Biochem second objective assessment review PDF

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review for the second OA to be able to narrow down the most important information they are looking for! helpful...

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Bohr Effect chart (low pH) - C- High CO2 H- High H+ A- Acidic R-Release of O2(rt. Shift) T- tense state (in tissues) Primary structure - Sequence of amino acids that make up a protein Secondary Structure - Sequence of amino acids fold. Tertiary Structure - -more folding in a 3D shape. -R groups (side chains) Quaternary Structure - Protein has more than 1 polypeptide chain. Chemical reaction -

-absorb and release energy -activation energy -energy is released (heat & light) when bonds are broken.

Exothermic reaction - Exo=to release Thermo=heat -chemical reaction that releases more energy than it absorbs (as heat & light) Example of exothermic reaction - Cellular respiration: breaks down glucose to make cellular energy Endothermic reaction - Endo=absorb Thermos=heat -absorbs more energy than it releases Example of endothermic reaction - Photosynthesis- takes in light to break down to create glucose Catalyst - Substance that will decrease the activation energy needed to start a chemical reaction Enzymes -

-catalysts used by cells -increase the rate of chemical reaction -specific to substrates

Enzyme structure -

-they are proteins -twist, fold, bend to final shape -shape attracts specific molecules

Substrate - Molecules that bind to the enzyme Active site - -location on enzyme where substrate binds

Function of DNA polymerase in process of PCR. - -increase expression -2 genes -SIRT1 & SIRT2 Function of a molecule - Structural component of the lipid bilayer How would lipid production in a cell change in order to maintain fluidity of its cell membrane as it adapts to lower temperatures? - Produce lipids with shorter fatty acid chains Function of cholesterol - Maintains membrane fluidity Lipid (fat) soluble vitamins - A, D, E, K What stimulates beta-oxidation of fatty acids? - An increase in NAD+ concentration in the mitochondrial matrix What occurs in an otherwise healthy person whose diet has very few carbs and high levels of fats? - Acetone is produced in the blood Amino acids - -Non-polar (hydrophobic) -Polar charged -Polar uncharged Which type of mammalian DNA damage repair requires the presence of the chromosome that is homologous to the damaged chromosome? - Recombination Xeroxerma Pigmentosum (XP) - A recessive genetic disease that occurs when one or more of the genes that perform nucleotide excision repair are nonfunctional Why do XP patients have a much higher incidence of skin cancer than the general population? The mutation of all other genes is higher due to failure to repair. Assuming 100% reaction efficiency, how many DNA copies are created after the completion of 4 complete PCR cycles? - 16 What is the function of DNA polymerase in the process of PCR? - It recognizes the primers and uses the available dNTPs to replicate the template DNA sequence. What difference in the regions of the SIRT1 & SIRT2 genes in people addicted to cocaine increases their expression? - The nucleosomes become more widely spaced. What occurs during the process of alternative splicing of RNA? - Alternate combinations of Exons within the same gene are linked together. Polypeptides - -functional proteins

-made of folded up polymers Elements - Substance that cannot be broken down into another substance by chemical reaction. Ionic bond - Actions share + & - charge Covalent bond - When atoms share electrons Hydrogen bond - Forms when portion of a polar molecule that is partially positive interacts with portion of a polar molecule that is partially negative Van der Waals interactions - Occur due to random, transient movements of electrons that at any given instant, give molecules regions of + & - charges. Amino acid - -has amino group (-NH2) -& a carbonyl group (-COOH) -cx. Based on side chains Elevated levels of AST & ALT - -indicates liver damage (When damaged, their protein contents can spill into blood stream) Which level of protein structure is disrupted through the hydrolysis of peptide bonds? - Primary Sickle cell disease - Caused by mutation in the Hgb-beta gene. (Causes cells to become rigid, sticky, misshapen.) Which force is most influential in determining the secondary structure of a protein? - Hydrogen bonding Hydrophobic effect - Tendency of non-polar substances to aggregate in an aqueous solution & exclude water molecules. Hydrophobic interaction - Mutation of gene for protein that leads to substitution of no polar amino acid with charged amino acid Dopamine - -neurotransmitter -variety of functions (including motor control) Parkinson's = decreases dopamine. Sinemet helps by increasing dopamine levels. Lactose breaks down into : - Glucose and galactose Frameshift mutation - -insertion or deletion of 1 or 2 nucleotides Missense mutation - -substitution of one amino acid for another -results in 10 different amino acids or 10 missense mutations

Nonsense mutation - -premature stop codon incorporated into the sequence -leads to a shorter protein Carbohydrates - -linear -CH2O formula -energy=glucose -structure=cellulose Lipids - -energy storage -signaling -high amount of C DNA - -twisted ladder -double helix -in nucleus -deoxyribose -bases= Anine, Thymine, Cytosine, Guarine -in all molecules -have nucleotides RNA - -plays "messenger" -in & outside nucleus -ribose -Adenine, Uracil, Guarine, Cytosine -mRNA=messenger (takes message to ribosome) -rRNA=ribosomal RNA -tRNA=transfers amino acids Transcription - -comes first! Transcribes DNA into message. (RNA polymerase will connect complementary bases. mRNA can go out of nucleus to attach to ribosome of rRNA) How do rising blood CO2 levels promote the deoxygenated confirmation of hemoglobin? - CO2 reacts with H2O in the blood & decreases pH, which promotes the dome confirmation of the heme group. How does hemoglobin keep blood pH neutral during exercise? - Deoxygenated hemoglobin binds to excess H+ What is occurring in surrounding tissues as the amount of hemoglobin saturated with oxygen increases? - The concentration of hydrogen ions decreases. Translation - -2nd step -builds protein (tRNA leaves behind its amino acid, built chain of amino acids)

Factors that favor the oxygenated form of hemoglobin: - -increased pH -decreased CO2 Which metal ion is bound to the porphyrin ring in hemoglobin? - Iron Which feature of hemoglobin makes it an effective O2 transport molecule? - It's affinity for O2 is regulated by pH. What is a temporary modification to protein structure by kinases that alters enzyme function? Phosphorylation Which type of inhibition occurs when a particular drug binds to the allosteric site of an enzyme and subsequently changes the enzyme's structure? - Noncompetitive Proteases - -a class of enzymes -hydrolyze protein strands into smaller units -increase pH= significant decrease in protease activity How do the rates of enzyme catalyzed reactions compare to those of corresponding uncatalyzed reactions? - They are 10^6 to 10^12 times faster. Which change will likely increase the activity of an enzyme currently at optimal conditions? Significantly increasing substrate concentrations What occurs immediately after the appropriate molecule enters the active site of the enzyme? The enzyme binds to the molecule to form an enzyme molecule complex. Are enzymes specific? - Yes What process is disrupted after a patient invests excessive antacid that neutralizes the pH of the stomach? - Protein catabolism In Alzheimer's patients, which biochemical event is responsible for their behavior? - Protein aggregation In which situation would altering a protein structure lead to a disease state? - A mutation aconitase blocks essential step in aerobic metabolism Which force is most influential in determining the tertiary structure of a protein? - Hydrophobic effect Quaternary structure - Large, functional protein structure composed or smaller proteins with multiple subunits. Primary - Level of protein structure established through the dehydration synthesis of peptide bonds

Describe the protein gradient of the proton that during aerobic metabolism. - There is a higher H+ concentration in the inter membrane space than in the matrix. Which complex polysaccharide acts as an energy storing molecule in the liver? - Glycogen How does insulin impact carbohydrate metabolism? - It stimulates the uptake of glucose from the blood by cells in the body. What occurs during the biochemical process of glucation? - A covalent bond forms between a sugar and a protein or liquid. Which metabolic pathway involves coenzyme A, NAD, & FAD? - Beta oxidation Which cellular condition prompts the cell to perform fermentation rather than the citric acid cycle? - Lack of O2 What causes the symptoms of NIDDM type 2? - There are not enough GluT4 transporters on plasma membranes. Which molecule is pyruvate directly converted to under aerobic conditions? - Acetyl CoA Which cellular organelle required for the citric acid cycle and electron transport chain is not present in RBCs? - Mitochondria Which molecule is replenished by fermentation? - NAD+ Which pathway is triggered by the intake of carbs during exercise? - Glycolysis How many ATP molecules are used in the conversion of pyruvate to glucose? - 6 Increased expression - Make proteins Decreased expression - Not making proteins Promoter - Start line Methylation - -methyl (CH3) -mRNA added to DNA or nuclosomes - causes decreased expression Base excision repair - -only 1 nucleotide damaged - remove and replace Nucleotide excision repair - -more than 1 nucleotide damaged -cut a sequence & replace that section

Mismatch repair - -happens in mistakes with DNA replication -DNA polymerase proofreads to see if make a right choice, but makes a mistake. -remove big section of damage and replace all of it Homologous recombination - -use 2nd copy of the DNA to copy back the correct info - double strand (cut DNA in 2), break Non-homologous end-joining - -happens before DNA replication -trim the ends-stuck back together PCR - -DNA replication in a test tube -Denature, Anneal, Elongation, Repeat Denature - -step 1 of PCR -increase heat to separate the DNA Anneal - -step 2 of PCR -use DNA primers that match the gene to find only the gene we want (ex: to find BRCA gene) Elongation - -step 3 of PCR -use DNA polymerase to make copies of our genes Which ingredients/molecules are required to set up a PCR? - -DNA polymerase (elongation) -DNA nucleotides (dNTPs) -primers (annealing) -template DNA (patient DNA) DNA polymerase always makes strands : - 5'-3' What breaks ionic bonds? - -pH changes -salt changes What breaks hydrogen bonds? - -pH and salt changes (Disulfide bonds broken by reducing agent) What breaks hydrophobic bonds? - Heat Types of bonds from strongest to weakest - -disulfide bond -ionic bond -hydrogen bond -hydrophobic bond Which bond is weakest, but have most influence on protein structure because of how many there are? - Hydrophobic bond

Quaternary Structure - -only some proteins will get here -2 or more subunits -proteins -Polypeptides (Example= myoglobin and hemoglobin) Hydrolysis - Broken peptide bonds Chaperones - Help fold proteins Denature - -have an environmental change that causes a protein to misfold or unfold. -breaking side change & secondary structure bonds -disulfide=reducing agent -ionic=pH or salt change -hydrophobic=heat change Degradation - Break peptide bonds (Hydrolysis) Aggregation - -proteins clump together in abnormal way (d/t hydrophobic interactions) Enzymes - -functional proteins -catalysts -reusable (can be recycled!) -specific -induced fit -work like assembly line (enzyme pathway) Feedback inhibition - -stop the enzyme "assembly line" because we have too much "product" -happens naturally to maintain homeostasis Competitive inhibition - -medicine/drugs -competitive inhibitor will bind to active site to prevent substrate from binding -(overcome inhibition by adding more substrate) Non-competitive inhibition - -more effective -bind to allosteric site of enzyme -changes the shape of the protein DNA - -phosphate + deoxyribose sugar + A/T/C/G -contains 2 strands -the strands are anti-parallel (opposite each other) : 5'-3' 3'-5' RNA - -phosphate + ribose sugar + A/U/C/G

-single strand (can fold back onto itself & form pairs between itself (stem-loop) Nucleotides - -contain one or more phosphates -a 5 carbon sugar and a nitrogen base -always in the 5' to 3' direction DNA organization - DNA is wrapped around proteins called histones -~nucleosomes-~chromatin fiber-~ chromosomes Pairing - DNA= A—T RNA= A—U Steps of DNA replication - -DNA is separated, creating a replication fork (by helicase) -primase attaches on RNA primer, where the replication starts -DNA polymerase adds bases to remaining of the strand until it reaches a stop codon. (This is done in fragments-"ozaki fragments" -DNA ligase seals the 2 strands forming a double helix Epigenetics - -involves packaging of DNA (packages are called nucleosomes. How tightly packed they are determines whether or not the gene is on or off) -loosely packed=transcription possible -tightly packed=transcription impeded Point mutations - When one of the DNA bases (nucleotides) are replaced with another, results in a different protein. Myoglobin - - 1 subunit - tertiary - used for O2 storage - in muscles -high affinity (how tightly it holds onto something) Hemoglobin - - 4 subunits -quaternary -for O2 transport -moving through blood from lungs to tissues -low affinity (because it gives O2 up) Heme - -special molecule inside the protein -iron (Fe) -where O2 binds -in myoglobin, carries 1 O2 -in hemoglobin carries 4 O2 CO - -carbon monoxide (1 O2) -poison!

-binds to hgb on the heme & blocks O2 from binding -has 200 x higher affinity -a competitive inhibitor -puts hgb into the R state (makes hgb want to bind hgb even more) -this is why it is so dangerous, our hgb picks it up instead of O2) 2, 3, BPG - -produced in our body naturally -similar function to H+ (stabilizes the T state) -produced in 2 cases (high altitudes & pregnancy) Hemoglobins role I'm CO poisoning - Hgb binds to CO with a higher affinity than O2 & stabilizes the R state What facilitates the transition of hgb from the R state to the T state? - An increase in the concentration of H+ Carbohydrate metabolism - 1. Glycolysis 2. Citric acid cycle (aerobic) 3. Electron transport chain (aerobic) 4. Firmentation (anaerobic) 5. Gluconeogenesis (anaerobic) What occurs during aerobic respiration? - NADH & FADH2 are produced from NAD & FAD during citric acid cycles. -NADH & FADH2 donate electrons to the ETC, re-engineering NAD & FAD. -O2 accepts electrons, producing water What directly provides the energy necessary for the conversion of ADP to ATP by ATP synthase? - Protons moving down a concentration gradient from the intermembrane space to the mitochondrial matrix. Cori Cycle - -muscle cells produce lactate which is then converted to glucose in the liver Exonuclease - During DNA replication, if an error is detected, DNA polymerase removes the nucleotides and replaces them with correct ones. Glyco/ gluco - Glucose Genesis - Make Lysis - Break Neo - New Insulin - -increase glucose in blood -fed state(after we eat, increase glucose=pancreas releases insulin)

-lets glucose into cells -signals for GluT4 to go to cell membrane Glycolysis - -break glucose -make ATP (useable energy) Glycogenesis - -store glucose as glycogen (short term storage) -in liver Fatty acid synthesis - - make fat from acetyl CoA -fats stored in triglycerides (3 fatty acids) -adipose tissue (long term storage) Glycogenolysis - Break glucose out of glycogen Gluconeogenesis - -make new glucose(from lactate) -acetyl CoA~pyruvate~glucose -glycerol (from triglycerides) -amino acids(last resort!) Beta oxidation - Break fats into acetyl CoA Fatty acid structures - -made up of carbonyl groups Saturated fatty acids - -no double bonds -maximum Hs Unsaturated fatty acid - -(not saturated with Hs) -at least 1 double bond -lose 2 Hs per double bond Essential - -we have to eat it (our bodies cannot make it) -omega 3 -omega 6 - essential for building other types of lipids Unsaturated fats - -natural (veg oils) -1 double bond Trans-unsaturated - -treat saturated with chemicals to switch hydrogen to other side -not natural! Build up in our body d/t doesn't recognize them. Fluidity - -more double bonds=always more fluid! -if same # double bonds, but shorter chain, will be MORE fluid! Poly unsaturated - -more than one double bond

Acetyl CoA - -2 carbons -attached to coenzyme A (to make sticky we need biotin) Beta oxidation - -breakdown of fats -occurs when we eat fats, or exercise -break beta bonds Oxidative damage to DNA can often result in the alteration of a single nucleotide. Which DNA repair mechanism would repair this type of damage? - Base excision repair What is the function of DNA polymerase in the process of PCR? - It recognizes the primers and uses the available dNTPs to replicate the template DNA sequence. Which structural level is impacted by denaturing a protein containing a single polypeptide? Tertiary Frying an egg changes the egg white from a clear liquid to an opaque solid. Which molecular change in the albumin protein causes this change in appearance? - Hydrophobic interactions form between denatured egg white proteins. Which features of a protein made of a single polypeptide chain is most directly responsible for its function? - Three dimensional structure Which reaction is responsible for the formation of polypeptides? - Dehydration How can alteration in protein structure lead to a disease state? - A mutation replaces an isoleucine with an aspartic acid in a transcription factor protein, which blocks the normal folding of the protein & its function in the expression of certain genes. Steps of DNA replication: -...