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142 Cards in this Set

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4 levels of structure in proteins
primary
secondary
tertiary
quaternary
The primary structure is a sequence of
unique, precisely defined amino acid sequence
amino acid sequence is important for which several reasons?
1) essential to to elucidating it mechanism of action

2) determines the 3-D
structure of protein

3) sequence determination is a component of molecular pathology
Two primary structure diseases
Sickle Cell Anemia
Cancer
Causes of sickle cell anemia and cancer
mutation of an amino acid that destroys the sequence of an amino acid chain. Sickle cell-mutation of Glu6 to Val
Cancer-Gly12 to Val
Four major protein secondary structures?
Alpha helix
Beta sheet
Turn
Coil
How many amino acids per turn in an alpha helix polypeptide cahin
3.6
In alpha helix structure where does the hydrogen bonding occur?
between the carboxy group and the amino hydrogen 4 amino acids along the chain
What direction of rotation are L amino acids found?
counterclockwise (right handed)
What two amino acids are not present in the alpha helix structure?
Proline and glycine
Why can't proline be found in the alpha helix structure?
It has an imino group. that group produces destablizing bending and interferes with they H bonding
Why can't glycine be found in the alpha helix structure?
It is much more flexible because it lack the R group.
It introduces a weakness in the cylindrical feature.
Turns and coils often contain which two amino acids?
Proline
Glycine
Turns will always be found going in what direction
antiparallel
Coils will always having which direction?
parallel
Silky, stretchy proteins are
alpha helix
Filmy like proteins are
beta sheet
Turns and coils often contain which two amino acids?
Proline
Glycine
Turns may be found in the
(function)
catalytic centre of an enzyme
coils function
add flexiblity to the protein and allows for conformational changes
Turns will always be found going in what direction
antiparallel
Coils will always having which direction?
parallel
Silky, stretchy proteins are
alpha helix
Filmy like proteins are
beta sheet
Turns may be found in the
(function)
catalytic centre of an enzyme
coils function
add flexiblity to the protein and allows for conformational changes
Hydrogen bonding in Beta sheets occure if
several strands lay next to each other
A normal brain prion consists of mostly
alpha helices and random coil
A model of disease causing prion has
extensive beta sheet structure
Diseased prions are more:
stiff, tends to aggregate, and has limited resistance to digestion by proteases
How do prion diseases propogate?
diseased prions promote refolding of normal prions into the diseased form
Example of prion diseases
Alzheimers (humans)
Scrapie (sheep)
Bovine Spongiform Encephalopathy (mad cow)
Chronic Wasting Disease (elk/deer)
4 components of amino acid
carbon centered
carboxyllic group
amino group
side chain
What amino acid's R chain is a Hydrogen
glycine
Amino acids link together to form?
peptide
The amino group is what charge.
at low pH and high concentration of H+
positve ion (basic)
the carboxyllic group is what charge.
at high pH and low concentration of H+
negative (acidic)
All 20 Amino Acids are chiral except
Glycine
CORN
L-amino acid
All amino acids are what form
L-form
What peptide antibiotics contain D amino acids?
gramicidin (neosporin component)

Actinomycin D
Why are peptide anitbiotics useful in humans?
They contain D amino acids and the body isnt used to breaking them down, so they have more longevity in the body.
what amino acids are non-polar
Glycine
alanine
Valine
Leucine
Methionine
Isoleucine
Proline
What amino acids are Aromatic?
Phenylalanine
Tyrosine
Tryptophan
what amino acids are polar?
Serine
Cysteine
Threonine
Asparagine
Glutamine
what amino acids are Postiviely charged
Lysine
Histidine
Arginine
what amino acids are negatively charged?
Aspartic acid
Glutamic acid
What two amino acids contain sulfur inside their chain?
methionine
cysteine
Which amino acid is cyclic?
Proline
Which amino acids have a side chain that allows it to be ionized?
Tyrosine
Cysteine
What are important characteristics of charged amino acids?
Hydrophillic surfaces in proteins
salt bridges in proteins
acid/base and covalent protein chemisty
The direction of the peptide bond is ____ terminal to ___ terminal
N-terminal to C-terminal
A protein is least soluble when the ___ = the ___
pH = proteins pI
Basic amino acids (positive charged) will be postively charged when
pH is < pKa value
Acidic amino acids (negative charge) will be negatively charged when
pH is > pKa value
What three ways are free amino acids used in the body?
protein and peptide synthesis
Essential Nitrogen-containing compounds
Energy Production
Amino acids that are converted to glucose or glycogen are called?
glucogenic amino acids
The glucogenic amino acids are:
Alanine
arginine
asparagine
cysteine
glutamine
glycine
histidine
hydroxyproline
methionine
proline
serine
valine
Amino acdis that give rise to Ketone bodies are called?
Ketogenic amino acids
The ketogenic amino acids are:
leucine
lysine
Amino acids that are both keotgenic and glucogenic are:
threonine
isoluecine
phenylalanine
tyrosine
tryptophan
Amino acids are used in energy production only under what condition
when we are starving
what are the essential amino acids?
isoleucine
leucine
lysine
methionine
phenylalanine
threonine
tryptophan
valin
What are the semi essential amino acids
histidine
arginine
What are the non essential amino acids?
Asparagine
Glutamine
Aspartate
Glutamate
Glycine
Alanine
Proline
Tyrosine
Cysteine
Serine
Tyrosine is biosynthesized from what?
Phenylalanine
Cysteine is biosynthesized from what?
Methionine
What is the recommended daily allowance of protein for an individual?
.8 g "high quality" protein per kg of weight
What type of diets have been used to discourage herpes breakouts?
High in Lysine low in arginine
What are the precursors for epinephrine?
Dopamine
Tyrosine

(adrenaline hormone)
what are the essential amino acids?
isoleucine
leucine
lysine
methionine
phenylalanine
threonine
tryptophan
valin
what is the precursor for dopamine?
Tyrosine

(neurotransmitter)
What are the semi essential amino acids
histidine
arginine
what is the precursor for Thyroxine?
Tyrosine

(thryoid hormone)
What are the non essential amino acids?
Asparagine
Glutamine
Aspartate
Glutamate
Glycine
Alanine
Proline
Tyrosine
Cysteine
Serine
Tyrosine is biosynthesized from what?
Phenylalanine
Cysteine is biosynthesized from what?
Methionine
What is the recommended daily allowance of protein for an individual?
.8 g "high quality" protein per kg of weight
What type of diets have been used to discourage herpes breakouts?
High in Lysine low in arginine
What are the precursors for epinephrine?
Dopamine
Tyrosine

(adrenaline hormone)
what is the precursor for dopamine?
Tyrosine

(neurotransmitter)
what is the precursor for Thyroxine?
Tyrosine

(thryoid hormone)
What are the precursors for Melatonin?
Serotonin
Tryptophan

(neurohormone)
what are the precursors for Niacin?
Tryptophan

(vitamin B3)
Whare is the precursor for Seratonin or 5HT?
Tryptophan

(neurotransmitter)
What is the precursor for GABA?
Glutamate acid

(neurotransmitter)
What is the precursor for Histamine?
Histidine

(allergy and stomach acid production)
where is Glycine found?
Its a CNS neurotransmitter found in the spinal fluid
What are Hydroxylysine and Hydroxyproline important for?
mainting collagen structure
what is carnitine used for?
Lys derivative
fatty acid transport
what is creatine use for?
It is converted into creatine phosphate and stored in the muscles, where it is used for energy
what is Taurine used for?
critical for bile acid synthesis and osmoregulation
what is Homocysteine?
associated with heart problems

(artheroslerosis, heart attacks, strokes, blood clot formation, alzheimers disease)
What are the precursors of aspartane?
aspartic acid
phenyl alanine
what is aspartane used for?
diet soda
sweeteners
what are the precursors for monosodium glutamate?
Glutamic acid
Sodium hydroxide
What is MSG?
used in chinese food
makes it taste better
What 3 amino acids are phosphorylated?
Serine
Threonine
Tyrosine
phenylketonuria occurs because of the the buildup of what amino acid?
phenylalanine
Phenylketonuria results from what
lack of enzyme to convert phenylalanine to tyrosine
Maple syrup disease is caused by lack of enzyme to metabolize which amino acids?
leucine
isoleucine
valine
What can be done to help children with maple syrup disease?
Vitamin B (thiamine) injections
dialysis
special artificial diet low in leucine, isoleucine, and valine
What is the synthetic form of Oxytocin?
Pitocin
what does pitocin do?
induces labor
builds trust and bonds
stimulates milk release
What does vasopressin do?
stimulates re-asorption of water in the kidney
Patients with what disease are deficient in vasopressin?
diabetes insipidus
they excrete large volumes of water
PRIALT contains
ziconotide
what is ziconotide
25 amino acid peptide
a non narcotic pain reliever
it must be administered intrathecally
What two barriers are there to peptide drugs?
Oral-digestive system designed to breakdown polypeptides into amino acids

Intestinal absorptive epithelium-most drugs are hypophillic so they cant pass the phosolipid bilayer
Peptide drug pros
High activity
High specificity
little nonspecific binding
minimum other drug interaction
less accumulation in tissue
less toxicity
less potent
biological and chemical diversity
Peptide drug cons
low oral bioavailability
injection required
less stable
difficult delievery and transportation through memrane
costly
less soluble
immunological risk
cleared form body quickly
What is an amino acid with both a postive and negative charge?
Zwitterion
All amino acids are chiral except which one?
glycine
What are Globular Proteins?
Tertiary structures that are:
compact
highly-folded proteins that are water soluble
What are Fibrous proteins?
Tertiary structures that are:
stiff
elongated proteins that tend to form insoluable fibers
Myoglobin
globular
Made to work with the other biological fluids
They are soluble
surfaces are hydrophillic insides are hydrophobic
ex.. insulin, hemoglobin, antibodies
Collagen
Fibrous
hair skin wool nails
is insoluble
What protein structure has multiple polypeptides
Quaternary
What is required to maintain collagen's quaternary structure?
lysyl hydroxylase
prolyl hydroxylase
What is vitamin C used for?
it is a cofactor for hydroxylation to maintain collagen's structure
Prolonged Vitamin C defiencey leads to what disease?
Scurvy
What is the complete or partial unfolding of a protein?
Denaturation
How can proteins be denatured?
Heat-molecular motion
Mechanical agitation-molecular motion
pH-ion and H-bond disruption
Detergents-hydrophobic disruption
Organic Solvents (acetone, alcohols, etc)-hydrophobic disruption
Chaotropic Agents (chaos causing)- 5-10 M urea or guanidinium ion appear to cause hydrophobic disruption
How can some proteins be renatured?
remove the denaturant

although most denaturation is irreversible
Where is Myoglobin found? and what is it used for?
Found in muscle cells

For O2 storage

single polypeptide
Where is Hemoglobin found? and what is it used for?
Found in red blood cells

For O2 transport to tissue

multi polypeptide
What cofactor does myglobin and hemoglobin need?
Heme
Heme is what type of Cofactor?
Prosthetic group
What is the polypeptide part of a conjugated protein?
Apoprotein
What is the complete biologically active protein conjugate?
Holoprotein
What is the Normal Hematocrit Range?
Female: 38-46%

Male: 42-53%
What is Anemia?
Deficiency of functional RBC's and or hemoglobin
What type of compound is Heme?
Aromatic
When Oxygen is coordinated to Iron, blood is what color?
Red
When Oxygen is not coordinated to iron, blood is what color?
Blue
What is used to overcome Carbon Monoxide Poisoning?
Exposure to O2 rapidly

Hyperbaric Chamber
Why do we get Carbon Monoxide poisoning?
CO has an affinity (it binds to) heme more than O2 binds to heme..so it gets in our blood stream.
Allosteric Activators?
compounds that bind at sites other than the active catalytic site and regualte the enzyme activity through conformational changes affecting the catalytic site
Hemoglobin exhibits?
allostery
What happens when O2 binds the heme iron to each protein?
hemoglobin undergoes conformational changes.

The hemoglobin binds the O2 more tightly
What is cooperative binding?
When first binding of O2 makes conformational changes to other subunits and allows binding for those subunits to be easier.
What are allosteric activators?
compounds bind at sites other than the active catalyitc site and regulate the enzyme through conformational changes