dipole dipole
additional COO or H3N makes a..(add some salt)
salt bridge
all amino acids have…(their make up)
a carboxylic group, an amine group, an R side chain, and an H all attached to central carbon
The principal classes of biomolecules are (PLNC)
proteins, carbohydrates, lipids, and nucleic acids
proteins do what for living things?
They provide structure (keratin) and support (actin filaments) to tissues and organs throughout our bodies. As hormones (oxytocin) and enzymes (catalase), they control aspects of metabolism
In body fluids, water-soluble proteins pick up other…
molecules for storage (casein) or transport (transferrin, Fe3+).
Proteins of the immune system provide
protection (Immunoglobulin G) against invaders, such as bacteria and viruses
proteins are polymers of what?
amino acids
Amino acids in proteins are located where?
alpha-amino (α-amino) acids because the amine group in each is connected to the alpha carbon
For 19 of these amino acids…
only the identity of the side chain attached to the carbon differs
The remaining amino acid not like the others..
proline, is a secondary amine whose nitrogen and carbon atoms are joined in a five-membered ring
The 20 α-amino acids that make up proteins are classified as…
neutral, acidic, or basic, depending on the nature of their side chains
The 15 neutral amino acids are further divided into…
those with nonpolar side chains and those with polar functional groups, such as amide or hydroxyl groups in their side chains
what enables proteins to perform their functions?
The sequence of amino acids in a protein and the chemical nature of their side chains
The intermolecular forces present between amino acids or between protein chains are (hivd)
hydrogen bonding, Van der Waals forces, ionic bonding, and disulfide bonds
The nonpolar side chains are described as hydrophobic or hydrophilic?
hydrophobic (water-fearing). To avoid aqueous fluids, nonpolar side chains gather into clusters to create a water-free environment.
The polar, acidic, and basic side chains are hydrophobic or hydrophilic?
The polar, acidic, and basic side chains are hydrophilic (water-loving). Attractions between water molecules and hydrophilic groups on the surface of folded proteins impart water solubility to the proteins
how many amino acids are chiral?
19, only gylcine is achiral
α-amino acids can exist as…(Lane likes the natural look)
D- or L-enantiomers.
Nature selectively uses only L-amino acids for making proteins
zwitter ion
A neutral dipolar ion that has one positive charge and one negative charge
because amino acids contain an acid and basic part, they can..
undergo an intramolecular acid-base reaction to form a zwitterion
intermolecular acid-base reaction gives amino acids many of the physical properties of…
salts: crystals, high melting points, and water solubility.
In acidic solution, amino acid zwitterions…
accept protons on their basic –COO– groups to leave only the positively charged –NH3+ groups
In basic solution, amino acid zwitterions…
lose protons from their acidic –NH3+ groups to leave only the negatively charged –COO– groups.
The isoelectric point (pI)describes…
the pH at which a sample of an amino acid has equal numbers of + and – charges
at the pI point…
the net charge of all the molecules of that amino acid in a pure sample is zero
Isoelectric points influence…
protein solubility and determine which amino acids in an enzyme participate directly in enzymatic reactions.
A dipeptide results from the formation of…(peppy opposites)
a peptide bond between the –NH2 group of one amino acid and the –COOH group of a second amino acid.
Three amino acids linked by peptide bonds will form..
a tripeptide
Any number of amino acids can link together to form a…
linear, chainlike polymer—a polypeptide.
Very large peptides (oligopeptides) contain..
hundreds of amino acids and are referred to as proteins.
A pair of amino acids can be combined to form…
two different dipeptides
Peptides and proteins are always written with the…
amino-terminal amino acid (N-terminal, the one with the free –NH3+) on the left and carboxyl-terminal amino acid (C-terminal, the one with the free –COO–) on the right.
The individual amino acids joined in the chain are referred to as..
residues
peptide naming
name the amino acid residues in order, starting at the N-terminus and ending with the C-terminus.
Primary structure (primary is most important)
Primary structure
is the sequence of amino acids in a protein chain.
Along the backbone of a protein is a…
chain of alternating peptide bonds and α-carbon atoms.
The amino acid side chains are located where?
substituents along the backbone, where they are bonded to the α−carbon atoms
The spatial arrangement of the polypeptide backbones of proteins determines…
secondary protein structure (2°)
The secondary structure includes…(2nd set of sheets)
wo kinds of repeating patterns known as the alpha-helix (α-helix) and the beta-sheet (β-sheet)
what holds the polypeptide chain in place? (What holds everything in place)
Hydrogen bonding between backbone atoms holds the polypeptide chain in place
Alpha-helix (α-helix)
A secondary protein structure in which a protein chain forms a right-handed coil stabilized by hydrogen bonds between peptide groups along its backbone
Beta-sheet (β-sheet)
A secondary protein structure in which adjacent protein chains either in the same molecule or in different molecules are held together by hydrogen bonds along the backbones, forming a flat sheetlike structure
Proteins are classified in several ways..(fg proteins)
one of which is to identify them as either fibrous proteins or globular proteins
Fibrous protein
A tough, insoluble protein whose protein chains form fibers or sheets
Globular protein (glob likes water)
A water-soluble protein whose chain is folded in a compact shape with hydrophilic groups on the outside
Tertiary protein structure (3°)
The way in which an entire protein chain is coiled and folded into its specific three-dimensional shape
native protein
A protein with the shape in which it functions in living systems
simple protein (simple residue)
A protein composed only of amino acids ex. ribonuclease
salt bridge
Where there are ionized acidic and basic side chains, the attraction between their positive and negative charges creates salt bridges
Amino acids with charged R groups will interact with…
water through hydrogen bonding
Hydrocarbon side chains are attracted to each other by which forces?
dispersion forces (primarily london dispersion), which can create a water-free pocket in the protein chain
Cysteine amino acid residues have side chains containing…
Cysteine amino acid residues have side chains containing thiol functional groups (–SH) that can react to form sulfur-sulfur bonds (–S–S–)
Disulfide bond
An S–S bond formed between two cysteine side chains that can join two separate peptide chains, or cause a loop in a single peptide chain
Ribonuclease is classified as a…
simple protein because it is composed only of amino acid residues
Conjugated amino acid has…(like a conjugated verb)
non-amino acid group in it, like hemoglobin or myoglobin - the heme group is the non-amino group.
casein - milk protein, has phosphate so it’s conjugated also.
lipoprotein - has lipids added
glycoproteins - have carbohydrate group in it
Quaternary protein structure (the final quarter)
Quaternary protein structure is the way in which two or more protein chains aggregate to form large, ordered structures
Polypeptides are primarily held together by ___forces
noncovalent forces, but covalent bonds and non–amino acid portions may also be incorporated
hemoglobin - hydrophilic or phobic?
The arms are hydrophilic, inside is hydrophobic.
a conjugated quaternary protein composed of four polypeptide chains (two each of two polypeptides called α-chain and β-chain) held together by hydrophobic interactions and four heme groups
hemoglobin in the lungs (and can carry how many molecules?)
O2 binds to Fe2+ so that each hemoglobin can carry a maximum of four O2 molecules
hemoglobin in tissue
In tissues in need of oxygen, O2 is released, and CO2 is picked up and carried back to the lungs
Hemoglobin is what type of protein? (not globular)
a cellular protein, normally found only inside cells and carried throughout the body inside red blood cells
Serum albumin is what type of protein?
it is referred to as a mobile protein because it is dissolved in an extracellular (outside the cell) fluid. It carries CO2 to the lungs for disposal
Collagen is the major part of what tissues?
connective tissues
The basic structural unit of collagen (tropocollagen) is…
three intertwined chains of about 1000 amino acids each. Each chain is loosely coiled in a left-handed (counterclockwise) direction
Primary structure is the…
sequence of amino acids connected by peptide bonds in the polypeptide chain, for example, Asp-Arg-Val-Tyr
Secondary structure is the
arrangement in space of the polypeptide chain, which includes the regular patterns of the α-helices and the β-sheet motifs (held together by hydrogen bonds between backbone carbonyl and amino groups in amino acid residues) plus the loops and coils that connect these segments
Tertiary structure is the
folding of a protein molecule into a specific three-dimensional shape held together by noncovalent interactions primarily between amino acid side chains that can be quite far apart along the backbone and, in some cases, by disulfide bonds between side-chain thiol groups
Quaternary structure is…
two or more protein chains assembled in a larger three-dimensional structure held together by noncovalent interactions
Digestion of proteins in the diet involves…(Need water to digest)
hydrolyzing peptide bonds in the stomach and small intestine, where the process is catalyzed by enzymes. Amino acids are absorbed through the wall of the intestine
Denaturationis the loss of…(you can’t denature the first evil)
secondary, tertiary, and quaternary protein structure that leaves primary structure intact because the peptide bond isn’t broken.
Solubility is often decreased by…
denaturation. Enzymes lose their catalytic activity and other proteins are not able to carry out biological functions when denatured
Most denaturation is irreversible or reveresable?
Most denaturation is irreversible, but renaturation is accompanied by recovery of biological activity
agents that cause denaturation (heat the mechanic)
Heat—The weak side-chain attractions in globular proteins are easily disrupted by heating.
Mechanical agitation—The most familiar example of denaturation by agitation is the foam produced by beating egg whites. Denaturation of proteins at the surface of the air bubbles stiffens the protein and causes the bubbles to be held in place
agents that cause denaturation 2 (even clean organic fruit)
Detergents—Even very low concentrations of detergents can disrupt the association of hydrophobic side chains.
Organic compounds—Polar solvents interfere with hydrogen bonding by competing for bonding sites.
agents that cause denaturation 3 (sweat salt)
pH change—Excess H+ or OH– ions react with basic or acidic side chains in amino acid residues and disrupt salt bridges.
Inorganic salts—High concentrations of ions can disturb salt bridges
the only acidic amino acids are…(ooh acid)
asperatic and glutamic - don’t need to remember, BUT the both have O= and OH as part of the side chain, which makes them acidic
the basic amino acids will always have…
a N in the side chain
alkyl side chain has…
ONLY C and Hs in it
at a low pH (acidic) basic groups would gain or lose an H+?
gain an H+
at a high pH, acids may gain or lose an H+? (high is the opposite on acid)
lose an H+, so HN3 becomes HN2
naming peptides
change last part to yl for all except the one at terminal C - keep that the full name. ex - alanine gylcine would be alanyl-glycine
each amino acid is a residue, so in tripeptide we have how many residues?
3
2-20 amino acids are called…(2 olga!)
oligopeptides
more than 20 amino acids are called…
proteins or polypeptides
quatranary structure can have how many chains of amino acids?
2, 3, or 4
both alpha and beta sheet are stabilized by what?
H bonding
the arrangement in beta sheets is which direction?
anti-parallel - this just means that the shape rotates C and N terminals at the curve. The C and Ns are facing each other.
keratins have mostly what structure? (KERATIN think opposite)
alpha helix - so they have a secondary structure
fibroin
silk, spider webs. has beta sheet structure
globular proteins are in what shapes?
globe-like 3-dimensional, some are alpha helix and/or beta sheet that is folded.
most enzymes are what proteins?
globular
forces in tertiary and quatranary structures only (tert and quat take LSD H)
Non-covalent forces***london forces, ionic forces - or salt bridge, and H-bonding, and disulfide (only with cysteine)
2 classifications based on location - on the move or staying put?
1) cellular and 2) mobile
mobile proteins
soluble and therefore globular. they are located on extra-cellular, which just means outside the cell. mostly carry CO2 from tissue to lungs
cellular protein
formed in cell
most abundant protein in mammals is…
collagen (30% of total protein)
collagen is globular or fibrous?
it is fibrous, made of 3 chains
where is collagen found in the body? (collagen cast baby CST BB)
skin, tendons, bones, blood vessels and connective tissue
what structure is collagen? (collagen is complex)
quatrenary
what structure is insulin?
quatrenary
what causes denaturation? (denature the MD at IHOP)
heat, mechanical (whisk), organic compound (adding vinegar to milk), inorganic salt, pH change, detergent.
the amino acid sequence naming is…
just the 3 letter abbreviation
how to tell if an amino acid side chain is non polar
the side chain will be MOSTLY C and H groups - 2 have Ns in the ring, but the majority of the side chain will be C and H
how to tell if a polar amino acid side chain is acidic
There are only 2 - it will have a C=O O group in the side chain, and the ending of the name will be acid
how to tell if a polar amino acid side chain is basic
it will have an NH2, NH3 or an N NOT attached to C=O or inside a cyclic. Inside a cyclic is not basic.
how to tell if an amino acid side chain is polar and neutral
it will either have an OH or SH group, OR an C=O attached to NH2 group
to figure out what type of bond will form, look at the…
side chains. 2 non-polar will form hydrophobic, acidic or basic and a neutral will form a salt bridge, and
if a C has a CH2, it cannot be…
chiral
the backbone of alpha helix and beta sheet is held together by what bonds?
hydrogen bonds
alpha helix is globular or fibrous?
both
beta sheets are globular or fibrous?
fibrous
tertiery structure is connected by what?
side chains. Alpha and beta are connected by amide and C=O bonds.
asparagine one letter code (No asperagus)
N
glutamine one letter code (Qnon glut)
Q
tyrosine one letter code (why tyro?)
Y
aspartic acid one letter code (Don’t be asperatic spaz)
D
glutamic acid one letter code (Exclude gluten, mic)
E
arginine one letter code (aRRR pirate)
R
lysine one letter code (Kut lyse)
K
examples of quaternary structures
hemoglobin and collagen
