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Bio-Chem 1 Test

What are the four bio molecules? Amino acids/proteins Carbohydrates Nucleotides/Nucleaic acids Lipids
The solvent in bio chemistry is what? Water
Switter ion has a positive and negative charge
True or false: Most amino acids are chiral compounds? True!
Alpha amino acids consist of a ____ and a ____ amine and a COO- group
aromatic amino acids absorb_____ by using a spectrograph or what ever its called.. UV light
Aromatic R groups? Tryptophan, Tyrosine, Phenyalanine
Positively Charged R groups Arginine, Lysine, Histidine
Negatively Charged R groups Aspartate, Glutamate,
Nonpolar alaphatic R groups Leucine, Iso-Leucine, alnine, glycine, Proline, Valine, Methionine (Dont like water, R groups form a hydrophobic interatction)
Polar, Uncharged R groups Serine, Threonine, Cysteine, Asparagine, Glutamine (Hydrogen Bonding)
Essential Amino Acids Valine, Leucine, Isoleucine, Methionine, Threonine, Phenylalanine, Tryptophan, Lysine
DNA------------>Proteins expression
DNA------>mRNA-------> Transcription, Translation
Uncommon amino acid selenocysteine
Metabolites Citrulline, Carnetine, Taurine, Creatine
L-Citrulline and Ornithine Intermediats of urea cycle
Carnitine Transfers FA across membranes into mitochondria so it can be used for energy production
Taurine: Bile acid (acts like soap and creaks up FA) Helps aid in digestion
Creatine: Intermediat storage of energy in muscles (skeletal)
PI PI= pka+pka2 Basic: pkR+pk2 -------- ------- 2 2 Acidic: pkR+pk1 --------- 2
Non covalent(weak interactions) in aqueous solutions: Hydrogen Bonding Ionic Bonding Hydrophobic Interaction (nonpolar function groups associate with each other, want to get away from H20) Vanderwalls forces
Proline: Only one where R group forms ring with alpha amino group
Gylcine Is chiral true or false? False
Methionine: Contains sulfure Theo ether
Cystenine: Second amino acid which contains sulfur. 2 cysteine--> disulfide bond
A280 is used to estimate the concentration of what? Protein concentration
Positively Charged R groups Nitrogen containing R groups, are basic in nature and can get positively charged when pronated Basic amino acids
Histidine: Very often found at the active site of enzymes. Enzymes are proteins that function as catalysts because pkR is close to 7
Negatively charged R group: Acidic Amino acid pkR is less then 7 ending with ate=acid
Olgopeptide: small polymer (with a few amino acids) Ex. oxytocin (hormone), 9 amino acids. Triggers contractions Bradykinin: 9 amino acids (inflamation)
polypeptide/Proteins Polypeptide: are less then or equal to 10,000g/mol Proteins: > 10,000 g/mol
Alanylglutamylglycyllysine 1 2 3 4 Produces 4 water molecules
HDL/LDL High density lipoprotein/ Low density lipoprotein
Proline: Restricts folding of backbone because a-N is part of backbone
Glycine: very small, vertually not steric hindered. allows for very narrow turns
Tryptophan: Very large, alot of steric hindrance, leads to some restrictions as to how the backbone can fold
Fibrous proteins: -Linear, long strands of polypeptides or proteins, forming "fibers" - Typically only one type of secondary structure - Functions: support shape and structure
Globular proteins: more or less spherical shape Much more complexity and variability with respect to secondary structure Functions: biocatalyst and regulation
Fibrous Proteins: -Keratin Structure- all alpha helix
Fibrous proteins: - silk fibroin all beta sheet
Fibrous proteins: -Collogen Struture: all alpha helix - triple helixes of poly peptides -Disulfide bond, H bonding
Ligand(Key) : Molecule (or ion) that can bind reversably to a protein creating quilibrium between protein & Ligand P+L ---->PL
Binding Site (Lock): -Where Ligands bind -Structure complimentry to structure of ligand -binding non covalent -a protein can have multiple binding sites and multiple ligands
Enzymes: E+S---->ES---->EP------> E+P = product (E= enzyme, S= Substrate)
Oxygen binding proteins: Oxygen bings at prosthetic group (Heme) (Porphyrine)ex. chlorophyll
Examples of globular proteins: Myoglobin/Hemoglobin
Myoglobin: -binds oxygen -contains a heme group(prosthetic)which is responsible for carrying oxygen molecules to muscles
Protein function: Oxygen wants the last electron in the outer shell of FE2 (attracted to the unpaired electron in FE2+) Free electron pars stabalize Fe2+
Ligand binding site: Theta= occupied binding sites/available binding sites
Allosteric effect: - Binding of a ligand leads to a... Confermation change of prtein structure and changes properties of other ligand binding sites within the protein
Allosteric effect: - In heoglobin Deoxyhemoglobin-->low affinity for oxygen; upon binding of one oxygen confirmation of hemoglobin changes-->increase in affinity for oxygen
Allosteric effect: Sigmoid bonding curves result from alosteric efects
BPG Bisphosphoglycerat -- -- ---
BPG (Bisphosphoglycerat): Allosteric activator of hemoglobin increase the sigmoid effect-->decrease the affinity for oxygen
Less Oxygen creates more? BPG
BPG effect on Hemoglobin: -Low O2 supplies for hours -[BPG] go up-->lower affinity for O2 -Change in [BPG] takes 24-48 hours (time it takesk to recover from altitude sickness)
High altitude for a long time: -More red blood cells -increase in Hemoglobin -increased # of binding sites
lifespan of a red blood cell: 120 days
Effect of pH on O2 binding of Hb: pH affects protenation of charged R groups--> changes in non covelant interactions pH decreases-->affinity for O2 decreases pH increases-->affinity for O2 increases
pH in blood: -Cellular respiration C6H12O6+6O2--->6CO2+6H2O (glucose) CO2+H2O-->H2CO3--> H+ + HCO3- <-- <-- (pH)
Stabalization of pH: -Buffers (phosphate, amino acid R groups) - about 30% of CO2 binds to Hb(and does not react with water) -about 10% will form carbonic acid
(In lungs) (In tissue) CO2 + H2O ---> H+ + HCO3- pH increases pH decreases pH effect= "BOHR effect"
Carbon Monoxide: -Oderless gas -Binds to Oxygen binding site, 240x more tightly bound then oxygen -prevents O2 from binding -Prevents switch to lower affinity state(hyperbola) -anemia ---> sigmoid binding curve
Hemoglobin: -Hb is transferred via the placenta from mother to child - About 30mmHg(4kpa) of hemoglobin in tissues and 80mmHg(13kpa) in lungs
Anemia: -iron defficiency -most common form -If iron is not present we cannot make hemoglobin, oxygen cant be transferred -Hb function is not altered-->alosteric affect of O2-->high and low affinity
Sickel Cell Anemia: -Under supply of oxygen -CO prevents switch to lower affinity state(hyperbola) -Sigmoid binding curve
Better to have anemia or CO poisoning? Anemia!
Fetal Hb: -Not bonding site for BPG -As soon as a baby is breathing-->gamma polypeptide NOT expressed and expression of beta polypeptide starts -alpha2gamma2: gamma polypeptide has slightly different AA sequence which leads to higher O2 affinity
Genetics sickle cell anemia: -Mutation in gene of Beta subunit (point mutation=1 base in DNA is changed) -Homozygous individuals(carry mutation on both chromosomes)at high risk
Genetics of sickle cell anemia: - Heterozygous/homozygous -Homozygous individuals(carry mutation on both chromosomes)at high risk -Heterozygous individuals(carry the sickle cell trait)
Heterozygous (carriers of sickle cell anemia) -Minimal Risk -Have protection from malaria
Malaria: Caused by a parasite called plasmodium which feeds on red blood cells
The configuration at the alpha-carbon of the vast majority of naturally occurring amino acids is_____? L-configuration
Threonine is an_______ amino acid Polar, uncharged R group
____ Has a pkR that is close to 7 and hence is commonly found at the active site of enzymes. Histidine
Hydrophobic interactions occur between ______ R-groups Nonpolar, aliphatic R groups
The only uncommon amino acid found in proteins that is modified pre-translation is_____? Selenocysteine
Carnitine (an uncommon amino acid) Transports fatty acids into the mitchondria
The pl of aspartate is______? (pK1=1.88, pK2=9.60, pKR= 3.65) Aspartate is a negatively charged R group. Negative=acidic PI calculations: -basic---> pkR+pk2/2 -acidic----> pkR=pk1/2 -neutral--> pk1+pk2/2
True or flase: Every peptide bond is an amide bond? TRUE!
What creats proteins? Ribosomes
Oligopeptide: -Small polymer (w/few amino acids) Ex. oxytocin(hormone)--> 9 AA's -Triggers contractions -Antiboitics->inhibit the growth of bacteria
Polypeptide: Less then or equal to 10,000 g/mol
Proteins: > then 10,000g/mol
Alanylglutamylglycyllysine ----- ------- ----- ----- Produces 4 water molecules
"Sub-Units" individual poly peptides encoded by seperate genes -become functional via further modification
Di-Sulfide bond: Covalent stabalizing factor to stabalize functional proteins (needs enzymatic action) --between polypeptides or within
Insulin was published in: 1953
The three dimensional structure of proteins: -Primary structure Amino acid sequence
The three dimensional structure of proteins: -Secondary structure Motives in confirmation found in many tertiery structures alpha-helix beta sheet
The three dimensional structure of proteins: - tertiary structure 3-D structure (confirmation) of a polypeptide and its prosthetic group
The three dimensional structure of proteins: -Quarterary structure 3-D arrangement of subunits, in a functional protein
Stabilizing forces: -Non covalent forces (form randomly) -Hydrogen bonding -Ionic Bonding -Hydrophobic Interactions -Vanderwalls forces
Protein backbone: Main stabilizing force is H-bonding Beta-confirmation= backbone
Tertiary and Quaternary structures: -Distant AA's can interact and cantribute to stabilization of 3D structure. - Noncovalent and covalent stabilizing forces
Proline: restricts folding of backbone because a-N is part of backbone
Glycine: Very small, virtually not sterically hindered; leads to some restrictions as to how the backbone can fold.
Tryptophan: Very large, very sterically hindered,leads to some restrictions as to how the backbone an fold
Collagen Biosynthesis: -A Ribosomes in the rough ER
Collagen Biosynthesis: -B 1st enzymatic modification -Hydroxylation -Vitaman C required
Collagen Biosynthesis: -C 2nd enzymatic modification -glycosylation (polydroxy compound)
Collagen Biosynthesis: -D 3rd enzymatic modification - Di-sulfide bonds between 3 modified polypeptides arargned in a triple helix
Collagen Biosynthesis: -E Pro-Collagen -In golgi vessicles
Collagen Biosynthesis: -F 4th enzymatic modification - in extra cellular matrix - removal of C and N terminous
Ligand Binding: The higher kd= the lower the affinity of the protein for the ligand. Lower kd= higher affinity of protein for ligand
kd: kd=[ligand] where 50% of binding site is occupied
Difficient in Vit C = ? Scurvy!! -Insuficient collagen
Symptoms of sickel cell anemia: Weakness, Muscle pain, Dizziness, Shortness of breath, Heart murmur, Death (often before age 15)
Death occuring from sickle cell anemia: -physical exertion -infection - Do to under supply of oxygen---> not enough ATP available in the cells - increased energy needs to heal the body
Created by: Jtanko23
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