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Flashcards in Proteins Deck (106):
1

Most abundant and functionally diverse molecules in living systems; Linear polymers of Amino Acids

Proteins

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Set of all the proteins expressed by an individual cell at a particular time

Proteome

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Aims to identify the entire complement of proteins elaborated by a cell under diverse conditions

Proteomics

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Structure of Amino Acids

1 carboxyl group (-COOH)1 amino group (-NH2)1 unique side chain (R-group)

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Amino Acids with Alipathic Side chains

Glycine (Gly, G)Alanine (Ala, A)Valine (Val, V)Leucine (Leu, L)Isoleucine (Ile, I)

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Amino Acids with Hydroxylic groups and Sulfur atoms

Serine (Ser, S)Threonine (Thr, T)Tyrosine (Tyr, Y)Cysteine (Cys, C)Methionine (Met, M)

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Amino Acids with Aromatic Side Chains

Histidine (His, H)Phenylalanine (Phe, F)Tyrosine (Tyr, Y)Tryptophan (Trp, W)Proline (Pro, P) - Imino Acid

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Amino Acids with Basic Groups

Arginine (Arg, R)Lysine (Lys, K)Histidine (His, H)

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Amino Acids with Acidic Groups and their Amides

Aspartic Acid (Asp, D)Asparagine (Asn, N)Glutamic Acid (Glu, E)Glutamine (Gln, Q)

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Net charge of zero at Physiologic pH; promote hydrophobic interactions; Cluster in the interior of the protein

Non-polar Side Chains

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Has the smallest at physiologic pH;Used in the first step of he synthesis

Glycine

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Carries nitrogen from peripheral tissues to the liver

Alanine

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Branched-chain amino acids whose metabolites accumulate in Maple Syrup Urine Disease

Valine, Leucine, Isoleucine

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Accumulate in Phenylketonuria

Phenylalanine

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Deficiency in Phenylalanine hydroxylase

Phenylketonuria

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Has the largest side chain; Precursor for Niacin, Serotonin and Melatonin

Tryptophan

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Transfer of methyl group as S-adenosylmethionine (SAM); Precursor of Homocysteine

Methionine

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Not an amino acid; Contributes to the fibrous structure of collagen and interrupts alpha-helices in globular proteins

Proline

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Zero net charge at physiologic pH; presence of side chains that can participate in hydrogen bonds

Uncharged Polar Side Chains

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Contains a sulfhydryl group that is an active part of many enzymes; 2 cysteines can be connected by covalent disulfide bond to form Cysteine

Cysteine

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Precursor of Dopamine, Norepinephrine, Epinephrine, Thyroxine and Melanin

Tyrosine

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Phosphorylation site of enzyme modification; Often linked to carbohydrate groups in glycoproteins

Serine

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Sites for O-linked glycosylation in Golgi Apparatus

Serine and Threonine

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Have a carbonyl group and an amide group that can also form hydrogen bonds

Asparagine and Glutamine

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Site for N-linked glycosylation in endoplasmic reticulum

Asparagine

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Deaminated by glutaminase resulting in the formation of ammonia; Major carrier of nitrogen to the liver from peripheral tissues

Glutamine

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Positively charged because of the amine group

Basic Amino Acids

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Precursor of Histamine; Used in the diagnosis of folic acid deficiency

Histidine

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Precursor of creatinine, urea and nitric oxide

Arginine

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21st Amino Acid?; found in handful of proteins, including certain peroxidases and reductases; a selenium atom replaces the sulfur of its structural analog, cysteine

Selenocysteine

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All amino acids are chiral EXCEPT

Glycine

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Defined as an atom in a molecule that is bonded to 4 different chemical species allowing for optical isomerism

Chiral Center

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Exact mirror images of each other

Stereoisomers/Optical Isomers/Enantiomers

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All amino acids in proteins

L-configuration

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Bacterial cell walls, antibiotics

D-configuration

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Chemical compound that has a total net charge of zero

Zwitterion

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pH where the zwitterion predominates

pI or Isoloelectric Point

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Which group accepts protons?

Amino group

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Which group donates protons?

Carboxylic acid group

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Amino acids that cannot be synthesized by the body and must come from diet

Essential Amino Acids

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Essential Amino Acids

PhenylalanineValineTryptophanThreonineIsoleucineMethionineHistidineArginineLeucineLysine

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Conditionally Non-essential Amino Acids

ArginineHistidine

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May be made in the body, but usually not enough

Arginine

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May be recycled, but should eventually be consumed since it is not made at all

Histidine

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Linear sequence of a protein's amino acids

Primary Structure

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Attach alpha-amino group of one amino acid to the alpha-carbonyl group of another; Very stable, can only be disrupted by hydrolysis through prolonged exposure to a strong acid or base at elevated temperatures; Polar and can form hydrogen bonds; Partial double bond character makes the bond rigid and planar; Generally in trans configuration

Peptide Bonds

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Sequencing of Polypeptides: N-terminal amino acid

Sanger's Reagent (1-fluoro-2,4-dinitrobenzene)Edman's Reagent (Phenylisothiocyanate)

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Sequencing of Polypeptides: C-terminal amino acid

HydrazineCarboxypeptidase

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The folding of short (3- to 30- residue) contiguous segments of polypeptide into geometrically ordered units

Secondary Structure

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Kinds of Secondary Structure

Alpha-helixBeta-pleated sheets

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Most common; R-handed spiral with polypeptide backbone core; Side chains extend outward; 3.6 amino acid per turn of the spiral

Alpha helix

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Surfaces appear flat and pleated; 2 or more peptide chains parallel to each other; Interchain and Intrachain bonds

Beta sheet

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Combinations of adjacent secondary structures such as beta-alpha-beta unit, greek key, beta-meander, beta-barrel

Motifs or Supersecondary Structures

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Overall 3-dimensional shape of the protein; Refers to the folding of domains and their final arrangement in the polypeptide

Tertiary structure

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Fundamental functional and 3-dimensional structure units of a polypeptide

Domains

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Specialized group of proteins required for the proper folding of many species of proteins; Prevents aggregation; Can also "rescue" proteins

Chaperones

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Structure of proteins consisting of more than one polypeptide chain; held together by noncovalent bonds

Quaternary Structure

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Precipitation of a protein so that it forms ordered crystals that can diffract x-rays

X-ray Crystallography

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Measures absorbance of radio frequency electromagnetic energy by certain atomic nuclei

Nuclear Magnetic Resonance Spectroscopy

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Molecular dynamics programs can be used to stimulate the conformational dynamics of a protein and the manner in which factors such as temperature, pH, ionic strength, or amino acid substitutions influence these motions

Molecular Modeling

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Disruption of a protein's structure; Unfolded and disorganized; Reversible

Denaturation

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Reasons for Denaturation

HeatOrganic solventsMechanical mixingStrong acids and basesDetergentsIons of heavy metals like lead and mercury

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Fatal neurodegenerative diseases characterized by spongiform changes, astrocytic gliomas and neuronal loss resulting from deposition of insoluble protein aggregates in neural cells

Prion Diseases

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The characteristic senile plaques and neurofibrillary bundles contain aggregates of the protein beta-amyloid

Alzheimer's Disease

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A complex of Protoporphyrin IX and ferrous iron

Heme

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Heme protein found exclusively in red blood cells; Composed of heme + 4 globin chains

Hemoglobin

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True or False: Hemoglobin is the major transporter of carbon dioxide in blood?

FalseMajor (75%) bicarbonate (HCO3)Minor (25%) hemoglobin (carbaminoHb)

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Hemoglobin Types: Conception up to 1st few months from Yolk sac

Embryonal hemoglobin (Hb Gower 1)

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Hemoglobin Types: First few months to after birth from Liver

Fetal Hemoglobin (HbF)

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Hemoglobin Types: 8th month onwards from Marrow

Hemoglobin A (HbA)

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Hemoglobin Types: Shortly after birth onwards from marrow

Hemoglobin A2 (HbA2)

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Hemoglobin Configuration: Low oxygen affinity

T (taut) form

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Hemoglobin Configuration: High oxygen affinity (300x)

R (relaxed) form

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Heme protein found in heart and skeletal muscle

Myoglobin

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Following massive crush injury, myoglobin released from damaged muscle fibers colors the urine dark red

Myoglobinuria

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Hemoglobin curve

Sigmoidal curve

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Myoglobin curve

Hyperbolic curve

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Factors whose interaction with one site of the hemoglobin affects the binding of oxygen to heme groups at other locations

Allosteric Effectors

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P50=pO2 at which Hb is 50% saturatedIncreased affinity=increased pO2Decreased affinity=decreased pO2

NORMAL O2 Dissociation Curve

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Increased P50Decreased affinityIncreased CO2, Decreased pH

Shift to the RIGHT O2 Dissociation Curve

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Decreased P50Increased affinityDecreased CO2, Increased pH

Shift to the LEFT O2 Dissociation Curve

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The deoxy form of hemoglobin has a greater affinity for protons than does oxyhemoglobin

Bohr Effect

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Stabilizes the T structure of hemoglobin by forming additional salt bridges that must be broken prior to conversion to the R state

2,3 Biphosphoglycerate

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Oxidized form of Hb (Fe3+) that does not bind O2 as readily but increase affinity for CN-; Symptoms of Methemoglobin include cyanosis, anxiety, headache and dyspnea; "Chocolate" cyanosis

Methemoglobin

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Hb bound to carbon monoxide instead of O2; Hb becomes "cherry pink" in color; CO has 200x greater affinity for Hb than O2 and acts as a competitive inhibitor of O2

Carboxyhemoglobin

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When blood glucose enters the erythrocytes, it glycosylates the epsilon-amino group of lysine residues and the amino terminals of hemoglobin

Glycosylated Hemoglobin (HbA1c)

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Cutoff of HbA1c

>/= 6.5%

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Level of HbA1c that has been shown to reduce microvascular and neuropathic complications of type 1 and type 2 diabetes

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Disorder characterized by an inherited defect in RBC membrane that renders the erythrocytes spheroidal, less deformable, and vulnerable to splenic sequestration and destruction

Hereditary Spherocytosis

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Disorders caused by either by: Production of a structurally abnormal Hb molecule or Synthesis of insufficient amounts of normal Hb subunits (Rarely both)

Hemoglobinopathies

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Cause: Point mutation in both genes coding for the beta-chain that results in a valine rather than a glutamate

Sickle Cell Disease

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Hemoglobin variant that has a single amino acid substitution in the 6th position of the beta-globin chain in which lysine is substituted for glutamate

Hemoglobin C Disease

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Inadequate synthesis of alpha chains leads to anemia due to beta-chain accumulation and precipitation

Alpha Thalassemia

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Inadequate synthesis of beta chains; Leads to anemia, accumulation of Hb Barts and alpha chain precipitation

Beta Thalassemia

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Most abundant protein in the body: A long stiff extracellular structure in which 3 polypeptides (alpha-chains) each 1000 amino acid in length are wound around one another in a triple helix

Collagen

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Collagen is rich in

GlycineProline

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Most common type of Collagen

Type I

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Results from inheritable defects in the metabolism of fibrillar collagen; Type III is most frequently affected

Ehlers-Danlos Syndrome

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Brittle bone Syndrome; Mutation in collagen genes result to bones that easily bend and fracture; Most common form is autosomal dominant with abnormal collagen type I

Osteogenesis imperfecta

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Hydroxylation of collagen is a post-translational modification requiring Ascorbic Acid

Scurvy

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A number of genetic disorders affecting the structure of type IV collagen fibers, the major collagen found in the basement membranes of renal glomeruli

Alport's Syndrome

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Characterized by kinky hair and growth retardation; Reflects a dietary deficiency of the copper required by lysyl oxidase, which catalyzes a key step in formation of the covalent cross links that strengthen collagen fibers

Menke's Syndrome

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The skin breaks and blisters as a result of minor trauma; the dystrophic form is due toMutations affecting the structure of Type VII collagen, which forms delicate fibrils that anchor the basal lamina to collagen fibrils in the dermis

Epidermolysis Bullosa

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Connective tissue protein with rubber-like properties, responsible for extensibility and elastic recoil in tissues

Elastin

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Autosomal dominant connective tissue disorder; Mutation in the fibrillin gene

Marfan Syndrome

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Alpha1-antitrypsin inhibits proteolytic enzymes from hydrolyzing and destroying proteins

Alpha1 Antitrypsin Deficiency