BIO 3342 Test 1

Distinguish between the 3 types of weak non-covalent bonds that support life functions; characterize a description of biological interaction as driven primarily by either hydrogen bonding, ionic bonding or the hydrophobic effect

Covalent bonds are where electron pairs are shared between pairs fo atoms Ionic bonds are attraction between fully charged components Hydrogen bonds are a weak attractive interaction that is between the unshared pair of outer electrons of a hydrogen atom and a second electronegative atom to form an attractive interaction In a hydrophobic interaction, non polar molecules are forced into aggregates which minimizes their exposure to the surrounding water molecules

List roles in sustaining life that are attributed to water and relate these roles to the molecular structure and bonding patterns of water (i.e. specific heat, heat of vaporization, solvent properties, etc)

Each molecule of water can form hydrogen bonds with as many as four other molecules producing a highly interconnected network of molecules Each hydrogen bond is formed with the partially positive hydrogen that is aligned with the partially negative oxygen. Hydrogen bonding is what allows water molecules to have an unusually strong tendency to adhere to one another When water is heated, most of the thermal energy is consumed in disrupting hydrogen bonds rather than molecular motion Evaporation takes a lot of energy because it involve the breaking of hydrogen bonds Water is able to dissolve in more types of substances than any other solvent Water plays a key role in maintaining the structure and function of macromolecules and the complexes that they form

by comparing the prevailing ratio of Products: Reactants to the Keq, determine whether a reaction will require an input of energy to proceed in the forward direction as written

Keq can be used to determine if a reaction is at equilibrium, to calculate concentrations at equilibrium, and to estimate whether a reaction favors products or reactants at equilibrium.

Name the bond that joins two monosaccharides within disaccharides or polysaccharides (i.e. beta-1, 4 glycosidic bond)

Monomers of glucose are joined by alpha 1,6 bonds if branched and alpha 1-4 glucosidic bonds Glycogen is joined via an alpha 1,4 glycosidic bond and a 1,6 glycosidic bond if branched Starch is linked by an alpha 1-4 glycosidic bond Disacharrides like lactose are joined via beta 1,4 glycosidic bonds and is composed of glucose and galactose Maltose is joined by alpha 1-4 glycosidic bonds and is made of 2 alpha D glucoses Sucrose is linked by alpha 1,2 glycosidic bonds and is made of alpha glucose and beta fructose

Categorize plant Kv, Na/glucose cotransporter, KcsA, Na/K ATPase, and glucose transporter as proteins that facilitate simple diffusion, non-mediated channel flow, passive mediated, active mediated or secondary active mediated transport of solute across the membrane; identify which of these integral membrane proteins bind/hydrolyze ATP

Passive diffusion and facilitated diffusion (passive transport) do not bind to ATP because they pass down their electrochemical gradient. Active transport does require the binding of ATP (Ex. Sodium potassium pump)

in which stage of catabolic metabolism (as presented in your textbook) does glycogen breakdown occur?

Phase I

In which stage of catabolic metabolism (as presented in your textbook) is the Electron Transport Chain at play?

Phase III

Distinguish symport and antiport in co-transport; Given a diagram or description of a scenario, identify symport, antiport and cotransport as well as whether the transport is passive, active or secondary active transport

Plant cells rely on secondary active transport systems to take up a variety of nutrients, including sucrose, amino acids, and nitrate. In plants, uptake of these compounds is coupled to the downhill, inward movement of H+ ions rather than Na+ ions. The secondary active transport of glucose into the epithelial cells of the intestine and the transport of sucrose into a plant cell are examples of symport, in which the two transported species (Na+ and glucose or H+ and sucrose) move in the same direction. Numerous cotransporters have been isolated that engage in antiport, in which the two transported species move in opposite directions. For example, cells often main- tain a proper cytoplasmic pH by coupling the inward, downhill movement of Na+ with the outward movement of H+. Cotransporters that mediate antiport are usually called exchangers. The three‐ dimensional structures of a number of secondary transporters have been solved in recent years, and, like the Na+/K+‐ATPase, they exhibit a transport cycle in which the protein's binding sites gain alternating access to the cytoplasm and the extracellular space.

Explain what is meant by "reduced carbon fuel" and rank carbon-based molecules according to their energy/reduction status

Plants have the capacity to use light energy to reduce carbon and fix it into CO2 Gain in electrons is reduction. Loss of electrons is oxidation

Order the steps from arrival of transcription-promoting factors at the eukaryotic DNA gene promoter to synthesis of an mRNA copy of the gene. Include the terms RNA polymerase II, elongation, promoter, nucleotides, and transcription factor.

Predict the impact of blocking or altering any of the above molecules/factors in transcription RNA polymerase 2 makes the RNA a. General transcription factors (TFs) i. Protein that binds to a eukaryotic promoter near the transcription start site and is a part of the basal transcription apparatus that indicates transcription ii. TFs + RNA pol + mediator= basal transcription apparatus § Basal transcription apparatus - complex of transcription factors, RNA polymerase, and other proteins that assemble on the promoter and are capable of initiating minimal levels of transcription iii. Required for transcription b. Transcriptional activator proteins (TAPs) i. Protein in eukaryotic cells that binds to specific DNA sequences and bring about higher levels of transcription by stimulating the assembly of the basal transcription apparatus at the start site. i. Stimulate assembly of basal transcription apparatus to increase transcription levels ii. Not required for transcription c. Remember that TFs and TAPs are specific to eukaryotes

List the types of cellular macromolecules and associate them with life functions/organelles; Contrast lipids with the other 3 classes of macromolecules.

Proteins (amino acids) Nucleic acids (nucleotides) Polymers of nucleotides that store and transmit genetic information DNA holds the genetic information in all other cellular organisms and some viruses RNA is the genetic material is some viruses Has C2 hydroxyl Composed of a phosphate group, sugar, and base Nucleobases are purines and pyrimidines Polysaccharides Lipids

Describe the directionality of RNA polymerase action with regard to the DNA as well as the RNA product. Include the terms: DNA template strand, DNA coding strand, DNA noncoding strand, mRNA, codons, 5'-3' and 3'-5'.

RNA reads 3--> 5 but builds 5 -->

Using Plant Kv channels as an example, explain how a channel can open and then close in response to a change in membrane potential (voltage gated channel -example of facilitated passive diffusion via ion channel); in particular, contrast the location, amino acid composition and roles of the 1) pore domain, 2) helices S1-S4 of the voltage sensing domain, and the inactivation peptide of the cytoplasmic portion of this voltage-gated channel; predict the impact of mutations in these channel

Sodium and potassium ion channels which respond to changes in membrane potential and can exist in closed, open, or inactivated states We go from -60 mv to +20 during depolarization which changes the flow of ions This channel is open only for a short period of time and is known as the ball and chain model where a positively charged ball domain held by a polypeptide chain moves back and forth within the cytoplasm. As the channel opens, the ball moves into the pore and inactivates the channel

As a part of catabolic metabolism, in which compartment of the cell is each of the following metabolites produced?

Succinate- mitochondria, Phase III Carbon dioxide-mitochondria, in Phase II and Phase III (pyruvateàacetyl CoA and in CAC) Fructose 1,6-bisphosphate-cytosol, Phase II ATP-cytosol and mitochondria, Phase II and Phase III (glycolysis, CAC and respiration-linked ATP synthesis by ATP synthase in the inner mitochondrial membrane) Glucose-6-phosphate, cytosol, Phase II Phosphoenolpyruvate, cytosol, Phase II Citrate, mitochondria, Phase III H20-prominently at the end of the ETC in the inner mitochondrial membrane, Phase III (though is a by-product of other reactions along the way)

identify sucrose and lactose as disaccharides joined by glycosidic bonds

Sucrose is glucose+ fructose and lactose is glucose and galactose Sucrose is joined by alpha 1,2 linkage whereas lactose is joined by beta 1,4 linkage

Relate the structure of an ion channel to the flow of ions through it using the KcsA K+ channel as an exemplar (this is facilitated passive diffusion via an ion channel); predict the impact of altering the composition of the Gly-Tyr-Gly-Val-Thr selectivity filter in terms of passage of K+ or whether larger or smaller ions would be more likely to pass in mediated diffusion

The carbonyl groups of the selectivity filter interact with the potassium ions Partially neg oxygens interact with potassium to form more stabilizing bonds à neg G value = spontaneous rxn Has the property of ion specificity which is the ability of a channel to allow a specific ion to enter while preventing all others from moving across The five amino acid sequence is known as the selectivity filter which determines the specificity of the filter for the ion channel for K+ ions Larger and smaller ions won't pass through the selectivity filter because it is not thermodynamically favorable bc it would require an input of energy

Explain what reaction coupling means.

The formation of glutamine is said to be coupled to the hydrolysis of ATP. As long as the ΔG for ATP hydrolysis is more negative than the ΔG for glutamine synthesis from glutamic acid is positive, the "downhill" ATP hydrolysis reaction can be used to drive the "uphill" synthesis of glutamine. To couple the two chemical reactions, the product of the first reaction becomes the reactant for the second. The bridge between the two reactions—glutamyl phosphate in this case—is called the common intermediate . What happens, in essence, is that the exergonic hydrolysis of ATP is taking place in two steps. In the first step, glutamic acid acts as an acceptor of the phosphate group, which is displaced by NH3 in the second step.

Describe three ways in which enzymes lower the free energy of activation

1. Substrate orientation Enzymes hold substrate in the optimal position for a reaction 2. Changing substrate reactivity Acidic or basic R groups can change the charge of a substrate Charged R groups may attack, bend, or link within the substrate Cofactors increase reactivity by removing or donating electrons 3. Inducing strain in the substrate Shifts in conformation to cause an induced fit between the enzyme and substrate

Discuss hydropathy plots as a technique used to predict transmembrane stretches of integral membrane proteins

A string of 20-30 hydrophobic amino acids as determined by hydropathy plots identifies a membrane spanning domain each site along a polypeptide is assigned a value that provides a measure of the hydrophobicity of the amino acid at that site as well as that of its neighbors. This approach provides a "running average" of the hydrophobicity of short sections of the polypeptide and guarantees that one or a few polar amino acids in a sequence do not alter the profile of the entire stretch. Hydrophobicity of amino acids can be determined using various criteria, such as their lipid solubility or the energy that would be required to transfer them from a nonpolar medium into an aqueous medium. Transmembrane segments are usually identified as a jagged peak that extends well into the hydrophobic side of the spectrum. How many times does it span the membrane?

Describe packaging of DNA within the nucleus using the terms chromosome, chromatin, nucleosome, histone and linker DNA. Include detail about the composition of nucleosomes and histones as well as the length of linker DNA.

Chromosomes are composed of DNA and associated proteins called chromatin Linker histone binds to the linker DNA that connects one nucleosome to the next Histones have large amounts of arginine and lysine. H1, H2A, H2B, H3, H4. Positve lysine is drawn to phosphate A nucleosome is about 200 bp of DNA wrapped around a positively charged histone Negatively charged sugar phsophate backbone is attached to histones Chromosomes consists of 1 covalently connected DNA molecule and associated proteins In prokaryotes, the DNA and proteins reside in the nucleoid

How is the generation of pluripotent stem cells different from the mechanism by which hematopoietic stem cells are obtained?

The generation of IPS cells does not require the use of an embryo HSC are generated from the bone marrow IPS cells can be generated from somatic cells

Interpret Kaplan-Meier plots of survival or disease-free survival data, especially plots of the impact of nutrient depravation or calorie restriction on survival

The initial idea that reduced caloric intake could lead to longer life came from studies in rats and mice. Feeding the animals 10-30 percent less food allowed them to have longer lives, with an increase in both the average lifespan as well as in the maximum lifespan. odel organism studies have also indicated that caloric restriction may increase the production of reactive oxygen.

Explain the patch clamp method and how it furthered understanding of ion channel gating

This is accomplished using very fine micropipette‐electrodes made of polished glass that are placed on the outer cell surface and sealed to the membrane by suction. The voltage across the membrane can be maintained (clamped) at any particular value, and the current originating in the small patch of membrane surrounded by the pipette can be measured Most of the ion channels that have been identified can exist in either an open or a closed confor- mation; such channels are said to be gated. The opening and clos- ing of the gates are subject to complex physiologic regulation and can be induced by a variety of factors depending on the particular channel.

Describe Cystic Fibrosis as a genetic disease of ion transport

cystic fibrosis, the best studied and most common inherited ion channel disorder, results from a defect in the ion channels of epithelial cells. in addition to functioning as a chloride channel, CFTR also (1) conducts bicarbonate (HCO3−) ions, (2) suppresses the activity of an epithelial Na+ ion channel (ENaC), and (3) stimulates the activity of a family of epithelial chloride/bicarbonate exchangers.

If given the names glucose-6-phosphate, fructose-1,6-bisphosphate, phosphoenolpyruvate, acetyl CoA, citric acid, succinate, or ETC Complexes, associate it with Phase I, II or III of metabolism

glucose-6-phosphate, fructose-1,6-bisphosphate, and phosphoenolpyruvate are stage 2 acetyl CoA is between stages 2 and 3 citric acid, succinate, or ETC Complexes are in the inner mitochondrial membrane is stage 3. Acetyl coA is a reduced carbon that helps create citrate

Using Na/K ATPase as an exemplar, explain how ATP hydrolysis can be coupled to movement of ions against their concentration gradient in primary active mediated transport

he Na+K+-ATPase pump helps to maintain osmotic equilibrium and membrane potential in cells. The sodium and potassium move against the concentration gradients. The Na+ K+-ATPase pump maintains the gradient of a higher concentration of sodium extracellularly and a higher level of potassium intracellularly

Explain the role of aquaporins in allowing water movement across membranes; describe the mechanisms whereby aquaporin selectively permits passage of water molecules (your explanation should include the identity of key amino acid residues); predict the impact of altering amino acids R206 (Arg), E152 (Glu) or E14 (Glu) on aquaporin function or of lack of aquaporin channels on the process of osmosis

many cells are much more permeable to water than can be explained by simple diffusion through the lipid bilayer. A family of small integral proteins, called aquaporins, allow the passive movement of water from one side of the plasma membrane to the other. Each aquaporin subunit (in the four‐subunit protein) contains a central channel that is lined primarily by hydrophobic amino acid residues and is highly specific for water molecules. At the narrow passageway are positively charged amino acid residues that prevent the movement of charged ions such as protons to keep it from disrupting the gradient used for ATP production

Which will cross a simple phospholipid bilayer more readily? A large nonpolar substance or a small nonpolar substance A charged small molecule or an uncharged small molecule Why?

membranes are highly permeable to small inorganic molecules, such as O 2 , CO 2, NO, and H 2 O, which are thought to slip between adjacent phospholipids. In contrast, larger polar molecules, such as sugars, amino acids, and phosphorylated intermediates, exhibit poor membrane penetrability. As a result, the lipid bilayer of the plasma membrane provides an effective barrier that keeps these essential metabolites from diffusing out of the cell. One measure of polarity or non polarity of a substance is the partition coefficient where the ratio of a solubility in a polar solvent to water are mixed. Greater lipid solubility= faster penetration. Another factor determining the rate of penetration is size. If two molecules have equal partition coefficients than the one with the smaller molecule will penetrate the membrane more rapidly than the larger one. - answer: small nonpolar and small uncharged

Explain how site-directed mutagenesis is used to characterize the role of specific amino acids in the enzyme active site

recent advances in DNA technology have allowed investigators to isolate an individual gene from human chromosomes, to alter its information content in a precisely determined way, and to synthesize the modi-fied protein with its altered amino acid sequence. This technique, which is called site‐directed mutagenesis the gene can be mutated in a way that substitutes an amino acid with different charge, hydrophobic character, or hydrogen‐bonding properties. For example, the drug Somavert, which was approved by the FDA in 2003, is a modified version of human growth hormone (GH) con-taining several alterations. GH normally acts by binding to a receptor on the surface of target cells, which triggers a physiological response. Somavert competes with GH in binding to the GH receptor, but interaction between drug and receptor fails to trigger the cellular response.

Compare and contrast the four ways that substance can move across the plasma membrane

simple diffusion through the lipid bilayer; simple diffusion through an aqueous, protein‐lined channel; diffusion that is facilitated by a protein transporter; and active transport, which requires an energy‐driven protein "pump" capable of moving substances against a concentration gradient - Passive diffusion does not require ATP nor an integral protein

Describe the primary features of Stages I, II, and III of metabolism

stage 1: macromolecules are hydrolyzed into their building blocks Stage 2: building blocks degrade into metabolites Occurs in the cytosol ATP gets produced via substrate level phosphorylation Stage 3: small molecular weight metabolites like Acetyl-CoA are further oxidized to make ATP

Explain what is meant by "structure based drug design" and offer an overview of the process.

structure‐based drug design , relies upon knowledge of the structure of the protein target. If the tertiary structure of a protein has been determined, research-ers can use computers to design "virtual" drug molecules whose size and shape might allow them to fit into the apparent cracks and crev-ices of the protein, rendering it inactive.

Offer 3 examples of the ways in which ion channels can be 'gated' and what it means to be gated; be able to identify these mechanisms in excerpts of scientific writing about ion channels

such channels are said to be gated. The opening and clos- ing of the gates are subject to complex physiologic regulation and can be induced by a variety of factors depending on the particular chan- nel. Three major categories of gated channels are distinguished: 1. Voltage‐gated channels whose conformational state depends on the difference in ionic charge on the two sides of the membrane. 2. Ligand‐gated channels whose conformational state depends on the binding of a specific molecule (the ligand), which is usu- ally not the solute that passes through the channel. Some ligand‐ gated channels are opened (or closed) following the binding of a molecule to the outer surface of the channel; others are opened (or closed) following the binding of a ligand to the inner surface of the channel. For example, neurotransmitters, such as acetylcho- line, act on the outer surface of certain cation channels, whereas? cyclic nucleotides, such as cAMP, act on the inner surface of cer- tain calcium ion channels. One of the most well studied ligand gated channels is acetylcholine receptor found on synaptic cells Acetylcholine receptors are ion channels that respond to the binding of neurotransmitter called acetylcholine When action potential arrives at the terminal end of the presynaptic nerve cell, it stimulates the release of vesicles containing acetylcholine which then diffuses across the synaptic cleft and bind to target receptors The receptor is a pentamer that consists of 4 subunits When acetylcholine is not bound to the channel, the channel is in its closed state. In this state, the cavity of the channel contains large, hydrophobic amino acids that repel polar ions and prevent them from passing across The open estate is when the internal cavity widens and allows ions to cross when acetylcholine binds and stimulates a conformational change 3. Mechano‐gated channels whose conformational state depends on mechanical forces (e.g., stretch tension) that are applied to the membrane. Members of one family of cation channels, for exam- ple, are opened by the movements of stereocilia (see Figure 9.46) on the hair cells of the inner ear in response to sound or motions of the head.

Identify the sources of variability in the monosaccharides group: hexoses (position of hydroxyl groups around chiral carbons and position of the carbonyl, position of the hydroxyl at ring closure—alpha vs beta)

sugars having five or more carbons spontaneously self‐react (Figure 2.12 c ) to produce a closed, or ring‐containing, molecule. Only a tiny fraction of sugar molecules in solution are found in the open‐chain linear form; the rest are in the ring form by convention, the molecule is called d ‐glyceraldehyde if the hydroxyl group of carbon 2 projects to the right, and l ‐glyceraldehyde if it pro-jects to the left As the backbone of sugar molecules increases in length, so too does the number of asymmetric carbon atoms and, consequently, the number of stereoisomers If the hydroxyl group of this carbon projects to the right, the aldose is a d ‐sugar; if it projects to the left, it is an l ‐sugar. The enzymes present in living cells can distinguish between the d and lforms of a sugar. the molecule is an α ‐pyranose when the OH group of the first carbon projects below the plane of the ring, and a β ‐pyranose when the hydroxyl projects upward.

Describe or sketch the general structure of the plasma membrane, including the lipid bilayer, cholesterol, glycolipids/glycoproteins, and integral, peripheral/amphipathic, channel and lipid-anchored membrane proteins.

the external surface of most membrane proteins, as well as a small percentage of the phospholipids, contain short chains of sugars, making them glycoproteins and glycolipids. Those portions of the polypeptide chains that extend through the lipid bilayer typically occur as α helices composed of hydrophobic amino acids. The two leaflets of the bilayer contain different types of lipids as indicated by the differently colored head groups. ( b) Molecular model of the membrane of a synaptic vesicle constructed using known structures of the various proteins along with information on their relative numbers obtained from the analysis of purified synaptic vesicles. The high protein density of the membrane is apparent. Most of the proteins in this membrane are required for the interaction of the vesicle with the plasma membrane. The large blue protein at the lower right pumps H + ions into the vesicle. This protein is present in the form of individual protein molecules and protein complexes that penetrate a fluid lipid bilayer. cellular membranes are dynamic structures in which the components are mobile and capable of coming together to engage in various types of transient or semipermanent interactions. The membrane is asymmetric as there are 1) different composition of lipids and glycolipids 2) difference is positioning and orientation of membrane proteins 3) difference in enzymatic activities on the inner and outer surfaces Functions as a protective barrier, transport, signal transduction, and energy storage The lipid bilayer serves primarily as a structural backbone of the membrane and pro-vides the barrier that prevents random movements of water‐soluble materials into and out of the cell. The proteins of the membrane, on the other hand, carry out most of the specific functions Integral proteins (Figure 4.13 a ) that penetrate the lipid bilayer. Integral proteins are transmembrane proteins ; that is, they pass entirely through the lipid bilayer and thus have domains that protrude from both the extracellular and cytoplasmic sides of the membrane. Some integral proteins have only one membrane‐spanning segment, whereas others are multispanning. Genome‐sequencing studies suggest that integral proteins constitute 25-30 percent of all encoded proteins and roughly 60 percent of all cur-rent drug targets Ex) porins are transmembrane integral proteins where the hydrophobic amino acids interact with hydrocarbon tails Prostaglandin is an integral protein that is not transmembrane Peripheral proteins (Figure 4.13 b ) that are located entirely outside of the lipid bilayer, on either the cytoplasmic or extracellular side, yet are associated with the surface of the membrane by noncovalent bonds. Can easily be removed by adding a salt solution or changing pH Can readily disassociate from the membrane Lipid‐anchored proteins (Figure 4.13 c ) that are located out-side the lipid bilayer, on either the extracellular or cytoplasmic surface, but are covalently linked to a lipid molecule that is situ-ated within the bilayer. Myelinated neurons have a high percentage of lipids bc of the crucial role in insulation Mitochondria membrane has a high percentage of proteins bc of mitochondrial function in the production of energy

Order the steps in the Na/K ATPase mechanism of action, including how Asp phosphorylation mediates ion pumping

- 3 Na+ bind - ATP hydrolysis and phosphorylation of pump at Asp - e1 becomes e2 - 3 Na are released and 2 K bind - Asp is dephosphorylated - e2 to e1 change - 2 K+ are released - ATP binding

Using the Na/glucose cotransporter as an exemplar, explain how ATP hydrolysis can be used to drive secondary active mediated co-transport of ions against their concentration gradient

- ATPases are membrane pumps that breakdown ATP molecules directly and use the energy stored to move molecules and ions against the electrochemical gradient. - Secondary transporters do not hydrolyze ATP directly, instead, they couple the non spontaneous flow of one molecule/ion with the spontaneous flow of a different molecule or ion - Antiporters allow it to move from high to low concentration by using the electrochemical gradient of one molecule to move a second type of molecule in the opposite direction - Symporters use the flow of one ion to move a different ion in the same direction against the concentration gradient

Phosphoglycerides are said to be amphipathic. Why? Refer to specific structures within phosphoglycerides.

- The phosphate containing head, at one end of the molecule, is highly water soluble thus hydrophilic. The fatty acid tails are hydrophobic and will not interact with water. - Phospoglycerides are arranged into a stable bilayer that keeps the fatty acid tails from interacting with water. This structure can form into a micelle. In a micelle, hydrophilic heads face out and fatty acid tails face inward.

Describe the structural features of triacylglycerides, fatty acids, phospholipids (phosphoglycerides and glycolipids), steroids, cholesterol and micelles; associate type of lipid with general function in cellular or organismal biology

- Carbohydrates function primarily as a short‐term, rapidly available energy source, whereas fat reserves store energy on a long‐term basis. - In many animals, fats are stored in special cells ( adipocytes ) whose cytoplasm is filled with one or a few large lipid droplets. Adipocytes exhibit a remark-able ability to change their volume to accommodate varying quanti-ties of fat. - Steroids are built around a characteristic four‐ringed hydrocarbon skeleton. One of the most important steroids is cholesterol , a compo-nent of animal cell membranes and a precursor for the synthesis of a number of steroid hormones, such as testosterone, progesterone, and estrogen - Phospholipid molecule resembles a fat (triacylglycerol), but has only two fatty acid chains rather than three; it is a diacylglycerol . The third hydroxyl of the glycerol backbone is covalently bonded to a phosphate group, which in turn is covalently bonded to a small polar group, such as choline

By comparing the prevailing ratio of Products: Reactants to the Keq, determine whether a reaction will release free energy as it proceeds in the forward or reverse directions as written. Label as endergonic or exergonic.

- Delta G<0 transformation is spontaneous (EXERGONIC) - Delta G>0 transformation requires energy input (ENDERGONIC) - When the free energies of products and reactants are equal, delta G=0

Examine the figure in your textbook highlighting the critical amino acids of the aquaporin channel. Which amino acid is "R" of R206 or "E" of E152 and E14? What do these amino acid have in common? Why does this matter?

- E is glutamic acid and R is arginine which are both polar charged amino acids The amino acid residues are highly specific and want to hydrogen bond. Yet the polar charged residues keep the polar uncharged residues from linking to hydrogen bond. This central amino acid pair, they say, restricts the behavior of water molecules in the center of the channel in such a way that prevents "proton jumping" yet keeps the water flowing.

Relate amphipathicity of phospholipids and integral membrane proteins to their localization in cell membranes; Predict the polarity of amino acids that compose integral membrane proteins or the impact of altering amino acid composition on membrane localization

- Each of these groups is small and hydrophilic and, together with the negatively charged phosphate to which it is attached, forms a highly water‐ soluble domain at one end of the molecule, called the head group - With fatty acid chains at one end of the molecule and a polar head group at the other end, all of the phosphoglycerides exhibit a distinct amphipathic character. - The phosphate containing head, at one end of the molecule, is highly water soluble thus hydrophilic. The fatty acid tails are hydrophobic and will not interact with water. - Phospoglycerides are arranged into a stable bilayer that keeps the fatty acid tails from interacting with water. This structure can form into a micelle. In a micelle, hydrophilic heads face out and fatty acid tails face inward. - A less abundant class of membrane lipids, called sphingolipids , are derivatives of sphingosine, an amino alcohol that contains a long hydrocarbon chain ( - Like membrane lipids, detergents are amphipathic, being composed of a polar end and a nonpolar hydrocarbon chain (see Figure 2.20 ). As a consequence of their structure, detergents can substitute for phospholipids in stabilizing integral proteins while rendering them soluble in aqueous solution (FIGURE 4.16 ). Once the proteins have been solubilized by the detergent, various analyses can be carried out to determine the protein's amino acid composition, molecular mass, amino acid sequence, and so forth.

What is the difference between a fatty acid, a triglyceride and a phosphoglyceride? What do they share in common?

- Fatty acids are long unbranched chains of hydrocarbons with a single carboxyl group at one end. - Lack double bonds= saturated - Triglycerides are composite molecules of fat which are made of a glycerol molecule linked by ester bonds to 3 fatty acids. - Phosphoglycerides are membrane phospholipids built on a glycerol backbone. - Unlike triglycerides which have 3 fatty aids, phosphoglycerides only have 2 fatty acid chains. The third carbon is occupied by a modified phosphate group - Triglycerides are not amphipathic but phosphoglcerides are - Fatty acid, triglyceride and phsophoglyceride all contain fatty acid components

Label a fatty acid structure as a cis unsaturated fatty acid, trans unsaturated fatty acid or a saturated fatty acid

- Fatty acids that lack double bonds, such as stearic acid (Figure 2.19 b ), are described as saturated ; those possessing double bonds are unsaturated . Naturally occurring fatty acids have double bonds in the cis configuration. Trans fatty acids are made through food processing. Saturated fatty acids lack double bonds and can therefore package tighter into a solid form such as fats. They also have a higher melting point due to the amount of energy required to break the bonds compared to that of unsaturated fatty acids - Cis ‐unsaturated fatty acids, on the other hand, have crooks in the chain at the sites of a dou-ble bond - Consequently, phospholipids with saturated chains pack together more tightly than those containing unsaturated chains. The greater the degree of unsaturation of the fatty acids of the bilayer, the lower the temperature before the bilayer gel - Another factor that influences bilayer fluidity is fatty acid chain length. The shorter the fatty acyl chains of a phospholipid, the lower its melting tempera-ture. The physical state of the membrane is also affected by cholesterol. Because of their orientation within the bilayer (Figure 4.7 ), cholesterol molecules disrupt the close packing of fatty acyl chains and interfere with their mobility.

How are symport and antiport similar? Different?

- In plants, uptake of these compounds is coupled to the downhill, inward movement of H + ions rather than Na + ions. The secondary active transport of glucose into the epithelial cells of the intestine and the transport of sucrose into a plant cell are examples of symport , In which the two transported species (Na + and glucose or H + and sucrose) move in the same direction. Numerous cotransporters have been isolated that engage in antiport , in which the two transportedspecies move in opposite directions.

Define the terms Vmax, Km and saturation with regard to enzymatically catalyzed reactions; Recognize evidence of Vmax and saturation on a graph of substrate concentration versus reaction velocity.

- KM is an important characteristic of enzyme-substrate interactions and is independent of enzyme and substrate concentrations. - KM is equal to the substrate concentration at which the reaction rate is half its maximal value. - The maximal rate, Vmax, is attained when the catalytic sites on the enzyme are saturated with substrate—that is, when [ES] = [E]T

macromolecules

- Lipids are a diverse group of nonpolar biological molecules whose common properties are their ability to dissolve in organic solvents, such as chloroform or benzene, and their inability to dissolve in water - Fats consist of a glycerol molecule linked by ester bonds to three fatty acids; the composite molecule is termed a triacylglycerol - Fatty acids are long, unbranched hydrocarbon chains with a single carboxyl group at one end (Figure 2.19 b ). Because the two ends of a fatty acid molecule have a very dif-ferent structure, they also have different properties. The hydrocar-bon chain is hydrophobic, whereas the carboxyl group ( —COOH ), which bears a negative charge at physiological pH, is hydrophilic. Molecules having both hydrophobic and hydrophilic regions are said to be amphipathic - Soaps owe their grease‐dissolving capability to the fact that the hydrophobic end of each fatty acid can embed itself in the grease, whereas the hydrophilic end can interact with the surrounding water. - Fatty acids differ from one another in the length of their hydro-carbon chain and the presence or absence of double bonds. Fatty acids present in cells typically vary in length from 14 to 20 carbons. Fats that are liquid at room temperature are termed oils - The hydrogenation process also converts some of the cis double bonds into trans double bonds, which are straight rather than kinked. This process generates partially hydrogenated or trans‐fats.

Distinguish between: Passive vs Active transport, non-mediated (channel flow) versus transporter-mediated flow across membranes

- Passive Transport can be either simple diffusion of molecules through the cell membrane, through specific channels or pores, or require the molecules to be carried through the cell membrane by a carrier molecule (mediated diffusion) but does not require energy. - Active Transport is the term used to refer to the movement of molecules when energy is required. The energy is in the form ATP (ATP is the abbreviated name for Adenosine-tri-phosphate, the form of energy which can be used by cells to perform cellular activity). - Mediated transport is more complex, only occurring in living matter, and involving the facilitation of movement by specific carriers, such as Permeases, Porters, Translocases, Translocators and Transporters. Glucose is a large molecule which must enter the cells in order to make energy, it is the molecule which is broken down to make energy in a form the cell can use (i.e. glucose is broken down to make ATP). As glucose is vital, it must be transported into cells at high speed and continuously. - Nonmediated transport involves simple diffusion, where chemicals move through a semi-permeable membrane, from an area of high concentration on one side, to an area of low concentration on the other. This type of transport is simple and will occur in even non-living situations. When molecules are transported against the concentration gradient (i.e. from low concentrations to high concentrations), we say active transport is occurring.

Compare and Contrast Kv and KcsA channels

- Potassium channels are a large family of ion channels that share a common property of selectivity for K+ over Na+ ions - Different in gating mechanisms as KcsA is opened by lowering pH and Kv is activated by cell membrane depolarization

In what ways do simple diffusion and simple diffusion through a channel differ? In what ways do facilitated diffusion through a carrier protein and active transport through a transporter protein differ? How are they alike?

- Simple diffusion is a spontaneous process in which the substance moves from a region of high to low concentration through the lipid bilayer. - Simple diffusion through a channel involves an integral membrane protein or cluster of proteins Both of these always move in one direction, down the concentration gradient. - Facilitated diffusion is where solute molecules need to bind to a transporter. Requires an energy pump to push substances against the concentration gradient - Active transport requires a protein transporter with a specific binding site and undergoes a change in affinity with energy released by an exergonic process. Movement can go in either direction - All of these are methods by which particles can move across the lipid bilayer

Given a particular membrane permeability and specific concentration gradient across a membrane, determine whether the solute must cross by diffusion, active transport or passive transport; Conversely, predict conditions required for a molecule to cross the membrane via these mechanisms

- Simple diffusion: small and nonpolar. DOes not use ATP - facilitated diffusion: polar molecules and larger ions; does not use ATP - Primary active transport: molecules moving against their gradient coupled to the hydrolysis of ATP. Uses ATP - Secondary active transport: Molecule going with+ molecule going against. Uses ATP

What are the sources of variation within the structures of the phosphoglyceride family of lipids?

- Sources of variation include length of the hydrocarbon chain, type of amino groups attached, whether or not a glycerol backbone exists sphingomyelin is the only phospholipid of the membrane that is not built with a glycerol backbone. - Sphingolipids and Ceramides are formed by the attachment of sphingosine to fatty acids. - If the substitution is a carbohydrate, then you will have a glycolipid - Ring arrangement: cholestrols hydrophobic rings are flat, rigid, and interfere with the movements of fatty acid tails of the phospholipids

Regarding the experiment depicted in Figure 4.21, what was the purpose of site-directed mutagenesis in this set of experiments? Also, why would an amino acid within the depicted protein be alkylated by NEM under one set of conditions but then Unreactive with NEM under a different set of circumstances?

- The purpose of site directed mutagenesis in these experiments was to determine which sites within the membrane are accessible to the aqueous environment and how this will change as the protein functions. In this case, they mutated and made different versions of permease. - Site directed mutagenesis can involve replacing specific amino acids with others to identify spatial relationships as well - The residues of the protein become alkylate by NEM in the presence of sugar. There was an increase in reactivity to NEM when the permeate was incubated with the sugar to be transported. - The results suggests that the presence of sugar introduces a conformational change in the permease.

Using chymotrypsin as an example, describe how specific amino acid residues form an active site for enzymatic catalysis (Figure 3.13); predict the effect of changing or altering the key active site amino acid residues

- a serine protease that catalyzes the cleavage of peptide bonds on the carboxyl side of hydrophobic amino acids. - utilizes covalent catalysis so that the active site contains a nucleophile that temporarily covalent bonds with the peptide substrate. It's the serine residue that acts as a nucleophile and attacks the carbonyl of the peptide bond. Histidine and aspartate help transform serine into an alkoxide so it can act as a nucleophile. The negatively charged aspartate side chain interacts with histidines hydrogen --> positions histidine in the correct orientation to interact with serine. The partial negative nitrogen interacts with the H of serine.

Relate the magnitude of the Keq to the standard free energy release of the reaction under standard conditions.

- neg Keq, neg delta G= exothermic à releases energy - pos Keq=pos delta G= endothermic à input energy

In which stage of catabolic metabolism (as presented in your textbook) does glycolysis occur?

2

In which stage of catabolic metabolism (as presented in your textbook) does respiration-linked ATP synthesis occur?

3

In which stage of catabolic metabolism (as presented in your textbook) does the Citric Acid Cycle occur?

3

In which stage of catabolic metabolism (as presented in your textbook) does the Krebs Cycle occur?

3

Explain what Is meant by stating that the genetic code Is triplet and overlapping/ What did the finding that DNA base compositions varied greatly among different organisms suggests about the genetic code?

A codon consists of 3 nucleotides hence triplet. It Is overlapping since there are since there are 20 amino acids but only 64 codons so many codons can code for the same amino acid. The genetic code Is universal

What Is a genome? How does the complexity of a bacterial genome differ from that of eukaryotic genomes?

A genome Is all of the genetic Information that an Individual Inherits from their parents. Eukaryotes have a membrane bound nucleus In which they package the DNA Into histones and wrap It to form chromosomes. Eukaryotes also store much more genetic material as well

If given the sequence of one strand of DNA, predict the sequence or base pair composition of the complementary strand.

A=T and C=G and it all adds up to 100%

When glucose is elevated in actively contracting muscles but ADP levels become elevated (ATP low) and oxygen is absent, which of the following is likely to occur?

ATP synthesis by substrate level phosphorylation in the cytosol Production of phosphoenolpyruvate

Define acid and base. Be able to recognize examples of functional groups acting as acids versus bases in an aqueous solution and relate the charge on the functional group to protonation status.

An acid is a molecule that is capable of donating a hydrogen A base is one that accepts a hydrogen NH3 is an acid but HN2 is a base

discuss the significance of fluidity in relation to the biological properties of the plasma membrane and relate lipid composition of the membrane to its fluidity.

Another factor that influences bilayer fluidity is fatty acid chain length. The shorter the fatty acyl chains of a phospholipid, the lower its melting tempera-ture. The physical state of the membrane is also affected by cholesterol. Because of their orientation within the bilayer (Figure 4.7), cholesterol molecules disrupt the close packing of fatty acyl chains and interfere with their mobility.

state whether reaction spontaneity implies rapid reaction; reject the idea that the value of ΔG correlates with net reaction velocity

Delta G does not imply a rapid reaction. Reaction rate is influenced by enzymes. Spontaneity depends on enthalpy and entropy.

how do diffusion and osmosis compare?

Diffusion moves substances from regions of high concentration to low concentration. Osmosis is the movement of water down a semipermeable membrane from a region of lower solute concentration to a region of higher solute concentration.

Describe the Watson-Crick model of DNA

Double helical- 2 polynucleotides spiral together Antiparallel strands run in opposite directions, complimentary to one another Hydrogen bonds between nitrogenous bases so A with T (2 bonds) and C with G (3 bonds)

what Is meant by the term DNA denaturation? How does denaturation depend on the GC content of the DNA? How does this variable affect the Tm?

Denaturation Is the ability of the DNA double helix to separate Into two component strands. Tm Is the melting temperature at which the shift In absorbance Is half completed. The higher the GC content of the DNA< the higher the Tm. This Increased stability of GC containing DNA reflects the presence of the hydrogen bond between the bases a compared with the AT pairs

Distinguish the terms diffusion and osmosis; Identify examples of diffusion or osmosis when presented with various scenarios in text or picture form

Diffusion is a spontaneous process in which a substance moves from a region of high concentration to a region of low concentration, eventually eliminating the concentration difference between the two regions - Water moves readily through a semipermeable membrane from a region of lower solute concentration to a region of higher solute concentration. This process is called osmosis, and it is readily demonstrated by placing a cell into a solution containing a nonpenetrating solute at a concentration different than that present within the cell itself. * passive diffusion

What Is meant by saying that a DNA strand has polarity? That the two strands are antiparallel? That the molecule has a major and minor groove? That the strands are complimentary to one another?

DNA strands have polarity because the phosphate groups give It a negative charge The strands are antiparallel because the two chains of the double helix run In the opposite direction The spaces between the different turns of the double helix have different width. The major groove Is wider and the minor groove Is narrower. Proteins that bind to DNA often fit Into these grooves so that It can read the nucleotide sequence without having to separate the strands The strands are complementary because the strands are fixed relative to one another

Relate mRNA coding sequence to protein primary sequence, including the roles of tRNA, rRNA, codons, anticodons, E P and A sites on ribosomes, amino acids, and catalysis of peptide bond formation by the ribosome Predict the impact of blocking the action of any of the above molecules in translation

Elongation is where amino acids are joined to create a polypeptide chain. Elongation requires (1) the 70s initiation complex; (2) tRNAs charged with their amino acids; (3) several elongation factors; (4) GTP. · A ribosome has three sites that can be occupied by tRNAs: the aminoacyl (A) site, the peptidyl (P) site and the exit (E) site. o Aminoacyl (A) site -w all charged tRNAs first enter the A site except the initiator tRNA o Peptidyl (P) site - tRNAs move from the aminoacyl (A) site to into the P site o Exit (E) site - the tRNA moves from the P site to the E site, from which it exits the ribosome · Step 1 of elongation: o After initiation, the fMet-tRNA is in the P site of the ribosome o EF-Tu + GTP + charged tRNA enter A site 1. EF-Tu - elongation factor Tu; protein taking part in the elongation stage of translation; forms a complex with GTP and a charged tRNA and then delivers the charged tRNA to the ribosome o GTP hydrolyzed to GDP and EF-Tu/GDP leaves · Step 2 of elongation: o Peptide bond forms between amino acids in P and A sites (peptidyl transferase is the enzyme that does this) o tRNA in P site releases its amino acid so now the peptide chain is entirely on the tRNA at the A site · Step 3 of elongation: o Translocation - the movement of the ribosome down the mRNA in the 5'® 3' direction. o Ribosome shifts down by one codon (translocation) with the help of EF-G and GTP o tRNA that was in P site is now in E site and then immediately leaves o A site is now available to receive the next charged tRNA and the cycle continues

State whether or not enzymes altering the Keq, ΔG°', ΔG, or time required for a reaction to reach equilibrium; State whether enzymes can convert a nonspontaneous reaction to a spontaneous reaction (i.e., alter Keq, ΔG°', or ΔG)

Enzymes CANNOT change the thermodynamics of a reaction: AGo or Keq • They CANNOT change the direction of a reaction or the position of the equilibrium. They DO increase the rate of the reaction by lowering the activation energy.

If 30% of the bases on a single DNA strand are T, then 30% of the bases on that strand are A. T/F

False because single stranded DNA Is not subject to any specific ratio

Glucose levels are elevated in actively contracting muscles. In these muscles cells, the level of ADP becomes elevated (because ATP is consumed/low). If oxygen is present, which of the following will occur?

Formation of pyruvate Increased ETC activity Increased ATP synthetase activity at the mitochondrial inner membrane

When blood glucose levels are low which of the following will happen in liver?

Gluconeogenesis Glycogen degradation Joining of two molecules of phosphoenolpyruvate

Identify starch (amylose/amylopectin), glycogen, cellulose and chitin as either nutritional or structural carbohydrates; Identify the monomers composing each molecule and the type of bond joining the monosaccharides

Glycogen and Starch are nutritional polysaccharides. Starch is made of branched amylopectin and unbranched amylose. Amylose require the breaking of alpha 1,4 glycosidic bonds. Amylopectin are linked by 1,6 glycosidic bonds 3 Glycogen is a branched polymer containing only one type of monomer: glucose (Figure 2.17 a ). Most of the sugar units of a glycogen molecule are joined to one another by α (1 → 4) glycosidic bonds (type 2 bond in Figure 2.17 a ). Branch points con-tain a sugar joined to three neighboring units rather than to two, as in the unbranched segments of the polymer. The extra neighbor, which forms the branch, is linked by an α (1 → 6) glycosidic bond (type 1 bond in Figure 2.17 a ). Starch is actu-ally a mixture of two different polymers, amylose and amylopectin. Amylose is an unbranched, helical molecule whose sugars are joined by α (1 → 4) linkages (Figure 2.17 b ), whereas amylopectin is branched. Amylopectin differs from glycogen in being much less branched and having an irregular branching pattern. Structural polysaccharides like cellulose, chitin, and GAGs are not able to be digested. Cellulose is connected by beta 1,4. cellulose consists solely of glucose monomers; its properties differ dramatically from these other polysaccharides because the glucose units are joined by β (1 → 4) linkages (bond 3 in Figure 2.17 c ) rather than α (1 → 4) linkages. Ironically, multicellular animals (with rare exception) lack the enzyme needed to degrade cellulose an unbranched polymer of the sugar N ‐acetylglucosamine, which is similar in structure to glucose but has an acetyl amino group instead of a hydroxyl group bonded to the second carbon atom of the ring.

Match glycolysis, TCA Cycle, ETC/Oxidative Phosphorylation of ATP, photosynthesis with the cellular location in which these pathways occur

Glycolysis occurs in the cytosol An important feature of glycolysis is that it can generate a lim-ited number of ATP molecules in the absence of oxygen. Neither the substrate‐level phosphorylation of ADP by 1,3‐bisphosphoglycerate nor a later one by phosphoenolpyruvate (step 10, Figure 3.24 ) requires molecular oxygen. Thus, glycolysis can be considered an anaerobic pathway to ATP production, indicating that it can pro-ceed in the absence of molecular oxygen to continue to provide ATP. Two molecules of ATP are produced by substrate‐level phospho-rylation during glycolysis from each molecule of glyceraldehyde 3‐phosphate oxidized to pyruvate. Krebs cycle and oxidative phosphorylation take place in the mitochondria glycolysis , occurs in the soluble phase of the cytoplasm (the cyto-sol) and leads to the formation of pyruvate. The second stage is the tricarboxylic acid (or TCA) cycle , which occurs within the mito-chondria of eukaryotic cells and the cytosol of prokaryotes and leads to the final oxidation of the carbon atoms to carbon dioxide. Most of the chemical energy of glucose is stored in the form of high‐energy electrons, which are removed as substrate molecules are oxidized during both glycolysis and the TCA cycle. It is the energy of these electrons that is ultimately used to synthesize ATP

Make predictions about the impact of changing temperature on the fluidity of membranes of varying lipid composition and/or the influence of changing lipid composition in fluidity

If the temperature of the bilayer is kept relatively warm (e.g., 37°C), the lipid exists in a relatively fluid state At this temperature, the lipid bilayer is best described as a two‐ dimensional liquid crystal. As in a crystal, the molecules still retain a specified orientation; in this case, the long axes of the molecules tend toward a parallel arrangement, yet individual phospholipids can rotate around their axis or move laterally within the plane of the bilayer. If the temperature is slowly lowered, a point is reached where the bilayer dis-tinctly changes (Figure 4.23 b ). The lipid is converted from a liquid crystalline phase to a frozen crystalline gel in which the movement of the phospholipid fatty acid chains is greatly restricted. The temperature at which this change occurs is called the transition temperature . The greater the degree of unsaturation of the fatty acids of the bilayer, the lower the temperature before the bilayer gels

Using glucose transporters as an exemplar, explain how an integral membrane protein can facilitate movement of a polar solute across the plasma membrane (as a facilitative transporter in facilitated passive diffusion)

In cotransport, the energy required to move one solute against its concentration or electrochemical gradient is provided by an ion moving into the cell down its electrochemical gradient. The ion that moves into the cell down its gradient is usually the same ion that is pumped out of the cell by an active transport pump: for example, Na+ in animal cells using the sodium-potassium pump, or H+ in plants and prokaryotes using the proton pump.In the case of the glucose-sodium cotransporter in animals, Na+ moves back into the cell down its electrochemical gradient, providing the energy for glucose to move into the cell against its concentration gradient. The energy for glucose transport into the cell is supplied indirectly by the sodium-potassium pump's hydrolysis of ATP, and directly by the Na+ electrochemical gradient created by the pump.

When blood glucose is elevated and ATP levels are adequate, which of the following is likely to happen in liver?

Increased glycogen synthesis

If given a stretch of dsDNA with one strand being designated the template/noncoding strand, produce the predicted transcribed mRNA coding sequence. If offered a ssDNA sequence, list the complementary DNA sequence in the order 5'-3'

MRNA corresponds with nontemplate coding strand

Rank a series of DNA fragments according to the predicted melting temperature (Tm) and be able to relate the annealing temperature of two strands of DNA to the bonding pattern between G/C and A/T. Conversely, among a group of DNA fragments or 'primers-DNA hybrids, predict which will require the most heat energy to melt OR which fragments will anneal first upon cooling.

Melting temperature is the amount of heat needed to melt half of the DNA into a single strand The heat to get the primer to lay down is the annealing temp Reduced temp favors hydrogen bonds therefore poly GC requires more heat bc it has more H bonds Lower temp is required to reanneal

Discuss the role of carbohydrates (glycolipids or glycoproteins) in the plasma membrane and relate presence/position on the membrane to function; compare presence on intracellular versus extracellular surface

Membranes contain carbohydrates covalently linked to lipids and proteins on the extracellular surface of the bilayer Glycoproteins have short, branched carbohydrates fir interactions with other cells and structures outside of the cell Glycolipids have larger carbohydrate chains that may be cell to cell recognition sites Glycolipids also play a role in cer-tain infectious diseases; the toxins that cause cholera and botulism both enter their target cell by first binding to cell‐surface ganglio-sides, as does the influenza virus. Can serve as identifier on cell surface The addition of carbohydrate, or glycosylation , is the most com-plex of these modifications. The carbohydrate of glycoproteins is pre-sent as short, branched hydrophilic oligosaccharides If the substitution is a carbohydrate, the molecule is a glycolipid . If the carbohy-drate is a simple sugar, the glycolipid is called a cerebroside ; if it is a small cluster of sugars that includes sialic acid, the glycolipid is called a ganglioside

Distinguish between the terms monosaccharides, disaccharides, and polysaccharides; aldoses and ketoses; trioses, tetroses, pentoses, hexoses and heptoses

Most sugars have the formula (CH2O)n. Trioses have 3 carbons, tetroses have 4 carbons and s on. If the carbonyl group is located internally, it's a ketose. If the carbonyl group is located terminally, its an aldose. Monosaccharides are a carbon backbone linked together in a linear array of single bonds. Molecules composed of only two sugar units are disaccharides and serve primarily as readily available energy stores. Polysaccharides are polymers of monosacharrides that take on different functions depending on linkages and folding. i.e. nutritional like glycogen, starch or structural like cellulose, chitin, and GAGS Carbohydrates (or glycans, as they are often called) include simple sugars (or monosaccharides ) and all larger molecules constructed of sugar building blocks. Carbohydrates function primarily as stores of chemical energy and as durable building materials for biological con-struction. Most sugars have the general formula (CH 2 O) n . The sugars of importance in cellular metabolism have values of n that range from 3 to 7. Sugars containing three carbons are known as trioses , those with four carbons as tetroses , those with five carbons as pentoses , those with six carbons as hexoses , and those with seven carbons as heptoses . Sugars tend to be highly water soluble due to all the hydroxyls

A fatty acid with a long hydrocarbon chain with no double bonds has a higher melting point than a fatty acid with a short hydrocarbon chain with many double bonds. Explain why. Your answer should reference vander Waals forces.

No double bonds means that the fatty acid is straight and has the potential to package tightly into solids such as fat. Saturated fatty acids usually have high melting points because the van der waal forces are closer together meaning they are harder to break the bonds part. Unsaturated fatty acids have the possibility of adding more hydrogen atoms. Since these are not packed as closely together, they often exist as liquids such as oil. Because double bonds can cause the fatty acids to fold the van der wall forces are weaker and it would take less energy to break the molecules apart.

Distinguish between a nucleic acid, nucleotides, nucleosides and nucleobases; distinguish between ribonucleic acid and deoxyribonucleic acid; categorize a nucleobase as either a purine or a pyrimidine

Nucleic acids are macromolecules constructed out of long chains ( strands ) of monomers called nucleotides . Nucleic acids function primarily in the storage and transmission of genetic information, but they may also have structural or catalytic roles. There are two types of nucleic acids found in living organisms, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA

Predict, from the structure of a solute whether or not it will diffuse passively across a simple phospholipid bilayer membrane; Predict rate of movement of small vs large vs polar vs nonpolar molecules across cell membranes

The lipid bilayer of the membrane is ideally suited to prevent the loss of charged and polar solutes from a cell. -its partition coefficient, which is the ratio of its solu- bility in a nonpolar solvent, such as octanol or a vegetable oil, to that in water under conditions where the nonpolar solvent and water are mixed together - consider polarity, size - Very small, uncharged molecules penetrate very rapidly through cellular membranes. Consequently, membranes are highly permeable to small inorganic molecules, such as O2, CO2, NO, and H2O, which are thought to slip between adjacent phospho- lipids. In contrast, larger polar molecules, such as sugars, amino acids, and phosphorylated intermediates, exhibit poor membrane penetrability.

Relate flow through ion channels to the membrane potential and concentration gradient that exists across the plasma membrane of cells

The magnitude and direction of the voltage across the plasma membrane are determined by the differences in concentrations of ions on either side of the membrane and their relative permeabilities. As described earlier in the chapter, the Na+/K+‐ATPase pumps Na+ out of the cell and K+ into the cell, thereby establishing steep gradients of these two ions across the plasma membrane

Examine Figure 4.4. Why could this structure be called a 'fluid mosaic'? Make specific references to the labeled components of the structure shown.

The plasma membrane is referred to as the fluid mosaic because it is made of phospholipids, proteins, and cholesterol. The plasma membrane is more than just a lipid bilayer. Cholesterol helps regulate molecules entering and leaving the cell. Proteins such as the glycoproteins, integral proteins and peripheral proteins help with transport and communication of lager molecules. Polypeptide chains can extend through the lipid bilayer as hydrophobic alpha helices. Phospholipids and glycolipids assemble into lipid bilayer.

Discuss an approach to the study of conformational changes of integral membrane proteins and the meaning of NEM adducts on amino acid residues

The purpose of site directed mutagenesis in these experiments was to determine which sites within the membrane are accessible to the aqueous environment and how this will change as the protein functions. In this case, they mutated and made different versions of permease. Site directed mutagenesis can involve replacing specific amino acids with others to identify spatial relationships as well The residues of the protein become alkylate by NEM in the presence of sugar. There was an increase in reactivity to NEM when the permeate was incubated with the sugar to be transported. The results suggests that the presence of sugar introduces a conformational change in the permease

Relate the structure of a fatty acid or triacylglyceride to its melting point and fluidity

The strength of intermolecular bonds and therefore fluidity depends on: 1) the length of fatty acids 2) degree of unsaturation 3) concentration of cholesterol - Longer fatty acids can form more LDFs than shorter ones so the presence of longer fatty acids decreases the fluidity and increases the Tm - Saturated fatty acids create a well structured arrangement of hydrocarbons. The straight chain hydrocarbons can form stronger IMFs with the nearby fatty acids which raises Tm and favors rigidity - A cis double bond in the hydrocarbon chain creates a jink in the chain that interferes with the well ordered structure which would favor membrane fluidity and lower Tm Cholesterol interferes with the regular interaction of fatty acids; however, it forms complexes with gyclosphingolipids. These complexes are called lipid rafts and make the membrane less fluid and more resistant to phase transitions - No double bonds means that the fatty acid is straight and has the potential to package tightly into solids such as fat. Saturated fatty acids usually have high melting points because the van der waal forces are closer together meaning they are harder to break the bonds part. Unsaturated fatty acids have the possibility of adding more hydrogen atoms. Since these are not packed as closely together, they often exist as liquids such as oil. Because double bonds can cause the fatty acids to fold the van der wall forces are weaker and it would take less energy to break the molecules apart hence lower melting point. - The physical state of the lipid of a membrane is described by its fluidity (or viscosity At this temperature, the lipid bilayer is best described as a two‐ dimensional liquid crystal. As in a crystal, the molecules still retain a specified orientation; in this case, the long axes of the molecules tend toward a parallel arrangement, yet individual phospholipids can rotate around their axis or move laterally within the plane of the bilayer. If the temperature is slowly lowered, a point is reached where the bilayer dis-tinctly changes - The lipid is converted from a liquid crystalline phase to a frozen crystalline gel in which the movement of the phospholipid fatty acid chains is greatly restricted. The temperature at which this change occurs is called the transition temperature . The transition temperature of a particular bilayer depends on the ability of the lipid molecules to be packed together, which depends in turn on the particular lipids of which it is constructed. - many of the most basic cellular processes, including cell movement, cell growth, cell division, formation of intercellular junctions, secretion, and endocyto-sis, depend on the movement of membrane components and would probably not be possible if membranes were rigid, nonfluid structures. - Maintenance of membrane fluidity is an example of homeostasis at the cellular level and can be demonstrated in various ways. For example, if the temperature of a culture of cells is lowered, the cells respond met-abolically. The initial "emergency" response is mediated by enzymes that remodel membranes, making the cell more cold resistant. Remodeling is accomplished by (1) desaturating single bonds in fatty acyl chains to form double bonds, and (2) reshuffling the chains between different phospholipid molecules to produce ones that contain two unsaturated fatty acids, which greatly lowers the melting temperature of the bilayer. Desaturation of single bonds to form double bonds is catalyzed by enzymes called desaturases

describe two methods that scientists use to study the ability of molecules to move within the plasma membrane and describe which form(s) of movement are commonly noted (transverse, lateral)

Transverse is when the outer leaflet flips into the inner leaflet. Happens at a much lower rate than that of lateral diffusion because during transverse diffusion, the polar head must travel through the nonpolar membrane which is energetically unfavorable To study the ability of molecules to move within the plasmid, a hydropathy plot is used where pos Gibbs free energy is hydrophobic and neg Gibbs free energy is hydrophilic. Lateral diffusion is when the bonds between the water molecules remain and the bonds between hydrocarbons remain so it requires less energy to move Proteins have much more extensive hydrophobic regions and therefore do not flip flop because they would have to overcome a higher free energy barrier

Describe the features of water that make it especially well suited as the 'solvent of life' and predict hydrogen bond formation between atoms of water molecules or between water molecules and polar functional groups within other cellular molecules such as amino acids, carbohydrates and nucleic acids.

Water is highly asymmetric with the O atom at one end and the two H atoms at the opposite end Each of the two covalent bonds in the molecule are highly polarized All three atoms in a water molecule are adept at forming hydrogen bonds

Describe two metabolic fates of glucose (glycolysis, glycogen) and predict which will predominate under conditions of low versus high ATP in muscle or high versus low glucose in liver

When ATP levels are low, ADP is high. Glucose is abundant. Glycogen and glucose are broken down in catabolic pathways to create ATP ATP used to drive the synthesis of glucose, glycogen in anabolic pathways. When ATP is abundant With so limited a supply, it is evident that ATP is not a molecule in which a large total amount of free energy is stored. The energy reserves of a cell are stored instead as polysaccharides and fats. When the levels of ATP start to fall, reactions are set in motion to increase ATP formation at the expense of the energy‐rich storage forms. Similarly, when ATP lev-els are high, reactions that would normally lead to ATP production are inhibited. The more hydrogen atoms that can be stripped from a "fuel" molecule, the more ATP that ultimately can be produced. Bernard concluded that various food materials (such as proteins) were carried to the liver where they were chemically converted to glucose and stored as glycogen. Then, as the body needed sugar for fuel, the glycogen in the liver was transformed to glucose, which was released into the blood-stream to satisfy glucose‐depleted tissues. In Bernard ' s hypothesis, the balance between glycogen formation and glycogen breakdown in the liver was the prime determinant in maintaining the relatively constant ( homeostatic ) level of glucose in the blood.

By comparing the prevailing ratio of Products: Reactants to the Keq, determine whether a reaction will proceed in the forward or reverse directions.

When Keq is greater than 1, the reaction will proceed in the forward direction. When Keq is less than 1, the reaction can proceed in the reverse direction. When Keq is equal to 1, the rate of products being formed is constant to the rate of reactants.

A cell placed in a hypertonic solution with shrink or swell?

When two compartments of different solute concentration are separated by a semipermeable membrane, the compartment of higher solute concentration is said to be hypertonic relative to the compartment of lower solute concentration, which is described as being hypotonic . When a cell is placed into a hypotonic solution, the cell rapidly gains water osmosis and swells

Define isotonic, hypotonic, hypertonic; Predict how a cell will react when placed into a hypertonic, isotonic or hypotonic solution

When two compartments of different solute concentration are separated by a semipermeable membrane, the compartment of higher solute concentration is said to be hypertonic (or hyperosmotic) relative to the compartment of lower solute concentration, which is described as being hypotonic (or hypoosmotic). When a cell is placed into a hypotonic solution, the cell rapidly gains water by osmosis and swells - In a hypertonic medium, recovery occurs as the cells gain ions from the medium. Once the internal solute concentration (which includes a high concentration of dissolved proteins) equals the external solute concentration, the internal and external fluids are isotonic (or isosmotic), and no net movement of water into or out of the cells occurs