MCAT Biochemistry

Isoelectric points (pI) for basic amino acid

(pKa, NH group + pKa R group) / 2 9 + 10.5 / 2 = 9.75 remember that basic amino acids has two NH2 groups that can become protonate and these are what you will use to calculate the PI which is usually the last two pKas used. amino acids with basic side chains have pI values well above 6

Isoelectric points (pI) for acidic amino acid

(pKa, R group + pKa, COOH group) / 2 Glutamic acid = 4.25 + 2.19/2 = 3.22 remember the acidic amino acids will loos their protons from the COOH grooups first so use their pKa to calculate Pi (usually first two) amino acids with acidic side chain have pI values below 6

Impact on activation energy: Exergonic reaction

- spontaneous -Delta G is negative (Gibbs free energy) but the enzymes do not alter this - Enzymes do not change the equilibrium as well - enzyme do alter the activation rate (kinetics) and can affect how quickly the reaction reaches equilibrium but not the equilibrium itself. Catalyses exert their effect by lowering the activation energy of a reaction

At pH 7 the charge on a glutamic acid molecule is -2 -1 0 +1

-1 Glutamic acid is acidic because of the extra carboxyl group. At neutral pH both carboxyl groups are deprotonated and thus negatively charged.

What are the steps of fatty acid synthesis?

-Activation -Bond formation -reduction -dehydration -second reduction

Uncompetitive Inhibition

-Bind only to the ES complex and essentially lock the substrate in the enzyme preventing its release. - bind at allosteric site -lower Km and Vmax -parrallel lines on both types of plots MM & LB

Covalently Modified Enzymes

-Can be activated by phosphorylation or dephospho rylation -cannot predict which one without experiment -Glycosylation- attachment of sugar moieties, and can tag an enzyme for transport within the cell or can modify portion activity and selectivity.

Temperature effects on enzyme activity

-Enzyme-Catalyzed reactions tend to double in velocity for every 10 Degrees C increase until the optimum temp is reached. After this activity falls sharply. - Some enzymes can regain function if cooled.

Which complexes are associated with each of the following? -Pumping a proton into the inter membrane space -Acquiring electrons from NADH -Acquiring electron from FADH2 -Having the highest reduction potential

-Pumping a proton into the inter membrane space: Complex I, III & IV -Acquiring electrons from NADH: Complex I -Acquiring electron from FADH2: Complex II -Having the highest reduction potential: Complex IV (reduction potentials increase along the ETC)

Mixed inhibition

-Results when the inhibitor can bind to either the enzyme or the Enzyme-Substrate complex -if it had affinity for both it would be noncompetitive inhibitor -mixed do not bind at the active site, but at an allosteric site -alters the value of Km depending not he preference of the inhibitor for the enzyme vs. ES complex - if it binds to the enzyme it increases the Km value (lowers affinity) -if it binds to the ES complex it lower the Km value (increase affinity) -either way Vmax is decreased

Zymogens

-Tripsinogen, which makes sure we don't digest our pancreas by and uncontrollable release of trypsin - (ogen)

Key features of the Watson-Crick Model

-Two strands of DNA are antiparallel: that is the strands are oriented in opposite directions. When one strand has polarity 5' to 3' down the page, the other strand has 5' to 3' up the page -The sugar - phosphate backbone is on the outside of the helix with the nitrogenous bases on the inside. -there are specific base-pairing rules, often referred to as complementary base-pairing. An adenine (A) is always base-paired with a thymine (T) via two hydrogen bonds. A guanine (G) always pairs with cytosine (C) via three hydrogen bonds -Total purines will be equal to total pyrimidines overall. This is known as Chargaff's Rules remember that hydrogen bonds make the G-C base pair interaction stronger.

Irreversible Inhibition

-acitive site is made unavailable for a long period of time or the enzyme is permanently alters. Example: Aspirin irreversibly modifies Cyclooxygenase-1 - primary drug mechanism

Noncompetitive Inhibition

-binds to the allosteric site instead of the active site which induces a change in enzyme conformation -it is noncompetitive because the two molecules do not compete for the same site, it also cannot be overcome by adding substrate because it doesn't affect it . -bind equally well to enzyme and ES complex -Decreases the measured Vmax, because there is less enzyme available to read: does not alter the Km

Damage to the cell can arise from and cause what?

-breaking of the DNA backbone -structural or spontaneous alteration of bases -incorporation of the incorrect base during replication Damage can cause increased risk for cancer

Salinity effects on enzyme activity

-increasing levels of salt can disrupt hydrogen and ionic bonds, causing a partial change in the conformation of the enzyme and in some cases causing denaturation

Competitive inhibition

-involve occupancy of the active site, substrate cannot access binding site if there is something in the way -can be overcome by adding more substrate so that the substrate-to-inhibitor ration is higher. -does not alter the value of Vmax because if enough substrate is added it would out compete the inhibitor and be able to run the reaction at maximum velocity -does increase the amount of Km

Allosteric Enzymes

-multiple binding sites -alternate between an active and inactive form (cannot carry out a reaction) - molecules that bind to these enzyme may be either allosteric activators or allosteric inhibitors -causes a conformation shift in protein -Activator will result in a shift that makes the active site more available for binding to the substrate -inhibitor will make it less available -both may also alter the activity of the enzyme -will have the S sigmoidal (S-shaped Curve) in a graph

When antibodies bind to their targets called antigens there can be three outcomes

-neutralizing the antigen, making the pathogen or toxin unable to ever its effect on the body -Marking the pathogen for destruction by other white blood cells immediately which is called Opsonization - Clumping together known as agglutinating the antigen and antibody into large insoluble protein complexes that can be phagocytized and digest by macrophages.

Stereochemistry of an amino acid

-the alpha carbon of amino acids are chiral as it has four different things attached -an exception does exist which is glycine (H-) as its R-group making it achiral -All chiral amino acids in eukaryotes are L-Amino groups, which means the amino group is drawn on the left in a Fischer Projection -All amino acids will have (S) configuration for almost all chiral amino acids, except cysteine which is still a L-amino acid it is just in (R) absolute configuration because the -CH2SH has priority over the -COOH group.

Use the date in below to calculate the Km for the enzyme [S] (mM) (V mmol/sec) .01----------------1 .05----------------9.1 .1------------------17 .5------------------50 1-------------------67 5-------------------91 10-----------------95 50-----------------99 100--------------100 Km= ? .5 1 10 50

.5 Recognize relationships more than using equations. You can see that as the substrate increases significantly, the rate has a small change. Vmax is near 100 , Vmax /2 = 50mmol/min = .5 mM

Steps in Replication

1.) Origin of replication --in prokaryotic cells it has one per chromosome --in eukaryotic cell it has multiple per chromosomes 2.) Unwinding of DNA double helix --both prokaryotic and eukaryotic cells use Helicase 3.) Stabilization of unwound template strands --both prokaryotic and eukaryotic cells use Single-stranded DNA binding proteins 4.)Synthesis of RNA primers --both use primes 5.)Synthesis of DNA --Prokaryotic cells use DNA polymerase III --Eukaryotic cells use DNA polymerase Alpha 6.) Removal of RNA primers --Prokaryotic cells - DNA polymerase I (5' - 3' exonuclease) -- Eukaryotic cells - RNase H (5' to 3' exonuclease) -Replacements of RNA with DNA --Prokaryotic cells - DNA polymerase I --Eukaryotic cells - DNA polymerase delta -Joining of Okazaki fragments --Both use DNA ligase -Removal of positive supercoils ahead of advancing replication forks -- DNA Topoisomerase, DNA Gyrase in prokaryotic cells -Synthesis of telomeres (ends of chromosomes, high GC) -- Not applicable in prokaryotes --Telomerase is used in Eukaryotes

Steps of Base Excision Repair

1.) the affected base is recognized and removed by a glycosylase enzyme, leavng being an apurinic/apyrimidinic (AP) site, also known as abasic site 2.) the AP site is recognized by an AP endonuclease that removes the damaged sequence form the DNA. 3.) DNA ligase and polymerase can then fill in the gap and seal the strand .

Consider a reaction catalyzed by enzyme A with a Km value of 5x10^-6M and Vmax of 20 mol/min At a concentration of 5x10^-6 m substrate the rate of the reaction will be 10 15 20 30 ----mmol/min

10 mmol/min Look at relationships : at 5x10^-6 enzyme A is working at 1/2 of it Vmax because the concentration is equal to the km of the enzyme therefor 1/2 of 20 is 10 Km= 1/2 Vmax

If a sample of DNA has 10% G what is the % of T?

10% G= 10% C thus %G+%C = 20% %A + %T = 80% Thus %T = 40%

Consider a reaction catalyzed by enzyme A with a Km value of 5x10^-6M and Vmax of 20 mol/min At a concentration of 5x10^-4 m substrate the rate of the reaction will be 10 15 20 30 ----mmol/min

20 AT 5X10^-4 there is 100 times more substrate than present at half maximal velocity. At high values (significantly higher than the Km) the enzyme is at or near it Vmax which is 20 mol/min

3-Phosphoglycerate Kinase

3-Phosphoglycerate Kinase transfers the high energy phosphate from 1,3-bisphosphoglcerate to ADP, formic ATP and 3-phosphoglycerate. This type of reaction in which ADP is directly phosphorylated to ATP using a high energy intermediate, this is referred to as substrate-level phosphorylation. In contrast to oxidative phosporyaltion in mitochondria, substrate level phosphorylations are not dependent on oxygen, and are the only means of ATP generation in an aerobic tissue.

3-phosphoglycerate kinase and pyruvate kinase each do what?

3-phosphoglycerate kinase and pyruvate kinase each perform substrate-level phosphorylation, placing an inorganic phosphate (Pi) onto ADP to form ATP.

At what pH can protein A best be obtained through Electrophoresis? A - pI= 4.5 B - pI= 6.0 C - pI= 9.5 2.5 3.5 4.5 5.5

5.5 in electrophoresis we attempt to separate out one component fro the others. Because we are attempting to only isolate A a pH that causes A to be negative while B and C are neutral or positive will be best. 5.5 does this. 4.5 would make A neutral thus it would not migrate across the gel

How many distinct tripeptides can be formed from one valine molecule, one alanine molecule and one leucine molecule. 1 3 6 27

6 3 x 2 x 1 = 6 VAl, VlA, ALV, AVL, LVA, and LAV

What are the stop codons?

61 codons code for one of the 20 amino acids the other three code for termination of translation which are the three stop codons. UGA, UAA and UAG

How many codons code for one of the 20 amino? Hoe many encode for termination of translation?

61 of the codons code for one of the 20 amino acids 3 codons encode the termination of translation

What three binding site is in the ribosome?

A - site P - site E - site APE

Which of the following DNA sequences would have the highest melting temperature? CGCAACCATCCG CGCAATAATACA CGTAATAATACA CATAACAAATCA

A .CGCAACCATCCG The melting temperature of DNA is the temperature at which a DNA double helix separates into two single strands (denatures) To do this the hydrogen bonds linking the base pairs must be broken. Cytosine binds to guanine with three hydrogen bonds, whereas adenine binds to thymine with two hydrogen bonds. The amount of heat needed to disrupt the bonding is proportional to the number of bonds. Thus the higher GC- content in a DNA segment the higher the melting point. HIGHER GC- content in a DNA segment the higher the melting point!!

What are the roles of each site in the ribosome?

A site: binds incoming aminoacyl-tRNA using codon-anticodon pairing P site: holds growing polypeptide until peptide transferase forms peptide bond and polypeptide is handed to A site E site: postranslational modifications include proper folding by chaperones, formation of quaternary structure, cleavage of proteins or signal sequences, and addition of other biomolecules

Mnemonic is isoelectric focusing

A+ Anode has acidic (H+ rich gel) and a (+) charge

LOOK AT 5 on page 321

A. The new ATP yield from glycolysis is 2 ATP per glucose.

A man collapses while running a marathon and is taken to the emergency room. His blood is found to be somewhat acidic. and further test show increased lactate dehydrogenese activity. This enzyme is involved in which of the following pathways? Anaerobic glycolysis B-Oxidation of fatty acids Citric acid cycle Pentose phosphate pathway

A. Anaerobic glycolysis Under normal conditions when oxygen is readily available the pyruvate generated in glycolysis enters the mitochondrion and is converted into acetyl-CoA by the action of pyruvate dehydrogenase. During strenuous exercise, particularly by individuals in poor physical condition, the oxygen demands of the skeletal muscle may exceed the ability of the heart and lungs to proved oxygen. In this setting, the muscles switch to anaerobic glycolysis, and the pyruvate that is produced is fermented to lactate by the action of lactic dehydrogenase.

Toposiomerases are enzymes involved in: DNA replicaiton and transcription Postranscriptional processing. RNA synthesis and translation Postranslational processing

A. DNA Replication and transcription Topoisomerases, such as prokaryotic DNA gyrase, are involved in DNA replication and mRNA synthesis (transcription). DNA gyrase is a type of topoisomerase that enhances the action of helicase enzymes by the introduction of negative supercoils into the DNA molecule. These negative supercoils facilitate DNA replication by keeping the strands separated and untangled

Missing nucleotide denoted by X on ATX & ATX What effect will this mutation have on the amino acid sequence of the protein encoded by the CFTR gene? Deletion of a phenylalanine residue with no changed in the C-terminus sequence. Deletion of a leucine residue with no change in the C-termius sequence. Deletion of a phenylalanine residue with a changed in the C-terminus sequence Deletion of a leucine residue with a changed in the C-terminus sequence.

A. Deletion of a phenylalanine residue with no changed in the C-terminus sequence.

Which of the following is true of diffusion and osmosis? Diffusion and osmosis rely on the electrochemical gradient of only the compound of interest Diffusion and osmosis rely on the electrochemical gradient of all compound in a cell Diffusion and osmosis will proceed in the same direction if there is only one solute Diffusion and osmosis cannot occur simultaneously

A. Diffusion and osmosis rely on the electrochemical gradient of only the compound of interest The movement of any solute or water by diffusion or osmosis is dependent only on the concentration gradient of that molecule and on membrane permeability .

Which of the following is LEAST likely to result from protein degradation and processing by the liver? Fatty acids Glucose Acetoacetate 3-Hydroybutyrate

A. Fatty acids is the least to result form protein degradation and processing by the liver. The degradation of protein and processing by the liver implies a prolonged starvation state: protein will not be used for energy unless absolutely necessary. Thus gluconeogenesis is the mot likely process. When gluconeogenesis is not possible, easily metabolized molecules, such as ketone bodies are synthesized. Fatty acids production occurs when energy is being stored: proteins would not be broken own to store energy in fatty acids.

Each of the following catalyzes a rate-limiting step of a carbohydrate metabolism pathway EXCEPT: Hexokinase Glycogen synthase Glucose-6-phosphate dehydrogenase Fructose-1,6-bisphosphatase

A. Hexokinase Hexokinase catalyses an important irreversible step of glycolysis, but it is not the rate limiting step. Phosphofructokinase--1 (PFK1) catalyzes the rate-limiting step of glycolysis.

Which of the following statements regarding polymerase chain reaction is FALSE? Human DNA polymerase is used because it is most accurate A primer must be prepared with a complementary sequence to part of the DNA of interest Repeated heating and cooling cycles allow the enzymes to act specifically and replaces helicase Each cycle of the polymerase chain reaction double the amount of DNA of interest

A. Human DNA polymerase is used because it is most accurate The polymerase chain reaction is used to clone a sequence of DNA using a DNA sample, a primer, free nucleotides, and enzyme. The polymerase from Thermus Aquaticus is used because the reaction is regulated by thermal cycling, which would denature human enzymes.

Statin drugs inhibit HMG-CoA reductase. As such they are likely prescribed for: Hypercholesterolemia (high cholesterol) Hypertriglyceridemia (high triacylglycerol) Hypocholesterolemia (low cholesterol) Visceral Adiposity (obesity)

A. Hypercholesterolemia (high cholesterol) Statins are drugs that are prescribed to treat high cholesterols and act as competitive inhibitors of HMG-CoA reductase. HMG-CoA reductase is the rate limiting enzyme of de novo cholesterol synthesis; inhibition of this enzyme lowers production of cholesterol, thus lowering overall levels of cholesterol.

The unique enzymes of gluconeogenesis are used to circumvent specific irreversible steps of glycolysis. Which of the following correctly paris an enzyme from glycolysis with its corresponding enzymes used in gluconeogenesis? Phosphofructokinase-1/fructose-1.6-bisphosphatase Pyruvate dehydrogenase / pyruvate carboxylase abd phosphoenolpyruvate carboxykinase Hexokinase/glucokinase Pyruvate kinase/ glucose-6-phosphatase

A. Phosphofructokinase-1/fructose-1.6-bisphosphatase

The dynamic properties of molecules in the cell membrane are most rapid in: Phospholipids moving within the plane of the membrane Phospholipids moving between the layers of the membrane Proteins moving within the place of the membrane Proteins exiting the cell through exocytosis

A. Phospholipids moving within the plane of the membrane Movement of individual molecules in the cell membrane will be affected by size and polarity, just as with diffusion. Lipids are much smaller than proteins in the plasma membrane and will move more quickly. Lipids will move fastest within the plane of the cell membrane because th polar head group does not need to pass through the hydrophobic tail regions in the same way that it would it it were moving between the membrane layers.

Enhancers are transcriptional regulatory sequences that function by enhancing the activity of: RNA polymerase at a single promoter site RNA polymerase at multiple promoter sites Spliceosomes and a lariate formation of the ribosome Transcription factors that bind to the promoter but not to RNA polymerase

A. RNA polymerase at a single promoter site Specific transcription factors bind to a specific DN sequence, such as an enhancer, and to RNA polymerase at a single promoter sequence. They enable the RNA polymerase to transcribe the specific gene for that enhancer more efficiently.

Which of the following statements conflicts with the fluid mosaic model? The cell membrane is static in structure Membrane components can be derived from multiple biomolecuels Hydrophobic interactions stabilize the lipid bilayer Proteins are asymmetrically distributed within the cell membrane.

A. The cell membrane is static in structure The fluid mosaic model accounts for a dynamic membrane. In this model, membrane components contain both fatty and carbohydrate-derived components, eliminating B. Further, the membrane is stabilized by the hydrophobic interactions of both fatty acid tails and membrane proteins, which may be found on the cytosolic or extracellular side of the membrane, or may run directly through the membrane. C&D are eliminated

What is the function of LCAT? LCAT catalyzes the production of cholesteryl esters LCAT catalyzes the production of cholesterol LCAT catalyzes the transfer of cholesteryl esters LCAT catalyzes the transfer of cholesterol

A. The function of LCAT is that it catalyzes the production of cholesteryl esters LCAT adds a fatty acid to cholesterol producing cholesteryl esters, which dissolve in the core of HDL, allowing HDL to transport cholesterol from the periphery to the liver.

What is the fate of long-chain fatty acids that are contained within micelles? Transport into chylomicrons released into the lymphatic system Transport into chylomicrons released into the circulatory system Direct diffusion across the intestine into the lymphatic system Direct diffusion across the intestine into the circulatory system

A. Transport into chylomicrons released into the lymphatic systems the fate of long chain fatty acids that are contained within micelles. Short-Chain fatty acids are soluble in the intestinal lumen, and thus do not interact with micelles as longer fatty acids chains do. The long chain fatty acids are taken up by the intestinal cells and packaged into triacylglycerols for transport as chylomicrons. Chylomicrons exit the intestine through lacteals that feed into the lymphatic system, which joins with the bloodstream in the base of the neck through the thoracic duct.

Tumor suppressor genes are most likely to result in cancer through: loss of function mutations gain of function mutations overexpression proto-oncogene formation

A. loss of function mutations Oncogenes are most likely to result in cancer through activation while tumor suppressor genes are most likely to result in cancer through inactivation

A eukaryotic cell has been found to exhibit a truncation mutation that creates an inactive RNA polymerase I enzyme. Which type of RNA will be affected by this inactivation? rRNA tRNA snRNA hnRNA

A. rRNA RNA polymerase I in eukaryotes is found in the nucleolus and is in charge of transcribing most of the rRNA for use during ribosomal creation. RNA polymerase II is responsible for hnRNA and snRNA. RNA polymerase III is responsible for rRNA and the 5s rRNA

Which amino acid is encoded by ATT

ATT; mRNA = AAU; Asparagine (Asn)

Which mRNA codon is the start codon, and what amino acid does it code for?

AUG the start codon and the amino acid it codes for is methionine.

How does acetyl-CoA shift the metabolism of pyruvate?

Acetyl- CoA inhibits pyruvate dehydrogenase complex while activating pyruvate carboxylase. The net effect is to shift burning pyruvate in the citric acid cycle to creating new glucose molecule for the rest of the body. The acetyl-CoA for this regulation comes predominantly from B-oxidation not glycolysis.

How does acetyl-CoA affect PDH complex activity? Why?

Acetyl-CoA inhibits the PDH complex. As a product of the enzyme complex, a buildup of acetyl-CoA from either the citric acid cycle or fatty acid oxidation signals that the cell is energetically satisfied and that the production of acetyl-CoA should be slowed or stopped. Pyruvate can then be used to form other products, such as oxaloacetate for use in glycogenesis.

Amino acids in acid or basic pH

Acidic - positive or protonated Basic- negative or deprotonated

Isoelectric focusing exploits what?

Acidic and basic properties of amino acid by separating them based on their pI (isoelectric points) to do this the proteins are places in a gel with a pH gradient (acidic gel at positive anode, basic gel at the negative cathode and neutral in the middle) The electric field is generated across the gel. As the proteins go to the specified charged cathode or anode, when the proteins reach the portion of the gel where the pH is equal to the pI the protein stops moving. so a protien stops when the pH = pI

Enzymes do what?

Act as catalysts -do not affect the thermodynamics of a reaction -Lower the activation energy -Increase the rate of the reaction - Are not changed or consumed in the reaction -will appear in reactants and products - Are -pH and temperature sensitive, with optimal activity at specific pH ranges and temperature -do not affect the overall delta G of the reaction - Are specific for a particular reaction or class of reactions

Activation domain allows what?

Activation domain allows for the binding of several transcription factors and other important regulatory protein., such as RNA polymerase and histone acetylases which function in the remodeling of the chromatin structure.

What can active transport be?

Active transport may be primary or secondary depending on the energy source. Secondary active transport can be further classified as symport and or antiport.

Active transport

Active transport requires energy in the form of ATP or an existing favorable ion gradient.

Activity Analysis

Activity is correlated with with concentration but is also affected by the purification methods used an the conditions of the assay. Reactions with color change have particular applicability because microarrays can rapidly identify the sample from a chromatographic analyst that contains the compound of interest.

Why are proteins analyzed after isolation?

After the first step being isolation the protein identify is confirmed by amino acid analysis or activity. The classification of their feature is generally desired.

Alanine

Ala A

What is the stereochemistry of amino acids?

All Chiral eukaryotic amino acids are L-Aminos, Glycine is not chiral. All chiral eukaryotic amino acids have (S)- configuration with the exception being Cysteine having R instead of S but still keeping L, this is due to the Thiol (SH) group having higher priority over the COOH- group.

Which of the following is a reason for conjugating proteins? I. to direct their delivery to a particular organelle II. to direct their delivery to the cell membrane III. to add a cofactor needed for their activity

All of them

Restriction endonucleases are used for which of the following? I. Gene therapy II. Southern blotting III. DNA repair

All three; Gene therapy, Southern Blotting and DNA repair utilize Restriction Endonucleases Endonucleases are enzymes that cut DNA. They are used by the cell for DNA repair. They are also used by scientists during DNA analysis, as restriction enzymes are endonucleases. Restriction enzymes are used to cleave DNA before electrophoresis and southern blotting, and to introduce a gene of interest into a viral vector for gene therapy

Regulated Enzymes

Allosteric Enzymes Covalently Modified Enzymes Zymogens

Alpha and Beta Anomerics

Alpha is less wanted because of the -OH in the axial form which adds steric hindrance Beta is wanted more due to the -OH in the equatorial position adding stability

Optical Isomers

Also known as stereoisomers which are compounds that have the same chemical formula: these molecules differ from one another only in terms of the spatial arrangement of their component atoms

Base Excision Repair

Alterations to bases can occur with other cellular insults. Example being thermal energy being absorbed by DNA and may lead to cytosine deamination. Cytosine deamination is the loss of an amino group from cytosine ad results in the conversion of cytosine to uracil. Uracil should not be found in DNA molecules and is thus easily detected as an error. This is repaired by base excision repair

What is alternative splicing?

Alternative splicing is the ability of some genes to use various combinations of eons to create multiple proteins from one hnRNA transcript. This increase protein diversity and allows a species to maximize the number of proteins it can create from a limited number of gees.

Chapter 1

Amino Acids, Peptides and Proteins

Transfereases examples

Aminotransferase can convert aspartate and alpha-ketoglutarate as a pair to glutamate and oxaloacetate These should be straight forwardly named don't forget Kinases is in this class as well for they transfer a Phosphate gout generally from ATP to a mother molecule

Which of the two forms of starch is more soluble in solution?

Amylopectin is more soluble in solution that amylose because of its branched structure. The highly branched structure of amylopectin decreases intermolecular bonding between polysaccharide polymers and increase interaction with the surround solution

Starches like amylose and amylopectin are broken down by enzyme in the body and are used as what?

Amylose is degraded by a-amylase and B-amylase. B-Amylase cleaves amylose at the nonreducing end of the polymer to yield maltose while a-amylase cleaves randomly along the chain to yield shorter polysaccharide chains, maltose and glucose

What is galactose?

An important source of galactose in the diet is the disaccharide "lactose" which is present in milk. Lactose is hydrolyzed to galactose and glucose by lactase, which is a brush-border enzyme of the duodenum.

Which of the following statement about enzyme kinetics is FALSE? An increase in the substrate concentration leads to proportional increases in the rate of the reaction Most enzymes operating in the human body work best at a temperature of 37 C An enzyme-substrate complex can either form a product or dissociate back into the enzyme and substrate Maximal activity of many human enzymes occurs around pH of 7.4

An increase in the substrate concentration leads to proportional increases in the rate of the reaction Most enzymes do opperate at maximal activity around a temp of 37 C and a pH of 7.4

What is the on-off switch that regulates gene expression levels?

An operon, which is a cluster of genes transcribed as a single mRNA; this particular cluster in E.coli is known as the trp operon

Where is Reannealing used?

Annealing of complimentary DNA strands is an important process in Polymerase Chain Reactions (PCR) and in the detection of specific DNA sequences using probe DNA

Immunoglobulins (antibodies)

Antibodies also known as immunoglobulin Ig are proteins produced by B-cells that function to neutralize targets in the body such as toxins and bacteria Y-shaped- made up of two identical heavy chains and two identical light chains -disulfide linkages and non-covalent interactions hold the heavy and light chains together Each antibody has an antigen-binding region at the tips of the Y, here there are specific polypeptide seqences that will bind one and only one specific antigenic sequence. The other part of the antibody is known as the constant region which is involved in recruitment and binding of other cells of the immune system such as macrophages.

Which of the following characteristics is NOT attributed to antibodies Antibodies bind to more than one distinct antigen Antibodies label antigens for targeting by other immune cells Antibodies can cause agglutination by interaction with antigen Antibodies have two heavy chains and two light chains

Antibodies bind to more than one distinct antigen is false.. Antibodies are specific to a single antigen They do label antigens for targeting They do cause agglutination in interaction They deff have two heavy chains and two light chains

Some enzymes require the presence of a nonprotein molecule to behave catalytically. An enzyme devoid of this molecule is called Holoenzyme Apoenzyme Coenzyme Zymoenzyme

Apoenzyme An enzyme devoid of its necessary cofactor is called an apoenzyme and is catalytically inactive

Apoproteins control what?

Apoproteins control interactions between lipoproteins

Arginine

Arg R -has three nitrogen atoms in side chain

Basic amino acids

Arginine Lysine Histidine have pI above 6 also have a side chain with differing amounts of nitrogen positive due to the Nitrogen groups in each of the 3

Think of Cooperativity as a party

As more people start arriving the atmosphere becomes more [R]elaxed and the party seems more appealing but as people start leaving the [T]ense host has to start cleaning up.

What is the relationship between osmotic pressure and the direction of osmosis through a semipermeable membrame?

As osmotic pressure increases, more water will tend to flow into the compartment to decrease solute concentration. Osmotic pressure is often considered a "sucking" pressure because water will move toward the compartment with the highest osmotic pressure.

Michaelis Menten plot of enzyme kinetics

As the amount of substrate increases the enzyme is able to increase its rate of reaction until it reaches a max enzymatic reaction rate (Vmax) and once reached adding more substrate will no increase the rate of reaction.

Chiral carbon number significance on the number of stereoisomers

As the number of chiral carbon increases, so too does the number of possible stereoisomers because on compound may have many diastereomers number of possible streamers of a compound can be calculated by 2^n where n is the number of chiral carbons in the molecule

Asparagine

Asn N -possess -OCNH2, this does not gain or lose protons and do not become charged

Aspartic acid (aspartate)

Asp D - has -COO- in side chain

Acidic Amino Acids

Aspartic acid (aspartate) Glutamic acid (glutamate) have pI below 6 have -COO- as their side chains negative due to the -COO-

Negatively Charged (Acidic) Side Chains

Aspartic acid- related to asparagine but have (-COO-) in side chain Glutamic acid- related to glutamine but have (-COO-) in side chain

Titration of Glycine - low to high pH

At low pH glycine exist as +NH3CH2COOH with it being fully protonated .5 equvalent point = pKa1 At neutral pH or added 1.0 equivalent of base the glycine exists as +NH3CH2COO- which is a zwitterion when the zwitterion exists the pH equals the isoelectric point (pI) of glycine 1.5 equvalent point = pKa2, here the zwitterion concentration equal the concentration of the fully deprotonated form At high pH or 2.0 equivalents of base the glycine is fully deprotonated NH2CH2COO-

5' CAP

At the end of the hnRNA molecules a 7-mtheylguanylate triphosphate cap is added. The cap is actually added during the process of transcription and is recognized by the ribosome as the binding site. It also protects the mRNA from degradation in the cytoplasm

A man is given antibiotics to treat a urinary tract infection and develops an episode of red blood cell lysis. Further studies show weakness of the plasma membrane and Heinz bodies. Which of the following enzymes is most likely defective in this patient? Fructose-1,6-bisphoshatase Glucose-6-phosphate dehydrogenase Hexokinase Pyruvate kinase

B Glucose-6-phosphate dehydrogenase Based on the question stem we can infer that the antibiotics must have been an oxidative stress on the patient.

Which of the following enzymes cleaves polysaccharide change and yields maltose exclusively? a-amylase B-amylase Debranching enzyme Glycogen phosphorylase

B-Amylase B-amylase cleaves amylose at the nonreducing end of the polymer to yield maltose exclusively a-amylase cleaves amylose anywhere along the chain to yield short polysaccharides, maltose and glucose. Debranching enzyme removes oligosaccharides from a branch in glycogen or starch Glycogen phosphorylase yields glucose 1-phosphate

B-Oxidation uses what?

B-oxidation uses cycles of oxidation, hydration, oxidation, and cleavage

Which fatty acid can be synthesized by humans? 12:0 16:0 16:1 18:3

B. 16:0 Humans can only synthesize one fatty acid, palmitic acid. Palmitic acid is fully saturated and therefore does not contain any double bonds. Palmitic acids has 16 carbons, and is synthesized from eight molecules of acetyl-CoA. In shorthand notation, palmitic acid is written as 16:0 (16 carbons: no double bonds)

A double stranded RNA genome isolated from a virus was found to contain 15 % uracil. What percentage of gaunine should exist in this viruses genome. 15% 35% 70% 85%

B. 35% Uracil must equal Adenine 15% or uracil means 15 % of Adenine =30% which leaves 70% 70/2= 35 % guanine and cytosine

A gene encodes a protein with 150 amino acids. There is one intron of 1000 base pairs (bp), a 5'-untranslated region of 100 bp, and a 3'-untranslated region of 200 bp. In the final mRNA, about how many bases lie between the start AUG codon and final termination codon? 150 450 650 1750

B. 450 The intron will not be a part of the final, processed mRNA, and the untranslated regions of the mRNA will not be trend into amino acids. Translation will begin with codon 1 (which would be AUG). Because there are 150 amino acids, we can surmise that there will be `150 codons. Each codon will use 3 nucleotides, so 150 x3 = 450 because codon 151 will be the stop codon.

You have just sequenced a piece of DNA that reads as follows: 5'--TCTTTGAGACATCC--3' What would the base sequence of the mRNA transcribed from this DNA be? 5'--AGAAACUCUGUAGG--3' 5'--GGAUGUCUCAAAGA--3' 5'--AGAAACTCTGTAGG--3' 5'--GGATCTCTCAAAGA--3'

B. 5'--GGAUGUCUCAAAGA--3' Remember that mRNA will be antiparallel to DNA. Our answer should be 5'--3' mRNA, with the 5' end complementary to the 3' end of the DNA that is being transcribed. Thus the mRNA transcribed from this strand will be 5'--GGAUGUCUCAAAGA--3' 5'--TCTTTGAGACATCC--3' ---sample being

Peptidyl transferase connects the carboxylate group of one amino acid to the amino group of an incoming amino acid.. What type of linkage is created in this peptide bond? Ester Amide Anhydride Ether

B. Amide Peptidyl transferase connects the incoming amino terminal to the previous carboxyl terminal; the only functional group listed here with a carbonyl and amino group is the amide. Peptide bonds are thus amide linkages

Which of the following is/are functions of NADPH in the cell? I. Antimicrobial resistance via bacterial destruction by bleach within lysosomes II. Involvement in the production of the precursors to steroid hormones III. Functional carriage of energy across organelle membranes for use within the mitochondria

B. Antimicrobial resistance via bacterial destruction by bleach within lysosomes & Involvement in the production of the precursors to steroid hormones NADPH has three primary functions: involvement in biosynthesis pf lipids and cholesterol, production of bactericidal bleach in the lysosomes of certain white blood cells, and maintenance of a supply of reduced glutathione for protection against free radical damage. Energy carriage is an important function of NADH not NADP

Where does B-oxidation of fatty acids occur within the cell? Cytosol Mitochondria Smooth Endoplasmic reticulum Plasma membrane

B. B-oxidation of fatty acids occurs within the Mitochondria B-Oxidation occurs within the mitochondria, along with the electron transport chain. In contrast, fatty acid synthesis occurs in the cytosol. Fatty acyl carriers like the carnitine shuttle allow entry into the mitochondrion for breakdown.

Which of the following is true about cholesterol? Cholesterol always increases membrane fluidity in cells Cholesterol is a steroid hormone precursor Cholesterol is a precursor for vitamin A, which is produce in the skin Cholesterol interacts only with the hydrophobic tails of phospholipids

B. Cholesterol is a steroid hormone precursor Cholesterol is a steroid hormone precursor that has variable effects on membrane fluidity depending on temperature, eliminating A. It interacts with both the hydrophobic tails and the hydrophilic heads of membrane lipids nulling D. Cholesterol is a precursor of Vitamin D not Vitamin A. Which can be produced in the asking in a UV - driven reaction

How do chylomicrons and VLDL differ? Chlyomicrons contain apoproteins, VLDL do not Chylomicrons are synthesized in the intestine, VLDL are synthesized in the liver. Chylomicrons transport triacylglycerol, VLDL transport cholesterol VLDL are another term for chylomicron remnants; they differ in age

B. Chylomicrons are synthesized in the intestine, VLDL are synthesized in the liver. Chylomicrons and VLDL are very similar. Both contain apolpoproteins and primarily transport triacylglycerols eliminating A & C. The only major difference between them is the tissue of origin. Chylomicrons transport dietary triacylglycerols and originate in the small intestine, while VLDL transport newly synthesized triacylglycerols and originate in the liver.

Which of the following is an ethical concern of gene sequencing? Gene sequencing is invasive, thus the potential health risks must be thoroughly explained Gene sequencing impacts relatives, thus privacy concerns may be raised Gene sequencing is very inaccurate, which increases anxiety related to findings Gene sequencing can provide false-negative results, giving a false sense of security

B. Gene sequencing impacts relatives, thus privacy concerns may be raised One of the primary ethical concerns rated to gene sequencing is the issue of consent and privacy. Because genetic screening provides information on direct relatives, there are potential violation of privacy in communicating this information to family members who may be at risk There are not significant physical risks and gene sequencing is fairly accurate

After an overnight fast, which of the following enzymes would be expected to have little if any physiological activity? Malate dehydrogenase Glucokinase a-ketoglutarate dehydrogenase Phosphofructokinase-1

B. Glucokinase After an overnight fast the liver is producing glucose and glucokinase activity would be significant. Glucokinase is used to trap extra glucose in liver cells as part of a storage mechanism: with low blood glucose, liver cells would be generating new glucose, not storing it. Malate dehydrogenase & a-ketoglutarate dehydrogenase are enzymes in the citric acid cycle.

Which of the following is true about glycerophospholipids? Glycerophospholipids can sometimes be sphingolipids, depending on the bonds in their head groups Glycerophospholipids are merely a subset of phospholipids Glycerophospholipids are used in the ABO blood typing system Glycerophospholids have one glycerol, one polar head group and one fatty acid tail

B. Glycerophospholipids are merely a subset of phospholipids Glycerophospholipids are a subset of phospholipids, as are sphingomyelins. Glycerophospholipids are never sphingolipids because they contain a glycerol backbone (rather than sphingosine or a sphingoid backbone) Eliminating A. Sphingolipids are used in the ABO blood typing system not glycerophospholipids eliminating C. glycerophospholipids have a polar head group, glycerol, and two fatty acid tails not one

After an overnight fast which of the following processes would be expected to occur at an elevated rate with the well-fed state? Glycolysis Glycogenolysis Glycogenesis Glycerol synthesis

B. Glycogenolysis After a fast, the liver must contribute glucose into the blood-stream through two main process; Glycogenolysis (early fasting intermediate) and gluconeogenesis (late fasting intermediate) The other processes would continue at normal basal levels or have decreased activity after a fast

Which of the following enzyme is NOT used for lipid digestion in the digestion tract? Pancreatic lipase Hormone-sensitive lipase Cholesterol esterace Colipace

B. Hormone-sensitive lipase is NOT used for lipid digestion in the digestion tract. Hormone-sensitive lipase responds to low insulin levels as well as cortisol and epinephrine to mobilize fatty acids form adipocytes. It is not involved in digestion, but rather mobilization of fatty acids.

Soap bubbles form because fatty acid salts organize into: Lysosomes Micelles Phospholipid bilayers Hydrogen bonds

B. Micelles Fatty acid salt micelles are responsible for the formation of soap bubbles. Fatty acids in soap are free fatty acids, not phospholipids

In a single strand of a nucleic acid, nucleotides are linked by: Hydrogen bonds Phosphodiester bonds Ionic bonds Van der Waals forces

B. Phosphodiester bonds Nucleotides bond together to form polynucleotides. The 3' hydroxyl group of one nucleotide's sugar joins the 5' hydroxyl group of the adjacent nucleotide's sugar by a phosphodiester bond Hydrogen bonding is important for holding complementary strands together, but does not play a role in the bonds formed between adjacent nucleotides on a single strand

The bulk movement of liquid into a cell through vesicular infolding is knowns as: Phagocytosis Pinocytosis Exocytosis Drinking

B. Pinocytosis The enodcytosis (bulk uptake through vesicle formation) of fluid is known as pinocytosis. Phagocytosis is the endocytotic intake of solids, while exocytosis is a method of releasing vesicular contents Drinking does not apply on a cellular level.

Which of the following is NOT a function of the cell membrane? Cytoskeletal attachment Protein synthesis Transport regulation Second messenger

B. Protein synthesis Ribosomes are the site of protein synthesis within a cell and are not coupled to the cell membrane. The cell membrane functions as a site for cytoskeletal attachment. A is accomplished through channels, transportersm and selective permeability, While the phospholipids act as a reagent for second messenger formation.

How does the inner mitochondrial membrane differ from the outer mitochondrial membrane? The inner mitochondrial membrane is more permeable and lacks cholesterol The inner mitochondrial membrane is less permeable and lacks cholesterol The inner mitochondrial membrane is more permeable and has cholesterol The inner mitochondrial membrane is less permeable and has cholesterol

B. The inner mitochondrial membrane is less permeable and lacks cholesterol The outer mitochondrial membrane is very permeable while the inner membrane is highly impermeable. The inner mitochondrial membrane is unique within the cell because it lacks cholesterol

Which of the following best describes the structure of steroids? Three clyclopentane rings, one cyclohexane ring Three cyclohexane rings, one cyclopentane ring Four carbon rings, differing in structure for each steroid Three cyclic carbon rings and a functional group

B. Three cyclohexane rings, one cylcopentane ring Although the oxidation status of these rings varies for different steroids, the overall structure does not, hence C.

Which lipid type is LEAST likely to contribute to membrane fluidity? Unstaturated glycerphospholipids Trans glycerophospholipids Cholesterol Unsaturated sphingolipids

B. Trans glycerophospholipids Compounds that contribute to membrane fluidity will lower the melting point or disrupt the crystal structure. Cholesterol and unsaturated lipids A & D are known to haver these functions. Trans glycerophospholipids tend to increase the melting point of the membrane and therefore decrease membrane fluidity.

During Saponification: Triaclyglycerols undergo a condensation reaction Triaclyglycerols undergo ester hydrolysis Fatty acid salts are produced using a strong acid Fatty acid salts are bound to albumin

B. Triacylglycerols undergo ester hydrolysis Saponification is the ester hydrolysis of tracylglycerols using a strong base like sodium or potassium hydroxide to form glycerol and fatty acid salts This is not a condensation reaction but it is a cleavage reaction Fatty acids do travel in the body bonded to serum albumin but is unrelated to saponification

Which of the statements regarding waxes is FALSE? Waxes generally have melting points above room temperature Waxes are produced only in plants and insects therefore must be consumed by humans Waxes protect against dehydration and parasites Waxes are esters of long-chain fatty acids and long-chain alcohols

B. Waxes are produced only in plants and insects therefore must be consumed by humans Waxes are also produced in animals for similar protective function. Cerumen or earwax is an example in humans

Double-stranded RNA cannot be translated by the ribosome and is marked for degradation in the cell. Which of the following strands of RNA would prevent mature mRNA in the cytoplasm from being transcribed. identical mRNA to the one produced antisense mRNA to the one produces mRNA with thymine substituted for uracil Sense mRNA to the one produced

B. antisense mRNA to the one produces the mRNA produced has the same structure as the sense strand of DNA (with uracils instead of thymine). Because bonding of nucleic acids is always complementary but antiparallel, the antisense strand of mRNA would be the one that binds to the produced mRNA, creating double-stranded RNA that is then degraded once found in the cytoplasm.

How is cDNA best characterized? cDNA results from a DNA transcript with noncoding regions removed. cDNA results from the reverse transcription of processesd mRNA cDNA is the abbreviation for deoxycytosine cDNA is the circular DNA molecule that from the bacterial gene

B. cDNA results from the reverse transcription of processesd mRNA cDNA which is complementary DNA is formed form a processed mRNA strand by reverse transcription. cDNA is used in DNA libraries and contains only the exons of genes that are transcriptionally active in the sample tissue

When trypsin convert chymotrypsinogen to chymotrypsin, some molecules of chymotrypsin bind to a repressor, which is turn binds to an operator region and prevents further transcription of trypsin. This is most similar to which of the following operons? trp operon during lack of tryptophan trp operon during abundance of tryptophan lac operons during lack of lactose lac operon during abundance of lactose

B. trp operon during abundance of tryptophan The example given is a sample of repression due to the abundance of a corepressor. In other words, this is a repressible system that is currently blocking transcription. For the trp operon, an abundance of tryptophan in the environment allows for the repressor to bind tryptophan and then to the operator site. This blocks transcription of the genes required to synthesize tryptophan within the cell. deamed a repressible system; the lac operon is an inducible system, in which an inducer binds to the repressor thus permitting transcription.

B vitamins

B1: Thiamine B2: Riboflavin B3: Niacin B5: Pantothenic acid B6: Pyridoxal Phosphate B7: Biotin B9: Folic acid B12: Cyanocobalamin

Esterification of Glucose

Because carbohydrates have hydroxyl groups they are able to participate in reactions with carboxylic acids and carboxylic derivatives to form esters. Similar to phosphorylation of Glucose

Key concept

Because glycolysis contains three irreversible step, different enzymes must exist in gluconeogenesis to allow the body to revert pyruvate to glucose.

Resonance in a peptide (amide) bond?

Because of the amide groups have delocalizable pi electrons in the carbonyl and in the lone pair on the amino nitrogen they can exhibit resonance and this give rise to the C-N bond in the amide having a partial double bond character between the oxygen and the nitrogen

Why are amino acids called "amphoteric species"?

Because they have both an acid group and a basic group carboxylic acid amino group meaning they can accept or donate a proton depending on the pH of the environment

Absolute configuration

Biochemists use the D - L method over the R - S method

Chapter 8

Biological membranes

Branched and unsaturated fatty acids require what?

Branched and unsaturated fatty acids require special enzymes.

Branching Enzyme

Branching enzyme, which moves a block of oligoglucose from one chain and adds it to the growing glycogen as a new branch using an a-1,6-glycosidic link.

Which of the following is not a method by which enzyme decrease the activation energy for biological reactions? Modifying the local charge environment Forming transient covalent bonds Acting as electron donors or recepts Breaking bond in the enzyme irreversibly to provide energy

Breaking bonds in the enzyme irreversibly to provide energy

The (DELTA) G of NADH reducing oxygen directly is significantly greater than any individual step along the electron transport chain. If this is the case, why does transferrin electrons along the ETC generate more ATP than direct reduction of oxygen by NADH?

By splitting up electron transfer into several complexes, enough energy is released to facilitate the creation of a proton gradient at many locationsm rather than just one. the greater the proton gradient is, the greater the ATP generation will be. Direct reduction of oxygen by NADH would release a significant amount of energy to the environment, resulting in inefficient electron transport.

Which of the following is LEAST likely to be the resting membrane potential of a cell -70 mV -55 mV 0 mV +35 mV

C. 0 mV Cell membranes are most likely to have a resting membrane potential that is nonzero because the resting membrane potential create a state that is capable of responding to stimuli. Signaling molecules and channels would not be as useful with a membrane potential of zero. The values given in the answer choices correspond to different stages of the action potential, but the key information is that a resting potential of 0 mV does not maintain gradients for later activity.

Which of the following statements about terpenes is FALSE? Terpenes are strongly scented molecules that sometimes serve protective functions Terpenes are steroid precursors A triterpene is made of three isoprene moieites, and there has 15 carbons Terpenes are made by plants and insects

C. A triterpene is made of three isoprene moieites, and there has 15 carbons A triterpene is made of six isoprene (one terpene contains two isoprene units) and therefore has a 30-carbon backbone

Which of the following best characterizes the process of fatty acid synthesis? Two reductions follow by a dehydration and bond formation Reduction following by activation, bond formation, dehydration, and reduction Activation followed by bond formation, reduction, dehydration, and reduction Activation followed by bond formation, oxidation, dehydration and reduction.

C. Activation followed by bond formation, reduction, dehydration, and reduction is the process of fatty acid synthesis The steps in fatty acid synthesis are -activation ( attachment to acyl carrier protein) -bond formation (between malonyl-CoA and the growing fatty acid chain) -reduction (of a carboxyl group) -dehydration -reduction (of a double bond. these are the steps in fatty acid synthesis

Which of the following biomolecules is LEAST likely to contain an aromatic ring? Proteins Purines Carbohydrates Pyrimidines

C. Carbohydrates Aromatic rings must contain conjugated pie electrons which require alternating single and multiple bonds, or lone pairs. In carbohydrate ring structures, only single bonds are present, thus preventing aromaticity. Nucleic acids contain aromatic heterocycles, while proteins will generally contain at least one aromatic amino acid. (tryptophan, phenylalanine, or tyrosine)

When fatty acid B-oxidation predominates in the liver, mitochondrial pyruvate is most likely to be: Carboxylated to phosphoenolpyruvate for entry into glucogneogensis Oxidative decarboxylated to acetyl-CoA for oxidation in the citric acid cycle Carboxylated to oxaloacetate for entry into gluconeogenesis Reduced to lactate in the process of fermentation

C. Carboxylated to oxaloacetate for entry into gluconeogenesis Pyruvate is converted primarily into three main intermediate, acetyl-CoA for the citric acid cycle; lactate during fermentation or oxaloacetate for glyconeogenesis (via pyruvate carboxylase). High levels of acetyl-CoA, which is produced during B-oxidation, will inhibit pyruvate dehydrogenase and shift the citric acid cycle to run in the reverse direction, producing oxaloacetae for glucogenesis. Acetyl-CoA also stimulates pyruvate carboxylase directly.

Why might uracil be excluded from DNA but NOT RNA? Uracil is much more difficult to synthesize than thymine Uracil bind adenine too strongly for replication Cytosine degradation results in uracil Uracil is used as a DNA synthesis activator

C. Cytosine degradation results in uracil One common DNA mutation is the transition from cytosine to uracil in the presence of heat. DNA repair enzymes recognize uracil and correct this error by excising the base and inserting cytosine. RNA exists only transiently in the cell, such that cytosine degradation is insignificant. Were uracil to be used DNA under normal circumstances, it would be impossible to tell if a base should be uracil or if it is a damaged cytosine nucleotide.

A student is trying to determine the type of membrane transport ocurring in a cell. She finds that the molecule to be transported is very large an polar, and when transported across the membrane, no energy is required. Which of the following is the most likely mechanism of transport? Active transport Simple diffusion Facilitated diffusion Exocytosis

C. Facilitated diffusion We are asked to identify the type of transport that would allow a large, polar molecule to cross the membrane without any energy expenditure. This scenario describes facilitated diffusion, which uses a transport protein (or channel) to facilitate the movement of large, polar molecules across the non polar, hydrophobic membrane. Facilitated diffusion like simple diffusion does not require energy.

During fatty acid mobilization, which of the following occurs? I. HSL is activated II. Free fatty acids are released III. Gluconeogenesis proceeds in adipocytes

C. HSL is activated & Free fatty acids are released during fatty acid mobilization. During fatty acids mobilization there is a breakdown of triacylglycerols in adipocytes by hormone-sensitive lipase (HSL). This breakdown results in the release of three fatty acids and a glycerol molecule. The glycerol may be used by the liver for gluconeogenesis, but adipocytes do not have the ability to carry our gluconeogenesis

Which of the following is true regarding Ketolysis? Ketolysis occurs only in the brain Ketolysis occurs in the liver Ketolysis generates acetyl-CoA Ketolysis increases glucose metabolism

C. Ketolysis generates acetyl-CoA Ketolysis is the breakdown of ketone bodies to acetyl-CoA for energy. This process occurs in the brain and muscle tissues, but cannot occur in the liver, which lacks an enzyme necessary for ketone body breakdown. Catalysis is not associated with an increase in glucose metabolism because it most often occurs under conditions of starvation

Which of the following statements about saturation is FALSE? It can describe the number of double or triple bonds in a fatty acid tail It determines at least one of the properties of membranes More saturated fatty acids make for a more fluid solution Fully saturated fatty acids have only single bonds

C. More saturated fatty acids make for a more fluid solution More saturated fatty acids make for a less fluid solution. This is because they can pack more tightly and form more noncovalent bond, resulting in more energy being needed to disrupt the overall structure

In the genetic code of human nuclear DNA, one of the codons specifying the amino acid tyrosine is UAC. If one nucleotide is changed, and the codon is mutated to UAG, what type of mutation will occur? Silent mutation Missense mutation Nonsense mutation Frameshift mutation

C. Nonsense mutation UAG is one of the three known stop codons so changing tyrosine to a stop codon must be a nonsense mutation.

An investigator is measuring the activity of various enzymes involved in reactions of intermediary metabolism. One of the enzymes has greatly decreased activity compared to reference value. The buffer of the assay contains citrate. which of the following enzyme will most likely the directly affected by the use of citrate? Fructose-2,6-bisphosphate Isocitrate dehydrogenase Phosphfructokinase-1 Pyruvate carboxylase

C. Phosphofructokinase-1 Citrate is produced by citrate synthase from acetyl-CoA and oxaloacetate. This reaction takes place in the mitochondria. When the citric acid cycle slows down, citrate accumulates. In the cytosol, it acts as a negative allosteric regulator of phosphofructokinase-1, the enzyme that catalyzes the rate limiting step of glycolysis.

Which of the following is NOT a cell-cell junction in animals? Desmonones Gap junctions Plasmodesmata Tight junctions

C. Plasmosdesmata Plasmodesmata are cell-cell junctions that are found in plants, not animal. Gap junctions, tight junctions, desmosomes, and hemidesmosomes are all found in animals, particularly in epithelia.

2,4-dienoyl-CoA reductase is used in the oxidation of: Saturated fatty acids Monounsaturated fatty acids Polyunsaturated fatty acids Cholesterol

C. Polyunsaturated fatty acids In order for the enzymes of fatty acid oxidation to operate, there can be at most one double bond in the area of enzyme activity, and it must be oriented between carbons 2 and 3. In order to accomplish this in monounsaturated fatty acids, an isomerase is employed. When there are multiple double bonds that fall within the enzymatic binding is, both an isomerase and 2,4-dienoyl-CoA reductase are required for the oxidative enzymes to act on the fatty acid. For this question simply recognize that dienoyl refers to having multiple double bonds is sufficient to arrive at the answer.

Which of the following enzymes is NOT involved in DNA replication? Primase DNA ligase RNA polymerase Telomerase

C. RNA polymerase During DNA replication the strands are separated by DNA helicase. At the replication fork, primase creates a primer for the initiation of replication which is followed by DNA polymerase. On the lagging strand Okazaki fragments form and are joined by DNA ligase. After the chromosome has been processed, the ends, called telomeres, are replicated with the assistance of the enzyme telomerase RNA polymerase, distinct from primase is responsible for transcription.

Why are triacylglycerols used in the human body for energy storage? They are highly hydrated and therefore can store lots of energy They always have short fatty acid chains for easy access by metabolic enzymes The carbon atoms of the fatty acid chains are highly reduced and therefore yield more energy upon oxidation Polysaccharides, which would actually be a better energy storage form, would dissolve in the body

C. The carbon atoms of the fatty acid chains are highly reduced and therefore yield more energy upon oxidation. Tiacylglycerols are highly hydrophobic and therefore not highly hydrated, eliminating A. The fatty acid chains produce twice as much energy as polysaccharides during oxidation because they are highly reduced. The fatty acid chains vary in length and saturation

Which of the following is true for amphipathic molecules? They form protective spheres in any solvent, with hydrophobic molecules interior and hydrophilic molecules exteriors They have two fatty acid chains and a polar head group They are important to the formation of the phospholipid bilayer and soap bubbles They have a glycerol bases

C. They are important to the formation of phospholipid bilayer and soap bubbles. Phopholipids are amphipathic, as are fatty acid salts. Although amphipathic molecules take spherical forms with hydrophobic molecules interior in aqueous solution as choice A says but it would be true in Non polar solvent B. describes phospholipids and sphingolipids D. describes triacylglycerols and phospholipids: both group do not include fatty acid salts

A researcher treats a solution containing animal cells with ouabain, a poisonous substance that interferes with the sodium-potassium ATPase embedded in the cell membrane, and the cell lyses as a result. Which of the following statements best describe ouabians effect? Treatment with ouabain result in high levels of extracellular calcium Treatment with ouabain results in high levels of extracellular potassium and sodium Treatment with ouabain increases intracellular concentrations of sodium Treatment with ouabain decreases intracellular concentrations of sodium.

C. Treatment with ouabain increases intracellular concentrations of sodium This question requires an understanding of osmosis and the action of the sodium-potassium pump. When a cell is placed in a hypertonic solution (solution having a higher solute concentration than the cell), fluid will diffuse our of the cell and result in cell shrinkage. When a cell is placed in hypotonic solution ( a solution having a lower solute concentration that the cell) fluid will diffuse from the solution into the cell, causing the cell to expand and possibly lyse. The sodium-potassium pump moved three sodium potassium pump by ouabain will cause a net increase in the sodium concentration inside the cell and water will diffuse in, causeing the cell to swell and then lyse

Val-tRNA^val is the tRNA that carries valine to the ribosome during translation. Which of the following sequences gives an appropriate anticodon for this tRNA? CAU AUC UAC GUG

C. UAC There are four different codons for valine: CUU, GUC, GUA and GUG. Through base-pairing, we can determine that the proper anticodon must end with AC. Remember that the codon and anticodon are antiparallel to each other, and that nucleic acids are always written 5'-3' on the MCAT. Therefore we are looking for an answer that ends with AC rather than starting with CA

Which of the following RNA molecules or proteins is NOT found in the spliceosome during intron excision? snRNA hnRNA shRNA snRNPs

C. shRNA (short hairpin RNA) is a useful tool used in RNA interference. it is not produced in the nucleus for use in the spliceosome. It targets mRNA to be degraded in the cytoplasm; it is not utilized in splicing of the hnRNA snRNA & snRNPs however do bind to the hnRNA to induce splicing

For a compound to be aromatic, all of the following must be true EXCEPT: the molecule is cyclic the molecule contains 4n + 2 pie electrons the molecule contains alternating single and double bonds the molecule is planar

C. the molecule contains alternating single and double bonds For a compound to be aromatic, it must be cyclic, planer and conjugate and contain 4n + 2 pie electrons. Yes conjugation is alternating single and double bonds but remember they can possess triple bonds.

Cell Adhesion Molecules

CAMs are proteins found on the surface of so cells and aid in binding the cell to the extracellular matrix of other cells Cadherins, Integrins, Selectins

Which amino acid is encoded by CCA

CCA; mRNA = UGG; Tryptophan (Trp)

CETP catalyzes what?

CETP catalyzes the transition of IDL to LDL by transferring cholesteryl esters from HDL

Which amino acid is encoded by CGC

CGC; mRNA= GCG Alanine; (Ala)

Which of the following is most likely to be found bound to a protein in the body? Sodium Potassium Chloride Calcium

Calcium Ions not readily accessible in the cytoplasm or extracellular space are likely to be bound to a binding protein. Calcium and Magnesium are protein bound but without knowing this the question can still be answered. Sodium and Potassium must exist in their free states to participate in action potentials. Chloride is readily excreted by the kidney which would not be true if it were protein bound. Calcium is used for muscle contraction and other processes that must be regulated

Chapter 10

Carbohydrate Metabolism II

Chapter 9

Carbohydrate Metabolsim I: Glycolysis, Glycogen, Gluconeogenesis and the Pentose Phosphate pathway

Chapter 10

Carbohydrate Metabolsim II: Aerobic Respiration

Chapter 4

Carbohydrate Structure and Function

What forms the protective glycoprotein coat and also function in cell recognition?

Carbohydrates form the protective glycoprotein coat and also function in cell recognition.

Carbohydrate Classification

Carbohydrates have many names and can be classified by the number of sugar moieities that make them up, the number of carbons in each sugar, the functional group present on the molecule and the stereochemistry of the sugar

During protein processing, what is the eventual fate of each of the following; Carbon Skeleton Amino group Side chains

Carbon Skeleton- is transported to the liver for processing into glucose or ketone bodies. Amino group- will feed into the urea cycle for excretion. Side chains- will be processed like amino groups, while other functional groups will be treated like the carbon skeleton

Carbon skeletons of amino acids are used for what? q

Carbon skeletons of amino acids are used for energy, either through gluconeogenesis or ketone body formation. Amino groups are fed into the urea cycle for excretion. The fate of a side chain depends on its chemistry.

At ph 10.5 - glycine which doesnt have an ionizable side chain

Carboxyl is already deprotonated to (-COO-) now we are above the pKa of amino group so it deprotonates as well becoming -NH2 Glycine for example is now negatively charged at basic pH

Catabolism of cellular proteins occurs when?

Catabolism of cellular proteins occur only under conditions of starvation

Hydrolases

Catalyst the breaking of a compound into two molecule using the addition of water.

Ligases

Catalyze addition or synthesis reactions, generally between large similar molecule and often require ATP. Often seen in nucleic acid synthesis or lyases if the molecules are small then use Lyases

Lyases

Catalyze the cleavage of a single molecule into two products, Do not require water as a substrate and do not act as an oxidoreductae It is common to do the reverse of a reaction so if the synthesis of two molecules are put into one then Lyases are still used but referred to as synthases

Transfereases

Catalyze the movement of a functional group from one molecule to another.

Isomerases

Catalyze the rearrangement of bonds within a molecule. can be classified as oxidoreductases, transferases, or lyases depending on mechanism Catalyze reactions between stereoisomers as well as constitutional isomers

Gene duplication

Cells can increase the expression of a gene product by duplicating the relevant gene.

Most important polysaccharides in biology

Cellulose Starch Glycogen all composed of entirely of D-glucose, but differ in configuration about the anomeric carbon and the position of glycosidic bonds polymer formation can either be linear or branched

Which of the following is not involved in cell migration? Dynein Flagella Actin Centrioles

Centrioles these are composed of microtubules and used in mitosis but not cell migration

Cooperativity enzyme kinetics

Certain enzymes do not show the normal hyperbola that is show in the Michaelis Menten graph of (V vs. [S]) but rather show a sigmoidal (s-shaped) kinetics owing to cooperativity among substrate site. Cooperative enzymes have multiple subunits and multiple active sites. Two states of enzymes exist: Low affinity tense state (T) or a high affinity relaxed state (R) Substrate encourages the transition of other subunits from the T state to the R state and increases likelihood of binding by other subunits. Loss of substrate can encourage the transition from the R state to the T state.

Collagen

Characteristics of trihelical fiber makes up most of the extracellular matrix of connective tissue provide strength and flexibility major component of bones, structure based on the abundance of the amino acid glycine. if glycine is replaced then this can lead to improper folding and then bone fragility

Chemical digestion of lipids occurs in the what, by what?

Chemical digestion of lipids occur in the small intestine and is facilitated by bile, pancreatic lipase, collapse, and cholesterol esterase

Cholesterol is what?

Cholesterol is present in large amounts and contributes to membrane fluidity and stability

How is cholesterol obtained?

Cholesterol may be obtained through dietary sources or through de novo synthesis in the liver.

How does cholesterol play a role in the fluidity and stability of the plasma membrane?

Cholesterol moderates membrane fluidity by interfering with the crystal structure of the cell membrane and occupying space between phospholipid molecule at low temperatures, and by restricting excessive movement of phospholipids at high temperatures. Cholesterol also provides ability by cross-linking adjacent phospholipids through interactions at the polar head group and hydrophobic interactions at the nearby fatty acid tail.

Chylomicrons are what?

Chylomicrons are the transport mechanism for dietary triacylglycerol molecules and are transported via the lymphatic system

What are the three main sites of regulation within the citric acid cycle? What molecules inhibit and activate the three main checkpoints?

Citrate synthase- Inhibitors= ATP, NADH, Succinyl-CoA, citrate.... Activators= None Isocitrate dehydrogenase- Inhibitors= ATP, NADH. Activators= ADP, NAD+ a-ketoglutarate complex- Inhibitors= ATP, NADHm succinyl-CoA..... Activators= ADP, CA2+

Cofactors and Coenzymes

Cofactors and Coenzymes are small in size so they can bind to active site of the enzyme -usually kept at low concentrations in cells -attached from low covalent bonds to strong

Which of the following proteins is most likely to be found extracellularly? Tubulin Myosin Collagen Actin

Collagen most prevalent extracellular proteins are keratin, elastin, and collagen Tubulin and actin are cytoskeletal proteins while, myosin is a motor protein

Reversible inhibitors

Competitive, Noncompetitive, Mixed, and Uncompetitive

What is the purpose of all the reactions that collectively make up the citric acid cycle?

Complete oxidation of carbons in intermediates to CO2 so that reduction reaction can be coupled with CO2 formation, thus forming energy carriers such as NADH and FADH2 for the electron transport chain.

Elastin

Component of extracellular matrix of connective tissue role is to stretch then recoil like a spring

Concentration gradients

Concentration gradients help to determine appropriate membrane transport mechanisms in cells.

Concentration Determination

Concentration is determined almost exclusively through spectroscopy. Proteins contain aromatic side chains can be analyzed with UV spectroscopy without any treatment: however this type of analysis is sensitive to contaminants Don't forget that proteins also cause colorimetric change with particular reactions most commonly the bradford protein assay.

Purine

Contain two rings in their structure. The two purines found in nucleic acids are Adenine (A) and Gaunine (G) both are found in DNA and RNA

What factors would cause an activity assay to display lower affinity than expected after concentration determination

Contamination of the sample with detergent or SDS could yield an artificially increased protein level, leading to lower activity than expected.

Affinity Chromatography

Customizable by the way we can use a creating a column with a high affinity for a certain protein. This can be accomplished by coating beads with a receptor that binds the protein or a specific antibody to the protein. in either case the protein is retained in the column. Elutents can be created with a specific pH or salinity level that disrupts the bonds between the ligand and the protein of interest. Elutents can be hard to remove from certain enzymes if they are inhibitors.

Cysteine

Cys C -has a thiol (-SH) in side chain that is weaker than the -OH meaning oxidation can occur to it.

Assigning D - L configuration

D - sugars have the hydroxide of their highest numbered chiral center on the right L- Sugars have that hydroxide on the left D & L are opposite from each other

Memorize the following common sugars tested on the MCAT

D-Fructose D-Glucose D-Galactose D-Mannose

For most cells, the extracellular calcium concentration is around 10,000 times higher than the intracellular calcium concentration. What is the membrane potential established by this electrochemical gradient? -123 mV -61.5 mV +61.5 mV +123 mV

D. +123 mV

Which stage of protein synthesis does NOT require energy? Initiation Elongation Termination All stages of protein synthesis require energy

D. All stages of proteins synthesis require energy they all need large amounts of energy

Which of the following could result from an absence of apolipoproteins? I. An inability to secrete lipid tranport lipoproteins II. An inability to endocytose lipoproteins III. A decreased ability to remove excess cholesterol from blood vessels.

D. An inability to secrete lipid tranport lipoproteins, An inability to endocytose lipoproteins and A decreased ability to remove excess cholesterol from blood vessels, all can result from an absence of apolipoproteins While the transport and lipid binding functions of most lipoproteins are independent of the apolipoprotein component, the interaction of these lipoproteins with the environment is controlled almost exclusively by apolipoproteins, and are unable to transfer lipids without specialized apoliproteins or cholesterol-specific enzymes.

Which of the following statements regarding differences between DNA and RNA is FALSE? In cells, DNA is double-stranded, whereas RNA is single-stranded DNA uses the nitrogenous base thymine: RNA uses uracil The sugar in DNA is deoxyribose; the sugar in RNA is ribose DNA strands replicate in a 5' to a 3' direction, whereas RNA is synthesized in a 3' to 5' direction

D. DNA strands replicate in a 5' to a 3' direction, whereas RNA is synthesized in a 3' to 5' direction is false In cells, DNA is double stranded, with a deoxyribose sugar and the nitrogenous bases A, T, C and G. RNA on the other hand is usually single stranded with a ribose sugar and the bases A, U , C and G Remember both DNA replication and RNA synthesis proceed in a 5' to 3' direction

When insulin is released, it acts to increase the absorption of glucose into skeletal muscle predominantly though which of the following transporters? GLUT 1 GLUT 2 GLUT 3 GLUT 4

D. GLUT 4 GLUT is an abbreviation for Glucose Transporter and describeds a family of sugar transporters with varying distributions and activities. GLUT 4 is found in adipose tissue and muscle, and mediates insulin-stimulated glucose uptake: in fact it is the only insulin-responsive glucose transporter. Insulin acts via its receptor to translocate GLUT 4 to the plasma membrane. GLUT 4 in skeletal muscle is also stimulated by excersise though an insulin independent pathway.

Which of the following is a sphingolipid? Lecithin Phosophatidylinostiol Cholesterol Ganglioside

D. Ganglioside Gangliosides, along with creamed, sphingomyelin and cerebrosides are sphingolipids.

After a large, well-balanced meal, all of the following substances would be expected to be elevated EXCEPT: Fatty acid Insulin Glucose Glucagon

D. Glucagon After a large meal, one would expect blood to contain high levels of nutrients such as glucose and fatty acids. as well as regulators telling the body to utilize and sore this fuel like insulin. Glucagon is a peptide hormone used to rase blood sugar levels by promoting, among other processes, glycogenolysis and gluconeogenesis. Glucagon should be elevated during a fast.

Which of the following is NOT a difference between Heterochromatin and Euchromatin? Euchromatin has areas that can be transcribed, whereas heterochromatin is silent Heterochromatin is tightly packed, whereas euchromatin is less dense Heterochromatin stains darkly whereas euchromatin stains lightly Heterochromatin is found in the nucleus, whereas euchromatin is in the cytoplasm

D. Heterochromatin is found in the nucleus, whereas euchromatin is in the cytoplasm Euchromatin has a classical "beads on a string" appearance that stains lightly, while heterochromatin is tightly packed and stains darkly. Heterochromatin is primarily composed of inactive genes or untranslated regions, while euchromatin is able to be expressed. All chromatin is found in the nucleus not the cytoplasm.

After a brief period of intense exercise, the activity of muscle pyruvate dehydrogenase is greatly increased. This increased activity is most likely due to: Decreased ADP Increased acetyl-CoA Increased NADH/NAD+ ratio Increased pyruvate concentration

D. Increased pyruvate concentration

Which of the following amino acids will provide the most energy when degraded? Glycine Alanine Valine Isoleucine

D. Isoleucine will provide the most energy when degraded. The energy contribution of an amino acid depends on its ability to be turned into glucose through gluconeogenesis (glycogenic amino acids), ketone bodies (ketogenic amino acids) or both. All of the amino acids listed in the answer choices are glycogenic: isoleucine is also ketogenic. The energy acquired from an amino acid will also depend on the number of carbons it can donate to these energy creating processes, which depends on the size of its side chain. isoleucine has the largest side chain of the answer choices and will thus contribute the most energy per molecule.

What role does peptidyl transferase play in protein synthesis? It transports the initiator ammoniacal-tRNA complex It helps the ribosome to advance three nucleotides along the mRNA in the 5' to 3' direction It holds the protein in its tertiary structure It catalyzes the formation of a peptide bond

D. It catalyzes the formation of a peptide bond Peptidyl transferase is an enzyme that catalyzes the formation of a peptide bond between the incoming amino acid in the A site and the growing polypeptide chain in the P site. Initiation and elongation factors help transport changed tRNA molecules into the ribosome and advance the ribosome down the mRNA transcript Chaperones maintains a proteins three dimensional shape as it is formed

Which of the following organs does NOT require a constant supply of glucose from the blood for energy during a fast? Red Blood cells Brain Pancreas Liver

D. Liver. The liver, like all cells, needs a constant supply of glucose; however, it is able to produce its own glucose through gluconeogenesis. The other cells listed here are absolutely dependent on a glucose source from the blood for energy, although they may also use other cells listed here.

During which phase of the cell cycle are DNA repair mechanisms lease active? G1 S G2 M

D. M phase Mismatch repair mechanisms are active during S phase (proofreading) and G2 phase (M2H2 and MLH1) . Nucleotide and base excision repair mechanisms are most active during the G1 and G2 phases. These mechanisms exist during interphase because they are aimed at preventing propagation of the error into daughter cells during M phase (mitosis)

The majority of triacylglycerols stored in adipocytes originate from: Synthesis in the adipocyte Dietary intake Ketone bodies Synthesis in the liver

D. Majority of triacylglycerols stored in adipocytes originate from - Synthesis in the liver The liver is the major metabolic organ in the body and is responsible for much of the synthesis and interconversion of fuel sources. Most of the triacylglycerols that are synthesized in the liver are transported as VLDL to adipose tissue for storage. Both the adipocytes and dietary intake constitute a minor source of triacylgcerols.

Which of the following statements regarding prostaglandins is FALSE? Prostaglandins regulate the synthesis of cAMP Prostaglandins synthesis is inhibited by NSAIDs Prostaglandins affect pain, inflammation and smooth muscle function Prostaglandins are endocrine hormones, like steroid hormones

D. Prostaglandins are endocrine hormones, like steroid hormones Prostaglandins are paracrine or autocrine signaling molecules, not endocrine -- they affect regions close to where they are produced, rather than affecting the entire body. Think of the swelling that happens when you bash your knee into your desk: your knee will swell, turn red and possibly bruise.

Resting membrane potential depend on: I. The differential distribution of ions across the membrane II. Active transport processes III. Selective permeability of the phospholipid bilayer.

D. Resting membrane potential depends on the differential distribution of ions across the membrane, Active transport processes and Selective permeability of the phospholipid bilayer. The polarization of the membrane at rest is the result of an uneven distribution of ions between the inside and outside of the cell. The difference is achieved through active pumping of ions (predominantly sodium and potassium) into and out of the cell and the selective permeability of the membrane, which allows certain certain ions to cross

Which of the following is NOT a type of glycolipid? Cerebroside Globoside Ganglioside Sphingomyelin

D. Sphingomyelin Glycolipids contain sugar moieties connected to their backbone. Sphingomyelin is not a glycolipid, but rather a phospholipid. This class can either have phosphatidylcholine or phosphatidylehtanolamine as a head group and therefore contains a phosphodiester, not glycosidic, bond

A membrane receptor is most likely to be a Embedded protein with catalytic activity Transmembrane proteins with sequestration activity Membrane-associated protein with sequestration activity Transmembrane protein with catalytic activity

D. Transmembrane protein with catalytic activity Membrane receptors must have both an extracellular and intracellular domain; therefore they are considered transmembrane proteins. In order to initiate a second messenger cascade, they typically display enzymatic activity, although some may act strictly as channels.

A biopsy is done on a child with an enlarged liver and shows accumulation of glycogen granules with single glucose residues remain at the branch points near the periphery of the granule. The most likely genetic defect is in the gene encoding: a-1,4 phosphorylase (glycogen phosphorylase) a-1,4:a-1,6 transferase (branching enzyme) a-1,4;a-1,6 transferase (part of the deb ranching enzyme complex) a-1,6 glucosidase (part of the debranching enzyme

D. a-1,6 glucosidase (part of the deb ranching enzyme) The pattern described for this childs glycogen demonstrates appropriate production: there are long chains of glucose monomers, implying that glycogen synthase works. During glycogenolysis it seems that the child is able to remove individual glucose monomers and process glycogen down to the branch point itself, which requires glycogen phosphorylase A and a-1,4:a-1,6 transferase C The metabolic problem here is removing the final glucose at the branch point, which is an a-1,6 link. This requires, a-1,6 glucosidase

Chapter 6

DNA & Biotechnology

How is supercoiling relieved?

DNA Topoisomerases introduce negative supercoils DNA Topoisomerases work ahead of helicase, nicking one or both strands, allowing relaxation of the torsional pressure and then resealing the cut strands.

Chromosomes

DNA is divided up among 46 chromosomes found in the nucleus of the cell.

What are DNA libraries?

DNA libraries arise from DNA cloning which are large collection of known DNA sequences; in sum these sequences could equate to the genome of an organism.

Where is mutation more likely to happen? Leading or lagging strand?

DNA ligase which closes the gaps between Okazaki fragments, lacks proofreading ability. Thus, mutations in the lagging strand is higher than the leading strand.

DNA Methylation

DNA methyaltion is involved in chromatin remodeling and regulation of gene expression levels in the cell. DNA methylases add methyl groups to cytosine and adenine nucleotides; methylation of genes is often linked with the silencing of gene expression. Heterochromatin regions of the DNA are much more heavily methylated, hindering access of the trasncriptional machinery to the DNA.

Replicating the ends of the chromosomes

DNA polymerase does a excellent job of synthesizing DNA but it unfortunately cannot complete synthesis of the 5' end of the strand.

If the DNA polymerase of humans cannot be used at high temperatures then what is?

DNA polymerase in humans does not work at high temperature so the DNA polymerase found in Thermus Aquaticus a bacteria that thrives in the hot springs of yellowstone at 70 C is used instead.

DNA Polymerase I does what?

DNA polymerase works in prokaryotes and fills in gaps left behind after RNA primer excision.

DNA polymerases Beta and epsilon participate in what?

DNA repair

DNA ligase does what?

DNA works in both prokaryotes and eukaryotes. Ligase seals the ends of the DNA molecules together, creating one continuous strand of DNA especially between Okazaki fragments.

Debranching Enzyme

Debranching Enzyme moves a block of oligoglucose form one branch and connects it to the chain using an a-1,4 glycosidic link. It also removes the branch point, which is connected via an a-1,6 glycosidic link, releasing a free glucose molecule.

Key concept of Debranching enzyme.

Debranching enzyme is actually made up of two enzymes with different functions; one moves the terminal end of a glycogen chain to the branch point (a-1,4; a-1,6 transferase) One removes the glucose monomer actually present at the branch point (a-1,6 glucosidase)

Enzymes increase the rate of the reaction by: Decreasing the activation energy Decreasing the overall free energy change of the reaction Increasing the activation energy Increasing the overall free energy change of the reaction

Decreasing the activation energy Remember they do not affect (delta G) free energy

Mutations

Degeneracy Wobble Missense mutation Nonsense Mutations Frameshift Mutations

Oxidoreductase examples

Dehydrogenase or Reductase If there is an Oxygen as the last electron accepter, the enzyme should have Oxidase in the name.

Denaturing

Denaturing is melting the double helix by condition that disrupt hydrogen bonding and base-pairing resulting in the melting of double helix into single strands that have separated from each other. None of the covalent links between the nucleotides in the backbone of the DNA break during this process.

Desomosomes and Hemidesmosomes do what?

Desmosomes and Hemidesmosomes anchor layers of epithelial tissue together.

What do digested lipids form?

Digested lipids form micelles for absorption or be absorbed directly.

Where does digestion of lipids begin?

Digestion of lipids occurs primarily in the mouth and stomach

Enzymes

Ea - decrease the activation energy Rate (forward) - enzymes increases this Rate (reverse) - enzymes increase this Keq remains unchanged for it doesn't affect equilibrium Delta G of rxn remains unchanged as well

DNA strand polarity

Each strand of DNA has distinct 5' and 3' ends creating polarity within the backbone. 5' will have an -OH or phosphate group bonded to C-5' of the sugar, while the 3' end has a free -OH on C-3 of the sugar.

Electrical potential of a membrane is what?

Electrical potential of a membrane at physiological temperature can be calculated using the Goldman-Hodgkin- Katz voltage equation, which is derived form the Nernst equation.

Embedded proteins

Embedded proteins are most likely part of a catalytic complex or involved in cellular communication.

What are the differences between Enzyme linked receptors and G protein coupled receptors

Enzyme linked receptors- -Auto-activity -Enyzmatic activity G protein coupled receptors- -two-protein complex -dissociation upon activation -trimer in common- -extracellular domain -transmembrane domain -ligand binding

Lock and Key Theory

Enzyme's active site being the (lock) Substrate being the (key)

Hormone are found in the body in very low concentrations, but tend to have a strong effect. What type of receptor are hormones most likely to act on? Ligand-gated ion channels Enzyme-linked receptors G protein-coupled receptor

Enzyme-linked receptors & G protein-coupled receptor These use second messenger systems while ion channels do no. For a ligand present in low quantities to have a strong action we expect it to initiate a second messenger cascade system not the actual second messenger systems

Chapter 2

Enzymes

Holoenzymes

Enzymes with their cofactor

Apoenzymes

Enzymes without their cofactor

What is the difference between esterification and glycoside formation?

Esterification is the reaction by which a hydroxyl group reacts with either a carboxylic acid or a carboxylic acid derivative to form an ester Glycoside formation refers to the reaction between an alcohol and a hemiacetal or hemiketal group on a sugar to yield an alkoxy group Alkoxy group is an alkyl (carbon and hydrogen chain) group singular bonded to oxygen thus: R-O. The range of alkoxy groups is great, the simplest being methoxy (CH3O-). An ethoxy group (CH3CH2O-)

How to find the start codon?

Every protein begins with methionine, the codon for methionine (AUG) is considered the start codon for translation of the mRNA into protein.

RNase H which is in eukaryotes does what?

Excises RNA primer

Extracellular ligands do what?

Extracellular ligands bind to membrane receptors, which function as channels or enzymes in second messenger pathways.

Facilitated diffusion

Facilitated diffusion uses transport proteins to move impermeable solutes across the cell membrane.

True or false: Bodily proteins will commonly break down to provide acetyl-CoA for lipid synthesis.

False. Proteins are more valuable to the cell than lipids thus they will not commonly be broken down for lipid synthesis.

True or False: All lipids enter the circulation through the lymphatic system

False. Small free fatty acids enter the circulation directly.

True or False: The Edman degradation proceeds from the carboxyl (C-) terminus

False. it proceed from the N- Terminus

Why are fatty acids used to create ketone bodies instead of creating glucose?

Fatty acdi degradation results in large amount of acetyl-CoA, which cannot enter the gluconeogenic pathway to produce glucose. Only odd-numbering fatty acids can act as a source of carbon for gluconeogenesis; even then, only the final malonly-CoA molecule can be used. Energy is packaged into ketone bodies for consumption by the brain and muscles.

Where does fatty acid oxidation occur?

Fatty acid oxidation occurs in the mitochondria following transport by the carnitine shuttle

What are fatty acids?

Fatty acids are carboxylic acids, typically with a single long chain, although they can be branched

Where are fatty acids synthesized?

Fatty acids are synthesized in the cytoplasm from acetyl-CoA transported out of the mitochondria.

Why must Pyruvate undergo fermentation for glycolysis to continue?

Fermentation must occur to regenerate NAD+, which is in limited supply in cells. Fermentation generates no ATP or energy carriers: it merely regenerates the coenzymes needed in glycolysis.

What does Nucleotide Excision Repair use?

First, specific proteins scan the DNA molecule and recognize the lesion because of a bulge in the strand. And then a Excision Endonuclease is used to make nicks in the phosphodiester backbone of the damaged strand on both sides of the thymes dimer and removes the defective oligonucleotide. DNA polymerase then fils in the gap by synthesizing DNA in the 5' to 3' direction. Then the nick in the strand is sealed by DNA ligase

Describe the role of floppiness and lipid rafts in biological memebranes.

Floppiness are responsible for the movement of phospholipids between the layers of the plasma membrane because it is otherwise energetically unfavorable. Lipid rafts are aggregates of specific lipids in the membrane that function as attachment points for other biomolecules and play roles in signaling.

What is the structure of the cell membrane?

Fluid mosaic model

To take away from the Michaelis-Menten graph

For a given conentration of enzyme the relationship generally graphs as a hyperbola. When substrate concentration is less than Km, changes in substrate conentration will greatly affect the reaction rate. At high substrate concentrator exceeding Km the reaction are increase much more slowly as it approaches vMax where it become dependent of the substrate concentration.

What is the primary method of transporting free fatty acids in the blood?

Free fatty acids remain in the blood, bonded to albumin and other carrier proteins. A much smaller amount will remain unbonded.

What is fructose?

Fructose is found in honey and fruit and as part of the disaccharide sucrose. Sucrose is hydrolyzed by the duodenal brush-boder enzyme sucrase, and the resulting monosaccharides, glucose and fructose are absorbed into the hepatic portal vein.

Fructose-1,6-biphosphatase

Fructose-1,6-biphosphatase converts fructors 1,6-bisphophate to fructose 6-phosphate bypassing phosphofructokinase-1. This is the rate-limiting step of gluconeogenesis. it is activated by ATP and glucagon indirectly. It is inhibited by AMP directly and insulting indirectly.

List the function, key regulators and if it is reversible: Glucokinase

Function of Glucokinase: Glucokinase also phosphoryaltes and "traps" glucose in liver and pancreatic cells, and works with GLUT 2 as part of the glucose sensor in B-islet cells. In liver cells Glucokinase is induced by insulin It is irreversible.

List the function, key regulators and if it is reversible: Hexokinase

Function of Hexokinase: Hexokinase phosphoryalates glucose to form glucose 6-phosphate, "trapping" glucose in the cell. Regulator of Hexokinase: it is inhibited by glucose 6-phosphate It is irreversible

List the function, key regulators and if it is reversible: Phosphofructokinase-1

Function of Phosphofructokinase-1: PFK-1 catalyzes the rate-limiting step of glycolysis, phosphorylating fructose 6-phosphate to fructose 1,6-biphosphate using ATP. PFK-1 is inhibited by ATP, citrate, and Glucagon, It is activated by AMP, fructose 2,6-bisphosphatem and insulin. It is irreversible

Regulator gene

Furthest upstream is the regulator gene, which codes for a protein known as the repressor.

Which of the following is NOT a component of all trimeric G proteins. G(a)-alpha G(b)-beta G(y)-gamma G(i)-inhibitor

G(i)-inhibitor is not a trimeric G protein a, b and y which are alpha, beta and gamma are apart of the Trimeric G protein Gs, Gi and Gq are subtypes of the G(a) subunit of the trimeric G proteins .

Which amino acid is encoded by GAT

GAT is a mRNA = AUC; Isoleucine (Ile)

Compare and contrast GLUT 2 and GLUT 4

GLUT 2 - TISSUE- liver and pancreas Km- HIGH Saturated at normal glucose levels? No, cant be saturated under normal physiological conditions. Responsive to insulin? No (but serves as glucose sensor to cause release of insulin in pancreatic B-cells) GLUT 4- TISSUE- Adipose tissue, muscle Km- Low Saturated at normal glucose levels? Yes, saturated when glucose levels are only slightly above 5 mM Responsive to insulin? Yes

What is GLUT 2 in Glucose Transport?

GLUT 2 is a low affinity transporter in hepatocytes and pancreatic cells. GLUT 2 is found in the liver (for glucose storage) and pancreatic B-islet cells (as part of the glucose sensor). It has a high kM. This mean that the liver will pick up glucose in proportion to its concentration in the blood (first-order kinetics) GLUT 2 serves along side the glycolytic enzyme glucokinase, serves as the glucose seniors for insulin release.

What is GLUT 4 in Glucose Transport?

GLUT 4 is found in adipose tissue and muscle and is stimulated by insulin. It has a low Km.

How does insulin promote glucose entry into cells?

GLUT 4 is saturated when glucose lesser only slightly above 5 mM, so glucose entry can only be increased by increasing the number of transporters. Insulin promotes the fusion of vesicles containing preformed GLUT 4 with the cell membrane.

Galactose is the C-4 epimer of glucose, structure shown in picture attached. What would galactose look like?

Galactose is a diasterieomer of glucose with the stereochemistry at C-4 (counting from the aldehyde) reversed. being able to identify C-4 is enough to answer this question, even without looking at the glucose molecule.

What is galactose phosphorylated by?

Galactose is phosphorylated by galactokinase, trapping it in the cell.

Contrast gap junctions and tight junctions.

Gap junctions allow for the intercellular transport of materials and do not prevent paracellular transport of material. Tight junctions are not used for intercellular transport but do prevent paracellular transport. Gap junctions are in discontinuous bunches around the cell, while tight junctions form bands aren the cell.

Gap junctions

Gap junctions allow for the rapid exchange of ions and other small molecules between adjacent cells

How are genes duplicated?

Genes can be duplicated in series on the same chromosome duplicated in parallel by opening the gene with helicases and permitting DNA replication only of that gene.

Glutamine

Gln Q -possess -OCNH2, this does not gain or lose protons and do not become charged

Glutamic acid (glutamate)

Glu E - has -COO- in side chain

Glucogenesis

Glucogenesis occurs in both the cytoplasm and mitochondria, predominantly in the liver. There is a small contribution from the kidneys. Most of glucogenesis is the revers of glycolysis, using the same enzymes.

Under what physiological condition should the body carry out gluconeogenesis?

Gluconeogenesis occurs when an individual has been fasting for >12 hours. To carry out gluconeogenesis, hepatic (and renal) cells must have enough energy to drive the process of glucose creations, which requires sufficient fat stores to undergo B-oxidaiton.

Glucose 6-phosphatase

Glucose 6-phosphatase converts Glucose 6-phosphate to a free glycose, bypassing glucokinase. It is found only in the endoplasmic reticulum of the liver.

Glutamic acid titration

Glutamic acid having two carboxyl groups and one amino group, the charge in its fully protonated state is still +1 It will lose its first proton normally as glycine does from the carboxyl group. At this point it is electrically neutral. It looses its second proton and become -1 but the second proton comes from the side chain carboxylic group not the amino group.

Glycine

Gly G - only achiral amino acid

Glyceraldehdye-3-phosphate dehydrogenase

Glyceraldehdye-3-phosphate dehydrogenase produces NADH, which can feed into the electron transport chain

Glyceraldehyde-3-phosphate Dehydrogenase

Glyceraldehyde-3-phosphate Dehydrogenase catalyzes an oxidation and addition of inorganic phosphate (Pi) to its substrate, glyceraldehdye 3-phosphate. This results in the production of a higher energy intermediate 1,3-bisphosphoglycerate and the reduction of NAD+ to NADH. If glycolysis is aerobic, the NADH can be oxidized by the mitochondrial electron transport chain, providing energy for ATP synthesis by oxidative phosphorylation.

Glycerophospholipds do what?

Glycerophospholipids replace one fatty acid with a phosphate group, which is often linked to other hydrophilic groups

Collagen consists of three helices with carbon backbones that are tightly wrapped around one another in a triple helix. Which of these amino acids is most likely to be found in the highest concentration in collagen? Proline Glycine Threonine Cysteine

Glycine Collagen has a triple helix, the carbon backbones are very close together. Thus steric hindrance is a potential problem. To reduce this we need a small side chain containing amino acid which glycine is a possible answer and it is the smallest so it could work the best.

Nonpolar, Nonaromatic side chains:

Glycine - contains just H (achiral) Alanine Valine leucine Isoleucine - all four have alkyl side chains containing one to four carbons Methionine- one of two that contain sulfur in its side chain Proline- forms a cyclic amino acid

Glycine as an example

Glycine requires that only the first two nucleotides of the codon be GG. The third nucleotide could be A, C, G, or U. The amino acid composition of the protein would remain the same.

Which two polysaccharides share all of their glycosidic linkage types in common? Cellulose and Amylopectin Amylose and Glycogen Amylose and Cellulose Glycogen and Amylopectin

Glycogen and Amylopectin Glycogen and Amylopectin are the only polysaccharide forms that demonstrate branching structure making them most similar in term of linkage. They both use a-1,4 and a-1,6 linkages Cellulose uses B-1,4 linkages and amylose does not contain a-1,6 linkages

Anderson disease (glycogen storage disease type IV) is a condition characterized by a deficiency in glycogen branching enzyme. Absence of this enzyme would be likely to cause all of the following effects EXCEPT.. Decreased glycogen solubility in human cells Slower action of glycogen phosphorylase Less storage of glucose in the body Glycogen devoid of a-1,4 linkages

Glycogen devoid of a a-1,4 linkages In Andersen's disease glycogen is less branched than normal thereby inducing lower solubility of glycogen. Branches reduced the interactions between adjacent changes of glycogen and encourage interactions with the aqueous environment. Smaller amount of branches meanthat glycogen phosphorylase has fewer terminal glucose monomers on which to act, making enzyme activity slower than normal overall. Without branches the density of glucose monomers cannot be as high: therefore the total glucose stored is lower than normal. We would expect normal a-1,4 linkages in th glycogen of an individual with andersens disease

Regarding glycogen and amylopectin, which of these two polymers would experience a higher rate of enzyme activity from enzyme that cleave side branches? Why?

Glycogen has a higher rate of enzymatic branch cleavage because it contains significantly more branching than amylopectin

What is the structure of Glycogen? What types of glycosidic links exist in a glycogen granule?

Glycogen is made up of a cored protein of glycogenin with linear chains of glucose emanating out from the center, connected by a-1,4 glycosidic links. Some of these chain are branched, which requires a-1,6 glycosidic links.

What are the two main enzymes of glycogenolysis and what does each accomplish?

Glycogen phosphorylase removes a glucose molecule from glycogen using a phosphate, breaking the a-1,4 link and creating glucose 1-phosphate. Debranching enzymes moves all of the glucose form a branch to a longer glycogen chain by breaking an a-1,4 link and forming a new a-1,4 link link to the longer chain. The branch point is left behind: this is removed by breaking the a-1,6 link to form a free molecule.

Glycogen phosphorylase

Glycogen phosphorylase removes singel glucose 1-phosphate molecules by breaking a-1,4 glycosidic links. In the liver, it is activated by glucagon to prevent low blood sugar; in exercising skeletal muscle, it is activated by epinephrine and AMP to provide glucose for the muscle itself.

What are the two main enzymes of glycogenesis, and what does each accomplish?

Glycogen synthase attaches the glucose molecules from UDP-glucose to the growing glycogen chain, forcing an a-1,4 link in the growing chain and moving a block of oligoglucose to another location in the glycogen granule. The oligoglucose is then attached with an a-1,6 link a-1,4 moves 4ward a-1,6 adds the branch into the mix.

Glycogen synthase

Glycogen synthase which creates a-1,4 glycosidic links between glucose molecules. It is activated by insulin in liver and muscle.

Glycogenesis

Glycogenesis is the production of glycogen using two main enzymes: Glycogen synthase & Branching enzyme

Glycogenolysis

Glycogenolysis is the breakdown go glycogen using two main enzymes: Glycogen phosphorylase and Debranching enzyme

Glycolysis

Glycolysis occurs in the cytoplasm of all cells, and does not require oxygen. It yields 2 ATP per molecule of glucose. Glycolysis is a cytoplasmic pathway that converts glucose into two pyruvate molecules, releasing a modest amount of energy captured in two substrate level phosphorylations and one oxidation reaction. Can occur anaerobically

Glucokinase is what?

Glycolytic enzyme Glucokinase is what converts glucose to glucose 6-phosphate. It is present in the pancreatic B-islet cells as part of the glucose sensor and is responsive to insulin in the liver. Anything with kinase in it, means it is an enzyme that catalyzes the transfer of phosphate groups from high energy to substrates. This is known as phosphorylation.

Hexokinase does what?

Glycolytic enzyme Hexokinase, which converts glucose to glucose 6-phosphate in peripheral tissue.

Phosphofructokinase-1 (PFK-1)

Glycolytic enzyme Phosphofructokinase-1 (PFK-1) is what phosphorylates fructose 6-phosphate to fructose 1,6-biphosphate in the rate-limitng step of glycolysis, PFK-1 is activated by AMP and fructose 2,6-biphosphate (F2,6-BP) and is inhibited by ATP and citrate.

Three G proteins

Gs- stimulates adenylate cyclase which increases levels of cAMP in the cell Gi- Inhibits adenylate cyclase which decreases levels of cAMP in the cell Gq- activates phospholipase C, which cleaves a phospholipid from the membrane to form PIP2. PIP2 is then cleaved into DAG and IP3: IP3 can open calcium channels in the endoplasmic reticulum increasing calcium level in the cell Mnemonic device for the G proteins functions: Gs: stimulates Gi: inhibits "Mind your Ps and Qs" Gq activates phospholipase C.

What are the five histones?

H2A, H2B H1, H3 & H4

What are the five histone proteins in eukaryotic cells? Which one is not part of the histone core around which DNA wraps to form Chromatin?

H2A, H2B, H1, H3, & H4 H1 is not part of the core and it wraps and seals the ends of the DNA

HDL is involved in what?

HDL is involved in the reverse transport of cholesterol

Under what conditions is HMG-CoA reductase most active? In what cellular region does it exist?

HMG-CoA reductase is most active in the absence of cholesterol and when stimulated by insulin. Cholesterol reduces the activity of HMG-CoA redactors which is located in the smooth endoplasmic reticulum

Aldonic acids are compounds that can be oxidized, and therefore act as reducing agents can be reduced, and therefore act as reducing agents have been oxidized and have acted as reducing agents have been oxidized and have acted as oxidizing agents

Have been oxidized and have acted as reducing agents Aldonic acids form after the aldehyde group on a reducing sugar reduces another compound, becoming oxidized in the process

Causes of denaturation

Heat and Solutes

What can cause Denaturing?

Heat, Alkaline pH and chemicals like formaldehyde and urea are commonly used

What is helicase?

Helicase is the enzyme responsible for unwinding the DNA, generating two single stranded template strand ahead of the polymerse.

Binding Proteins

Hemoglobin, calcium binding proteins, DNA binding proteins and others each has an affinity curve for its molecule of interest. A transport protein which must be able to bind or unbind its target to maintain steady state concentrations is likely to have varying affinity depending on the enviromental conditions

Compare & Contrast Heterochromatin and Euchromatic

Heterochromatin is Dense, Dark and is Silent during Transcriptional activity Euchchromatin is Uncondensed, Light and Active during Transcriptional activity

What are the function and key regulators of the following enzymes? Which ones are reversible?

Hexokinase Glucokinase Phosphofructokinase-1 Glyceraldehyde-3-phosphate dehydrogenase 3-phosphoglycerate kinase Pyruvate kinase

What property of telomeres and centromeres allows them to stay tightly raveled, even when the rest of the DNA is uncondensed?

High G-C content increases hydrogen bonding, making the association between DNA strands very strong at telomeres and Centromeres.

Histidine

His H -has aromatic ring with two nitrogen atoms, one being positive and the other not until under acidic conditions .

Which of these amino acids has a side chain that can become ionized in cells. Histidine Leucine Proline Threonine

Histidine Histidine has a nitrogen that can be protonated Ionizable amino acids: Tyrosine Cysteine Arginine Lysine Histidine Aspartic and Glutamic acid

Homo vs hetero - polysaccharide

Homopolysaccharide is when it is completely composed of glucose or any other monosaccharide Heteropolysaccharide is when it is made of more than one type of monosaccharide

What is the Fischer Projection?

Horizontal line are wedges = coming out of the page Vertical lines are dashes = into the page these allow people to study and identify enantiomers

Mnemonic for glycolysis

How Glycolysis Pushes Forward the Process: Kinases Hexokinase Glucokinase PFK-1 Pyruvate Kinases

What is hybridization?

Hybridization is the joining of complementary base pair sequences. This can be DNA-DNA or DNA-RNA recognition. Used in PCR and southern blotting

An alpha helix is most likely to be held together by disulfide bonds hydrophobic effets hydrogen bonds ionic attractions between side chains

Hydrogen bonds Disulfide bridge and hydrophobic effects are involved in tertiary structures not secondary. also they are too far part to participate in strong interactions in secondary structure

How does prokaryotic DNA differ from eukaryotic DNA? I. Prokaryotic DNA lacks nucleosomes II. Eukaryotic DNA has telomeres III. Prokaryotic DNA is replicated by different DNA polymers IV. Eukaryotic DNA is circular when not restricted by centromeres

I, II, & III. Prokaryotic DNA lacks nucleosomes Eukaryotic DNA has telomeres Prokaryotic DNA is replicated by different DNA polymers Prokaryotic DNA is circular and lacks histone proteins, and thus does not form nucleosomes. Both prokaryotic and eukaryotic DNA are replicated by DNA polymerases, although these polymerases differ in identity. Eukaryotic DNA is organized into chromatin, which can condense to form linear chromosomes Only prokaryotes have circular chromosomes Only eukaryotic DNA has telomeres.

The cyclic forms of monosaccharides are I. Hemiacetals II. Hemiketals III. Acetals

I. & II. Monosaccharides can exist as hemiacetals or hemiketals. depending on whether they are aldoses or ketoses. When a monosaccharide is in its cyclic form, the anomeric carbon is attached to the oxygen in the ring and a hydroxyl group. hence it is only a hemiacetal or hemiketal because an acetal or metal would require the -OH group to be converted to another -OR group.

Steroid hormones are steroids that: I. Have specific high affinity receptors II. Travel in the bloodstream from endocrine glands to distant sites III. Effect gene transcription by binding directly to DNA

I. & II. C.) Steroid hormones are produced in endocrine glands and travel in the bloodstream to bind high affinity receptors in the nucleus. The hormones receptor binds to DNA as part of the hormone-receptor complex. but the hormone itself does not

IDL is the what?

IDL is the VLDL remnant in transition between triacylglycerol and cholesterol transport; it picks up cholesteryl esters from HDL

Which of the following is correct about fat-soluble vitamins? I. Vitamin E is important for calcium regulation II. Vitamin D protects against cancer because it is a biological antioxidant III. Vitamin K is necessary for the post translational introduction of calcium binding sites IV. Vitamin A is metabolized to retinal, which is important for sight

III. & IV. Vitamin K is necessary for the post translational introduction of calcium binding sites. Vitamin A is metabolized to retinal, which is important for sight Vitamin A is metabolized to retinal which is important for sight. Vitamin D is metabolized to calcitriol, which is important for calcium regulation Vitamin E is made up of tocopherols, which are biological antioxidants, helps reduce caner risk by taking out free radicals with the aromatic ring it has Vitamin K is necessary for the introduction of calcium binding sites such as during the post translational modification of prothrombin

Which of the following is/are true about sphingolipids? I. They are all phospholipids II. They all contain a sphingosine backbone III. They can have either phosphodiester or glycosidic linkages to their polar head groups

III. They can have either phosphodiester or glycosidic linkages to their polar head groups Sphingolipids can either have a phosphodiester bond therefore be phospholipids or have a glycosidic linkage and therefore be glycolipids Not all sphingolipids have a sphingosine backbone

Codons

If a gene is a "sentence" describing a protein, then its basic unit is a three letter "word" known as the codon, which is translated into and amino acid. Each codon consists of three bases; thus there are 64 codons. All codons are written in the 5'--3' direction, and the code is unambiguous. in that each codon is specified for one an only one amino acid.

Deeper look into pI focusing

If we have a protein with a pI of 9 then it will stop at pH of 9, but if we place this pH of 9 having protein in the area with pH is 7 it will have more protons around it causing it to have a positive charge and be attracted to the negative cathode which is on the basic side of the gel and when it reaches the pH 9 area the charge dissociates and the protein becomes neutral again. remember the pH of each end -acids have more protons which carry a positive charge, thus the cathode which is negatively charged -bases have negative charged OH- ion which are attracted to the anode which is positively charged

Isoleucine

Ile I

Induced Fit Model

Image the enzyme is a stress ball and the substrate is a stressed kid. The student wants to relax so picks up a stress ball and starts squeezing, causing both to change conformation and shape In this case the substrate (student) has induced a changed int the shape of the enzyme (ball), this also requires energy and therefore this part of the reaction is endergonic, but letting go of the ball doesnt require that much energy and it Exergonic. once the student lets go we have out desired product, a relaxed student and the ball returns to shape just like enzymes

Cyclic sugar molecules end form

In glucose the a-anomer has the -OH group of C-1 Trans to the -CH2OH substituent (axial and down) Where the B-anomer has the -OH group of C-1 cis the -CH2OH substituent (equatorial and up)

In the absence of Oxygen what occurs beside Glycolysis?

In the absence of Oxygen Fermentation will occur. The key fermentation enzyme in mammalian cells is lactate dehydrogenase, which oxidizes NADH to NAD+, replenishing the oxidized coenzyme for glyceraldehyde-3-phosphate dehydrogenase.

What conditions and hormones promote lipid mobilization form fat stores?

In the post absorptive and prolonged fasting states, lipid mobilization is favored. A decrease in insulin levels, as well s an increase in epinephrine or cortisol, will increase lipid mobilization from adipocytes.

What happens in the spliceosome?

In the spliceosome, small nuclear RNA (snRNA) molecules couple with proteins known as small nuclear ribonulceoproteins (snRNPs) The snRNA/snRNP complex recognizes both the 5' and 3' splice sites of the introns. These noncoding sequences are excised in the form of a lariat and then degraded.

Inactivation of both alleles or mutations of tumor suppressor genes known as antiocogenes leads to what?

Inactivation of both alleles leads to loss of function and mutations of these genes result in loss of tumor suppression activity

Mismatch Repair

Incorporate the enzymes encoded by genes MSH2 & MLH1, which detect and remove errors introduced in replication that were missed during the S phase of the cell cycle. These enzymes are homologues of MutS & MutL in prokaryotes, which serve a similar function.

Falling levels of glucose cause an increase in what?

Increase in cyclic AMP (cAMP) when glucose level fall. this then binds to CAP inducing a conformational changed in CAP that allows it to bind the promoter region of the operon, further increasing transcription of the lactase gene.

What are the two types of operons?

Inducible systems Repressible systems

What is said to be compared to inducible systems?

Inducible systems are analogous to competitive inhibition for enzyme activity. As the concentration of the inducer increases, it will pull more copies of the repressor off of the operator region, freeing up those genes for transcription. this allows for products to be produced only when they are needed.

What are the three steps of initiation?

Initiation Elongation Termination

The three stages of translation?

Initiation Elongation Termination

What are the specialized factors for Initiation, Elongation, and Termination?

Initiation- intiation factors Elongation - elongation factors Terminaiton - release factors GTP for each step.

Key concept

Insulin acts to lower blood sugar levels/ the couterregulatory hormones, which include glucagon, epinephrine, cortisol, and growth hormone act to rase blood sugar levels by stimulating glycogenolysis and gluconeogenesis.

Surface vs Interior of protein

Interior: long alkyl chain possessing proteins such as alanine, isoleucine, leucine, valine, and phenylalanine are on the interior. These are strongly hydrophobic and thus more likely to be found on the interior Surface: amino acids with positively charged side chains- histidine, arginine and lysine. Plus negatively charged Aspargine, glutamine, glutamate and aspartate are hydrophilic thus on the inside. Charged side chains- outside Noncharged alkyl chains- inside

Keratin

Intermediate filament proteins found in epithelial cells Contribute to the mechanical integrity of the cell and also function as regulatory proteins -in hair and nails

How to guess how an amino acid will react..

Ionizable groups tend to gain protons under acidic conditions and lose them under basic conditions low pH- protonated high pH- deprotonated Also remember pKa, if pH is less than pKa a majority of species will be protonated. If the pH is higher than the pKa a majority of species will be deprotonated

Gel Electrophoresis

Is the technique used to separate macromolecules such as DNA and proteins by size and charge. All molecules of DNA are negatively charged because of the phosphate groups in the backbone of the molecule, so all DNA strands will migrate toward the anode of an electrochemical cell. agarose gel the longer the DNA the slower it will migrate

What enzyme catalyzes the rate-limiting step of the citric acid cycle?

Isocitrate dehydrogenase

What separation method can be used to separate proteins based on their Isoelectric points? pI

Isoelectric focusing and ion-exchange chromatography both separate based on charge. The charge of a protein in an environment is determined by its isoelectrical point (pI)

How does the gel for isoelectric focusing differ from the gel for traditional electrophoresis? Isoelectric focusing uses a gel with much larger pore sizes to allow fro complete migration isoelectric focusing uses a gel with SDS added to encourage a uniform negative charge isoelectric focusing uses a gel with a pH gradient that encourages a variable charge The gel is unchanged in isoelectrical focusing: the protein mixture is treated before loading.

Isoelectrical focusing uses a gel with a pH gradient that encourages a variable charge. When a protein is in a region with a pH above its pI it is negatively charged and moves toward the anode. When it is in a pH region below the pI it is positively charged and moves toward the cathode. The the pH = pI the protein is halted

How does one isolate the DNA of interest

It is referred to as a vector, forming a recombinant vector. Vectors are usually bacterial or viral plasmids that can be transferred to a host bacterium after insertion of the DNA of interest

What is hnRNA?

It is the primary transcript formed when the DNA double helix reforms. mRNA is derived from hnRNA via postranscriptional modifications.

How does the enzyme discriminate which is the template strand and which is the incorrectly paired daughter strand?

It looks at the level of methylation; the template strand has existed in the cell for a longer period of time, and therefore is more heavily methylated. The template strand is the more methylated one!!

From a metabolic standpoint does it makes sense for carbohydrates to get oxidized or reduced? What is the purpose of this process?

It makes sense for carbohydrates to become oxidized while reducing other groups. This is the case because aerobic metabolism requires reduced forms of electron carriers to facilitate processes such as oxidative phosphorylation. Because carbohydrates are a primary energy source they are oxidized

What conditions and tissues favor ketogenesis? Ketolysis?

Ketogenesis is favored by a prolonged fast and occurs in the liver. It is stimulated by increasing concentrations of acetyl-CoA. Ketolysis is also favored during a prolonged fast, but is stimulated by a low-energy state in muscle an brain tissues and does not occur in the liver.

Ketolysis is what?

Ketolysis regenerates acetyl-CoA for use as an energy source in peripheral tissues.

Ketones is reducing sugars

Ketones give positives to Tollens and Benedicts test Ketones cannot be oxidized to Carboxylic acids but they can Tautomerize to form aldoses under basic condition via ketolenol shifts When in alludes form they can react with Tollen and Benedict to form carboxylic acids

Ketose sugar may have the ability to act as reducing sugars. Which process explains this? Ketose sugars undergo tautomerization The ketone group is oxidized directly Ketose sugars undergo anomerization The ketone group is reduced directly

Ketose sugars undergo tautomerization. Ketose sugars under tautomerization, a rearrangement of bonds to undergo keto-enol shift. This forms an aldose, which then allow then to act as reducing sugars. A ketone group alone cannot be oxidized.

Michaelis Constant

Km after deriving it, Km can be understood to be the substrate concentration at which half of the enzymes activity sites are full ( hall of the stress balls). used to compare enzymes affinity The enzyme with higher Km has the lower affinity for its substrate because it requires a higher substrate concentration to be half saturated. The Km value is intrinsic property of the ES system and cannot be altered by changing the concentration of substrate or enzyme low kM reflects high affinity for the substrate

L-amino acid and D-amino acid

L=NH2 is drawn on the left D=NH2 is drawn on the right remember that cysteine is still L-amino acid it just has (R) configuration

What proteins are specific to the formation and transmission of cholesterol esters, and what are their functions?

LCAT catalyzes the esterification of cholesterol ro form cholesterol esters, CETP promotes the transfer of cholesterol esters from HDL to IDL, forming LDL.

LCAT catalyzes what?

LCAT catalyzes the formation of cholesterol esters for transport with HDL

LDL does what?

LDL primarily transports cholesterol for use by tissues

What is the lac operon induced by?

Lac operon is induced by the presence of lactose; thus these genes are only transcribed when it is useful to the cell.

Example of an inducible system?

Lac operon, which contains the gene for lactase. bacteria can digest lactose, but it is more energetically expensive than digesting glucose. Therefore, bacteria only want to use this option if lactose is high and glucose is low.

Feed-forward regulation

Less often, enzymes may be regulated by intermediates that precede the enzyme in the pathway.

Leucine

Leu L

What does a (alpha) a-1,6 linkage mean in talking about disaccharides?

Linkages are named for the configuration of the anomeric carbon and the numbers of the hydroxyl-contatining carbon a-1,6 this is formed between two D- molecules, the a-anomeric carbon of the first glucose (C-1) attaches to C-6 of the second glucose. The second glucose can be either a-or B- (alpha or beta) anomer if it occurs between two anomeric carbons, it must be specified in the name. a,a-1,1 linkage

Chapter 5

Lipid Structure and Function

Chapter 11

Lipid and Amino Acid Metbolism

What are lipid rafts?

Lipid rafts are collections of similar lipids with or without associated proteins that serve as attachment points for other biomolecules; these rafts often serve in signaling.

Lipids are mobilized from adipocytes by what?

Lipids are mobilized from adipocytes by hormone-sensitive lipase

Lipids are mobilized from lipoproteins by what?

Lipids are mobilized from lipoproteins by lipoprotein lipase.

List the following membrane components in order from most plentiful to least plentiful: carbohydrates, lipids, proteins, nucleic acids.

Lipids, including phospholipids, cholesterol and others are most plentiful: Proteins, including transmembrane protein (channels and receptors), membrane associated protein and embedded proteins are next most plentiful: Carbohydrates including the glycoprotein coat and signaling molecules are next. Nucleic acids are essentially absent.

Lipoproteins are synthesized primarily by which two organs?

Lipoproteins are synthesized primarily by the intestine and liver.

Where are long chain fatty acids absorbed?

Long chain fatty acids are absorbed as micelles and assembled into chylomicrons for release into the lymphatic system.

The conversion of ATP to cyclic AMP and inorganic phosphate is most likely catalyzed by which class of enzyme? Ligase Hydrolase Lyase Transferase

Lyase Lyases are responsible for breaking down a single molecule into two molecule without the addition of water or transfer of electrons.

Lysine

Lys K -has a terminal primary amino group (on end)

Which amino acids contribute most significantly to the pI of a Protein. Lysine Glycine Arginine pick any combination of 1 option to 2 or all of them.

Lysine and Arginine pI is determined by the number of acidic and basic amino acids a protein has. basic amino acids being: arginine, lysine, and histidine. Acidic amino acids being: Aspartic acids and glutamic acid Glycine has a hydrogen R group so it doest contribute much of anything.

Lysine titration

Lysine has two amino groups and one carboxyl group so the charge in its fully protonated state is +2 not +1 First loosing the proton off the carboxylic group around pH 2 brings charge to +1 Second loosing the proton off the main amino group around pH 9 and charge is neutral Third becomes negative when it loses the proton on the amino group in the side chain around 10.5

In lysine the pKa of the side chain is about 10.5. Assuming that the pKa of the carboxyl and the amino groups are 2 and 9 respectively, the pI of lysin is closest to. 5.5 6.2 7.4 9.8

Lysine is basic so its pI is above 6 and its pKa equation is NH group + R group /2 = 9 + 10.5 /2 = 9.8 \ It has a basic side chain so we ignore the pKa of the carboxyl group If it had an acidic side chain we would igrnore the pKa of the amine group

Which of the following is digestible by humans and is made up of only one type of monosaccharide? Lactose Sucrose Maltose Cellobiose

Maltose While maltose and cellobiose both have the same glucose subunits, only maltose is digestible by humans because the B-glycosidic linkage in colonies cannot be cleaved in the human body,

Splicing: Introns and Exons

Maturation of the hnRNA includes splicing of the transcript to remove noncoding sequences (introns) and ligate coding sequences (exons) together Splicing is accomplished by the spliceosome

Membrane associated proteins do what?

Membrane associated proteins may act as recognition molecules or enzymes.

Membrane potential is what?

Membrane potential is maintained by the sodium-potassium pump and leak channels.

Three types of RNA

Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA)

Methionine

Met M -one of two amino acids that contain Sulfur in side chain

Describe the structure of a micelle

Micelles are collections of lipids with their hydrophobic ends oriented toward the center and their charged ends oriented toward the aqueous environment. Micelles collect lipids within their hydrophobic centers.

What are the two categories of expressed point mutations?

Missense Mutation Nonsense Mutation

What is a Missesne mutation?

Missense is a mutation where one amino acid substitutes for another

What other molecules can be used to make acetyl-CoA and how does the body perform this conversion for each?

Molecule and how the body makes it Fatty Acids- Shuttle acyl group from cytosolic CoA-SH to mitochondrial CoA-SH via carnitine; then undergo B-oxidation Ketogenic amino acids- Transaminate to lose nitrogen; convert carbon skeleton into ketone body, which can be converted into acetyl CoA Ketones- Reverse of ketone body formation Alcohol- Alcohol dehydrogenase and acetaldehyde dehydrogenase convert alcohol into acetyl-CoA

Reactions of Monosaccharides

Monosaccharides contain alcohols, and either aldehydes or ketones so they undergo the same reaction that they do when present in other compounds. Includes: oxidation and reduction, esterification, and nucleophilic attack (creating glycosides)

Cyclic sugar molecule formation

Monosaccharides contain both a hydroxyl group (OH-), which can serve as a nucleophile and a carbonyl (C=) group which is the most common electrophile By knowing this the monosaccharides can undergo intramolecular reactions to form cyclic Hemiacetals & Hemiketals The only stable molecules that are stable in solution are six and five membered rings When whether a hemiacetal or hemiketal is formed the carbonyl carbon becomes chiral in the process and is referred to as the anomeric carbon

Disaccharides

Monosaccharides react with alcohols to form acetals. Glycosidic bonds formed between hydroxyl groups of two monosaccharides result in the formation of a disaccharide can have a 1,2:1,4:1,6 linkage Formation of an a- or B- glycosidic linkage is nonspecific in that the anomeric carbon of a cyclic sugar can react with any hydroxyl group on any other sugar

pH effects on enzyme activity

Most enzymes also depend on pH in order to function proper. -pH affects the ionization of the active site also can lead to denaturation -Pepsin works well in the stomach and has a miximal activity of pH around 2 -Pancreatic enzyme work in small intestines and best around 8.5

Which of the following is least likely to cause denaturations of proteins? Heating the protein to 100 degrees C Adding 8M urea Moving it to a more hypotonic enviromnent Adding a detergent such as sodium dodecyl sulfate

Moving it to a more hypotonic environment High temps, solutes, and detergents and denature a protein

A reaction that uses H+/H2O makes two cyclic sugar molecules with the hydroxyl group in on in axial position and equatorial position in the other molecules. Aldehyde formation Hemiacetal formation Mutarotaiton glycosidic bond cleavage

Mutaroation In solutionm the hemiacetal ring of glucose will break open spontaneously and then re-form. When the ring is broken, bond rotation occurs between C-1 and C-2 to produce either the a- or the B- anomer.

The formation of a-D-glucopyranose from B-D-glucopyranose is called Glycosidation Mutarotation Enantiomerization Racemization

Mutarotation Mutarotation is the interconversion between anomers of a compound Enantiomerization and Racemiation are related Glycosidation is the addition of a sugar to another compound

Oncogenes

Mutated genes that cause cancer

What is the difference between NADPH and NADH?

NAD+ is an energy carrier NADPH is used in biosynthesis in the immune system and to help prevent oxidative damage

What are the three primary functions of NADPH?

NADPH is involved in -lipid biosynthesis -bactericidal bleach formation in certain white blood cells -maintenance of glutathione stores to protect against reactive oxygen species.

Four groups attached to alpha carbon in an amino acids:

NH2 Carboxylic acid H R group but if glycine it has -H as side chain

In the equation A-->B-->C Substrate C is an allosteric inhibitor to enzyme 1 (A-->B). Which of the following is another mechanism necessarily cause by substrate C? Competitive Inhibition Irreversible Inhibition Feedback Enhancement Negative Feedback.

Negative Feedback By limiting the activity of enzyme 1 the rest of the pathway is slowed which is the definition of negative feedback

Feedback inhibition

Negative Feedback as well. helps maintain homeostasis, for example once we have enough of a given product we want to turn off the pathway that creates the product rather than creating a new more. - in this the product may bind to the active site of an enzyme or multiple enzymes that acted earlier thereby competitively inhibiting these enzymes and making them unavailable for use

What happens from the reduction in which binding of a protein reduces transcriptional activity?

Negative control

What is a negative control system?

Negative control system requires binding of a protein to the operator site to decrease transcription

What type of operon is the lac operon?

Negative inducer system

What type of operon is the trp operon?

Negative repressible system

Do amino acids have to always have the amino and carboxyl groups on the same carbon?

No, for example neurotransmitter gama-aminobutyric. This amino acid is connected to the gamma carbon. Three carbons away from the carboxyl group. But the MCAT focusses on the 20 essential alpha amino acids that are encoded by the human genetic code.

Chapter 3

Non-enzymatic Protein Function and Protein Analysis

Enantiomers

Nonidentical, non-superimposable mirror images of each other Keep in mind that any molecule that contains chiral carbons and no internal plane of symmetry has an enantiomer

What is a Nonsense mutation?

Nonsense is a mutation where the codon now encodes for a premature stop codon (known as truncation mutation as well)

Key concept-

Of all enzymes that the MCAT is most likely to test you on, the rate limiting enzymes for each process are at the top of the list. Glycolysis- Phosphofructokinase-1 Fermentation: lactate dehydrogenase Glycogenesis: glycogen synthase Glycogenolysis: glycogen phosphorylase Glucogenesis: fructose-1-6 bisphosphatase Pentose Phosphate Pathway: glucose-6-phosphate dehydrogenase.

How does translation begin?

Once the mRNA transcript is created and processed, it can exit the nucleus through nuclear pores. Once in the cytoplasm, mRNA finds a ribosome to begin the process of Translation.

Oncogenes vs. Mutated tumor suppression genes

Oncogenes promote the cell cycle while mutated tumor suppression can no longer slow the cell cycle. Oncogenes are like stepping on the gas while mutations are like cutting the breaks.

Osmosis

Osmosis describes the diffusion of water across a selectively permeable membrane.

Osmotic pressure is a what?

Osmotic pressure is a colligative property, which is the pressure applied to a pure solvent to prevent osmosis and is used to express the concentration of the solution.

Enzyme class names

Oxidoreductases Transferases Hydrolases Lyases Isomerases Ligases mnemonic devce: Lil' Hot

DNA polymerases delta and epsilon are assisted by what?

PCNA protein which assembles into a trimer to form the sliding clamp. The clamp helps to strengthen the interaction between these DNA polymerases and the template strand

Where is PFK2 found?

PFK is found in the liver.

Passive transport

Passive transport does not require energy because the molecule is moving down its concentration gradient or from an area with higher concentration to an area of low concentration.

Phenylalanine

Phe F -smallest of the aromatics

A particular alpha helix is known to cross the cell membrane. Which of these amino acids is most likely to be found in the transmembrane portion of the helix Glutamate Lysine Phenylalanine Aspartate

Phenylalanin if it is going to cross the transmembrane it will most likely be exposed to a hydrophobic enviroment so we would need to pick an amino acid with a hydrophobic side chain

Hydrolases examples

Phosphatase- cleave a phosphate group from another molecule Peptidase, Nucleases and Lipases

Phosphofructokinase-2 (PFK-2)

Phosphofructokinase-2 (PFK-2) is what produces the F2,6-BP that activates PFK-1. IT is activated by insulin and inhibited by glucagon.

Phospholipids do what?

Phospholipids move rapidly in the plane of the membrane through simple diffusion.

When lipids leave the stomach, what stages of digestion have been accomplished? What enzymes are added to accomplish the next phase?

Physical digestion is accomplished in the mouth and the stomach, reducing the particle size. Beginning in the small intestine, pancreatic lipase, collapse, cholesterol esterase, and bile assist in the chemical digestion of lipids. In the more distal portion of the small intestine, absorption occurs.

What is a mutation that affects one of the nucleotides in a codon?

Point mutation because these point mutations can affect the primary amino acid sequence of the protein they are called expressed mutations.

Difference between point mutation and frameshift mutation?

Point mutations occur when one nucleotide is changed. Frameshift mutation occurs when some number of nucleotides are added to or deleted from the mRNA sequence -Insertion or Deletion will shift the reading frame (three nucleotides of a codon) resulting in changes in the amino acid

Native PAGE

Polyacrylamide gel electrophoresis (PAGE) is used to analyze proteins in Native states. Unfortunately this is limited by the varying mass to charge and mass to size ratios of cellular proteins because multiple different proteins may experience the same level of migration PAGE is most useful to compare the molecular size or the charge of proteins known to be similar in sized from other methods like SDS-PAGE or size exclusion chromatography

What does Polymerase III (prokaryotes) and DNA polymerases alpha (eukaryotes) do?

Polymerase III (prokaryotes) and DNA polymerases alpha (eukaryotes) adds nucleotides to growing daughter strand.

Proteins; Primary and secondary structure

Primary - linear arrangement of amino acids coded in an organisms DNA, listed from N- terminus to the C- terminus. This is stabilized by the formation of covalent peptide bonds between adjacent amino acids. Secondary - Alpha helices and Beta pleated sheets - alpha helices, rodlike structure in which the peptide chain coils clockwise around a central axis, stabilized by hydrogen bonds. The a-helix is important in the structure of Keratin. - beta pleated sheets, can be parallel or antiparallel, the chain laying along side one another forming rows or strands held together by hydrogen bonds as well. The h bonds result in the shape of B pleated sheets.

Compare the two types of active transport. What is the difference between symport and antiport?

Primary active tranport uses ATP as an energy source for the movement of molecules against their concentration gradient, while secondary active transport uses an electrochemical an electrochemical gradient to power the transport. Symport moves both particles in secondary active transport across the membrane in the same direction, while antiport moves particles across the cell membrane in opposite directions

Which of these is most likely to be preserved when a protein is denatured? Primary Secondary Tertiary Qauternary

Primary structure denaturing never breaks the peptide bonds so primary structure will remain most likely

Proline

Pro P

What is the initial amino acid in prokaryotes and eukaryotes?

Prokaryotes = N-formulmethionine (fMET) Eukaryotes = methionine

What repair(s) is used if DNA polymerase makes a mistake?

Proofreading Mismatch Repair Nucleotide Excision Repair Base Excision Repair

Protein digestion occurs where?

Protein digestion occurs in the small intestine

Protein isolation

Proteins and other biomolecules are isolated from body tissues or cell cultures by cell lysis and homogenization which is crushing, grinding or blending the tissue of interest into an evenly mixed solution. Centrifugation can then isolate the proteins before another isolation technique must be used -isolation techniques are electrophoresis and chromatography

Isoelectric Focusing

Proteins can be separated on the basis of their isoelectric point (pI) Remember the pI is the pH last which the protein or amino acid is electrically neutral (Zwitterion) or in which the amino group is protonated, carboxyl group is deprotonated and any side chain is electrically neutral. Remember the calculation of pI? for basic amino acid- (NH pka + R group pka)/2 = pI -above 6 for acidic amino acid (R group pka + COOH group pka)/2 = pI below 6

Which protein properties allow UV spectroscopy to be used as a method of determining concentration. Proteins have partially planar characteristics in peptide bonds Globular proteins cause scattering of light Proteins contain aromatic groups in certain amino acids All organic macromolecules can be assessed with UV spec

Proteins contain aromatic group in certain amino acids UV spec is used better with conjugated systems of double bonds Peptide bonds may have resonance but this isn't adequate for UV absorption Aromatic systems are conjugated and phenyaline, tyrosine and tryptophan all contain aromatic structures.

What are the two families of nitrogen containing bases found in nucleotides?

Purines and Pyrimidines

As the new phosphodiester bond is made what is released?

Pyrophosphate (PPi) is released

What is the overall reaction of the pyruvate dehydrogenase complex?

Pyruvate + CoA-SH + NAD+ --> acetyl-CoA + CO2 + NADH + H+

Pyruvate Kinase

Pyruvate Kinase is the last enzyme in aerobic glycolysis, it catalyzes a substrate level phosphorylation of ADP using the high energy substrate phosphoenolpyruvate (PEP). Pyruvate Kinase is activated by fructose 1,6-bisphosphate form the PFK-1 reaction. This is referred to as fee-forward activation, meaning that the product of an earlier reaction of glycolysis (fructosese 1,6-bisphosphate) stimulates, or prepares, a later reaction in glycolysis (by activating pyruvate kinase)

The three irreversible steps of glycolysis most be bypassed by different enzymes:

Pyruvate carboxylase Fructose-1,6-biphosphatase Glucose 6-phosphatase

What are the four enzymes unique to gluconeogenesis? Which irreversible glycolytic enzymes do they replace?

Pyruvate carboxylase - replaces Pyruvate kinase Phosphoenolpyruvate carboxykinase (PEPCK) - Pyruvate kinase Fructose-2,6-bisphosphatase - replaces Phosphofructokinase-1 Glucose-6-phosphatase replaces Glucokinase

Pyruvate carboxylase

Pyruvate carboxylase converts pyruvate into oxaloacetate, which is converted to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase(PEPCK) . Together, these two enzyme bypass pyruvate kinases. Pyruvate carboxylase is activated by acetyl-CoA from B-oxidation; PEPCK is activated by glucagon and cortisol.

Pyruvate dehydrogenase

Pyruvate dehydrogenase refers to a complex of enzymes that convert pyruvate to acetyal-CoA It is stimulated by insulin and inhibited by acetyl-CoA

What are the three types of RNA Polymerases in the transcription of mRNA?

RNA Polymerase I: is located in the nucleolus and synthesizes rRNA RNA Polymerase II: is located in the nucleus and synthesizes hnRNA and some small nuclear RNA (snRNA) RNA Polymerase III: is located in the nucleus and synthesizes tRNA and some rRNA

Which direction does RNA Polymerase travel and why?

RNA Poymerase travels along the template strand in the 3'--5' direction, which allows for the construction of transcribed mRNA in the 5'--3' direction. Remember that RNA polymerase does not proofread its work, so the synthesized transcript will no be edited.

Chapter 7

RNA and the Genetic Code

When starting Transcription, where does RNA polymerase bind?

RNA polymerase II binds to the TATA boxm which is located within the promoter region of a relevant gene, at about -25

How is RNA synthesized?

RNA polymerase located genes by searching for specialized DNA regions known as the promoters. Does not require a primer to start In eukaryotes RNA polymerase II is the main player in transcribing mRNA and its binding site in the promoter region is known as the TATA Box.

What is the backlash of gene therapy?

Randomly integrated DNA possess a risk of integrating near and activating a host ocogene. Among children treated for SCID a small number have developed Leukemias. (cancer of white blood cells.)

What are the reactants of the pyruvate dehydrogenase complex? What are the products?

Reactants of the pyruvated dehydrogenase complex are- Pyruvate, NAD+ and CoA are the reactants of the PDH complex Products of the pyruvated dehydrogenase complex are- Acetyl-CoA, NADH, and CO2 are the products.

Tollens Reagent and Benedicts Reagent

Reagents used to detect the presence of reducing sugars. Tollens - utilizes Ag(NH3)2+ as an oxidizing agent. If positive aldehydes reduce Ag+ to metallic silver Benedicts- when used the aldehyde group of an aldose is readily oxidized which is indicated by a red precipitate of Cu2O

What is Recombinant DNA technology?

Recombinant DNA technology allows a DNA fragment from any source to be multiplied by either gene cloning or (PCR) This provides the mean of analyzing and altering genes and proteins. As well as genetic testing such as carrier detection and prenatal diagnosis of genetic diseases; it is also useful for gene therapy.

Tips on the Configurations

Remember if they differ at only one chiral carbon then they are epimers Remember also that a compound can only have one enantiomers but multiple diastereomers depending on how many chiral carbons are inverted between the two molecules

Activation energy

Remember that thermodynamics relates the relative energy states of a reaction in terms of its products and reactants. Endergonic reaction - requires energy input Exergonic reaction - energy is given off

Remember!

Remember the other physiological changes that promote a right shift of the oxygen dissociation curve (Bohr effect) -High 2,3-BPG -Low pH -High [H+] -High pCO2 These all occur during exercise giving the mnemonic; Exercise is the RIGHT thing to do.

DNA replication: what helps it?

Replisome or replication complex is a set of specialized proteins that assist the DNA polymerase. The begin the process of replication DNA unwinds at points called origins of replication. The generation of new DNA proceeds in both directions creating replication forks on both sides of the origin.

Ribosomal RNA (rRNA)

Ribosomal RNA is synthesized in the nucleolus and functions as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm.

What is the Ribosome and its function?

Ribosome is composed of proteins and rRNA. The function of the ribosome is to bring the mRNA message together with the charged aminoacyl-tRNA complex to generate the protein.

What is the function of sodium dodecyl sulfate (SDS) in SDS-PAGE

SDS solubilizes proteins to give them uniformly negative charges, so the separation is based purely on size. SDS is a detergent and will digest proteins to form micelles with uniform negative charges. Because the protein is sequestered with in the micelle other factors such as charged the protein and the shape have minimal role during separation. With this they can be modeled as being spheres and dependent only on size.

Saturated vs. Unsaturated fatty acids?

Saturated fatty acids have no double bonds between carbons. Unsaturated fatty acids have one or more double bonds.

Why D and L configuration?

Scientists used glyceraldehyde to learn about the optical rotation of sugars. The results of this early study led to the D & L naming. D-Glyceraldehyde was later determined to exhibit a positive rotation and L-Glyceraldehyde had a negative rotation. + & - cannot be determined by the D & L configuration but must be determined experimentally

Serine

Ser S -possess -OH group, very polar

Polar Side Chains- nonaromatic

Serine- Threonine- -both possess -OH in side chains, in turn making them extremely highly polar and able to h-bond Asparagine- Glutamine- -have amide side chains that do not gain or lose protons with changes in pH and do not become charged Cysteine- -has a thiol (-SH) group in side chain, remember that the group (-SH) is weaker than (-OH0 which leaves cysteine prone to oxidation, the only amino acid that uses (R)-configuration

Where are short chain fatty acids absorbed?

Short chain fatty acids are absorbed across the intestine into the blood

What proteins are required to hold the strands apart?

Single-stranded DNA-binding proteins will bind to the unraveled strand, preventing both the reassociation of the DNA strands and the degradation of DNA by nucleases.

What role do promoter sites have?

Site of RNA polymerase binding (similar to promoters in eukaryotes) further upstream from structural gene

Which of the following method would be best to separate large quantities of the following proteins Protein A - pI=6.5, 28000MM Protein B - pI=6.3 70000 Protein C - pI= 6.6 200,000 Ion-Exchange chromatography Size-exclusion chromatography isoelectric Focusing Native page

Size exclusion Chromatography The proteins only differ on their molecular weight. pI values are really close so ion-exchange is not a good choice. The question specifies "large quantity" which is yielded better through chromatography than PAGE because anything that is utilizing the gel will handle a small volume of protein,

SDS-PAGE

Sodium Dodecyl Sulfate - polyacrylamide gel electrophoresis is a useful too to separate proteins on the basis of mass alone. Starts like PAGE but adds SDS a detergent that disrupts all nonequivalent interactions

Sphingolipids

Sphingolipids are sites of biological recognition at the cell surface and can be bonded to various head groups and fatty acids this have a sphingosine or sphenoid backbone as opposed to the glycerol backbone of glyverophospholipids can be either phospholipids containing a phosphodiester linkage or Glycolipids containing glycosidic linkages to sugars. Sphingolipids are divided into four subclass differing by their head group

Mutarotations

Spontaneous change between open and closed forms of hemiacetal rings when exposed to water occur more rapidly when catalyzed with an acid or base In solution a-anomeric configuraiton is less favored because the hydroxyl group of the anomeric carbon is axial, adding to the steric strain of the molecule.

Starch

Starches are polysaccharides that are more digestible by humans because they are linked a-D-glucose monomers. Plants store starch as amylose, a linear glucose polymer linked via a-1,4 glycosidic bonds. Another types of starch is amylopectin which starts off with the same type of linkage that amylose exhibits but also contain branches via a-1,6 glycosidic bonds Iodine- is a well known reagents that test for the presence of starch and does so by fitting inside then helix conformation amylose typically makes forming a starch iodine complex.

Nomenclature of Carbohydrates

Start with monosaccharides, the simplest containing 3 carbon atoms are called trioses. Then the 4, 5, and 6 carbon atom containing carbohydrates called tetroses, pentoses, and hexoses. if they contain and aldehyde then they are called Aldoses along with ketone containing called Ketoses example 6 carbon sugar and an aldehyde = aldohexose 5 carbon sugar and a ketone = ketopentose Numbering of carbons is same as organic basic rules with the carbonyl carbon being the most oxidized and hence will have the lowest number possible

Proteins involved in biosignaling can have functions in what?

Substrate binding or enzymatic activity

Important Disaccharides

Sucrose Lactose Maltose

What happens when the helicase unwinds the DNA strands?

Supercoiling occurs and is wrapping of DNA on itself as its helical structure is pushed even further toward the telomeres during replication.

A graph shows kinetic date obtained for flu virus enzyme activity as a function off substrate concentration in the presence and absence of two antiviral Drugs Look on page 67 in biochem Which statement is true? Both drugs are noncompetitive inhibitors of the viral enzyme Tamiflu increases the Km value for the substrate compared to Relenza Relenza increases the Vmax value for the substrate compared to Tamiflu Both drugs are competitive inhibitors of the viral enzyme

Tamiflu increases the Km value for the substrate compared to Relenza This is a hallmark of Competitive inhibition Noncompetitive inhibitors result in decreased Vmax and the same Km as the graph depicts as well but it isn't an answer One is competitive (Tamiflu) and the other is noncompetitive (relenza) ruling out A B. is true C. is false for Relenze decreases the Vmax. Remember if it goes up the y- axis it is decreasing the Vmax not increasing for it it 1/vmax D is wrong because one is a competitive and the other is noncompetitive

Structural proteins

Tendons, Ligaments and basement membranes are all proteinaceous. Primary structural proteins are Collagen, Elastin, Keratin, Actin, and Tubulin -These have high repetitive secondary structures and a super secondary structure- referred to as a motif.

Proteins: Tertiary and Qauternary structures

Tertiary- 3-D shape and determined by hydrophilic and hydrophone interaction between R groups of amino acids. The 3-D shaped is determined by moving the philic to the outside and the phobics to the inside - presence of disulfide bonds, these create loops in the protein chain. these also determine how wavy or curly hair is. The more bonds the curlier it is. To form a disulfide bond you need to lose two protons and two electrons. (Oxidation) Qauternary- this is where the function of the protein comes from. - can induce cooperativity or allosteric effects. - Hemoglobin and antibodies contain 4 subunits.

Which enzyme is responsible for trapping fructose in the cell? What enzyme in fructose metabolism results in a product that can feed directly into glycolysis, linking the two pathways?

The "Trapping" enzyme is: Fructose is phosphorylated by fructokinase, trapping it in the cell (with a small contribution from hexokinase). The "Linking" enzyme is: Aldolase B produces dihydroxyacetone phosphate (DHAP) and glyceraldehyde (which can be phosphorylated to form glyceraldehyde 3-phosphate), which are glycolytic intermediates, thus linking the pathways.

Which enzyme is responsible for trapping galactose in the cell? What enzyme in galactose metabolism results in a product that can feed directly into glycolysis, linking the two pathways? "Trapping" enzyme? ____ "Linking" enzyme? _____

The "Trapping" enzyme is: Galactose is phosphorylated by galactokinase, trapping it in the cell. The "Linking" enzyme is: Galactose 1-phosphate uridyltransferase produces glucose 1-phosphate, a glycolytic intermediate, thus linking the pathways.

What are the three biding sites for tRNA in the Ribosome?

The A site (aminoacyl), P site (peptidyl) and E site (exit) APE

Why is the a-anomer of D-glucose less likely to form than the B-anomer? The B-anomer is preferred for metabolism The B-anomer undergoes less electron repulsion The a-anomer is the more stable anemia The a-anomer forms more in L-glucose

The B-anomer undergoes less electron repulsion The hydroxyl group on the anomeric carbon of the B-anomer is equatorial thereby creating less non-bonded strain than the a-anomer, which has the -OH group of the anomeric carbon in the axial position.

What is the difference between the ETC an oxidative phosphorylation? What links the two?

The ETC is made up of the physical set of inter membrane proteins located on the inner mitochondrial matrix, and they undergo oxidation-reduciton reactions as they transfer electrons to oxygen, the final electron acceptor. As electrons are transferred, a proton-motive force is generated in the inter-membrane space. Oxidative phosphorylation is the process by which ATP is generated via harnessing the proton gradient and it utilizes ATP synthase to do so.

A protein collected through affinity chromatography displays no activity even though it is found to have a high concentration using the Bradford protein assay. What best explains this finding? The bradford reagent was prepared incorrectly The active sit is occupied by a free ligand The protein is bound to the column The protein doe not catalyze the reaction of interest

The active site is occupied by a free ligand. Activity and concentration are correlated. Since we have a high concentration we expect a high activity unless the protein is damaged or inactivated in some way. The protein could have been inactivated by a detergent, pH change or Heat, but these aren't any of the answers. We must thing about the procedure, Protein elutes off an affinity column by binding free ligand. In this situation the binding may not have been reversed and thus the free ligand computers for the active site of the enzyme lowering the activity.

What does the addition of water allow in termination?

The addition of this water molecule allows transferase and termination factors to hydrolyze the completed polypeptide caring from the final tRNA. The polypeptide chain will then be released from the tRNA in the P site, and the two ribosomal subunits will dissociate.

A certain cooperative enzyme has four subunits, two of which are bound to substrate. Which of the following statements can be made? The affinity of the enzyme for the substrate has increased The affinity of the enzyme for the substrate has just decreased The affinity of the enzyme for the substrate is at the average for this enzyme class The affinity of the enzyme for the substrate is greater than with one substrate bound

The affinity of the enzyme for the substrate is greater than with one substrate bound Cooperative enzyme demonstrate a changed in affinity for the substrate depending on how many substrate molecules are bound and whether the last change was accomplished because a substate molecules was bound or left the active site of the enzyme Remember that an enzyme with two subunit occupied must have a higher affinity for the substrate than the same enzyme with only one subunit occupied

What happens to the bacterium after isolated?

The bacterium are then grown in colonies and a colony containing the recombinant vector is isolated Using antibiotics can kill off all the colonies not containing the recombinant vector.. This resulting colony can then be grown in large quantities.

Adding concentrated strong base to a solution containing an enzyme often reduces enzyme activity to zero. In addition to causing protein denaturation which of the following is another plausible reason of the loss of enzyme activity? Enzyme activity, once lost, cannot be recovered The base can cleave peptide residues Adding a base catalyzes protein polymerization Adding a base tends to deprotonate amino acids on the surface of proteins

The base can clean peptide residues enzyme activity can be recovered if lost D. is true but doesnt explain why.

Why is it necessary that fetal hemoglobin does not bind 2,3-BPG?

The binding of 2,3-BPG decreases hemoglobin's affinity for oxygen. Fetal hemoglobin must be able to "steal" oxygen from maternal hemoglobin at the placental interface; therefore, it would be disadvantageous to lower its affinity for oxygen.

The brain can derive its energy from what?

The brain can derive up to two-thirds of its energy from ketone bodies during prolonged starvation.

Where does the bulk of protein digestion occur?

The bulk of protein digestion occurs in the small intestine

Cell (plasma) membrane

The cell-plasma membrane is often described as a semipermeable phospholipid bilayer. The phrase along describes both the function and structure of the cell membranes: as a semipermeable barrier, it chooses which particles can enter and leave the cell at any point in time.

What is the Coding Strand (sense strand)

The coding strand of DNA is not used as a template during transcription. Because the coding strand is also complementary to the template strand, it is identical to the mRNA transcript except that all the Thymine nucleotides in DNA have been replaced with uracil in the mRNA molecule.

To identify aromatic rings to be aromatic

The compound is cyclic The compound is planar The compound is conjugated (has alternating single and multiple bonds or lone paris, The compound has 4n+2 (where n is any integer) pie electrons. This is called Huckel's rule

What role does the electron transport chain play in the generation of ATP?

The electron transport chain generates the proton-motive force, an electrochemical gradient across the inner mitochondrial membrane, which provides the energy for ATP synthase to function

What is the first step in replication of DNA?

The first step in replication of DNA is actually to lay down an RNA primer. DNA cannot be synthesize de novo; that is it needs another molecule to hook on. Thus primase synthesizes a short primer in the 5' to 3' direction to start replication on each strand.

Consider a biochemical reaction A-->B which is catalyzed by A--B Hydrogenase. Which of the statement is true? A. The reaction will proceed until the enzyme concentration decreases B. The reaction will be most favorable at 0 degrees C C. A Component of the enzyme is transferred from A to B D. The free energy of the catalyzed reaction is the same for the uncatalyzed reaction

The free energy of the catalyzed reaction is the same for the uncatalyzed reaction Enzymes catalyze reactions by lowering the activation energy, and are not changed or consumed While the activation energy is lowered the free energy of the reaction remains unchanged in the presence of an enzyme

Role of structural gene?

The gene of interest; its transcription is dependent on the repressor being absent from the operator site.

How does the ideal temperature for a reaction change with and without an enzyme catalyst? The ideal temperature is generally higher with a catalyst than without. The ideal temperature is generally lower with a catalyst than without The ideal temperature is characteristic of the reaction not the enzyme No conclusion can be made without known the enzyme type

The ideal temperature is generally lower with a catalyst than without Rate of reaction increases with temperature because of the increased kinetic energy of the reactants, but reaches a peak temperature because the enzyme denatures with the disruption of hydrogen bonds at high temperature. In absence of enzyme the peak temperature is much hotter. Increasing the temperature of a reaction increases chance of achieving the activation energy, but the enzyme catalyst would typically reduce the activation energy.

What distinguishes the inner mitochondrial membrane from other biological membranes? What is the pH gradient between the cytoplasm and the inter membrane space?

The inner mitochondrial membrane lacks, cholesterol, which differentiates it from most other biological membranes. There is no pH gradient between the cytoplasm and the inter membrane space because the outer mitochondrial membrane has such high permeability to biomolecules

What is the key enzyme in cholesterol biosynthesis?

The key enzyme in cholesterol biosynthesis is HMG-CoA reductase.

What is the strand that is copied in a direction opposite the direction of the replication fork?

The lagging strand, On this side of the replication fork, the parental strand has 5' to 3' polarity. DNA polymerase cannot simply read and synthesize on this strand. Because DNA polymerase can only synthesize in the 5' to 3' direction from a 3' to 5' template, small strands called Okazaki fragments are produced.

What is the strand that is copied in a continuous fashion, in the same direction as the advancing replication fork?

The leading strand, This parental strand will be read 3' to 5' and its complement will be synthesized in a 5' to 3' manner.

How is fructose phosphorylated?

The liver phosphorylates fructose using fructokinase to trap it in the cell.

What is the main function of the cell membrane?

The main function is to protect the interior of the cell from the external environment.

Based on its needs, which of the two shuttle mechanisms is cardiac muscle most likely to utilize? Why?

The malate-aspartate shuttle. Because this mechanism is the more efficient one, it makes sense for a highly aerobic organ such as the heart to utitlize it in order to maximize its ATP yield

How is the resting membrane potential maintained?

The membrane potential, which results from a difference in the number of positive and negative charges on either side of the membrane, is maintained primarily by the sodium-potassium pump, which moves three sodium ions out of the cell for every two potassium ions pumped in, and to a minor extent by leak channels that allow the passive transport of ions

Wha is in the phospholipid bilayer?

The phospholipid bilayer includes proteins and distinct signaling areas within lipid rafts. within lipid rafts. Carbohydrates associated with membrane-bound proteins create a glycoprotein coat. The cell wall of plants, bacteria, and fungi contain higher levels of carbohydrates.

What is the primary thermodynamic factor responsible for passive transport?

The primary thermodynamic favor responsible for passive transport is entropy.

What are two potential drawbacks of affinity chromatography?

The protein of interest may not elute from the column because is affinity is too high or it may be permanently bound to the free receptor in the eluent.

What is the ratio of free fatty acids to glycerol produced through lipid mobilization?

The ratio of free fatty acids to glycerol is 3:1. A triacylglycerol molecule is composed of glycerol and three fatty acids.

Initiation

The small ribosomal subunit binds to the mRNA. In prokaryotes the small subunit binds to the Shine-Dalgarno sequence in the 5' untranslated region of the mRNA. In eukaryotes, the small subunit binds to the 5' cap structure. The charged initiator tRNA binds to the AUG start codon through base-pairing with its anticodon within the P site of the ribosome.

Telomeres

The solution for our cells is a simple repeating unit (TTAGGG) at the end of the DNA forming a telomere. Some of the sequence lost in each round of replication and be replaced by the enzyme telomerase. Telomerase is highly expressed in rapidly diving cells. -shortening of telomeres contributes to aging

What are the five steps int he addition of acetyl-CoA to a growing fatty acid chain?

The steps in the attachment of acetyl-CoA to a fatty acid chain are attachment to acyl carrier protein, bond formation between molecules, reduction of a carboxyl group, dehydration, and reduction of a double bond.

Which of the following factors determine an enzyme's specificity? The three dimensional shape of the active site The Michaelis constant The type of cofactor required for the enzyme to be active The prosthetic group to the enzyme

The three dimensional shape of the active site No matter which explanation we are discussing (lock & key or induced fit, the active site determines which substrate the enzyme will react with

What are the two major metabolic products of the pentose phosphate pathway? (PPP)

The two major metabolic products of the pentose phosphate pathway are ribulose 5-phosphate and NADPH.

Equation and use of number of the electrophoresis

The velocity of the migration known as the migration velocity of a molecule , V, is directly proportional to the electric field strength, E, and to the net charge on the molecule, Z, and is inversely proportional to a frictional coefficient, F, which depends on the mass and shape of the migrating molecules. V= Ez/F

Which of these statements concerning peptide bonds is false. Their formation involves a reaction between an amino and a carboxyl group They are the primary bonds that hold amino acids together They have partial double bond character Their formation involves hydration reactions

Their formation involves hydration reactions Peptide bonds are primary covalent bonds between the amino acids that make up the proteins and involve condensation reactions, have a partial double bond character because the double bond resonates between C=O and C=N.

How does B-Oxidation of unsaturated fatty acids differ from that of saturated fatty acids?

There is an additional isomerase and an additional reductase for the B-Oxidation of unsaturated fatty acids, which provide the stereochemistry necessary for further oxidation.

How many times are they repeated and for what?

These steps are repeated eight times to form palmitic acid, the only fatty acid that humans can synthesize.

Titrations of amino acids with charged side chains

These will have an extra step, examples being glutamic acid and lysine

Which of the following statements is most likely to be true of non polar R group in aqueous solution? They are hydrophilic and found buried within proteins They are hydrophilic and found on protein surfaces They are hydrophobic and found buried within proteins They are hydrophobic and found on protein surfaces.

They are hydrophobic and found buried within the proteins Non polar groups are not capable of forming dipoles or hydrogen bonds, this makes them non polar.

All of the following are true of epimers EXCEPT: They differ in configuration about only one carbon They usually have slightly different chemical and physical properties They are diastereomers (exception of glyceraldehyde) They have equal but opposite optical activities

They have equal but opposite optical activities Epimers are monosaccharide diastereomers that differ in their configuration about only one carbon. As with all diastereomers, epimers have different chemical and physical properties, and their optical activities have no relation to each other.

Ways to view the Poly-A-Tail

Think of the poly-a-tail as a fuse for a time bomb for the mRNA transcript; as soon as the mRNA leaves the nucleus, it will seat to get degraded from its 3' end. The longer the poly-a-tail the more time the mRNA will be able to survive before being digested in the cytoplasm. The tail also assists with export of the mature mRNA from the nucleus.

How does one adapt to high altitudes? Low pO2

This involves -Increased respiration -Increased oxygen affinity of hemoglobin (initial) -Increase rate of glycolysis -Increased (2,3-BPG) in RBC (over a 12-24hour period) -Normalized oxygen affinity for hemoglobin resored by the increased level 2,3-BPG -Increased hemoglobin (over days to weeks)

Termination

This is when any of the three stop codons moves into the A site, a protein called release factor binds to the termination codon, causing a water molecule to be added to the polypeptide chain.

Threonine

Thr T -possess -OH group, very polar

Aromatic having side chains

Three amino acids have uncharged aromatic side chains Tryptophan- being the largest and has a double ring system that contains a nitrogen. Phenylalanine- has a benzyl side chain, non polar Tyrosine- which is Phenylalanine but adding a -OH group to it, the -OH makes it polar

Which of these amino acids has a chiral carbon in it side chain? I. Serine II. Threonine III. Isoleucine

Threonine and Isoleucine -all have amino acids have chiral carbons, only glycine doesnt but there are only two with chiral carbons in their side chains and that is Threonine and Isoleucine

Tight junctions

Tight junctions prevent paracellular transport, but do not provide intercellular transport.

Prosthetic group

Tightly bound cofactors or coenzymes are necessary for enzyme function

Amino acid composition

To determine the primary structure of a protein, sequential digestion of the protein with specific cleavage enzymes is used. small proteins are best analyzed with the Edman degradation which uses cleavage to sequence proteins of up to 50 to 70 amino acids. This degradation slecetively and sequentially removes the N-Terminal amino acid of the protein and viewed by mass spec Large proteins would need to be digested with chymotrypsin, trypsin and cyanogen bromide. these cleve the proteins at specific amino acids creating smaller fragments. That then can be read by the Edman degradation. This breaks disulfide links and salt bridges so their positions cannot be determined By combing this and PCR researchers can determine where on a chromosome the gene coding a particular protein resides

Proteins Analysis

To study the structure, function, or quantity is often of interest for a researcher of a commercial laboratory.

Transcription factors

Transcription factors are transcription-activating proteins that search the DNA looking for specific DNA-binding motifs.

Key concept of Transcription

Transcription is subject to the 5'--3' rule just like DNA synthesis. Synthesis of nucleic acids always occurs in the 5'--3' direction

Transcription

Transcription is the creation of mRNA from a DNA template. While mRNA is the only type of RNA that carries information from DNA directly, there are many other types of RNA that exist, two of which will play important role during protein translation: transfer RNA and ribosomal RNA

First step of Transcription and outcome

Transcription only produces a copy of only one of two strands of DNA. Initiation of transcription- enzymes such as helicase & topoisomerase are involved in unwinding the double stranded DNA and preventing formation of supercoils.

Central dogma of molecular biology

Transfer of genetic information use this to memorize the flow of genetic information from DNA to Protein

What is Translation?

Translation is the process of converting the mRNA transcript into a functional protein. Translation is a complex process that requires mRNA, tRNA, ribosomes, amino acids, and energy in the form of GTP.

What are the three classes of membrane proteins? How are they each most likely to function?

Transmembrane proteins are most lily to serve as channels or receptors. Embedded membrane proteins are most likely to have catalytic activity linked to nearby enzymes. Membrane associated (peripheral) proteins are most likely to be involved in signaling or are recognition molecules on the extracellular surface.

Transmembrane proteins do what?

Transmembrane proteins can have one or more hydrophobic domains and are most likely to function as receptors or channels.

How do transport kinetics differ from enzymatic kinetics?

Transport kinetics display both Km and Vmax values. They also can be cooperative, like some binding proteins. However transporters do not have analogous Keq values for reactions because there is no catalysts

Which of the following is least likely to be required for a series of metabolic reactions? Tracylglycerol acting as a coenzyme Oxidoreductase Enzyme Magnesium acting as a cofactor Transferase enzymes

Triacylglycerol acting as a coenzyme Triglycerides are unlikely to act as coenzymes for a few reasons, their large size, neutral charge, and ubiquity in cells. Cofactors and coenzyme are small in size such as metal ions. (C) They would expect to use B and D as oxidation-reduction reactions and movement of functional groups

Define Triacylglycerols and free fatty acids

Triacylglycerols and free fatty acids act as phospholipid precursors and are found in low levels in the membrane.

What are the two main methods of energy storage in the body?

Triacylglycerols in adipose tissue or Carbohydrates in glycogen Each has advantages and disadvantages Glycogen offers access to metabolic energy in a faster water soluble form: however because of its low energy density glycogen can only provide energy for a bit less than one day

Tryptophan

Trp W -Largest of the aromatics

True or False: Fatty acids are synthesized in the cytoplasm and modified by enzymes in the smooth endoplasmic reticulum.

True

True or False: In size exclusion chromatography, the largest molecules elute first

True. The small pores in size-exclusion chromatography trap smaller particles retaining them in the column in beads.

Tyrosine

Tyr Y -Phenylalanine but with a -OH group

Stop Codons are:

UAA,UGA and UAG

Stop codon mnemonic device

UAA- U Are Annoying UGA- U Go Away UAG- U Are Gone

Nucleotide Excision Repair

UV light induces the formation of dimers between adjacent thymine residues in DNA. The formation of thymine dimers interferes with DNA replication and normal gene expression and sitarist the shape of the double helix. Thymine dimers are eliminated from DNA by a Nucleotide Excision Repair (NER) mechanism, which is a cut-and-patch process.

Which ion channels are responsible for maintaining the resting membrane potential. Ungated Channels Voltage-gated channels Ligand-gated channels No ion channels are involved in maintenance of the resting membrane potential

Ungated Channels Ungated Channels permit free flow of ions, while the sodium-potassium pump is also active and correct for this leakage. Ligand gate and Voltage gated channels are involved in cell signaling and in the pacemaker potentials of certain cells. They cause deviation from not maintenance of the resting membrane potential.

What type of ion channel is open all time?

Ungated channels are always open

Three types of Ion Channels

Ungated, Voltage gated, and Ligand-Gated channels Ion channels are usually drug targets in the treatment of everything from heart disease (calcium channel blockers), to seizures (sodium channel blockers), to irritable bowl syndrome (acetylcholine receptor/cation channel blockers)

Unsaturated fatty acids use what during cleave?

Unsaturated fatty acids use an isomerase and an additional reductase during cleavage.

Mechanism of Enzyme activity

Uses a substrate and the enzyme to form the enzyme substrate couplex Active site- location within the enzyme where the substrate is held during the chemical reaction

Histone acetylation

Using the coactivators such as histone acetylates, which are involved in chromatin remodeling. Acetylation of histone proteins decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA, resulting in an open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA

VLDL transports what?

VLDL transports newly synthesized triacylglycerol molecules from the liver to peripheral tissues in the bloodstream

Valine

Val V

Watson--Crick Model

Watson and Crick were able to deduce the double helical nature of DNA and propose specific base pairing that would be that basis of a copying mechanism.

Waxes are what?

Waxes are present in very small amounts, if at all: they are most prevalent in plants and function in waterproofing and defense.

List the function, key regulators and if it is reversible: Pyruvate kinase

What is the function of: Pyruvate kinase Pyruvate kinase performs another substrate-level phosphorylation, transferring a phosphate from phosphoenolpyruvate (PEP) to ADP, forming ATP and pyruvate. It is activated by fructose 1,6 -bisphosphoglycerate. It is reversible.

List the function, key regulators and if it is reversible: 3-phosphoglycerate kinase

What is the function: 3-phosphoglycerate kinase 3-phosphoglycerate kinase performs a substrate-level phosphorylation, transferring a phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. It is reversible.

List the function, key regulators and if it is reversible: Glyceraldehyde-3-phosphate dehydrogenase

What is the function: Glyceraldehyde-3-phosphate dehydrogenase Glyceraldehyde-3-phosphate dehydrogenase generates NADH while phosphorylating glyceraldehyde 3-phosphate to 1,3-biphosphoglycerate. It is reversible.

Proofreading

When the complementary strands have incorrectly paired bases, the hydrogen bonds between the stand can be unstable and this lack of stability is detected as the DNA passes through this part of the polymerase. The incorrect base is excised and can be replaced with he correct one.

Mnemonic device for Transcription

When we transcribe information, we use the same language to write it down. Translation is exactly what it says: we are changing the language. RNA translation changes the language from nucleotides to amino acids.

Order the lipoproteins from greatest percentage of protein to least percentage of protein. Circle the molecules

With respect to protein content, HDL>LDL>IDL>VLDL>Chylomicrons. VLDL and chylomicrons are the primary triacylglycerol transporters. HDL and LDL are mostly involved in cholesterol transport.

What is wobble and what role does it serve?

Wobble refers to the fact that the third base in a codon often plays no role in determining which amino acid is translated from that codon. Ex: any codon starting with CC codes for proline regardless of which base is in the third "wobble" position.

High blood sugar causes damage to what?

You need to maintain 100 mg/dL or 5.6mM and high blood sugar can cause long term damage to the retina, kidney, blood vessels and nerves.

What are the two domains of transcription factors?

a DNA-binding domain and an activation domain.

Column Chromatography

a column is filled with silica or alumna beads as an adsorbent and gravity moves the solvent and compounds down the column. Size and polarity have a role in how fast a compound moves through the polar silica or alumina bead: the less polar the compound the faster it can elute through the column (short retention rate) useful in biochemistry because it can be used to separate and collect other macromolecules besides proteins such as nucleic acids

What recognizes the codon of mRNA during Translation?

a complementary anti-codon on a transfer RNA (tRNA). this anticodon sequence allow the tRNA to pair with the codon in the mRNA.

Heterochromatic

a small percentage of chromatin that remains compacted during interphase, heterochromatin appears dark under light microscopy and is transcriptionally silent. Heterochromatin consists of DNA with highly repetitive sequences.

DNA-binding domain bind to what?

a specific nucleotide sequence in the promoter region or to a DNA response element to help in the recruitment of transcriptional machinery a DNA response element is a sequence of DNA that binds only to specific transcription factors

One thing lipids all share in common

a tail composed of long chain fatty acids and vary by their degree of saturation and length, this determines how the molecule will behave.

Chromatography

a tool that uses physical and chemical properties to separate and identify compound from a complex mixture . Same concept of the protein moving to the region it is similar to (size, shape et) and will stick there

Remember?

a-1,4 keeps the same branch moving 4ward (moved and added in a slightly different location) a-1,6 puts a branch in the mix. (creates a branch)

Carboxylation

addition of carboxylic acid groups, usually to serve as calcium-binding sites

Prenylation

addition of lipid groups to certain membrane bound enzymes

Glycosylation

addition of oligosaccharides as proteins pass through the ER and golgi apparatus to determine cellular determination

Phosphorylation

addition of phosphates by protein kinases to activate or deactivate proteins

Glycerophospholipids

all Glycerophospholipids are phospholipids but not all phospholipids are glycerophospholipids These contain a glycerol backbone bonded by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head head groups can be positively, negatively or neutrally charged

pKa values of an amino acid

all amino acid have at least two groups that can be deprotonated so they all have at least two pKa values pKa1 which is for the carboxylic acid = around 2 pKa2 which is for the amino group = between 9-10 ' if they have an ionizable side chain they will have 3 pKa values

Complex carbohydrates

all carbohydrates with at least two sugar molecules linked together

Repressible system

allow constant production of a protein product. different form inducible systems, the repressor made by the regulator gene is inactive until it binds to a corepressor. serve as negative feedback final product can serve as a corepressor. as its levels increase, it can bind the repressor and the complex will attach to the operator region to prevent further transcription of the same gene.

What are the 5 DNA polymerases in eukaryotic cells?

alpha, beta, gamma, delta and epsilon.

Triacylglycerols

also called triglycerides, and are composed of three fatty acids bonded by ester linkages to glycerol. nonpolar and hydrophobic, this contributes to their insolubility in water as the polar hydroxyl groups of the glycerol component and the polar carboxylates of fatty acids are boned together decreasing their polarity can be observed as tiny droplets in the cytosol in animals these are called adipocytes and store large amounts of fat and are found under the skin in plants triacylglycerols are found in seeds as oils Tracyglycerols travel bidirectionally in the bloodstream between the liver and adipose tissue.

Size-Exclusion Chromatography

also uses beads that have tiny pores of varying sizes and are placed into a column. The tiny pores allow small compound to enter the beads thus slowing them down. Large compounds cannot fit into the beads so they are passed on. Remember that in this type only small compounds are slowed down and retained longer.

Peptide bond formation

amide bond formed between the -COO- group of one amino acid and the NH3+ of another. Happens through condensation or dehydration reactions because it results in the removal of a water molecule (H2O) the electrophile carbonyl carbon on the first amino acid is attacked by the nucleophile amino group on the second amino acid. after than the hydroxyl group of the carboxylic acid is kicked off. this leaves a N-C terminus possessing peptide the N terminus will be the amino terminus the C terminus will be the carboxyl terminus

What does the aminoacyl-tRNA synthetase do?

aminoacyl-tRNA syntheses transfers the activated amino acid to the 3' end of the correct rRNA. Each tRNA has a CCA nucleotide sequence where the amino acid binds. The high energy aminoacyl-tRNA bond will be used to supply the energy needed to create a peptide bond during translation

Membrane-spanning domain

anchors the receptor in the cell membrane

Euchromatin

appears light, uncondensed and expressed. -contains genetically active DNA

Terpenes

are a class of lipids built from isoprene (C5H8) moieties and share a common structural pattern with carbons grouped in multiple of five produced by mostly plants and some insects and are strong scented a terpene is numbered by the isoprene units present a single terpene unit has ate isoprene units Monoterpenes (C10H16) which are abundant in both essential oils, also contains two isoprene units Sesquiterpenes (one and a half) contain three isoprenes Diterpenes contain four Triterpenes contain six isoprenes Carotenoids like C-caroten and Luetin are tetraterpenes and have eight isoprene units.

G Protein-Coupled Receptors

are a large family of integral membrane proteins involved in signal transduction -characterized by their seven membrane-spanning alpha-helices -utilize Heterotrimeric G protein to transmit signals to an effector in the cell -named G proteins because of their intracellular link to guanine nucleotides (GDP & GTP) remember that binding of a ligand increases the affinity of the receptor of the G protein. Binding of the G protein represents a switch to the active state and affects the intracellular signaling pathway

Centromeres

are a region of DNA found in the center of chromosomes -sites of construction for their noticeable indentions -centromeres, the center of chromosomes are composed of heterochromatin, which is in turn composed of tandem repeat sequences that also contain high G-C content. centromeres allow the two sister chromatids to remain connected until microtubules separate the chromatids during anaphase.

Transgenic Mice

are altered at their germ line by introducing a cloned gene into fertilized ova or into embryonic stem cells. This cloned gene is known as transgenic.

Enzyme Kinetics

are dependent on factors like environmental conditions and concentrations of substrate and enzyme Stress ball connection- The stress the student (substrate up takes from the ball (enzyme) is dependent on the size and shape of ball as well as level of stress.

Restriction Enzymes (restriction endonucleases)

are enzymes that recognize specific double stranded DNA sequences. These sequences are palindromic, meaning that the 5' to 3' sequence of one strand is identical to the 5' to 3' sequence of the other strand. Restriction Enzymes are isolated from bacteria, which are their natural source. These can cut through the backbones of the double helix.

Waxes

are esters of long chain fatty acids with long chain alcohols function as protection for both plants and animals

Nucleotides

are formed when one or more phosphate groups are attached to the C-5 of a nucleoside. Adenosine Di- and Tri (ADP an ATP) gain their name from the number the phosphate groups attached to the nucleoside adenosine Nucleotides are the building block of DNA

Cofactors-

are generally inorganic molecules or metal ions and are often ingested as dietary minerals

Gangliosides

are glycoplipids that have polar head groups composed of oligosaccharides with one or more NANA or silica acid molecules at the terminus and a negative charge use glycosidic linkage play a big role in cell interaction, recognition, and signal transduction are gangly as in they have the most complex structure and functional groups, so they go in all directions

Steroids

are metabolic derivatives of terpenes and are very different from the lipids mentioned earlier in this chapter in both structure and function. structurally have four cycloalkane rings fused together: three cyclohexane and one cyclopentane functionality is determined by the oxidation status of these rings as well as the functional group they carry steroids are non polar

Knockout mice

are mice in which as gene has been intentionally deleted (knocked out)

Major and Minor grooves

are often sites for protein binding,

DNA (Deoxyribonucleic acid) RNA (Ribonucleic acid)

are polymers, each with distinct roles, that together create the molecules integral to life in all living organisms.

Prostaglandins

are produced by almost all cells in the body. 20-carbon molecules are unsaturated carboxylic acids derived from arachidonic acid and contain one five carbon ring paracrine and autocrine signaling molecules in many tissues the function of prostaglandins is to regulate the synthesis of cyclic adenosine monophosphate cAMP which is an intracellular messenger.

Ion Channels

are proteins that create specific pathways for charged molecules three groups that have different mechanisms of opening but all permit facilitated diffusion of charged particles.

DNA polymerases

are responsible for reading the DNA template, or parental strand and synthesizing the new daughter strand. DNA polymerase can read the template strand in the 3' to 5' direction while synthesizing the complementary strand in the 5' to 3' direction.

Glycosphingolipids

are sphingolipids with head groups composed of sugars bonded by glycosidic linkages are not phospholipids, and are found on the outer surface of the plasma membrane and can be further classified as cerebroside and globosides

Steroid hormones

are steroids that act as hormones meaning that stye are secreted by endocrine glands into the bloodstream and then travel on protein carriers to distant sites, where they can bind to specific high-affinity receptors and alter gene expression levels. examples: testosterone, estrogens, cortisol, aldosterone

Sphingomyelins

are the major class of sphingolipids that are also phospholipids, either have -choline or -amine as their head group and content a phosphodiester bond. have zero net charge major components in the plasma membranes of cells producing myelin (oligodendrocytes & Schawnn Cells)

Free Fatty Acids

are unesterified fatty acids with a free carboxylate group

Elongation Factors

assist by locating and recruiting aminoacyl-tRNA along with GTP while helping to remove GDP once the energy has been used.

What is the orientation of the interaction between tRNA pairing with the codon in mRNA?

because base-pairing is involved, the orientation of this interaction will be antiparallel. ex; the aminoacyl tRNA Ile-tRNA^Ile has an anticodon sequence 5'--GAU--3', allowing it to pair with the isoleucine codon 5'--AUC--3'

Proto-oncogenes

before the genes are mutated they are called photo oncogenes like proto-type the invention used before others are made

Process of Chromatography

begins by placing the sample onto a solid medium called the stationary phase or adsorbent. Next run the mobile phase through the stationary phase. This will allow the sample to run through the stationary phase or elute. Depenind on affinity for the stationary phase and mobile phase, different substances will migrate through at different speeds. Components that have high affinity for stationary phase- barely migrate at all. Components that have high affinity for mobile phase - will migrate much more quickly All chromatography is about is the affinity of a substance for the mobile and stationary phases, except for size exclusion chromatography.

Selectins

bind to carbohydrate molecules that project from other cell surfaces weakest formed by the CAMs. expressed in white blood cells and the endothelial cells that line blood vessels Like integrins they play a role in host defense, inflammation, and white blood cell migration

Ligand-Gated Channels

binding of a specific substance or ligand to the channel causes it to open to close Neurotransmitters for example act as ligand gated channels at the postsynaptic membrane. - GABA binds to a chloride channel and opens it. Km and Vmax parameters that apply to enzymes are also applicable to transporters such as ion channels in membranes. Kinetics of transport can be derived from the Michaelis-Menten and Lineweaver-Burk equations, where Km refers to the solute concentration at which the transporter is functioning at half of its maximum activity.

The lac operon is assisted by by..

binding of the catabolite activator protein (CAP) CAP is used by E.coli when glucose levels are low to signal that alternative carbon sources should be used.

What role does an operator site have?

binding site for repressor protein upstream from structural gene

How do frameshift mutations occur?

by Insertions or Deletions and shift the reading frames known as the three nucleotides of a codon

How are each type of amino acids activated?

by a different aminoacyl-tRNA synthetase it requires two high energy bonds from ATP, implying that the attachment of the amino acid is an energy rich bond.

How does the DNA bring the enhancer and promoter regions for a gene together?

by creating a hairpin loop

What is the easiest way the MCAT draws monosaccharides?

by using the Fischer Projections

Messenger RNA (mRNA)

carries the information specifying the amino acid sequence of the protein to the ribosome. mRNA is transcribed from template DNA strand by RNA polymerase enzymes in the nucleus of cells. mRNA is the only type of RNA that contains information that is translated into proteins: to do so it is read in three nucleotide segments termed codons. In eukaryotes mRNA is monocistronic, meaning that each mRNA molecule translates into only one protein product. In prokaryotes mRNA may be polycistronic and starting the process of translation at different location in the mRNA can result in different proteins.

Oxidoreductases

catalyze oxidation-reduction reactions: transfer of electrons between biological molecuels. often have a cofactor that acts as an electron carrier such as NAD+ or NADP In reactions catalyzed by this the electron donor is known as the reductant and the electron accepter is known as the oxidant

Vitamin E

characterizes a group of closely related lipids called tocopherols and tocotrienols characterized by a substituted aromatic ring with a long isoprenoid side chain and are characteristically hydrophobic. it contains a alcohol but overall it is hydrophobic due to the long tail The aromatic ring reacts with free radicals, destroying them and this prevents oxidative damage, and important contributor the development of cancer and aging.

Structural genes

code for the protein of interest

Nucleoside

composed of a five-carbon sugar (pentose) bonded to a nitrogeneous and are formed by covalently linking the base to C-1 of the sugar. carbons are marked with a prime symbol to distinguish from the nitrogenous base.

Peptides

composed of amino acid subunits called residues Dipeptides- 2 amino acid residues Tripeptides- 3 Oligo - 20 residues Longer than 20 = Polypeptides

Pyrimidine

contain only one rind in their structure. They are Cytosine (C), Thymine (T) and Uracil (U). Cytosine is found in both DNA and RNA Thymine is only found in DNA Uracil is only found in RNA CDR TD UR

phospholipids

contain: phosphate and alcohol that comprise the polar head group, joined to a hydrophobic fatty acid tail by phosphodiester linkages

Protein Structure

determined through X-ray Crystallography and nuclear magnetic resonance spectroscopy (NMR) X-ray crystallography is most reliable and common method, it measures electron density on an extremely high resolution scale and can also be used for nucleic acids

Epimers

differ in exactly one chiral center

Motor proteins

display enzymatic activity acting as Atlases that power the conformational change necessary for motor function responsible for muscle contraction and cellular movement

Lineweaver-Burk plots

double reciprocal of the Michaelis-Menton equation. intercept of the x axis is -(1/Km ), intercept of the y axis (1/Vmax) used to determine the type of inhibition that an enzyme is experiencing because Vmax and Km can be compared without estimation.

Feedback Regulation

enzyme regulation by products further down a given metabolic pathway

Remember complementary!!

example: 5'-ATCG-3' will be complementary to 5'-CGAT-3'

Promoter site

further upstream is the promoter site, which is similar in function to promoters in eukaryotes: it provides a place for RNA polymerase to bind.

Voltage-Gated Channels

gates are regulated by potential change near the channel example- neurons possess voltage-gated sodium channels these are closed are resting conditions but membrane depolarization causes a protein conformation change that allows them to quickly open and then quickly close as the voltage increases. -Pace maker current- as the voltage drops these channels open to bring the cell back to the threshold and dire another action potential

Glyceraldehyde

glyceraldehyde is a polyhydroxylated aldehyde or known as an aldose. numbering in this structure will start with the aldehyde containing carbon, it being C-1

Cadherins

group of glycoproteins that mediate calcium dependent cell adhesion usually hold similar cells together, such as epithelial cells different cells use different type of Cadherins E-Cadherins- epithelial N-Cadhersin - Nerve cells

Integrins

group of proteins that all have two membrane spanning chains call a and b or alpha and beta can promote cell division, apoptosis, or other processes

Cerebrosides

have a single sugar also is neutral

Ungated Channels

have no gates therefore unregulated example - ungated potassium channels, which mean there will be an efflux of potassium ions though these channels unless potassium is at equilibrium

Fully saturated fatty acid tails

have only single bonds; the carbon atom is considered saturated when it is bonded to four other atoms with no pi bonds have greater Van Der Waals forces

Enzyme linked receptors

have three primary protein domains -membrane spanning domain, -ligand-binding domain, -catalytic domain

Globosides

have two or more sugars alos is neutral

histone deactylation

histone deactylases are proteins that function to remove acetyl groups from histones, which results in a closed chromatin conformation and decrease in gene expression levels n the cell.

Other groups attached to the alpha carbon other than amino group and carboxyl group

hydrogen atom and a side chain, also known as a R group which is specific to each amino acid. The R group determines the function

How are nucleic acids classified?

if the pentose is ribose, the nucleic acid is RNA; if the pentose is deoxyribose then it is DNA

Using Chargaff's Rules

in double stranded DNA purines=pyrimidine %A=&T %G=%C

In Inducible systems what occurs?

in inducible system, the repressor is bonded tightly to the operator system and thereby acts as a roadblock so RNA polymerase is unable to get from the promoter to the structural gene because the repressor is in the way.

Fat-soluble vitamins

include A, D, E and K

Unsaturated fatty acid

includes one or more double bonds, these double bonds introduce kinks into the fatty acid chain which makes it difficult for them to stack and solidify tend to be liquid at room temp

Glycogen

is a carbohydrate storage unit in animals. It is similar to starch except it has more a-1,6 glycosidic bonds, this makes it a highly branched compound Branching optimizes the energy efficiency of glycogen and makes it more soluble in solution, thereby allowing more glucose to be stored in the body.

Vitamin K

is a group of compounds including phylloquinone (K1's) and the menaquinones (K2's) vital to the postranslational modifications required to from prothrombin and important clotting factor for blood.

Cholesterol

is a steroid or primary importance, is a major component of the phospholipid bilayer and is responsible for mediating membrane fluidity Cholesterols are amphipathic molecules contain both hydrophilic and hydrophobic components These interactions between these heads allows it to maintain constant fluidity in cell membranes, helps to prevent solidifying in the cold and prevents it form being too permeable in hot conditions Cholesterols is a precursor of steroid hormones, bile acids, and vitamin D

DNA cloning

is a technique that can produce large amounts of a desired. Often the DNA to be cloned is present in a small quantity and is part of a heterogeneous mixture containing other DNA sequences. The goal is to produce large amount of homogeneous DNA for other applications.

Elongation

is a three step cycle that is repeated for each amino acid added to the protein after the initiator methionine. During elongation, the ribosome moves in the 5' to 3' direction along the mRNA, synthesizing the protein from its amino (N-) to carboxyl (C-) terminus.

Polymerase Chain Reaction (PCR)

is an automated process that can produce millions of copies of a DNA sequence without amplifying the DNA in bacteria. PCR is used to identify criminal suspects, familial relationships and disease-causing bacteria and viruses. PCR requires primers that are complementary to the DNA that flanks the region of interest, nucleotides (dATP, dTTP, dCTP, dGTP) and DNA polymerase. this will need heat to help the DNA double helix melt apart.

The backbone of DNA

is composed of alternating sugar and phosphate groups; it determines he directionality of the DNA and is always read from 5' to 3'. it is formed as nucleotides are joined by 3' - 5' phosphodiester bonds. That is a phosphate group links the 3' carbon of one sugar to the 5' phosphate group of the next incoming sugar in the chain. DNA and RNA strands are negative charged because of the negative charge from the phosphate.

When glucose is in a straight-chain formation, it: is an aldoketose is a pentose has five chiral carbons is one of a group of 16 stereoisomers

is one of a group of 16 stereoisomers Glucose is an aldohexosem meaning it has one aldehyde group and six carbons. To calculate it remember that it has 6 carbons but only 4 are chiral so 2^4 = 16. So it has 16 stereoisomers

Transfer RNA (tRNA)

is responsible for converting the language of nucleic acids to the language of amino acids and peptides. Each tRNA molecule contains a folded strand of RNA that includes a three-anticodon The anticodon recognizes and pairs with the appropriate codon on an mRNA molecule while in the ribosome. There are 20 amino acids in eukaryotic proteins, each of which is represented by at least one codon. To become part of a nascent polypeptide in the ribosome, amino acids are connected to a specific tRNA molecule; such tRNA molecules are said to be charged or activated with an amino acid.

Saponification

is the ester hydrolysis of triacylglycerols using a strong base using Lye which is sodium or potassium hydroxide result is the basic cleavage of the fatty acid leaving the sodium salt of the fatty acid and glycerol soaps act as surfactant which lower the surface tension at the surface of a liquid, serving as a detergent or emulsifier.

Pinocytosis

is the ingestion of liquid into the cell in vesicles formed form the cell membrane and phagocytosis is the ingestion of larger, solid molecules.

Phosphofructokinases 1 (PFK-1)

is the rate limiting enzyme and main control point in glycolysis. In this reaction fructose 6-phosphate is phosphorylated to fructos 1,6-biphosphate using ATP. PFK 1 is inhibited by ATP and citrate and activated by AMP. This makes sense because the cell should turn off glycolysis when it has sufficient energy (high ATP) and turn on glycolysis when it need energy (high AMP) Citrate is an intermediate of the citric acid cycle so high levels of citrate also imply that the cell is producing sufficient energy.

Dihydroxyacetone

is the simplest ketone sugar (kettles) the carbonyl is the most oxidized: in this case the lowest number it can be assigned is C-2 this is true for almost every ketose

Jacob-Monod Model

is used to describe the structure and function of operons. In this model, operons contain: -structural genes -operator site -promoter site -regulator gene

Southern Blotting

is used to detect the presence and quantity of various DNA strands in a sample. DNA is cut by restriction enzymes and then separated by a gel electrophoresis. then it is separated to a membrane retaining the separation. The membrane is probed with copies of a single stranded DNA sequence. and its complementary sequence and form double stranded DNA. Probes are labeled with radioisotopes or indicator proteins.

Where is tRNA found?

it is found in the cytoplasm and is the second most abundant type of RNA in the cell, after mRNA

Why is a TATA box named "TATA"

it is named for its high concentration of Thymine and Adenine bases

In what direction is DNA written

it is written in the 5' to 3' end, thus written 5'--ATG-- 3' or simply ATG. But can be written in slightly different ways - if written backwards, the ends must be labeled: 3'--GTA--5' -The position of phosphates may be shown: pApTpG -"d" may be used a shorthand for deoxyribose: dAdTdG

Ketone bodies form when?

ketones form during a prolonged starvation state due to excess acetyl-CoA in the liver. (Ketogenesis)

Polysaccharides

long chains on monosaccharides linked together by glycosidic bonds.

What are the roles of the three main types of RNA?

mRNA carries information from DNA by traveling from the nucleus where it is transcribed to the cytoplasm where it is translated tRNA translates nucleic acids to amino acids by pairing its anticodon with mRNA codons; it is charged with amino acid which can add to the growing peptide chain. rRNA forms much of the structural and catalytic component of the ribosome, and acts as a ribozyme to create peptide bonds between amino acids

Key concept of mRNA...

mRNA is the messenger of genetic information. DNA codes for proteins but cannot perform any of the important enzymatic reactions that protein are responsible for in cells. mRNA takes the information from the DNA to the ribosomes, where creation of the primary protein structure occurs.

Enhancers

made up of many response elements, allows for the control of one genes expression by multiple signals. Signal molecules as an example, cAMP, cortisol, and estrogen, bind to specific receptors. Receptors of the examples given being, CREB, cocorticoid receptor, and the estrogen receptor.

Cellulose

main structural component of plants -is a homopolysaccharide -is a change of B-D-glucose molecules linked by B-1,4 glycosidic bonds, with hydrogen bonds holding the actual polymer chains together for support. humans cannot digest cellulose because we lack the cellulase enzyme responsible for hydrolyzing cellulose to glucose monomers. This means cellulose found in fruits and vegetables serves as a great source of fiber in our diet drawing water into the gut.

Actin

makes up microfilaments and the thin filaments in myofibrils most abundant proteins in eukaryotic cells have a positive and negative side, which allows them to travel unidirectionally along an actin filament like a one way street

Tubulin

makes up microtubules, which provide structure, also helps in chromosome separation in mitosis and meiosis

Electrophoresis

method of separated proteins and works by subjecting compounds to an electric field which moves them accordion got their net change and size Negatively charged compounds migrate toward the positive charged anode and Positively charged compounds move toward the negative charged cathode uses polyacrylamide gel as the medium, this gel is porous which solidifies at room temperature. Anions to anodes Cations to Cathodes

Substrates are..

molecules of which enzymes acts upon, a given enzyme will only catalyze a to a single reaction or class of reactions with these substrates, known as enzyme specificity

Amino acids

molecules that contain two functional groups: an amino group and a carboxyl group (-NH2) and a carboxyl group (-COOH) alpha amino acids will be the focus in biochemistry and this is when the two are bonded to the same carbon.

Oxidation and Reduction of Monosaccharides

most important biochemical reactions in the human body is the oxidation of carbohydrates in order to yield energy. \ Aldoses containing an aldehyde can be oxidized to form a carboxylic acid and are called aldonic acids. Thus since they are oxidized they are considered reducing agents any hemiacetal ring is considered a reducing sugar when the aldose is in ring form, oxidation yields a lactone instead which are cyclic esters with a carbonyl group persisting on the anomeric carbon.

Kinesins and Dyeins

motor proteins associated with microtubules, have two heads, at least one remains attached to the tubulin at all times Kinesins play key role in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis Dyeins are involved in the sliding movement of cilia and flagella both are important for vesicle transport in the cell but opposite way Kinesins bring vesicles toward positive end Dyeins bring vesicles toward negative end

What are the benefits of native PAGE compared to SDS-PAGE.

native PAGE allows a complete protein to be recovered after analysis and determines the size of proteins. SDS-PAGE can be used to eliminate conflation from mass-to-charge ratios

trp operon acts as what?

negative repressible system. When tryptophan is high in the local environment it acts as a repressor to bind to the operator site. Thus the cells turns off its machinery to synthesize its own tryptophan.

Histones are an example of what?

nucleoproteins which are proteins that associate with DNA other nucleoproteins are acid-soluble and tend to stimulate processes such as transcription

Gene therapy

offeres potential cures of individuals with inherited diseases. Gene therapy is intended for diseases in which a given gene is mutated or inactive, giving rise to pathology. To be useful Gene therapy would have to possess efficient gene delivery vectors must be used to transfer the cloned gene into the target cell. Viruses naturally infect cells to insert their own genetic material, most gene delivery vectors is use are modified viruses.

Vitamin A

or carotene, is an unsaturated hydrocarbon that is important in vision, growth and immune function. most significant is the aldehyde form of A and it retinal, which is a component of the light sensing molecular system in the human eye Carrots

Vitamin D

or cholecalciferol, can be consumed or formed in a UV light driven reaction in the skin. in liver or kidney D is converted to calcitriol, the biologically active form of D. Calcitriol increase calcium and phosphate uptake in the intestines, which promotes bone production. Rickets is caused by a lack of vitamin D Milk

Energy storage of Triacylglycerols

oxidation of Triacylglycerols yield twice the amount of energy per gram as carbohydrates, making this a far more energy dense storage mechanism. click right for the structure

What are some tumor suppressor genes?

p53 & Rb (retinoblastoma) these encode proteins that inhibit the cell cycle or participate in DNA repair processes Function to stop tumor progression and are sometimes called antiocogenes.

3' Poly-A-Tail

polyadenosyl (poly-A) tail is added the 3' end of the mRNA transcript and protects the message agains rapid degradation. It is composes of adenine and bases.

What is a system in which the binding of a molecule increases transcription?

positive control

What is a positive control system?

postive control system requires the binding of a protein to the operator site to increase transcription.

Myosin

primary motor protein that interacts with actin each subunit has a single head and neck movement in the neck is responsible for the power stroke of sarcomere contraction

Biosignaling

process in which cells receive and act on signals Proteins participate in biosignaling in different capacities including acting as extracellular ligands, transporters for facilitated diffusion, receptor proteins and second messengers

What do rRNA function as?

rRNA function as ribozymes; that is, enzymes made of RNA molecules instead of peptides. rRNA helps catalyze the formation of peptide bonds and is also important in splicing out its own introns within the nucleus.

Tautomerization

rearrangement of bonds in a compound usually by moving a hydrogen and forming a double bond In the case of ketones, the ketone group picks up a hydrogen while the double bond is moved between two adjacent carbons resulting in an enol. Which is a compound with a double bond and an alcohol group

Mnemonic for Purine and Pyrimidines

remember to CUT the PYE (Cytosine, Uracil, Thymine are pyrimidines) Pie has only one ring of crust as do Pyrimidines. PURe As Gold (Adenine and Guanine are purines) Also think of gold wedding rings for their are two of them in every marriage.

DNA polymerase gamma does what?

replicates mitochondrial DNA

What property of protein-degesting enzymes allows for a sequence to be determined without fully degrading the protein? Selectivity Sensitivity Turnover Inhibtion

selectivity The selective cleavager of proteins by digestive enzymes allows fragments of different lengths with known amino acids endpoints to be created. By cleaving with different enzymes, a basic outline of the amino acid can be created

Mutations in the Wobble lead to what?

silent or degenerate, which means there is not effect on the expression of the amino acid and therefore no adverse effects on the polypeptide sequence.

Coenzymes-

small organic groups, which are vitamins or derivativs of vitamin such as NAD+, FAD and Coenzyme A (vitamin C) Fat soluble Vitamins A, D, E and K are better regulated by partition coefficients Enzymatic reactions are not restricted to a single cofactor or coenzyme.

Some Restriction Enzymes yield what?

some yield sticky ends on the fragments, which are advantageous in facilitating the recombination of a restriction fragment with the vector DNA.

Signaling lipids

steroids, prostaglandins and fat-soluble vitamins as well as terpenes

Ligand-binding domain

stimulated by the appropriate ligand and induces a congregational change that activate the catalytic domain.

What is the A site?

the A site holds the incoming aminoacyl-tRNA complex. This is the next amino acid that is being added to the growing chain and is determined by the mRNA codon within the A site.

Histones

the DNA that makes up a chromosome is wound around a group of small basic proteins called histones forming chromatin. -there are 5 histones proteins found in eukaryotic cells -two copies each of the histone proteins H2A, H2B, H3 and H4 for a histone core and about 200 base pairs of DNA are wrapped around this protein complex, forming a nucleosome. -H1 the last histone seals off DNA as it enters and leaves the nucleosome adding stability to the structure.

What is the E site?

the E site is where the now inactivated (uncharged) tRNA pauses transiently before exiting the ribosome. As the now uncharged tRNA enters the E site, it quickly un binds from the mRNA and is read to be recharged

What is the P site?

the P site holds the tRNA that carries the growing polypeptide chain: it is also where the first amino acid (methionine) binds because it is starting the polypeptide chain. A peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site. This requires peptide transferase, an enzyme that is part of the large subunit. GTP is used for energy during the formation of this bond.

Concentrations of [S] & [E]

the concentrations of the enzyme and substrate affect how quickly a reaction will occur. Lets say we have 100 stress balls (enzyme) and only 10 frustrated students (substrates) to derive stress relief from. This represents a high enzyme concentration relative to substrate, now that we have many active sites (student letting go and feeling relaxed) in a chemical sense we would reach equilibrium quickly. as we add more substrates (students) the rate of the reaction increases. However if we add more people and start approaching 100 student we reach a maximal rate of relaxation. Unlike before inviting more student into the room will not change the rate of the reaction. It cannot go any faster once it reaches saturation and at this rate the enzyme is working at maximal velocity. The only way to increase Vmax is by increasing the enzyme concentration.

Reannealing

the denatured single stranded DNA can be brought back together if the denaturing condition is slowly removed. heat denatured DNA is slowly cooled

Degeneracy

the genetic code is degenerate because more than one codon can specify a single amino acid all amino acids, except for methionine and tryptophan are encoded by multiple codons, the first two bases are usually the same and the third base in the codon is variable

Is the replication process known as Semiconservative or Conservative?

the replication process is termed as semiconservative because one parental strand is retained in each of the two resealing identical double stranded DNA molecules.

The result of transcription is what?

the result is a single strand of mRNA, synthesized from one of the two nucleotide strands of DNA called the template strand or antisense strand. The newly synthesized mRNA strand is both antiparallel and complementary to the DNA template strand

Once opened by helicase what happens?

the unpaired strands of DNA are very sticky in a molecular sense. The free purines and pyrimidines seek out other molecules with which to hydrogen bond.

What is the third position referred to as?

the wobble position, wobble is an evolutionary development designed to protect against mutation in the coding regions of our DNA.

What is the second function of Telomeres?

their high G-C content creates exceptionally strong strand attractions at the end of chromosome s to prevent unraveling; think of telomeres as knotting off the end of the chromosome.

Gene amplification

there are times however, when the expression must be increased or amplified, in response to specific signals such as hormones, growth factors, and other intracellular conditions. Eukaryotic cells accomplish this through enhancers and gene duplication.

At pH of 1 - glycine which doesnt have an ionizable side chain

there will be plenty of protons in the solution, since we are below the pKa of the amino group the amino group will be protonated (-NH3+) and thus positively charged. this is also below that of the carboxyl group then it too will be fully protonated (-COOH) thus neutral

Endocytosis & Exocytosis

these are methods of engulfing material int cells or releasing material to the exterior of cell, both via the cell membrane.

Terpenes and Terpenoids

these are the precursors to steroids and other lipid signaling molecules and have varied independent functions

Positively Charged (Basic) side chains

these have positive charged nitrogen atoms Lysine- has a terminal primary amino agroup Arginine- has three nitrogen atoms in its side chain, the positive charge being delocalized over all three Histidine- has an aromatic ring with two nitrogen atoms, it is positive by how one nitrogen is protonated and the other isn't until given acidic conditions, giving it two side chains

What are the proteins in the cell membrane roles?

they act as transporters, cell adhesion, molecules, and enzymes.

Where does the ADP and ATP gain their energy from?

they are high energy compounds because of the energy associated with the repulsion between closely associated negative charges on the phosphate groups.

What are chaperones?

they assist in protein folding process

Michaelis Menten equation

this equation describes how the rate of the reaction (V) depends on the concentration of both the enzyme (E) and the substrate (S) which form the product (P) Enzyme substrate complexes form at a rate of k1 . The ES complex can either dissociate at a rate k2 or turn into E + P at a rate k3

At pH of 7 - glycine which doesnt have an ionizable side chain

this is far above the pH of Carboxylic acid group Carboxyl group deprotonates (-COO-) but we are still below the pKa of the amino group so it will remain (-NH3+) Called a Zwitterion, posessing a (-) & (+) charge

Glycoside Formation

this is when hemiacetals react with alcohols to form acetals The anomeric hydroxyl group is transformed into an alkoxy group yielding a mixture of a- and B- acetals with water as a leaving group The carbon-oxygen bonds are called glycosidic bonds and the acetals formed are glycoside This is a dehydration reaction thus breaking a glycosidic bond requires hydrolysis

Bradford protein assay

this mixes a protein in a solution with blue dye. Turning the protonated form from dark green to blue when mixed with the protein. Increased protein concentration correspond to a larger concentration of blue dye in solution.

Operatore site

this operator site is upstream of the structural gene and is a non transcribable region of DNA that is capable of binding a repressor protein.

Trimeric G Protein Cycle

three subunits are alpha, beta and gamma In inactive form the alpha subunit bind GDP and in a complex with Beta and Gamma as well When a ligand binds to the GPCR the receptor becomes acitvated and in turn engages the corresponding G protein. This replaces GDP with GTP and the alpha subunit dissociates itself from beta and gamma. This activated alpha subunit alters the activity of adenylate cyclase and if the alpha subunit is (As) then the enzyme is activated or stimulated. If the a subunit is Ai then the enzyme is inhibited. Once GTP on the activated alpha subunit is dephosphorylated to GDP the alpha subunit will rebind to the beta and gamma rendering the protein inactive once again.

How does one remove the block in an inducible system?

to remove the block, an inducer must bind the repressor protein so that RNA polymerase can move down the gene.

What role does a regulator gene have?

transcribed to form repressor protein furthest upstream

Facilitated Diffusion

type of passive transport which is the diffusion of molecule down a concentration gradient through a pore in the membrane created by this transmembrane protein. -used for molecule that are impermeable to the membrane (large, polar or charged) - this diffusion allows integral membrane proteins to serve as channels for these substrates to avoid the hydrophobic fatty acid tails of the phospholipid bilayer

Colloid

uniform mixture, oil and water separate but add soap or a detergent and it becomes a colloid this occurs by the formation of micelles: tiny aggregates of soap with the hydrophobic tails turned inwards and the hydrophilic heads turned outward, shielding the hydrophobic lipid tails and allowing for overall salvation

Ion-Exchange Chromatography

use beads and are put in the column that are coated with charged substances so they attract or bind compounds that have an opposite charge. Example- a + charged column will attract and hold a negatively charged protein as it passes through the column, either increasing its retention time or retaining it completely. A salt it used to elute the molecule that have stuck to a column

Catalytic Domain

when activated this often result in the initiation of a second messenger cascade. Receptore Tyrosine Kinases (RTK) for example are composed of a monomer that dimerizes upon ligand binding this dimer is the active form that phosphorylates additional cellular enzymes, including the receptor itself.

DNA alpha and delta do what?

work together to synthesize both the leading and lagging strands; DNA polymerase delta also fills in the gaps left behind when RNA primers are removed

In a neutral solution, most amino acids exist as: positively charged compounds zwitterions negatively charged compounds hydrophobic molecules

zwitterions zwitterions are when there is a neutrality between the carboxyl being deprotonated (-COO-) and the amino staying protonated