Chapter 3: Protein Structure and Function Flashcards
building blocks of proteins in living organisms
amino acids
how many amino acids can be found in nature
500 amino acids
number of amino acids the human genetic code directly encodes
20 amino acids
must be obtained from the diet
essential amino acids
can be synthesized in the body
non-essential amino acids
aliphatic amino acids
- alanine
- glycine
- isoleucine
- leucine
- proline
- valine
aromatic amino acids
- phenylalanine
- tryptophan
- tyrosine
acidic amino acids
- aspartic acid
- glutamic acid
basic amino acids
- arginine
- histidine
- lysine
hydroxylic amino acids
- serine
- threonine
suflur-containing amino acids
- cysteine
- methionine
amidic amino acids
- asparagine
- glutamine
What are the nine (9) essential amino acids? (PriVaTe ThIM HiLL)
- Phenylalanine
- Valine
- Tryptophan
- Threonine
- Isoleucine
- Methionine
- Histidine
- Lysine
- Leucine
What are the 11 non-essential amino acids?
(Almost All Girls Go Crazy After Going To A Pretty Shop)
- Alanine
- Arginine
- Glycine
- Glutamine
- Cysteine
- Asparagine
- Glutamic Acid
- Tyrosine
- Aspartic Acid
- Proline
- Serine
often referred to as the 21st amino acid
Selenocysteine
glycine
gly
alanine
ala
valine
val
leucine
leu
isoleucine
Ile
methionine
met
tryptophan
trp
phenylalanine
phe
proline
pro
serine
ser
threonine
thr
cysteine
cys
tyrosine
tyr
asparagine
asn
glutamine
gln
aspartic acid
asp
glutamic acid
glu
lysine
lys
arginine
arg
histidine
his
where is the word protein derived from
Greek, proteios
proteios
first
What are proteins
- large molecules made up of chains of amino acids
- found in every cell in the body
- involved in most of body’s functions and life processes
- sequence of amino acids is determined by DNA
Different classes of proteins
- structural
- contractile
- transport
- storage
- hormone
- enzyme
- protection
provide structural components
structural protein
examples of structural protein
- collagen
- keratin
collagen examples
- tendons
- cartilage
keratin examples
- hair
- skin
- wool
- nails
make muscles move
contractile protein
examples of contractile protein
- myosin
- actin
myosin and actin
contract muscle fibers
carry essential substances throughout the body
transport protein
examples of transport proteins
- hemoglobin
- lipoproteins
hemoglobin
transports oxygen
lipoproteins
transports lipids
store nutrients
storage proteins
examples of storage proteins
- casein
- ferritin
casein
stores protein in milk
ferritin
stores iron in spleen and liver
regulate body metabolism and the nervous system
hormone
examples of hormone
- insulin
- growth hormone
insulin
regulates blood glucose level
growth hormone
regulates body growth
catalyze biochemical reactions in the cells
enzymes
example of enzymes
- sucrase
- trypsin
sucrase
catalyzes hydrolysis of sucrose
trypsin function
catalyzes hydrolysis proteins
recognize and destroy foreign substances
protection proteins
example of protection protein
immunoglobulins
immunoglobulins
stimulate immune responses
structure, characteristic, and classes of amino acids differ in
R groups
amino acids vary in
- size
- shape
- charge
- polarity
- solubility in water
attached to four different substituents
α-Carbon
Four substiuents of amino acids
- hydrogen atom
- carboxyl group
- amino group
- R group
nonionic form:
amino group
NH2
nonionic form:
carboxyl group
COOH
Zwitterionic form:
amino group
NH3+
Zwitterionic form:
carboxyl group
COO-
two forms of amino acid
- nonionic form
- Zwitterionic form
compounds that form amino acids
- amine
- acid
α-amino acids
amine is adjacent to the carboxylate group
19 out of the 20 amino acids are __
stereoisomers
amino acid that is not a stereoisomer
Glycine
compounds that have the same constitution but differ in the spatial arrangement of their atoms
stereoisomers
α-carbon of amino acids is __
chiral
chiral molecules
nonsuperimposable on their mirror images
achiral molecules
superimposable on their mirror images
have the hydroxy group attached to the left side of the asymmetric carbon furthest from the carbonyl
L isomers
have the hydroxy group on the right side
D isomers
where do the differences of amino acids depend upon
side-chain R groups
Amino acids form classes based on what?
polarity of side chains
Nonpolar
hydrophobic R groups
Polar neutral
- high affinity for water
- not ionic at pH
Polar acidic
- ionized carboxyl groups
- negatively charged
Polar basic
- basic as side chain reacts with water to release hydroxide ion
- positively charged
What are the polar uncharged amino acids
- serine
- threonine
- asparagine
- glutamine
- tyrosine
- cysteine
R groups of polar uncharged amino acids
- OH
- amide group
- sulfhydryl/ thiol groups
- H-bond with water
where are polar uncharged amino acids found
surface of globular proteins
polar uncharged amino acids are __ in aqueous solutions
soluble
bears hydroxylic R group
- serine
- threonine
has amide-bearing side chain
- asparagine
- glutamine
- has a phenolic group
- together with aromatic groups of F and W, acounts for most of UV absorbance and fluorescence exhibited by proteins
tyrosine
tyrosine account for most of what
- UV absorbance
- fluorescence
exhibited by proteins
forms a disulfide bond to another residue through oxidation of their thiol groups
cysteine
how does the cysteine form a disulfide bond to another
through oxidation of thiol groups
what is formed between two cysteine residue after oxidaton of their thiol groups
disulfide bond
non-polar/hydrophobic amino acids
aliphatic
1. glycine
2. alanine
3. valine
4. leucine
5. isoleucine
6. methionine
7. proline
aromatic
1. phenylalanine
2. tryptophan
aliphatic non-polar/hydrophobic amino acids
- glycine
- alanine
- valine
- isoleucine
- leucine
- proline
- methionine
aromatic non-polar/hydrophobic amino acid
- phenylalanine
- tryptophan
where are non-polar/hydrophobic amino acids found
- globular proteins
- insoluble core
has the smallest possible side chain, an H atom
glycine
has methyl group -CH3
alanine
has aliphatic hydrocarbon side chain
valine
has isomeric butyl groups
- leucine
- isoleucine
has thiol ether side chain that resembles an n-butyl group in many of its physical properties
methionine
methionine: C and S have nearly equal __ and S is about the size of a __ __
- electronegativities
- methylene group
cyclic secondary amino acid has conformational constraints imposed by the cyclic nature of its pyrrolidine side chain, which is unique among the standard amino acids
proline
side chain” from the α carbon connects to the nitrogen
pyrrolidine loop
has phenyl moiety
phenylalanine
with indole group, contain aromatic side chains, which are characterized by bulk as well as nonpolarity
tryptophan
D (position)
dexter (right)
L (position)
laevus (left)
electrically charged amino acids
Negative (acidic)
1. aspartic acid
2. glutamic acid
Positive (basic)
1. lysine
2. arginine
3. histidine
- negatively charged above pH 3
- aspartic acid
- glutamic acid
in its ionized state, aspartic acid is often referred to as what?
aspartate
in its ionized state, glutamic acid is often referred to as what?
glutamate
positively charged at pysiological pH values
- lysine
- arginine
- histidine
what kind of side chain does lysine have
butylammonium side chain
what group does arginine have
guanidino group
guanidino group contains __ __ __, rather than only one as in the lysine side chain, it shows a more diverse chemistry
two reactive nitrogens
what does histidine carry
imidazolium moiety
glycine one letter
G
alanine one letter
A
valine one letter
V
leucine one letter
L
isoleucine one letter
I
methionine one letter
M
proline one letter
P
phenylalanine one letter
F
tryptophan one letter
W
serine one letter
S
threonine one letter
T
asparagine one letter
N
glutamine one letter
Q
tyrosine one letter
Y
cysteine one letter
C
lysine one letter
K
arginine one letter
R
histidine one letter
H
aspartic acid one letter
D
glutamic acid one letter
E
Animal protein: complete
- egg
- milk
- meat, fish, poultry
Animal protein: incomplete
gelatin (denatured collagen)
what is missing in gelatin
Trp
vegetable protein: incomplete
Grains
- wheat
- corn
- rice (brown, white)
- oats
Legumes
- beans
- peas
Nuts
- almonds
- walnuts
what is missing in grains
lys (wheat, rice, oats)
lys, trp (corn)
what is missing in legumes
met (peas)
met, trp (beans)
what is missing in nuts
lys, trp
top 10 complete vegetarian protein foods with all the essential amino acids
- firm tofu
- lentils
- low-fat yogurt
- cottage cheese
- green peas
- squash and pumpkin seeds
- quinoa
- peanut butter
- eggs
- mushrooms
chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O)
peptide bond
how is peptide bond formed
dehydration synthesis
what does peptide bond have that limits rotation about this bond
partial double bond
what is formed from the condensind or dehydrating of two amino acids
dipeptide
amino acid with free -NH3+
amino terminal amino acid
short for amino terminal amino acid
N-terminal
amino acid with free -COO-
carboxyl terminal amino acid
short for carboxtyl terminal amino acid
C-terminal
how are amino acid structures written
N-terminal on the left
unbranched chain of amino acids
polypeptide chain
may consists of one or more polypeptide chains
protein
read from N to C terminal
simple peptide
naming:
ex. alanine
alanyl
naming peptides
- far AA residue retains the name of amino acids
- all AAs (except trp) –> -ine or -ic acid is replaced by -yl
- tryptophan –> tryptophanyl
naming:
ex. glycine
glycyl
naming:
ex. serine
seryl
naming:
ex. alanine, glycine, serine
alanylglycylserine
(Ala-Gly-Ser)
4 steps of writing strucutre of peptides
- write backbone
- add oxygens to carboxyl carbons, and hydrogens to amino nitrogens
- add hydrogens to alpha-carbon
- add side chains
backbone of peptide
N-C-C-N-C-C-N-C-C
peptide chain of nine amino acid residues
nonapeptide
examples of nonapeptides
- oxytocin
- vasopressin
where do oxytocin and vasopressin differ
amino acid position
- 3
- 8
stimulates uterine contraction in labor
oxytocin
- antidiuretic hormone
- regulates blood pressure by adjusting amount of water reabsorved by kidneys
vasopressin
Variety of Functions of Peptides
- hormones and pheromones
- neuropeptides
- antibiotics
- protection
hormones and pheromones
- insulin (think sugar)
- oxytocin (think childbirth)
- sex-peptide (think fruit fly mating)
neuropeptides
substance P (pain mediator)
antibiotics
- polymyxin B (Gram - bacteria)
- bacitracin (Gram + bacteria)
ex. of toxins that protection proteins defend against
- amanitin
- conotoxin
- chlorotoxin
amanitin
mushrooms
conotoxin
cone snails
chlorotoxin
scorpions
fewer than 50 amino acids
peptides
2 amino acids
dipeptides
3 amino acids
tripeptides
more than 10 amino acids
polypeptides
more than 50 amino acids
proteins
proteins are typically __ to __ amino acids linked together
100 - 10,000 amino acids
how are chains of proteins synthesized
based on specific bodily DNA
Functions of proteins
- enzymes
- defense proteins
- transport proteins
- regulatory proteins
- structural proteins
- movement proteins
- nutrient proteins
are biological catalysts
enzymes
include antibodies which are specific protein molecules produced by specialized cells of the immune system in response to foreign antigens
defense proteins
other term for antibodies
immunoglobulins
__ has regions that precisely fit and bind to a single __
- antibody
- antigen
carry materials from one place to another in the body
transport proteins
- carry lipids, vitamins, minerals, and oxygen in the body
- act as pumps in cell membranes, transferring compounds from one side of the cell to the other
transporters
responsible for transport and storage of oxygen in higher organisms, respectively
- hemoglobin
- myoglobin
myoglobin
1 subunit
1 heme group
hemoglobin
4 subunits
4 heme groups
- control many aspects of cell function, including metabolism and reproduction
- we can only function within limited set of conditions
regulatory proteins
where are insulin released
beta cells of pancreas
where are glucagon released
alpha cells of pancreas
promotes growth
growth hormone
regulate blood glucose
insulin and glucagon
regulates the body’s metabolic rate
thyroxine
regulate blood calcium
- calcitonin
- parathormone
regulates fluid and electrolyte balance
antidiuretic hormone
provide mechanical support to large animals and provide them with outer coverings
structural proteins
hair and fingernail are composed of what
keratin
necessary for all forms of movement
movement proteins
how do muscles move
interaction of actin and myosin proteins
serve as sources of amino acids for embryos or infants
nutrient proteins
examples of nutrient storage proteins
- egg albumen
- casein in milk
Levels of protein structure
- primary
- secondary
- tertiary
- quaternary
primary structure
amino acid residues
secondary structure
three-dimensional spatial arrangements
tertiary structure
polypeptide chain
quaternary structure
assembled subunits
bond that holds primary structure
peptide bonds
smalles protein
insulin (51 amino acids in two chains)
what links the two chains of insulin
cysteine (disulfide) cross links
bonds in secondary strucure
hydrogen bond
(-NH group of peptide bond and carbonyl oxygen of another peptide bond)
two regular arrangements in secondary structure
- α-Helix
- beta sheet
stabilized by hydrogen bonds between nearby residues
α-Helix
stabilized by hydrogen bonds between adjacent segemtns that may not be nearby
beta sheet
most common type of secondary structure
α-Helix
shape of α-Helix
coiled, helical
important features of α-Helix
- amide H and carbonyl O involved in H bonds
- carbonly O links to amide H, 4 AA away
- H bonds parallel to long axis of helix
- right handed
- 5.4 angstorms repeat distance
- 3.6 amino acids per turn
second most common secondary structure appears similar to folds of fabric
β-pleated sheet
two possible orientations of β-pleated sheet
- parallel
- antiparallel
if the N-termini are head-to-head
parallel
if the N-terminus of one chin is aligned with the C-terminus of the other
antiparallel
- gives a specific three dimensional shape of the polypeptide chain
- involves interactions and cross links between different parts of peptide chain
tertiary structure
tertiary structure is stabilized by what
- hydrophobic and hydrophilic interactions
- salt bridges
- hydrogen bonds
- disulfide bonds
globular tertiary structure forms spontaneously and is maintained by what
interactions among side chains or R groups
between two cysteine residues
disulfide bridges
S-S linkage can occur within the same chain
intrachain
S-S linkage can occur between 2 or more chains
interchain
ionic interaction/electrostatic attraction between ionic side chains -COO- and - NH3+
salt bridges
interaction between polar residue chains
hydrogen bonds
interaction between nonpolar groups attracted by mutual repulsion of water
hydrophobic interactions
results from the aggregation of two or more polypeptide subunits
quaternary structure
fibrous protein of three polypeptides that are supercoiled like a rope
collagen
globular protein with two copies of two kinds of polypeptides
hemoglobin
Two major classes of protein
- fibrous proteins
- globular proteins
- typically insoluble inw ater and serve structural roles
- 3D structure is usually long and rod shaped
fibrous proteins
- coiled into compact shapes with hydrophilic outer surfaces making them water-soluble
- compact shape like a ball with irregular surfaces
- enzymes
globular proteins
α-keratin function
tough, rigid, hard (nails, horns)
α-keratin structure
- cross-linked α-helixes
- rigid linker (S–S)
collagen function
tensile strength, non-stretching (tendons, cartilage)
collagen structure
- cross linked triple-helixes
- flexible linker (Lys-HyLys)
silk fibroin function
soft, flexible non-stretchy (egg sac, nest, web)
silk fibroin structure
- non-covalently held β-sheets
- van der Waals interaction
shape of globular proteins
roughly circular
shape of fibrous proteins
long strands
amino acid sequence globular
irregular and wide range of R groups
amino acid sequence fibrous
repetitive with limited range of R groups
function globular
physiological/functional
function fibrous
structural
examples of globular
- hemoglobin
- enzymes
- insulin
- immunoglobulin
examples of fibrous
- collagen
- keratin
- myosin
- actin
- fibrin
solubility globular
generally soluble in water
solubility fibrous
generally insoluble in water
chemistry of permanent waving
- reduce
- curl
- oxidize
