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Bio-Chem 1 Test
| Question | Answer |
|---|---|
| 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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