Proteins – Chemistry

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nucleoside
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contain purine/pyrimidine base covalently bonded to a sugar
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nucleotide
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monomer of nucleic acids, nucleoside to which 1-3 Phosphate groups are covalently bonded
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nucleic acids
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polymer of nucleotides covalently linked by phosphodiester bonds. 2 Types: deoxyribonucleic and ribonucleic acids
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deoxyribonucleic acid (DNA)
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double-stranded nucleic acid molecule composed of repeating nucleotides
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ribonucleic acid (RNA)
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single-stranded nucleic acid molecule found in every living cell
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gene
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single-stranded section of DNA, codes for proteins
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chromosomes
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linear double-stranded DNA molecules that carry all of an organisms genetic info. During cell division a new copy of chrom. is produced for new cell, thereby conserving genetic info.
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metabolism
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sum of all biochem. reactions that occur w/in cell. Includes building up and breaking down of 4 key bio. molecules
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nitrogenous base
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heterocyclic amines, consists of carbon and nitrogen
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purines
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contain 2 ring structures fused together
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pyrimidines
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contain 1 ring structure
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Chemical components of nucleotides
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a) pentose sugar
b) 1 to 3 phosphate groups (-PO4 ^3-)
c) nitrogenous base
d) double-stranded DNA, purine complementary paired to pyrimidine
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DNA components
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1) nitrogenous bases
a)adenine b)guanine c)thymine d)cytosine

2)pentose sugar
3)phophate groups [-PO4 ^3-]

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DNA structure
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1) double helix
2)nitrogen pairing always complementary, A-T and C-G, held together by weak hydrogen bonds. Called complementary base pairing.
3) 6×10^9 nucleotides in human DNA, called genome. Within genome are genes, code for proteins. Contains about 30,000 genes.
4)2 pairs of 23 chromosomes, 46 total. 23 from mom, 23 from dad.
5)mutation, change in DNA sequence. Can result in nucleotide substitutions, insertions, or deletions. Can have no effect, loss of protein function, or creation of new function.
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ribonucleic acid (RNA) components
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1)nitrogenous base
a)adenine b)guanine c) uracil (replaces thymine) d)cytosine

2)pentose sugar
3)phosphate groups

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RNA structure
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1)single stranded
2)complementary base pairing, A-U and G-C
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messenger RNA (mRNA)
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carries genetic info. for protein from DNA to ribosomes
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ribosomal RNA (rRNA)
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major structural and functional component of ribosomes. Are “platforms” on which protein synthesis occurs
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transfer RNA (tRNA)
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in protein synthesis, role is to deliver correct amino acid to ribosome for incorporation into new protein molecule
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Transcription DNA–>RNA
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a) gene (single strand of DNA) serves as a template for synthesis of RNA molecule. RNA produced will complement DNA coding.
b) occurs in cell nucleus and is catalyzed by enzyme RNA polymerase. Final RNA product is exported from nucleus to cell cytoplasm.
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Translation mRNA–>protein
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a) mRNA is used as template to synthesize protein
b) occurs in cell cytoplasm on ribosomes.
c)converts sequence of nucleotides in mRNA into sequence of amino acids synthesize new polypeptide. Every 3 mRNA nucleotides encode single amino acid, this sequence is called codon.
d) tRNA decodes info. in mRNA into amino acid sequence by recognizing codon thru complementary base pairing
e) each tRNA binds 1 specific amino acid, recognizes one codon thru complementary base pairing. Results in correct amino acid being delivered to ribosomal complex and being incorporated in correct order into new protein
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replication
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a) DNA is copied. Bases for biological inheritance in all living organisms as cells must replicate DNA before dividing
b) occurs in nucleus
c)DNA strands separated, permits enzyme DNA polymerase to produce 2 complementary base paired DNA strands.
d)each DNA molecule will include 1 of the original strands and 1 new complementary strand. Process is semiconservative in nature.
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protein
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polymer of amino acids covalently joined by peptide bonds. Chemical elements in all proteins: Carbon, hydrogen, oxygen, and nitrogen. 20 common amino acids, rep. by single letter or 3 letter abbrev., have variable radical-R group. Over 50,000 estimated human proteins.
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R group
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either hydrophobic/hydrophilic, can be acidic/basic. Chemical properties result in protein’s function.
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amino acids
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monomeric subunit of proteins, composed of central carbon atom bonded to amino group (-NH2), carboxyl group (-COOH), hydrogen atom, and variable radical group of atoms denoted by letter R.
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peptide bond
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covalent bond formed btwn carboxyl group of 1 amino acid and amino group of another. Polymers, of more than 2 amino acids are called polypeptides instead of proteins.
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zwitterion
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ion that has both pos. and neg. charge. At physiological pH, amino acids form these as amino group is protonated and carboxyl group is dissociated
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denaturation
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process which organized structure of protein is disrupted. Results in loss of function that is often permanent.
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acute phase reactants
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group of proteins whose plasma concentrations change following trauma, burns, infection, inflammations, and other related conditions.
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cryoglobulins
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abnormal globulins occassionally encountered in serum can precipitate when serum is cooled to low temp. but redissolved when serum is rewarmed to body temp. (37 deg. Cel)
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immunoglobulins
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group of plasma proteins that recognize and bind foreign antigens. aka antibodies.
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protein primary structure
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linear sequence of amino acids (i.e. polypeptide) held together by peptide bonds
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protein secondary structure
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folding of primary structure of protein, this folding is caused by noncovalent interactions, principally hydrogen bonds. Alpha helix and beta pleated sheet.
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protein tertiary structure
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overall 3-dimensional folding of polypeptide resulting from additional folding beyond the secondary structure, caused by noncovalent interactions
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protein quanternary structure
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overall 3-dimensional folding of 2 or more polypeptides together
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globular proteins
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have relatively short primary structures (i.e. amino acid sequences), they constitute most of the proteins in body and circulating in your serum. Have compact, spherical, 3-dim. structure, and are generally soluble in salt solutions.
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examples of globular proteins
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albumin, antibodies, nearly all enzymes, hormones, and hemoglobin.
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fibrous proteins
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usually relatively long and are arranged in fibers/sheets that contain extensive amounts of one form of secondary structure. Insoluble in salt solutions, represent principal structural proteins of body.
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examples of fibrous proteins
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collagen, elastin, keratin, actin, and myosin
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Protein functions
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1) main component of immune system (antibodies)
2) catalyze biochem. reactions (enzymes)
3) transport molecules thruout body (hemoglobin)
4) regulatory roles (insulin hormone)
5) structure (keratin, collagen)
6) necessary for all forms of movement (actin, myosin)
7) nutrients (albumin and casein)
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hemoglobin (Hb)
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oxygen-carrying protein found in red blood cells (erythrocytes), tetrameric protein containing 4 heme groups. Composed of 2 pairs of identical polypeptides. Lifespan is 120 days (RBC).
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functions of hemoglobin
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gas transport and acid/base balance
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gas transport
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involves transport of critical gas molecules. Hb reversibly transports O2 from lungs to tiss. of body. Hb can bind up to 4 O2 molecules. Oxygenated Hb/oxyhemglobin will travel to tiss. of body where needed, will release O2 molecules. Hb facilitates extraction of CO2 from tiss. back to lungs where it can be expelled. 5-10% of CO2 is associated with Hb.
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acid/base balance
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assists in maintaining balance of blood. Hb is import. intracellular buffer. Hb readily accepts H+, forming deoxyhemoglobin (HHb), which is hemoglobin not bounded to O2 but capable of forming bond when O2 is available. Balance is maintained by binding/releasing H+ resulting from accumulation of acids as result of normal human metabolic processes.
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components of hemoglobin
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4 subunits, each contain 1 heme and 1 globin
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heme
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protoporphyrin IX ring, pyrrole rings are cyclic compounds that serve as building blocks for porphyrins, formed by linkage of 4 tetra pyrrole rings w/ 8 hydrogen ions. Single Fe ion will bond to center of ring to create heme group.
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Fe^+2 (ferrous) ion
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allows O2 to reversibly bind and be transported thruout tissues of body. Ferric iron (Fe^+3) will complex to protoporphyrin ring but cannot bind O2, must be reduced. Blood contains majority of total iron present in body.
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globin
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protein portion of molecule, composed of 2 pairs of polypeptide chains, contains 2 alpha and 2 beta globin polypeptides
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sites for heme synthesis
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bone marrow, Hb production begins in rubricyte and continuous thru reticulocyte stage of RBC development. Stored iron is released from cell and delivered to maturing cell. Protoporphyrin IX ring combines with iron in mitochondria.
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heme synthesis
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consists of an 8 step biochem. pathway which requires 8 diff. enzymes; 4 are located in mitochondria and 4 in cytosol.
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Aminolevelunic acid (ALA) synthase
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enzyme that catalyzes in initial step in porphyrin synthesis. Rate limiting step in heme synthesis. Final product in pathway, heme, inhibits this enzyme and is example of feedback inhibition.
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Lead inhibition
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inhibits all steps in porphyrin synthesis by denaturation of enzymes involved
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myoglobin
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heme monomeric protein found in muscle tiss., contains one polypeptide and one protoporphyrin ring. Serves as reserve supply of O2. Greater affinity for O2 than Hb and requires lower O2 pressure to realse O2.
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Factors affecting oxygen transport
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based on affinity for Hb to reversibly bind oxygen. Hemoglobin’s affinity is dependent on partial pressure of oxygen (pO2), pH, temperature, and concentrations of 2,3-diphosphoglycerate (2,3 DPG)
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partial pressure of oxygen
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P50 value is conventional index at which hemoglobin is 50% saturated with O2. Occurs at PO2 of 27mmHg. Decreased P50 is a shift to left, with increased affinity of hemoglobin, and impaired oxygen release to tiss. Increase of P50 is a shift to right, resulting in decreased oxygen affinity and increased release of oxygen, eases delivery of oxygen to tiss.
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P pH (Bohr Effect)
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a) Increased blood acidity will decreaese pH causing a shift to right and lowering of Hb affinity for O2.
b) Decreased blood acidity will increase pH causing shift to left, increase of Hb affinity for O2.
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Christian Bohr
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1904, discovered increase in blood CO2 levels would result in lowering pH of blood and require more O2 to be delivered to cells
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temperature
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a) as body temp. increases, Hb more readily releases O2, causes shift to right of curve.
b) as body temp. decreases, Hb less readily releases O2, causes shift to left of curve.
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2,3-Diphosphoglycerate (2,3-DPG)
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RBC’s contain a lot. Most important factor in oxygen transport, phosphate which is present in human RBC at about same molar ratio as Hb. Binds to deoxyhemoglobin but not oxygenated form, diminished oxygen affinity of Hb, shifts dissociation curve to right. Essential in enabling Hb to unload O2 into tiss. that need it most. When pH drops, oxygen diss. curve moves to right, but resulting inhibition of binding to Hb corrects shift by an equal change to left.
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Types of Human Hemoglobin
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Hb A, Hb A2, Hb A1c, Hb F.
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hemoglobin A
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comprised of 2 alpha and 2 beta chains. Most common form of adult Hb. A2 is 2 alpha and 2 delta chains.
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hemoglobin A1c
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non enzymatic modification Hb A that has been glycosylated. Often assayed via chromatography/electrophoresis. Concentrations serve as indicator for prolonged high glu. concentrations, increase can be seen in insulin-depen. diabetics. When previous 120 days glu. values was also elevated.
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hemoglobin F
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major Hb of fetal life. Newborns (<1 month) reps. 70-90% of total Hb but then signif. declines and is replaced by adult Hb, after age 3 decreases less than 0.4% (adult range).
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billirubin
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degradation product of heme portion of Hb. Protoporphyrin is converted into biliverdin then into bilirubin. It is the breakdown product of normal heme catabolism, yellow pigment that is released into blood stream where it binds with albumin. It is picked up by cells of liver and secreted with bile into intestines, further metabolized into urobilinogen, which is excreted in feces.
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factors that denature proteins
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1) heat
2) organic solvents like alcohol
3) detergents
4) salting out
5) pH changes
6) heavy metals (mercury and lead)
7) mechanical stress
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heat
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as temp. increases molecular motion increases. Weak hydrogen bonds will be disrupted by increased temps.
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organic solvent (i.e. alcohol)
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polar solvents disrupt hydrogen bonds in proteins as well as form new hydrogen bonds
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detergents (soap)
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have both a hydrophobic region and polar region. Can disrupt existing hydrogen bonds, also disrupting hydrophobic interactions import. to protein structure
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salting out
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high concentrations of salts can dehydrate protein making it less soluble. Salts are used to change solubility of proteins and can be used to precipitate them.
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simple proteins
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yield only amino acids upon hydrolysis
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examples of simple proteins
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albumin, insulin, and fibrinogen
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conjugated proteins
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upon hydrolysis yield amino acids and nonprotein substance.
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glycoproteins
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contain covalently link carb. residues that make up small % by weight of molecule.
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phosphoproteins
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have covalently linked phosphate groups
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lipoproteins
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contain covalently linked lipid molecules, like cholesterol, triglyceride, and phospholipids.
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metalloproteins
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contain ions and are often colored, like hemoglobin in RBC and chlorophyll in plants
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essential amino acids
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must be provided in adult diet since human body cannot synthesize them.
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8 amino acids that are essential
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isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
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nonessential amino acids
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human body is able to synthesize, there are 12.
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liver
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most import. site for protein production. Enzymes regulate concentration of essential amino acids.
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liver’s use of amino acids
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1)growth, maintenance, and repair
2)enzyme production
3)albumin
4)lipoproteins
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growth, maintenance, and repair
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liver makes many secreted proteins used for within the body
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enzyme production
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liver produces variety of enzymes that catalyze wide range of biochem. reactions.
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albumin
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liver is the only source, the most abundant serum protein.
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lipoproteins
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transport hydrophonic lipids such as HDL and LDL in blood.
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basic process of protein catabolism
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1) begins with digestion of food
2) stomach, intestines, and pancreas all secrete proteolytic enzymes which eventually breakdown protein into free amino acids
3a) removal of amino group -NH2, converted by a series of biochem reactions into urea since NH3 is very very toxic, known as urea cycle.
3b) urea is waste product of degradation of amino acids into CO2 and NH3. Synthesized in liver and transported in blood to kidneys where it is turned into urine.
4) Breakdown of carbon backbone, converted into:
pyruvate, acetyl CoA, Krebs cycle intermediates (keto acids), free amino acids, and ultimately into fat or glu.
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methods of protein analysis
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1) protein electrophoresis
2) biuret method
3) turbidimetry and nephelometry
4) albumin:globulin (A:G) ratio
5) kjeldahl procedure
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protein electrophoresis
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separates proteins based upon their electrical charge. 5 distinct protein zones.
a) Albumin (normally largest fraction)
b) alpha 1-globulins
c) alpha 2-globulins
d) beta globulins
e) gamma globulins
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biuret method
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most widely used procedure, measures total protein.
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turbidimetry and nephelometry
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used to measure light scatter by Beer’s Law. Can be used in automated systems. Precipitation of proteins is typically done by adding sulfosalicylic/tricholoracetic acid
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turbidimetry
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measures decreased in amount of light as it passes thru particulate solution, used to measure small particles that reduce amount of light that passes thru sample and scatter light. Measured with simple spectrophotometer.
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nephelometry
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used to measure amount of light as it scattered as it passes thru particulate solution, used to measure large parts. that deflect light forward. Intensity of light scatter is directly proportional to concentration of parts.
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albumin:globulin (A:G) ratio
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Division of albumin by globulin levels. Provides sensitive indicator for disease detection, ranges from 1.5-2.5 in healthy individuals. Calc. by subtracting albumin levels from total protein level gives indirect estimate of globulin levels. Increases in gamma globulins directly proportional to presence and severity of disease. Albumins inversely proportional. Low ratios can be seen in liver disease, burns, malnutrition, diarrhea, myeloma, and lymphomas.
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kjeldahl procedure
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measures total nitrogen, majority of nitrogen in body comes from protein catabolism. Used as reference against other methods for protein analysis.
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functions of albumin
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1) primary contributor to COP, responsible fo 80% of COP.
2) source of free amino acids when catabolized
3) major transport protein of large organic anions in blood
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clinical signif. of albumin
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hypoalbuminemia, low levels of albumin in blood
hyperalbuminemia, elevated levels
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clinical signif. of hypoalbuminemia
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liver disease, acute phase response, nephrotic syndrome, and other protein loss syndromes
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clinical signif. of hyperalbuminemia
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dehydration and artificial increase may result after prolonged tourniquet application during venipuncture.
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prealbumin physiology
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a) tryptophan rich tetrameric glycoprotein
b) mainly synthesized in liver
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prealbumin function
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serves as carrier protein for thyroid hormones (T3, T4) and vitamin A. Can also be used to asses nutritional status.
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clinical signif. of prealbumin
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decreased in number of liver diseases due to impaired synthesis. Increased in ppl who are receiving steroids. Can also be synthesized by cells of choroid plexus.
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antibody
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group of plasma proteins (immunoglobulins) that are produced by B lymphocytes due to exposure to an antigen. Reacts to a specific antigen.
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antigen
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substance that stimulates antibody formation and has ability to bind to an antibody.
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phenylketonuria (PKU)
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metabolic disorder in which there is genetic deficiency of enzyme phenylalanine hydroxylase
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maple syrup urine disease (MSUD)
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autosomal recessive metabolic disorder in which there is genetic deficiency in enzyme that degrades branched chain amino acids. Results in accumulation of valine, leucine, and isoleucine in blood and associated keto acid metbolites in urine. Condition is characterized by poor feeding, vomiting, lack of energy, seizures, and mental issues.
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clinical signif. of maple syrup urine disease
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leads to severe brain damage and may result in death. Variant forms appear later in childhood, typically less severe. Restrict food containing branched chain AA’s leucine, isoleucine, and valine in food like milk, meat, and eggs. Diet must be adhered to strictly and permanently.
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hypoproteinemia
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decrease in total serum protein levels in blood, especially albumin
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clinical signif. of hypoproteinemia
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1) starvation/nutritional deficiency of essential amino acids
2) excessive loss in urine due to renal disease/poor absorption of AA’s.
3) chronic liver disease
4) inflammatory conditions
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hyperproteinemia
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increase in total serum protein levels in blood
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clinical signif. of hyperproteinemia
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1) dehydration
2) increased synthesis of gamma globulins as would occur in acute phase response
3) measurement of unexpected protein such as fibrinogen
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porphyrias
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group of diseases associated with hereditary and acquired deficiencies in heme biosynthetic pathway. Sufficient enzyme activity even in dysfunctional enzymes that will support heme biosynthesis. Accumulation of porphyrins that are toxic to tiss. in high concentrations. Symptoms and treatment are not all same, some are cutaneous in nature and will manifest on skin. Exposure to light can result in swelling, itchy skin, and fluid accumulation. aka photoporphyrias
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porphyrinuria
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excessive excretion of 1 or more porphyrins in urine
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porphyrinemia
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presence of porphyrin in plasma or serum
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porphyrin disorder (hereditary)
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genetic disorders arising from impaired activity of enzymes in synthesis of heme
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porphyrin disorder (aquired)
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More common form, from lead poisoning, chronic renal failure, iron deficiency, and liver disease.
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thalassemias
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groups of inherited anemic diseases, most common genetic disorders in world. Derived from globin genetic mutations that result in little to none globin protein being produced. If alpha and beta chains are absent or in low levels then it affects Hb’s ability to bind and transport oxygen. Conditions include enlarged spleen or requiring blood transfusions.
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sickle cell anemia
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Hb S represents sickled RBC and is most common abnormal type of hemoglobin. Results from single mutation in beta globin gene that causes Hb structure to sickle under hypoxic conditions. If not managed, can be life threatening.
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caraminohemoglobin (CO2Hb)
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compound of carbon dioxide and Hb, approx 70-85% of CO2 is processed as bicarbonate and expired from lungs. Approx. 10-20% of CO2 binds to each globin chain of Hb molecule.
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methemoglobin (M-Hb)
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compound of Hb where 1 or more iron molecule is oxidized from ferrous state to ferric state. Oxidized iron can’t bind oxygen. Levels are maintained at less than 1% by diff. enzyme systems found within RBC
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sulfhemoglobin (S-Hb)
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green pigmented compound formed by addition of hydrogen sulfide molecule to Hb. Irreversible oxidation and conversion persists thruout life of erythrocyte. Appears after exposure to certain drugs or chemicals, or occupational exposure to sulfur.
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carboxyhemoglobin (COHb)
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compound formed by binding of carbon monoxide to heme iron. Hb has 200 times greater affinity for carbon monoxide than oxygen. Carbon monox. creates stronger bond with Hb, because of this carbon monox. is released at exponentially slower rate than oxygen. Individuals poisoned by carbon monox. exhibit “cherry red” color.
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Cryoglobulin pathophysiology
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abnormal globulins occasionally encountered in serum which can precipitate when serum is cooled to low temp. but re-dissolved when serum is rewarmed to body temp. (37 deg. C) Result of polymerization of immunoglobulins. Cryoglobulin complexes deposit on vessel walls causing inflammation. Vasculitis can lead to renal damage/neurological diseases
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clinical signif. cryoglobulin pathophysiology
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frequently seen in myeloma, macroglobulinemia, and some autoimmune diseases.
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Structure of immunoglobins (Ig)
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1)2 diff. polypeptide chains held together by disulfide bonds:
2 light chains, and 2 heavy chains

2)light chain; one variable domain and one constant domain

3)heavy chains; one variable domain, responsible for formation of specific antigen binding sites; and three constant domains, region of Ab that varies little within Ig class

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functions of immunoglobins
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1) neutralize toxic substances
2)facilitate phagocytosis
3) kill pathogens, often by activation of complement system
4) combine with antigen on cellular surface and cause destruction of these cells either extra/intravascularly
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5 classes of immunoglobins
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IgG, IgM, IgA, IgD, and IgE

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