Biochemistry Flashcards
What is the stereochemistry of all chiral eukaryotic amino acids?
L, (S)
the exceptions is cysteine (its R group is higher priority than the carboxylic acid group)
Which amino acids are nonpolar, nonaromatic?
glycine, alanine, valine, leucine, isoleucine, methionine, proline
Which amino acids are aromatic?
tryptophan, phenylalanine, tyrosine
Which amino acids are negatively charged/acidic?
aspartate, glutamate
Which amino acids are positively charged/basic?
lysine, arginine, histidine
What is the isoelectric point (pI)?
The pH at which the molecule is electrically neutral
pI for neutral amino acid = pKa,NH3+group + pKa,COOHgroup / 2
pI for acidic amino acid = pKa,Rgroup + pKa,COOHgroup / 2
pI for basic amino acid = pKa,NH3+group + pKa,Rgroup / 2
What is the primary structure of proteins?
the linear sequence of amino acids in the chain
What is the secondary structure of proteins?
the local structure determined by nearby amino acids
alpha-helix, beta-pleated sheet
What role does proline serve in the secondary structure of proteins?
it creates kinks in alpha-helices and turns in beta-pleated sheets
What is the tertiary structure of proteins?
the proteins three-dimensional shape
What is the quaternary structure of proteins?
an aggregate of smaller globular peptides, or subunits, and represents the functional form of the protein
(only exists for proteins with more than one polypeptide chain)
What does diploid and haploid mean?
diploid (2n): cells that contain two copies of each chromosome
haploid (n): cells that contain only one copy of each chromosome
What happens in the G1 stage of the cell cycle?
the cell grows and performs its normal functions. DNA is examined and repaired
What happens in the S stage of the cell cycle?
DNA is replicated
What happens in the G2 stage of the cell cycle?
The cell continues to grow and replicates organelles in preparation for mitosis. Cell continues to perform its normal functions.
What happens in the M phase of the cell cycle?
Mitosis (cell division) occurs.
What happens in prophase of mitosis?
Chromosomes condense, nuclear membrane dissolves, nucleoli disappear, centrioles migrate to opposite poles and begin forming the spindle apparatus
What happens in metaphase of mitosis?
Chromosomes gather along the metaphase plate in the center of the cell under the guidance of the spindle apparatus
What happens in anaphase of mitosis?
Sister chromatids separate, and a copy of each chromosome migrates to opposite poles
What happens in telophase and cytokinesis of mitosis?
Chromosomes decondense, nuclear membrane reforms, nucleoli reappear, spindle apparatus breaks down, cell divides into two identical daughter cells
What is the difference between homologous chromosomes and sister chromatids?
homologous chromosomes are related chromosomes of opposite parental origin. Sister chromatids are identical copies of the same DNA that are held together at the centromere.
What is the difference between prophase I of meiosis and prophase of mitosis?
homologous chromosomes come together as tetrads during synapsis; crossing over
What is the difference between metaphase I of meiosis and metaphase of mitosis?
homologous chromosomes line up on the opposite sides of the metaphase plate, rather than individual chromosomes lining up on the metaphase plate
What is the difference between anaphase I of meiosis and anaphase of mitosis?
homologous chromosomes separate from each other; centromeres do not break
What is the difference between telophase I of meiosis and telophase of mitosis?
chromatin may or may not decondense; interkinesis occurs as the cell prepares for meiosis II
What is the function of Leydig cells?
Leydig cells secrete testosterone and other male sex hormones (androgens)
What is the function of Sertoli cells?
Sertoli cells nourish sperm during their development
What is the acrosome and what organelle forms the acrosome?
The acrosome contains enzymes that are capable of penetrating the corona radiata and zona pellucida of the ovum, permitting fertilization to occur. It is a modified Golgi apparatus
Describe the follicular phase of the menstrual cycle
Egg develops, endometrial lining becomes vascularized and glandularized. FSH concentrations increase, LH concentrations stay the same, estrogen concentrations decrease then increase, and progesterone concentrations decrease
Describe the ovulation phase of the menstrual cycle
Egg is released from follicle into peritoneal cavity. FSH concentrations increase, LH concentrations drastically increase (spike), estrogen concentrations increase, and progesterone concentrations decrease
Describe the luteal phase of the menstrual cycle
Corpus lute produces progesterone to maintain endometrium. FSH concentrations decrease, LH concentrations stay the same, estrogen concentrations increase, and progesterone levels increase
Describe the menses phase of the menstrual cycle
Shedding of the endometrial lining. FSH concentrations decrease, LH concentrations decrease, estrogen concentrations decrease, and progesterone concentrations decrease
What are the important properties of enzymes/catalyst?
they lower the activation energy
they increase the rate of the reaction
they do not alter the equilibrium constant
they are not changed or consumed in the reaction (which means they will appear in both the reactants and products)
they are pH and temperature sensitive, with optimal activity at specific pH ranges and temperatures
they do no affect the overall ΔG of the reaction
they are specific for a particular reaction or class of reactions
What are oxidoredictases?
enzymes that catalyze oxidation-reduction reactions; that is, the transfer of electrons between biological molecules
What are transferases?
enzymes that catalyze the movement of a functional group from one molecule to another (kinases are a member of this class and catalyze the transfer of a phosphate group)
What are hydrolases?
enzymes that catalyze the breaking of a compound into two molecules using the addition of water
What are lyases?
enzymes that catalyze the cleavage of a single molecule into two products
What are isomerases?
enzymes that catalyze the rearrangement of bonds within a molecule
What are ligases?
enzymes that catalyze addition or synthesis reactions, generally between large similar molecules, and often require ATP
How do the lock and key theory and induced fit model differ?
Lock and Key: active site of enzyme fits exactly around substrate, no alterations to tertiary or quaternary structure of enzyme, less accurate model
Induced Fit: active site of enzyme molds itself around substrate only when substrate is present, tertiary and quaternary structure is modified for enzyme to function, more accurate model
What do cofactors and coenzymes do? How do they differ?
Cofactors and coenzymes both act as activators of enzymes. Cofactors tend to be inorganic (minerals), while coenzymes tend to be small organic compounds (vitamins). In both cases, these regulators induce a conformational change in the enzyme that promotes its activity. Tightly bound cofactors or coenzymes that are necessary for enzyme function are termed prosthetic groups
What is the Michaelis-Menten equation?
v=vmax[S] / Km + [S]
What are the effects of increasing [S] on enzyme kinetics?
increasing [S] has different effects, depending on how much substrate is present to begin with. When the substrate concentration is low, an increase in [S] causes a proportional increase in enzyme activity. At high [S], however, when the enzyme is saturated, increasing [S] has no effect on activity because vmax has already been attained
What are the effects of increasing [E] on enzyme kinetics?
Increasing [E] will always increase vmax, regardless of the starting concentration of enzyme
How are Michaelis-Menten and Lineweaver-Burk plots similar? How are they different?
Both Michaelis-Menten and Lineweaver-Burk relationships account for the values of Km and vmax under various conditions. They both provide simple graphical interpretations of these two variables and are derived from the Michaelis-Menten equation. However, the axes of these graphs and visual representation of this information is different between the two. The Michaelis-Menten plot is v vs [S], which creates a hyperbolic curve for monomeric enzymes. The Lineweaver-Burk plot, on the other hand, is 1/v vs 1/[S], which creates a straight line
What does Km represent? What would an increase in Km signify?
Km is a measure of an enzyme’s affinity for its substrate, and is defined as the substrate concentration at which an enzyme is functioning at half of its maximal velocity. As Km increases, an enzyme’s affinity for its substrate decreases.
What do the x and y intercepts in a Lineweaver-Burk plot represent?
The x-intercept represents -1/Km and the y-intercept represents 1/vmax
What is enzyme cooperativity?
Cooperativity refers to the interactions between subunits in a multisubunit enzyme or protein. The binding of substrate to one subunit induces a change in the other subunits from the T (tense) state to the R (relaxed) state, which encourages binding of substrate tot he other subunits. In the reverse direction, the unbinding of substrate from one subunit induces a change from the R to T in the remaining subunits, promoting unbinding of substrate from the remaining subunits
What are the effects of temperature on the function of enzymes?
as temperature increases, enzyme activity generally increases (doubling approximately every 10 degrees C). Above body temperature, however, enzyme activity quickly drops off as the enzyme denatures
What are the effects of pH on the function of enzymes?
Enzymes are maximally active within a small pH range; outside of this range, activity drops quickly with changes in pH as the ionization of the active site changes and the protein is denatured
What are the effects of salinity on the function of enzymes?
Changes in salinity can disrupt bonds within an enzyme, causing disruption of tertiary and quaternary structure, which leads to loss of enzyme function
What is the ideal temperature for most enzymes in the body?
37 C = 98.6 F = 310 K
What is the ideal pH for most enzymes in the body?
7.4
What is the ideal pH for gastric enzymes?
around 2
What is the ideal pH for pancreatic enzymes?
around 8.5
What is feedback inhibition?
Feedback inhibition refers to the product of an enzymatic pathway turning off enzymes further back in the same pathway. This helps maintain homeostasis: as product levels rise, the pathway creating that product is appropriately downregulated
Of the four types of reversible inhibitors, which could potentially increase Km?
A competitive inhibitor increases Km because the substrate concentration has to be higher to reach half the maximum velocity in the presence of the inhibitor. A mixed inhibitor will increase Km only if the inhibitor preferentially binds to the enzyme over the enzyme-substrate complex
What is irreversible inhibition?
Irreversible inhibition refers to the prolonged or permanent inactivation of an enzyme, such that it cannot be easily renatured to gain function
What are some examples of transient enzyme modifications?
allosteric activation or inhibition
What are some examples of covalent enzyme modification?
phosphorylation and glycosylation
Why are some enzymes released as zymogens?
Zymogens are precursors of active enzymes. It is critical that certain enzymes (like the digestive enzymes of the pancreas) remain inactive until arriving at their target site
How do cytoskeletal proteins differ from motor proteins?
Cytoskeletal proteins tend to be fibrous with repeating domains, while motor proteins tend to have ATPase activity and binding heads. Both types of protein function in cellular motility
True or false: motor proteins are not enzymes
False. An enzyme is a protein or RNA molecule with catalytic activity, which motor proteins do have. Motor function is generally considered non enzymatic, but the ATPase functionality of motor proteins indicates that these molecules do have catalytic activity
What could permit a binding protein involved in sequestration to have a low affinity for its substrate and still have a high percentage of substrate bound?
If the binding protein is present in sufficiently high quantities relative to the substrate, nearly all substrate will be bound despite a low affinity
What are the three main classes of cell adhesion molecules and what type of adhesion does each class form?
Cadherin: two cells of the same or similar type using calcium
Integrin: one cell to proteins in the extracellular matrix
Selectin: one cell to carbohydrates, usually on the surface of other cells
When an antibody binds to its antigen, what are the three possible outcomes of this interaction?
Antigen-antibody interactions can result in neutralization of the pathogen or toxin, opsonization (marking) of the antigen for destruction, or creation of insoluble antigen-antibody complexes that can be phagocytized and digested by macrophages (agglutination)
Contrast enzyme-linked receptors with G protein-coupled receptors
Enzyme-linked receptors: auto activity, enzymatic activity
G protein-coupled receptors: two protein complex, dissociation upon activation, trimer
Both: extracellular domain, transmembrane domain, ligand binding
What type of ion channel is active at all times?
ungated channels are always open
How do transport kinetics differ from enzyme 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 catalysis
What separation methods can be used to isolate a protein on the basis of isoelectric point?
Isoelectric focusing and ion-exchange chromatography both separate proteins based on charge; the charge of a protein in any given environment is determined by its isoelectric point (pI)
What are the relative benefits of native PAGE compared to SDS-PAGE?
Native PAGE allows a complete protein to be recovered after analysis; it also more accurately determines the relative globular size of proteins. SDS-PAGE can be used to eliminate conflation from mass-to-charge ratios
What are two potential drawbacks of affinity chromatography?
The protein of interest may not elute from the column because its affinity is too high or it may be permanently bound to the free receptor in the eluent
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
Why are proteins analyzed after isolation?
Protein isolation is generally only the first step in an analysis. The protein identity must be confirmed by amino acid analysis or activity. With unknown proteins, classification of their features is generally desired
What factors would cause an activity assay to display lower activity 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 (because the protein concentration was calculated as higher than its actual value). Alternatively, the enzyme could have been denatured during isolation and analysis
True or false: the Edman degradation proceeds from the carboxy (C-) terminus
False. The Edman degradation proceeds from the amino (N-) terminus
What type of receptors are hormones most likely to act on?
enzyme-linked receptors and G protein-coupled receptors
What amino acids contribute most significantly to the pI of a protein?
Lysine and arginine
How does the gel for isoelectric focusing differ from the gel for traditional electrophoresis?
Isoelectric focusing uses a gel with a pH gradient that encourages a variable charge
Which protein properties allow UV spectroscopy to be used as a method of determining concentration?
Proteins contain aromatic groups in certain amino acids
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 these findings?
The active site is occupied by free ligand
What property of protein-digesting enzymes allows for a sequence to be determined without fully degrading the protein?
selectivity
What is the name for a five-carbon sugar with an aldehyde group? A six-carbon sugar with a ketone group?
aldopentose; ketohexose
Explain the relationship between the carbonyl carbon, anomeric carbon, and the alpha and beta forms of a sugar molecule
During hemiacetal or hemiketal formation, the carbonyl carbon becomes chiral and is termed the anomeric carbon. The orientation of the -OH substituent on this carbon determines if the sugar molecule is the alpha or beta anomer
Explain 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
What purpose do Tollen’s reagent and Benedict’s reagent serve? How do they differ from each other?
Tollen’s reagent and Benedict’s reagent are used to detect the presence of reducing sugars. Tollen’s reagent is reduced to produce a silvery mirror when aldehydes are present whereas Benedict’s reagent is indicated by a reddish precipitate of Cu2O
From a metabolic standpoint, does it make 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.
Which of the two forms of starch is more soluble in solution? Why?
Amylopectin is more soluble in solution than amylose because of its branched structure. The highly branched structure of amylopectin decreases intermolecular bonding between polysaccharide polymers and increases interaction with the surrounding solution
Regarding glycogen and amylopectin, which of these two polymers should experience a higher rate of enzyme activity that cleave side branches? Why?
Glycogen has a higher rate of enzymatic branch cleavage because it contains significantly more branching than amylopectin
Define amphipathic
molecules that have both hydrophilic and hydrophobic regions
What determines the properties of lipids?
Lipid properties - for all categories of lipids - are determined by the degree of saturation in fatty acid chains and the functional groups to which the fatty acid chains are bonded
Which components of membrane lipids contribute to their structural role in membranes? Which components contribute to function?
Membrane lipids are amphipathic: they have hydrophilic heads and hydrophobic tails, allowing for the formation of bilayers in aqueous solution. The fatty acid tails form the bulk of the phospholipid bilayer, and play a predominantly structural role. On the other hand, the functional differences between membrane lipids are determined by the polar head group, due to its constant exposure to the exterior environment of the phospholipid bilayer (remember, this can be either the inside or outside of the cell). The degree of unsaturation of fatty acid tails can also play a small role in function.
What is the difference between a sphingolipid that is also a phospholipid and one that is NOT?
The difference is the bond between the sphingosine backbone and the head group. When this is a phosphodiester bond, it’s a phospholipid. Nonphospholipid sphingolipids include glycolipids, which contain a glycosidic linkage to a sugar.
Name the three main types of sphingolipids and their characteristics.
Sphingomyelin: phospholipid, functional groups include phosphatidylethanolamine/phosphatidylcholine
Glycosphingolipid: glycolipid, functional groups include sugars (mono- or polysaccharide)
Ganglioside: glycolipid, functional groups include oligosaccharides and N-acetylneuraminic acid (NANA)
What would happen if an amphipathic molecule were placed in a nonpolar solvent rather than an aqueous solution?
In a nonpolar solvent, we would see the opposite of what happens in a polar solvent like water: the hydrophilic, polar part of the molecules would be sequestered inside, while the nonpolar, hydrophobic part of the molecule would be found on the exterior and exposed to the solvent.
How many carbons are in a diterpene?
A diterpene has 20 carbon molecules in its backbone. One terpene unit is made from two isoprene units, each of which has five carbons and eight hydrogens.
What is the difference between a steroid and a steroid hormone?
A steroid is defined by its structure: it includes three cyclohexane rings and a cyclopentane ring. A steroid hormone is a molecule within this class that also functions as a hormone, meaning that it travels in the bloodstream, is active at low concentrations, has high-affinity receptors, and affects gene expression and metabolism.
NSAIDS block prostaglandin production in order to reduce pain and inflammation. What do prostaglandins do to bring about these symptoms?
Prostaglandins regulate the synthesis of cAMP, which is involved in many pathways, including those that drive pain and inflammation.
What are the names and functions of the four fat-soluble vitamins?
Vitamin A (carotene): as retinal: vision, as retinoic acid: epithelial development
Vitamin D (cholecalciferol): as calcitriol: calcium and phosphate regulation
Vitamin E (tocopherols): antioxidants, using aromatic ring
Vitamin K (phylloquinone and menaquinones): posttranslational modification of prothrombin (an important clotting factor in the blood), addition of calcium-binding sites on many proteins
How does the human body store spare energy? Why doesn’t the human body store most energy as sugar?
The human body stores energy as glycogen and triacylglycerols. Triacylglycerols are preferred because their carbons are more reduced, resulting in a larger amount of energy yield per unit weight. In addition, due to their hydrophobic nature, triacylglycerols do not need to carry extra weight from hydration.
Describe the structure and function of triacylglycerols.
Triacylglycerols, also called triglycerides, are composed of a glycerol backbone esterified to three fatty acids. They are used for energy storage.
What bonds are broken during saponification?
The ester bonds of triacylglycerols are broken to form a glycerol molecule and the salts of fatty acids (soap).
Why does soap appear to dissolve in water, and how is this fact important to cleaning?
Soap appears to dissolve in water because amphipathic free fatty acid salts form micelles, with hydrophobic fatty acid tails toward the center and carboxylate groups facing outward toward the water. Fat-soluble particles can then dissolve inside micelles in the soap-water solution and wash away. Water-soluble compounds can freely dissolve in the water.
What is the difference between a nucleoside and a nucleotide?
Nucleosides contain a five-carbon sugar (pentose) and nitrogenous base. Nucleotides are composed of a nucleoside plus one to three phosphate groups.
What are the base-pairing rules according to the Watson-Crick model?
A pairs with T (in DNA) or U (in RNA), using two hydrogen bonds. C pairs with G, using three hydrogen bonds.
What are the three major structural differences between DNA and RNA?
DNA contains deoxyribose, while RNA contains ribose. DNA contains thymine, while RNA contains uracil. Usually, DNA is double-stranded, while RNA is single-stranded.
How does the aromaticity of purines and pyrimidines underscore their genetic function?
The aromaticity of nucleic acids makes these compounds very stable and unreactive. Stability is important for storing genetic information and avoiding spontaneous mutations.
If a strand of RNA contained 15% cytosine, 15% adenine, 35% guanine, and 35% uracil, would this violate Chargaff’s rules?
This does not violate Chargaff’s rules. RNA is single-stranded, and thus the complementarity seen in DNA does not hold true. For single-stranded RNA, %C does not necessarily equal %G; %A does not necessarily equal %U.
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?
The five histone proteins are H1, H2A, H2B, H3, and H4. H1 is the only one not in the histone core.
Compare and contrast heterochromatin and euchromatin based on the following characteristics: density of chromatin packing, appearance under light microscopy, transcriptional activity.
Density of chromatin packing: heterochromatin are dense, while euchromatin are not dense (uncondensed)
Appearance under light microscopy: heterochromatin are dark, while euchromatin are light
Transcriptional activity: heterochromatin are silent, while euchromatin are active
What property of telomeres and centromeres allows them to stay tightly raveled, even when the rest of DNA is uncondensed?
Hight GC-content increases hydrogen bonding, making the association between DNA strands very strong at telomeres and centromeres.
What is the function of helicase and is it found in prokaryotes, eukaryotes, or both?
Helicase is found in both and its function is to unwind the DNA double helix
What is the function of single-stranded DNA-binding protein and is it found in prokaryotes, eukaryotes, or both?
Single-stranded DNA-binding protein is found in both and its function is to prevent reannealing of DNA double helix during replication
What is the function of primase and is it found in prokaryotes, eukaryotes, or both?
Primase is found in both and its function is to place ~10-nucleotide RNA primer to begin DNA replication
What is the function of DNA polymerase III and is it found in prokaryotes, eukaryotes, or both?
DNA polymerase III is found in prokaryotes and its function is to add nucleotides to the growing daughter strand
What is the function of DNA polymerase α (alpha) and is it found in prokaryotes, eukaryotes, or both?
DNA polymerase α is found in eukaryotes and its function is to add nucleotides to the growing daughter strand
What is the function of DNA polymerase I and is it found in prokaryotes, eukaryotes, or both?
DNA polymerase I is found in prokaryotes and its function is to fill in gaps left behind after RNA primer excision
What is the function of RNase H and is it found in prokaryotes, eukaryotes, or both?
RNase H is found in eukaryotes and its function is to excise RNA primer
What is the function of DNA ligase and is it found in prokaryotes, eukaryotes, or both?
DNA ligase is found in both and its function is to join DNA strands (especially between Okazaki fragments)
What is the function of DNA topoisomerases and is it found in prokaryotes, eukaryotes, or both?
DNA topoisomerase is found in both and its function is to reduce torsional strain from positive supercoils by introducing nicks in DNA strand
Between the leading strand and the lagging strand, which is more prone to mutations? Why?
The lagging strand is more prone to mutations because it must constantly start and stop the process of DNA replication. Additionally, it contains many more RNA primers, all of which must be removed and filled in with DNA.
What is the function of a telomere?
Telomeres are the end of eukaryotic chromosomes and contain repetitive sequences of noncoding DNA. These protect the chromosome from losing important genes from the incomplete replication of the 5’ end of the DNA strand
What is the difference between an oncogene and a tumor suppressor gene?
Oncogenes (or, more properly, photo-oncogenes) code for cell cycle-promoting proteins; when mutated, a photo-oncogene becomes an oncogene, promoting rapid cell cycling. Tumor suppressor genes code for repair or cell cycle-inhibiting proteins; when mutated, the cell cycle is allowed to proceed unchecked. Oncogenes are like stepping on the gas pedal mutated tumor suppressor genes are like cutting the brakes.
How does DNA polymerase recognize which strand is the template strand once the daughter strand is synthesized?
The parent strand is more heavily methylated, whereas the daughter strand is barely methylated at all. This allows DNA polymerase to distinguish between the two strands during proofreading.
Which phase of the cell cycle does the repair mechanism of DNA polymerase (proofreading) function? What are the key enzymes or genes specifically associated with the mechanism?
Phase of the cell cycle: S
Key enzymes/genes: DNA polymerase
Which phase of the cell cycle does the repair mechanism of mismatch repair function? What are the key enzymes or genes specifically associated with the mechanism?
Phase of the cell cycle: G2
Key enzymes/genes: MSH2, MLH1 (MutS and MutL in prokaryotes)
Which phase of the cell cycle does the repair mechanism of nucleotide excision repair function? What are the key enzymes or genes specifically associated with the mechanism?
Phase of the cell cycle: G1, G2
Key enzymes/genes: excision endonuclease
Which phase of the cell cycle does the repair mechanism of base excision repair function? What are the key enzymes or genes specifically associated with the mechanism?
Phase of the cell cycle: G1, G2
Key enzymes/genes: glycosylase, AP endonuclease
What is the key structural difference in the types of lesions corrected by nucleotide excision repair vs. those corrected by base excision repair?
Nucleotide excision repair corrects lesions that are large enough to distort the double helix; base excision repair corrects lesions that are small enough not to distort the double helix
When creating a DNA library, what are some of the advantages of genomic libraries? What about cDNA libraries?
Genomic libraries include all of the DNA in an organism’s genome, including noncoding regions. This may be useful for studying DNA in introns, centromeres, or telomeres. cDNA libraries only include expressed genes from a given tissue, but can be used to express recombinant proteins or to perform gene therapy
What does PCR accomplish for a researcher? What about southern blotting?
PCR increases the number of copies of a given DNA sequence and can be used for a sample containing very few copies of the DNA sequence. Southern blotting is useful when searching for a particular DNA sequence because it separates DNA fragments by length and then probes for a sequence of interest.
During DNA sequencing, why does the DNA polymer stop growing once a dideoxyribonucleotide is added?
Dideoxyribonucleotides lack the 3’ -OH group that is required for DNA strand elongation. Thus, once a dideoxyribonucleotide is added to a growing DNA molecule, no more nucleotides can be added because dideoxyribonucleotides have no 3’ -OH group with which to form a bond
What is the difference between a transgenic and a knockout mouse?
Transgenic mice have a gene introduced into their germ line or embryonic stem cells to look at the effects of that gene; they are therefore best suited for studying the effects of dominant alleles. Knockout mice are those in which a gene of interest has been removed, rather than added.
What is the role of mRNA?
mRNA carries information from DNA by traveling from the nucleus (where it is transcribed) to the cytoplasm (where if is translated).
What is the role of tRNA?
tRNA translates nucleic acids to amino acids by pairing its anticodon with mRNA codons; it is charged with an amino acid, which can be added to the growing peptide chain
What is the role of rRNA?
rRNA forms much of the structural and catalytic component of the ribosome, and acts as a ribozyme to create peptide bonds between amino acids
Which mRNA codon is the start codon, and what amino acid does it code for? Which mRNA codons are the stop codons?
The start codon is AUG, which codes for methionine
The stop codons are UAA, UGA, UAG
For a silent (degenerate) mutation, what changes in DNA sequence are observed, and what effect does it have on the encoded peptide?
Change in DNA sequence: substitution of bases in the wobble position, introns, or noncoding DNA
Effect of encoded protein: no change observed
For a missense mutation, what changes in DNA sequence are observed, and what effect does it have on the encoded peptide?
Change in DNA sequence: substitution of one base, creating an mRNA codon that matches a different amino acid
Effect of encoded protein: one amino acid is changed in the protein; variable effects on function depending on specific change
For a nonsense mutation, what changes in DNA sequence are observed, and what effect does it have on the encoded peptide?
Change in DNA sequence: substitution of one base, creating a stop codon
Effect of encoded protein: early function of protein; variable effects on function, but usually more severe than missense mutations
For a frameshift mutation, what changes in DNA sequence are observed, and what effect does it have on the encoded peptide?
Change in DNA sequence: insertion or deletion of bases, creating a shift in the reading frame of the mRNA
Effect of encoded protein: change in most amino acids after the site of insertion or deletion; usually the most severe of the mutations
What is wobble, and what role does it serve?
Wobble refers to the fact that the third base in a codon plays no role in determining which amino acid is translated from that codon. For example, any codon starting with “CC” codes for proline, regardless of which bas is in the third (wobble) position. This is protective because mutations in the wobble position will not have any effect on the protein translated from that gene
What is the role of RNA polymerase I?
RNA polymerase I synthesizes most rRNA.
What is the role of RNA polymerase II?
RNA polymerase II synthesizes mRNA (hnRNA) and snRNA.
What is the role of RNA polymerase III?
RNA polymerase III synthesizes tRNA and some rRNA
What are the three major post transcriptional modifications that turn hnRNA into mature mRNA?
Splicing: removal of introns, joining of exon; uses snRNA and snRNPs in the splice some to create a lariat, which is then degraded; exon are ligated together
5’ cap: addition of a 7-methylguanylate triphosphate cap to the 5’ end of the transcript
3’ poly-A tail: addition of adenosine bases to the 3’ end to protect against degradation
What is alternative splicing, and what does it accomplish?
Alternative splicing is the ability of some genes to use various combinations of exon to create multiple proteins from one hnRNA transcript. This increases protein diversity and allows a species to maximize the number of proteins it can create from a limited number of genes.
What are the three steps of translation?
Initiation, elongation, and termination
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 from peptide bond and polypeptide is handed to A site
E site: transiently holds uncharged tRNA as it exits the ribosome
What are the major posttranslational modifications that occur in proteins?
Posttranslational modifications include proper folding by chaperones, formation of quaternary structure, cleavage of proteins or signal sequences, and addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)
What type of operon is the trp operon? The lac operon?
The trp operon is a negative repressible system
The lac operon is a negative inducible system
From 5’ to 3’, what are the components of the operon, and what are their roles?
Regulator gene: transcribed to from repressor protein
Promoter site: site of RNA polymerase binding (similar to promoters in eukaryotes)
Operator site: binding site for repressor protein
Structural gene: the gene of interest; its transcription is dependent on the repressor being absent from the operator site
What is a positive control system?
Positive control systems require the binding of a protein to the operator site to increase transcription
What is a negative control system?
Negative control systems require the binding of a protein to the operator site to decrease transcription
What is an inducible system?
the system is normally “off” but can be made to turn “on” given a particular signal
What is a repressible system?
the system is normally “on” but can be made to turn “off” given a particular signal
In an enhancer, what are the differences between signal molecules, transcription factors, and response elements?
Signal molecules include steroid hormones and second messengers, which bind to their receptors in the nucleus. These receptors are transcription factors that use their DNA-binding domain to attach to a particular sequence in DNA called a response element. Once bonded to the response element, these transcription factors can then promote increased expression of the relevant gene.
By what histone modifications can genes be silenced in eukaryotic cells? Would these processes increase the proportion of heterochromatin or euchromatin?
Histone deacetylation and DNA methylation will both down regulate the transcription of a gene. These processes allow the relevant DNA to be clumped more tightly, increasing the proportion of heterochromatin.
Describe the role of flippases and lipid rafts in biological membranes
Flippases 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
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 proteins (channels and receptors), membrane-associated proteins, and embedded proteins, are next most plentiful; carbohydrates, including the glycoprotein coat and signaling molecules, are next; nucleic acids are essentially absent
How can you tell if fatty acids are saturated or unsaturated?
Unsaturated fatty acids have a kink in their chain due to double bonds
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 molecules at low temperatures, and by restricting excessive movement of phospholipids at high temperatures. Cholesterol also provides stability by cross-linking adjacent phospholipids through interactions at the polar head group and hydrophobic interactions at the nearby fatty acid tail.
What are the three classes of membrane proteins? How are they each most likely to function?
Transmembrane proteins are most likely 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.
Contrast gap junctions and tight junctions
Gap junctions allow for the intercellular transport of materials and do not prevent paracellular transport of materials. 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 around the cell
What is the primary thermodynamic factor responsible for passive transport?
The primary thermodynamic factor responsible for passive transport is entropy
What is the relationship between osmotic pressure and the direction of osmosis through a semipermeable membrane?
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.
Compare the two types of active transport. What is the difference between symport and antiport?
Primary active transport uses ATP as an energy source for the movement of molecules against their concentration gradient, while secondary active transport uses an electrochemical gradient to power the transport. Symport moves both particles in secondary active transport across the membrane in the same direction, while anti port moves particles across the cell membrane in opposite directions.
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.
What distinguishes the inner mitochondrial membrane from other biological membranes? What is the pH gradient between the cytoplasm and the intermembrane 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 intermembrane space because the outer mitochondrial membrane has such high permeability to biomolecules (the proton-motive force of the mitochondria is across the inner mitochondrial membrane, not the outer mitochondrial membrane)
Compare and contrast GLUT 2 and GLUT 4
Important tissues: GLUT 2; liver, pancreas. GLUT 4; adipose tissue, muscle
Km: GLUT 2; high (15 mM). GLUT 4; low (5mM)
Saturated at normal glucose levels? GLUT 2; no, cannot be saturated under normal physiological conditions. GLUT 4; yes, saturated when glucose levels are only slightly above 5mM.
Responsive to insulin? GLUT 2; no (but serves as glucose sensor to cause release of insulin in pancreatic beta-cells). GLUT 4; yes
How does insulin promote glucose entry into cells?
GLUT 4 is saturated when glucose levels are 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
What is the function and key regulators of the enzyme hexokinase? Is it reversible?
Hexokinase phosphorylates glucose to form glucose 6-phosphate, ‘trapping” glucose in the cell. It is inhibited by glucose 6-phosphate. It is irreversible.
What is the function and key regulators of the enzyme glucokinase? Is it reversible?
Glucokinase also phosphorylates and “traps” glucose in liver and pancreatic cells, and works with GLUT 2 as part of the glucose sensor in beta-islet cells. In liver cells, it is induced by insulin. It is irreversible.
What is the function and key regulators of the enzyme phosphofructokinase-1 (PFK-1)? Is it reversible?
PFK-1 catalyzes the rate-limiting step of glycolysis, phosphorylating fructose 6-phosphate to fructose 1,6-biphosphate using ATP. It is inhibited by ATP, citrate, and glucagon. It is activated by AMP, fructose 2,6-biphosphate, and insulin. It is irreversible.
What is the function and key regulators of the enzyme glyceraldehyde-3-phosphate dehydrogenase? Is it reversible?
Glyceraldehyde-3-phosphate dehydrogenase generates NADH while phosphorylating glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate. It is reversible.
What is the function and key regulators of the enzyme 3-phosphoglycerate kinase? Is it reversible?
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.
What is the function and key regulators of the enzyme pyruvate kinase? Is it reversible?
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-bisphosphate. It is irreversible.
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.
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.
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: galactose is phosphorylated by galactokinase, trapping it in the cell
“Linking” enzyme: galactose-1-phosphate uridyltransferase produces glucose 1-phosphate, a glycolytic intermediate, thus linking the pathways
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?
“Trapping” enzyme: fructose is phosphorylated by fructokinase, trapping it in the cell (with a small contribution from hexokinase)
“Linking” enzyme: 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
What are the reactants of the pyruvate dehydrogenase complex? What are the products?
Pyruvate, NAD+, and CoA are the reactants of the PDH complex. Acetyl-CoA, NADH, and CO2 are the products
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 satisfies 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 gluconeogenesis.
What is the structure of glycogen? What types of glycosidic links exist in a glycogen granule?
Glycogen is made up of a core protein of glycogenin with linear chains of glucose emanating out from the center, connected by alpha-1,4 glycosidic links. Some of these chains are branched, which requires alpha-1,6 glycosidic links.
What are the two main enzymes of glycogenesis, and what does each accomplish?
Glycogen synthase attaches the glucose molecule from UDP-glucose to the growing glycogen chain, forming an alpha-1,4 link in the process.
Branching enzyme creates a branch by breaking an alpha-1,4 Lin in the growing chain an moving a block of oligoglucose to another location in the glycogen granule. The oligoglucose is then attached with an alpha-1,6 link.
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 alpha-1,4 link and creating glucose 1-phosphate.
Debranching enzyme moves all of the glucose from a branch to a longer glycogen chain by breaking an alpha-1,4 link and forming a new alpha-1,4 link to the longer chain. The branch point is left behind; this is removed by breaking the alpha-1,6 link to form a free molecule of glucose.
Under what physiological conditions 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 creation, which requires sufficient fat stores to undergo beta-oxidation.
What are the four enzymes unique to gluconeogenesis? Which irreversible glycolytic enzymes do they replace?
Pyruvate carboxylase replaces pyruvate kinase
Phosphoenolpyruvate carboxykinase (PEPCK) replaces pyruvate kinase
Fructose-1,6-bisphosphatase replaces phosphofructokinase-1
Glucose-6-phosphatase replaces glucokinase
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 from burning pyruvate in the citric acid cycle to creating new glucose molecules for the rest of the body. The acetyl-CoA for this regulation comes predominantly from beta-oxidation, not glycolysis.
Given that glycogen storage disorder von Gierke’s disease affects the last enzyme of gluconeogenesis, predict the associated metabolic derangement that occurs.
The last enzyme in gluconeogenesis is glucose-6-phosphatase so patients with von Gierke’s disease are unable to perform gluconeogenesis in addition to glycogenolysis. This means patients will be unable to produce glucose during periods of fasting (resulting in hypoglycemia). Furthermore, given a blocker in the gluconeogenic pathway, a buildup of intermediates (including lactate resulting in lactic acidosis) would also be expected.
What are the two major products of the pentose phosphate pathway (PPP)?
The two major metabolic products of the pentose phosphate pathway are ribose 5-phosphate and NADPH
What are three primary functions of NADPH?
NADPH is involved in lipid biosynthesis, bactericidal bleach formation in certain white blood cells, and maintenance of glutathione stores to protect against reactive oxygen species.
What is the overall reaction of the pyruvate dehydrogenase complex?
pyruvate + CoA-SH + NAD+ –> acetyl-CoA + CO2 + NADH + H+
What other molecules can be used to make acetyl-CoA, and how does the body perform this conversion for each?
Molecule: fatty acids. Mechanism: shuttle acyl groups from systolic CoA-SH to mitochondrial CoA-SH via carnitine; then undergo beta-oxidation
Molecule: ketogenic amino acids. Mechanism: transaminate to lose nitrogen; convert carbon skeleton into ketone body, which can be converted into acetyl-CoA
Molecule: ketones. Mechanism: reverse of ketone body formation
Molecule: alcohol. Mechanism: alcohol dehydrogenase and acetaldehyde dehydrogenase convert alcohol into acetyl-CoA
Mnemonic to remember the substrates of the citric acid cycle
Please Can I Keep Selling Seashells For Money, Officer?
Pyruvate Citrate Isocitrate alpha-Ketoglutarate Succinyl-CoA Succinate Fumarate Malate Oxaloacetate
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 reactions can be coupled with CO2 formation, thus forming energy carriers such as NADH and FADH2 for the electron transport chain.
What enzyme catalyzes the rate-limiting step of the citric acid cycle?
isocitrate dehydrogenase
What are the three main sites of regulation within the citric acid cycle? What molecules inhibit and activate the three main checkpoints?
Citrate synthase: inhibited by ATP, NADH, succinylcholine-CoA, citrate and has no activators
Isocitrate dehydrogenase: inhibited by ATP and NADH and activated by ADP and NAD+
alpha-ketoglutarate complex: inhibited by ATP, NADH, and succinylcholine-CoA and activated by ADP and Ca2+
What complex(es) of the electron transport chain are associated with pumping a proton into the intermembrane space?
complexes I, III, and IV
What complex(es) of the electron transport chain are associated with acquiring electrons from NADH?
complex I
What complex(es) of the electron transport chain are associated with acquiring electrons from FADH2?
complex II
What complex(es) of the electron transport chain are associated with having the highest reduction potential?
complex IV (reduction potentials increase along the electron transport chain)
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.
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 utilize it in order to maximize its ATP yield.
What is the difference between the electron transport chain and oxidative phosphorylation? What links the two?
The electron transport chain is made up of the physical set of intermembrane proteins located on the inner mitochondrial matrix, and they undergo oxidation-reduction reactions as they transfer electrons to oxygen, the final electron acceptor. As electrons are transferred, a proton-motive force is generated in the intermembrane space. Oxidative phosphorylation is the process by which ATP is generated via harnessing the proton gradient, and it utilizes ATP synthase to do so.
The ∆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 transferring 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 locations, 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.
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, colipase, cholesterol esterase, and bile assist in the chemical digestion of lipids. In the more distal portion of the small intestine, absorption occurs.
True or false: all lipids enter the circulation through the lymphatic system
False. Small free fatty acids enter the circulation directly
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.
A diabetic patient begins insulin injections for management of blood glucose levels. What is the expected impact on the patient’s weight?
An increase in insulin levels will increase lipid storage and decrease lipid mobilization from adipocytes, leading to weight gain in diabetic patients who begin insulin injections
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
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
Order the lipoproteins from greatest percentage of protein to least percentage of protein. Circle the molecules that are primarily involved in triacylglycerol transport
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
Lipoproteins are synthesized primarily by which two organs?
Lipoproteins are synthesized primarily by the intestine and liver
When physicians order a lipid panel to evaluate a patient, which value do the prefer to see over a minimum threshold rather than below a maximum?
HDL is often considered “good” cholesterol because it picks up excess cholesterol from blood vessels for excretion. Because of this crucial role, HDL values are checked for being over a minimum value
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 reductase, which is located in the smooth endoplasmic reticulum
What proteins are specific to the formation and transmission of cholesteryl esters, and what are their functions?
LCAT catalyzes the esterification of cholesterol to form cholesteryl esters. CETP promotes the transfer of cholesteryl esters from HDL to IDL, forming LDL.
What are the five steps in the 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 carbonyl group, dehydration, and reduction of a double bond.
How does β-oxidation of unsaturated fatty acids differ from that of saturated fatty acids?
There is an additional isomerase and an additional reductase for the β-oxidation of unsaturated fatty acids, which provide the stereochemistry necessary for further oxidation
True or false: fatty acids are synthesized in the cytoplasm and modified by enzymes in the smooth endoplasmic reticulum
True
What are ketone bodies?
Ketone bodies are essentially transportable forms of acetyl-CoA. They are produced by the liver and used by other tissues during prolonged starvation
Why are fatty acids used to create ketone bodies instead of creating glucose?
Fatty acid degradation results in large amounts of acetyl-CoA, which cannot enter the gluconeogenic pathway to produce glucose. Only odd-numbered fatty acids can act as a source of carbon for gluconeogenesis; even then, only the final malonyl-CoA molecule can be used. Energy is packed into ketone bodies for consumption by the brain and muscles.
What conditions and tissues favor ketogenesis? Ketolysis?
Ketogenesis is favored by 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 lower-energy state in muscle and brain tissues and does not occur in the liver.
True or false: bodily proteins will commonly be broken 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
Where does the bulk of protein digestion occur?
The bulk of protein digestion occurs in the small intestine
During protein processing, what is the eventual fate of each of the following components: carbon skeleton, amino group, and side chains?
The carbon skeleton is transported to the liver for processing into glucose or ketone bodies. The amino group will feed into the urea cycle for excretion. Side chains are processed depending on their composition. Basic side chains will be processed like amino groups, while other functional groups will be treated like the carbon skeleton
What conditions does ∆G˚’ adjust for that are not considered with ∆G˚?
∆G˚’ adjusts only for the pH of the environment by fixing it at 7. Temperature and concentrations of all other reagents are still fixed at their values from standard conditions and must be adjusted for if they are not 1 M.
Why can heat be used as a measure of internal energy in living systems?
The cellular environment has a relatively fixed volume and pressure, which eliminates work from our calculations of internal energy; if ∆U = Q - W and W = 0, ∆U = Q
Complete the following table relating the change in entropy and enthalpy of a reaction with whether the reaction is spontaneous:
+∆H, +∆S:
+∆H, -∆S:
-∆H, +∆S:
-∆H, -∆S:
+∆H, +∆S: spontaneous at high temperatures
+∆H, -∆S: nonspontaneous
-∆H, +∆S: spontaneous
-∆H, -∆S: spontaneous at low temperatures
How does coupling with ATP hydrolysis alter the energetics of a reaction?
ATP hydrolysis yields about 30 kJ/mol of energy, which can be harnessed to drive other reactions forward. This may either allow a nonspontaneous reaction to occur or increase the rate of a spontaneous reaction
Explain why ATP is an inefficient molecule for long-term energy storage?
ATP is an intermediate-energy storage molecule and is not energetically dense. The high-energy bonds in ATP and the presence of a significant charge make it an inefficient molecule to pack into a small space. Long-term storage molecules are characterized by energy density and stable, nonrepulsive bonds, primarily seen in lipids
What is an advantage of analyzing the half-reactions in biological oxidation and reduction reactions?
Analyzing half-reactions can help to determine the number of electrons being transferred. This type of analysis also facilitates balancing equations and the determination of electrochemical potential if reduction potentials are provided.
Name three soluble electron carriers and their relevant metabolic pathways in the cell.
NDAH: glycolysis, fermentation, citric acid cycle, electron transport chain
NADPH: pentose phosphate pathway, lipid biosynthesis, bleach formation, oxidative stress, photosynthesis
Ubiquinone (CoQ): electron transport chain
Cytochromes: electron transport chain
Glutathione: oxidative stress
Provide an example of disequilibrium that is maintained at the expense of cellular energy
Any excitable cell is maintained in a state of disequilibrium. Classic examples include muscle tissue and neurons. In addition, cell volume and membrane transport are regulated by the action of the sodium-potassium pump, which can maintain a stable disequilibrium state in most tissues
What tissue is least able to change its fuel source in periods of prolonged starvation?
Cells that rely solely on anaerobic respiration are the least adaptable to different energy sources. Therefore, red blood cells are the least flexible during periods of prolonged starvation and stay reliant on glucose.
During what stage is there the greatest decrease in the circulating concentration of insulin?
During the postabsorptive state, there is the greatest decrease in insulin levels. The concentrations of the counterregulatory hormones (glucagon, cortisol, epinephrine, norepinephrine, and growth hormone) begin to rise.
Describe the primary metabolic function of insulin
Insulin promotes glucose uptake by adipose tissue and muscle, glucose utilization in muscle cells, and macromolecule storage (glycogenesis, lipogenesis).
Describe the primary metabolic function of glucagon
Glucagon increases blood glucose levels by promoting glycogenolysis, gluconeogenesis, lipolysis, and ketogenesis.
Describe the primary metabolic function of cortisol
Cortisol increases lipolysis and amino acid mobilization, while decreasing glucose uptake in certain tissues and enhancing the activity of other counterregulatory hormones.
Describe the primary metabolic function of catecholamines
Catecholamines increase glycogenolysis in muscle and liver and lipolysis in adipose tissue
Describe the primary metabolic function of thyroid hormones (T3/T4)
Thyroid hormones increase basic metabolic rate and potentiate the activity of other hormones
Thyroid storm is a potentially lethal state of extreme hyperthyroidism in which T3 and T4 levels are significantly above normal limits. What vital sign abnormalities might be expected in a patient with thyroid storm?
Thyroid storm presents with hyperthermia (high temperature), tachycardia (fast heart rate), hypertension (high blood pressure), and tachypnea (high respiratory rate)
What is the preferred fuel for most cells in the well-fed state? What is the exception and its preferred fuel?
The preferred fuel for most cells in the well-fed state is glucose; the exception is cardiac muscle, which prefers fatty acids
What organ consumes the greatest amount of glucose relative to its percentage of body mass?
The brain consumes the greater amount of glucose relative to its percentage of body mass
Describe the major metabolic functions of the liver.
The liver is responsible for maintaining a steady-state concentration of glucose in the blood through glucose uptake and storage, glycogenolysis, and gluconeogenesis. The liver also participates in cholesterol and fat metabolism, the urea cycle, bile synthesis, and the detoxification of foreign substances.
How is the respiratory quotient expected to change when a person transitions from resting to brief exercise?
As a person begins to exercise, the proportion of energy derived from glucose increases. This transition to almost exclusively carbohydrate metabolism will cause the respiratory quotient to approach 1.
True or false: body mass can be predicted by the leptin receptor phenotype and caloric intake alone
False; energy expenditure, genetics, socioeconomic status, geography, and other hormones also play a role in body mass regulation.
True or false: it is easier to gain weight than to lose weight
True; the threshold is lower for uncompensated weight gain than it is for uncompensated weight loss. Therefore, it is easier to surpass this threshold and gain weight than to lose weight
If you were designing a study to assess metabolism, which measurement method would you choose?
The methods described in the text include chemical analysis, which is objective and can quantify specific metabolic substrates, products, and enzymes; calorimetry, which is most accurate for basal metabolic rate but also most expensive; respirometry, which provides basic information about fuel sources; and caloric analysis at constant weight (food and exercise logs). which is the least invasive.
