BIO 3342 Exam I

Based upon the external amino acids on a surface of a tertiary or quaternary, predict whether that portion of the protein is more likely to be embedded in membrane or at the surface exposed to aqueous cytosol.

(Embedded in membrane) Hydrophobic amino acids will move away from aqueous cytosol and bury themselves in the center of the protein. (At the surface) Hydrophilic amino acids will interact with cytosol, tend to be located on the outer surface of the protein

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' --> Transcription uses one of the two exposed DNA strands as a template; this strand is called the template/noncoding strand. The RNA product is complementary to the template strand and is almost identical* to the other DNA strand, called the nontemplate (or coding) strand * all of the T nucleotides are replaced with U nucleotides.

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 mechanism

- 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

Contrast the conditions under which bright-field, phase-contrast, DIC, electron, or fluorescence microscopy would be most beneficial; Select the best type of microscopy for a given experimental goal

1. Bright-field microscopy - for transparent specimen made visible by staining, or naturally pigmented specimen 2. Phase - contrast microscopy - best for viewing transparent objects WITHOUT having to stain them 3. Differential Interference Contrast (DIC) - best for living and unstained organisms and to distinguish novel/contrasting organisms 4. Electron microscopy - best for subcellular structures, bacterium, & objects that need a large amount of resolution 5. Fluorescence microscopy - best to image and tag specific features of small specimen & subcellular structures

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 its protonation status(protonated vs deprotonated; neutral, positive or negative charge.)

An acid is a molecule that is capable of donating a hydrogen A base is one that accepts a hydrogen Functional Groups: 1. Alcohols - polar, negative, become protonated to water, which is a better leaving group. Alcohols also can become deprotonated in the presence of a strong base. 2. Ether - slightly polar, ether molecule is subject to reacting with strong acids and serves as a Lewis base. 3. Carboxylic acids, polar, deprotonated 4. Amines - neutral, protonated

Be able to recognize the identity of each of the 20 amino acids and their 1 and 3 letter abbreviations; Categorize each amino acid R group as nonpolar, polar or charged(ionizable)based upon its name alone(different books use different categories. For BIO 3342, use the information in the power point provided.)

Nonpolar, Hydrophobic R groups: Alanine, Valine Phenylalanine, Tryptophan, Leucine, Isoleucine, Methionine (MALPTI) Polar, Uncharged, hydrophilic R groups: Serine, Threonine, Tyrosine, Glutamine, Asparagine (ASGTT) Hydrophilic, Positively charged R groups: Lysine, Arginine, Histidine (HAL) Hydrophilic, Negatively charged R groups: Aspartate, Glutamate (AptG) "Other" Amino Acids: Cysteine, Glycine, Proline (PGC)

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) The purines in DNA are adenine and guanine, the same as in RNA. The pyrimidines in DNA are cytosine and thymine; in RNA, they are cytosine and uracil.

Explain how PCR can be used as a "semi-quantitative" measure of the concentration of specific DNA fragments in a solution and be able to interpret semi-quantitative RT-PCR data. Describe the process from lysing cells to reading the agarose gel.

PCR can be "semi - quantitative" in that it is used to determine how much of a specific nucleotide sequence is in a mixed sample 1. Denaturation (96 °C): Heat the reaction strongly to separate, or denature, the DNA strands. This provides single-stranded template for the next step. Annealing (55 - 65°C): Cool the reaction so the primers can bind to their complementary sequences on the single-stranded template DNA. Extension (72 ° C, ): Raise the reaction temperatures so Taq polymerase extends the primers, synthesizing new strands of DNA. DNA fragments of the same length form a "band" on the gel,

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 in some viruses Nucleobases are purines and pyrimidines Polysaccharides (monosaccharides) Lipids - hydrophobic, made up of fatty acids, some can be amphipathic

Explain how PCR is used to amplify specific regions of nucleic acid

RNA can be converted into cDNA. CDNA can serve as a template in PCR, band density confers relative abundance of mRNA

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.

Describe the flow of information in a cell from DNA to RNA to protein including the terms: transcription, translation, transcription start site, transcription terminator, mRNA, translation start site, stop codon, tRNA, rRNA, ribosome, ribozyme, codon, anticodon, amino acid and peptide bond formation.

Transcription (DNA to RNA): 1. Transcription uses one of the two exposed DNA strands as a template; this strand is called the template strand. 2. The RNA is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate (or coding) strand 3. in the newly made RNA, all of the T nucleotides are replaced with U nucleotides. 4. RNA polymerase binds to the DNA of the gene at a region called the promoter 5. basal (general) transcription factors & RNA polymerase bind to the promoter first, at the TATA box, and proceed along the transcription start site 6. RNA polymerase "walks" along one strand of DNA, known as the template strand, in the 3' to 5' direction 7. Transcription is terminated once polymerase transcribes a sequence of DNA known as a terminator. 8. The polyadenylation signal is recognized by an enzyme that cuts the RNA transcript nearby, releasing it from RNA polymerase 9. the RNA transcript (pre-mRNA) is processed, A 5' cap is added to the beginning of the RNA transcript, and a 3' poly-A tail is added to the end. Translation: 1. In translation, the codons of an mRNA are read in order (from the 5' end to the 3' end) by molecules called transfer RNAs, or tRNAs 2. Each tRNA has an anticodon, a set of three nucleotides that binds to a matching mRNA codon through base pairing 3. tRNAs bind to mRNAs inside the ribosome 4. the tRNA carrying the first amino acid (methionine) attaches to the small ribosomal subunit, binding to the 5' end of the mRNA 5. "walk" along the mRNA in the 3' direction, stopping when they reach the start codon (AUG) 6. First tRNA starts in P site, second in corresponding A site 7. Formation of the peptide bond that connects one amino acid to another. This step transfers the methionine from the first tRNA onto the amino acid of the second tRNA in the A site. 8. Once the peptide bond is formed, the mRNA is pulled onward through the ribosome 9. Termination happens when a stop codon in the mRNA (UAA, UAG, or UGA) enters the A site

Compare and contrast the various types of stem cells highlighted in your text and explain the importance of cell differentiation within a eukaryotic organism; Define pluripotent vs multipotent; Select the best type/method of stem cell harvest for a given experimental/therapeutic goal if given a list of options

multipotent - capable of differentiating into two or more mature cell types pluripotent - capable of differentiating into every cell type Types of Stem Cells: hematopoietic stem cells (HSCs ) - blood forming cells in the bone marrow (used for bone marrow transplants & leukemia treatment, allogenic) mesenchymal stem cell (MSC) - isolated from fat tissue, used for autologous therapies ** MSCs and HSCs are considered adult stem cells embryonic stem cells (ES) - isolated from blastocysts are pluripotent, can be "customized" via somatic cell nuclear transfer (SCNT), can cause teratoma (tumor) threat, used to regenerate or repair diseased tissue and organ Induced pluripotent cells (iPS cells) - can be generated from somatic cells and are pluripotent like ES cells. (Disease treatment iPS cells can be differentiated into specialized cell types affected by particular disease)

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, researchers can use computers to design "virtual" drug molecules whose size and shape might allow them to fit into the apparent cracks and crevices of the protein, rendering it inactive.

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

template strand to mRNA sequence: T ---> A, & A -----> U always write as 5' to 3' for final answer If given nontemplate strand, just replace the Ts with Us

Determine whether a cyclic monosaccharide or disaccharide is in the alpha or beta form

α‐pyranose, when the OH group of the first carbon projects below the plane of the ring -β‐pyranose when the hydroxyl projects upward.

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 example , 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

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

Label depictions or text descriptions of protein as primary, secondary, tertiary or quaternary protein structures. Be able to describe subunits, monomers, dimers, heterodimers, homodimers, trimers, and so on.

- Primary is the order of amino acids that form a peptide bond - Secondary structure is the conformation in the polypeptide chain - linked by covalent disulfide/noncovalent bonds - Tertiary Structure is the overall three-dimensional structure resulting from conformations of entire polypeptide - Quaternary Structure is the complexes of three dimensional structures - Subunits are complexes of more than one polypeptide chain Monomers have 1, Dimers have 2 subunits, trimers have 3 Homodimers are identical subunits joining together, heterodimers are different subunits joining together.

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 primer-DNA hybrids, predict which will require the most heat energy to melt OR which fragments will anneal first upon cooling

- The melting temperature (Tm) of the DNA means "the temperature at which the half of the Double Stranded DNA becomes Single Strand DNA - Tm = 4(G+C) +2(A+T) Increased hydrogen bonding within a strand of DNA will increase the melting point. The DNA segment with the most guanine-cytosine base pairs will have the highest melting point (due to having more H bonds) Annealing temperature is 5 degrees less than the melting temperature

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.

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

- negative Keq, negative delta G= exothermic, releases energy - positive Keq, positive delta G= endothermic, input energy

List the fundamental properties shared by all cells, explaining their importance and offering/identifying examples of manifestation of these properties; Characterize a unit as a living cell or not

1. Cells are highly complex & organized 2. Cells possess a genetic program and a means to use it 3. Cells reproduce 4. Cells acquire and utilize energy 5. Cells carry out chemical reactions 6. Cells engage in mechanical activities 7. Cells respond to stimuli 8. Cells self regulate 9. Cells evolve Identifying aspect of a cell: 1. Plasma membrane/outer covering - separates the cell's interior from its surrounding environment 2. cytoplasm - consisting of a jelly-like region within the cell in which other cellular components are found 3. DNA - genetic material 4. Ribosomes - particles that synthesize proteins

List the three tenets of the cell theory.

1. Cells are the fundamental unit of life 2. All organisms are composed of cells 3. All cells come from preexisting cells

List and be able to identify the 6 most commonly employed model organisms for researching cellular biology(Fig. 1.18); Select the best model organism for addressing a particular experimental goal given a list of options

1. Escherichia coli (E. coli) - rapid growth and the ability to express proteins at very high levels 2. Saccharomyces cerevisiae (yeast) - contains a surprising number of proteins that are homologous to proteins in humans; ideal for the identification of genes through the use of mutants. 3. Arabidopsis thaliana (mustard plant) - small genome, raid regeneration time & large seed production 4. Caenorhabditis elegans (nematode) - consists of a defined number of cells (roughly 1000) develops into precise pattern of cell divisions. easily cultured, can be kept alive in a frozen state, has a transparent body wall, a short generation time, and facility for genetic analysis. 5. Drosophila melanogaster (fruit fly) - small but complex eukaryote that is readily cultured in the lab,. favored for study of genetics, molecular biology of development & neurological basis of simple behavior. Certain larval cells have giant chromosomes, whose individual genes can be identified for studies of evolution and gene expression. 6. Mus musculus (mouse) - easily kept and bred in the laboratory. Thousands of different genetic strains have been developed. "Nude mouse" develops without a thymus gland so is able to accept human tissue grafts that are not rejected.

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

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

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 usually 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 certain calcium ion channels 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 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.

Rank the amino acids according to likelihood of being found within the core of tertiary structures or at the interface between monomers in quaternary structures; Predict the impact of changing the chemical character of key amino acid residues on protein structure

Amino acids found at the core of amino acid structures are likely to be nonpolar and hydrophobic (amino acids like Alanine, Valine Phenylalanine, Tryptophan, Leucine, Isoleucine, Methionine) Amino acids found between monomers will be more polar and charged (Lysine, Arginine, Histidine, Aspartate, Glutamate) Changing the chemical character could effect overall structure and function of a protein (ex: sickle cell)

Explain how centrifugation can be used to isolate specific subcellular compartments of cell lysates(cytosol, mitochondrial, microsomes, nucleus); Predict what the pellet and supernatant will contain if you spin lysate at 1,000 x g, 20,000 x g, and/or100,000 x g and explain why; List steps required to isolate nuclei (or mitochondria or microsomes or cytosol) from other cellular structures

A cell is broken by mechanical homogenization , various membranous organelles become fragmented, form spherical membranous vesicles. the cell homogenate is first subjected to low‐speed centrifugation to pellet larger particles, such as nuclei and mitochondria This leaves the smaller vesicles (microsomes) in the supernatant The microsomes can be removed from the supernatant by centrifugation at higher speeds for longer periods of time 500-1,000 x g—nuclear & unbroken cell pellet, supernatant: mitochondria , endoplasmic reticulum, plasma membrane, cytoplasm (postnuclear) ~20,000 x g----mitochondria, lysosomes, peroxisome pellet, supernatant: microsomes (postmitochondrial) ~50-80,000 x g----microsomal fraction, contains fragments of plasma membrane, smooth and rough ER; supernatant: free ribsomes, large macromolecules 200,000 X g free ribosomes, large macromolecules, viruses supernatant = cytosol; pellet contains large protein complexes

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.

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

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.

Give two ways in which a reaction with a positive standard free energy change (+ΔG°') could be made to proceed in the forward direction; Relate your answer to the term actual free energy change (ΔG)

A way to control the standard free energy change is to manipulate the concentration of the products and reactants. This can be done by: 1. Increasing the concentration of products 2. Decreasing the concentration of reactants

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 for DNA, should add up to 100%

Offer an example of recombinant DNA and give 3 methods by which human-plasmid DNA can be generated(i.e. ligation of restriction digest fragments, PCR products, or cDNA library into the plasmid)

An example of recombinant DNA can be present in crops that are genetically modified to be w/o seeds. The 3 methods that human - plasmid DNA can be generated are: 1. Ligation of restriction digest fragments: - Obtain the coding sequence - Ligate the coding sequence into an expression vector 2. PCR Products - PCR exponen8ally amplifies the quan8ty of targeted - cDNA fragment-Specific fragment targeted using forward and reverse primers - Isolated fragments can be digested for liga8on into cloning vector 3. cDNA library into the plasmid - mRNA reverse transcribed (RT) to create cDNA -cDNA molecules ligated into plasmids -Screen colonies

State whether or not enzymes alter 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: delta G or Keq They also 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.

Explain how the phrase "form dictates function" applies to proteins and how site-directed mutagenesis could be used to support the statement.

Can be used to cause a mutation that substitute an amino acid with different charge, properties, hydrophobic character and see what effect that substitution has on the structure and function of the modified protein

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 component 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

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.

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- Osmosis: 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 Define isotonic, hypotonic,

Using the term Km, describe how two enzymes might have the same Vmax (at saturating substrate concentrations) but different reaction velocities at low substrate concentration. Recognize evidence of Km on a graph of substrate concentration versus reaction velocity.

Enzymes can have the same Vmax but different reaction velocities due to competitive inhibitors With a competitive inhibitor, the reaction can eventually reach its normal Vmax but it takes a higher concentration of substrate to get it there. Vmax is unchanged, but the apparent Kmax is higher. (on a graph, Km is Vmax/2)

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

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 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. Aminoacyl (A) site -where all charged tRNAs first enter the A site except the initiator tRNA Peptidyl (P) site - tRNAs move from the aminoacyl (A) site to into the P site Exit (E) site - the tRNA moves from the P site to the E site, from which it exits the ribosome· Step 1 of elongation: After initiation, the fMet-tRNA is in the P site of the ribosome EF-Tu (elongation factor) + GTP + charged tRNA enter A site 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 GTP hydrolyzed to GDP and EF-Tu/GDP leaves· Step 2 of elongation: Peptide bond forms between amino acids in P and A sites (peptidyl transferase is the enzyme that does this) tRNA in P site releases its amino acid, peptide chain is entirely on the tRNA at the A site Step 3 of elongation: Translocation - the movement of the ribosome down the mRNA in the 5'® 3' direction Ribosome shifts down by one codon (translocation) with the help of EF-G and GTP tRNA that was in P site is now in E site and then immediately leaves A site is now available to receive the next charged tRNA and the cycle continues

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 double 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 temperature. 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.

In detail, explain 2 methods by which protein coding DNA sequence can be cloned in an expression vector for expression in bacterial cells(specifically, compare the PCR based versus cDNA library-based approaches described in class); use the terms mRNA, reverse transcriptase, restriction enzymes, primers, screen, ligate and a DNA plasmid vector to describe the methods. (Ask)

For PCR: - PCR amplifies cDNA of interest: Restriction enzymes cut DNA into two pieces at or near that site. Many restriction enzymes produce cut ends with short, single-stranded overhangs

Identify starch (amylose/amylopectin), glycogen, cellulose and chitinas 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 Glycogen is a branched polymer containing only one type of monomer: glucose Most of the sugar units of a glycogen molecule are joined to one another by α (1 → 4) glycosidic bonds Branch points contain 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 Starch is actually 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 rather than α (1 → 4) linkages 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 limited 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 glycolysis can be considered an anaerobic pathway to ATP production, indicating that it can proceed in the absence of molecular oxygen to continue to provide ATP. Two molecules of ATP are produced by substrate‐level phosphorylation 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 cytosol) and leads to the formation of pyruvate. The second stage is the tricarboxylic acid (or TCA) cycle , which occurs within the mitochondria of eukaryotic cells, 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

Identify glucose, galactose, mannose and fructose as hexoses and ribose as a pentose.

Hexoses (C6H12O6): Glucose, Galactose, Mannose and Fructose Pentose (C5H10O5): Ribose

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)

Hydrogen bonding can yield: -High specific heat - High boiling point - High surface tension - High heat of vaporization - Good solvent for polar solutes 1. 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 (High surface tension) 2. When water is heated, most of the thermal energy is consumed in disrupting hydrogen bonds rather than molecular motion (high boiling point) 3. The high boiling point of water makes it resistant to temperature change, allowing life forms to maintain relatively constant internal temperatures (high specific heat) 4. Evaporation takes a lot of energy because it involve the breaking of hydrogen bonds (high heat of vaporization) 5. Each molecule of water can form hydrogen bonds with as many as four other molecules producing a highly interconnected network of molecules .Water is able to dissolve in more types of substances than any other solvent (Good solvent for polar solutes) 6. Water plays a key role in maintaining the structure and function of macromolecules and the complexes that they form.

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

Hydrogen bonds: Hydrogen bears partial positive charge when covalently bonded to an electronegative atom - can approach a second electronegative atom to form an interaction Ionic Bonds: - Attraction between charged atoms - Share electrons (unequally) to create opposing charges Van der Waals Interactions: - Two very close nonpolar molecules with transitory dipoles within covalent can have a weak attractive force Hydrophobic effect: nonpolar molecules forced into aggregates to reduce exposure to water due to hydrophobic interaction ** Protein folding is primarily to due to hydrophobic effect, Ionic and hydrogen bonds refine macromolecular structure, Noncovalent ionic bonds between DNA and protein in a supramolecular structure

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 stateAt 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 distinctly 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 greater the degree of unsaturation of the fatty acids of the bilayer, the lower the temperature before the bilayer gels describe two methods that

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 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.

Compare and contrast subcellular structures of bacterial, plant, and animal cells (Table 1.1); associate the organelles with their cellular functions

In eukaryotic cells: 1. Division of cells into nucleus and cytoplasm, separated by a nuclear envelope containing complex pore structures 2. Complex chromosomes composed of DNA & associated proteins, capable of compacting into mitotic structures 3. includes endoplasmic reticulum, Golgi complex, lysosomes, endosomes, peroxisomes, and glyoxisomes 4. Specialized cytoplasmic organelles for aerobic respiration (mitochondria) and photosynthesis (chloroplasts) 5. Complex cytoskeletal system (including actin filaments, intermediate filaments, and microtubules) and associated motor proteins 6. Complex flagella and cilia 7. Can preform phagocytosis 8. Cellulose - containing cell walls (in plants) 9. Cell division using a microtubule - containing mitotic spindle that separates chromosomes 10. Presence of two copies of genes per cell (diploidy), one from each parent 11. Presence of three different RNA synthesizing enzymes (RNA polymerases) 12. Sexual reproduction requiring meiosis and fertilization In both prokaryotes and eukaryotes: 1. Plasma membrane 2. Genetic information encoded in DNA 3. Similar mechanisms of transcription and translation 4. Shared metabolic pathways 5. Similar apparatus for conservation of chemical energy as ATP (located in the plasma membrane of prokaryotes and the mitochondrial membrane of eukaryotes) 6. Similar mechanism of photosynthesis (between cyanobacteria and green plants) 7. Proteasomes (protein digesting structures) of similar construction 8. Cytoskeletal filaments built of proteins similar to actin and tubulin

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)

In hexoses (C6H12O6), hexoses can be aldoses or ketoses (position of carbonyl group) , The most common hexoses are glucose, galactose, mannose, and fructose. The first three are aldoses, whereas fructose is a ketose. Position of hydroxyl groups groups around chiral carbons change the type of hexose that it is. For example, fructose has a hydroxyl group around the top of a chiral carbon, and glucose has a carbonyl group at the top instead. 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 projects 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 stereo isomers 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 l forms 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.

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. Vmax is the maximum rate of an enzyme catalysed reaction i.e. when the enzyme is saturated by the substrate. ([ES] = [E]T)

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.

Define site-directed mutagenesis and the purpose of the technique

Makes copies of vector containing wild type sequence using primers with mismatches The newly synthesized strands contain mutation introduced in the primer Used to study the impact of amino acid substitution

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 certain infectious diseases; the toxins that cause cholera and botulism both enter their target cell by first binding to cell‐surface gangliosides, as does the influenza virus Can serve as identifier on cell surface The addition of carbohydrate, or glycosylation , is the most complex of these modifications. The carbohydrate of glycoproteins is present as short, branched hydrophilic oligosaccharides If the substitution is a carbohydrate, the molecule is a glycolipid . If the carbohydrate 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

Compare and contrast the size (using the units: microns, nanometers or Angstroms)and functions of prokaryotic cells and eukaryotic cells (Figure 1.19; be able to use terms micron, nanometer or Angstrom in making the size comparisons between cell types and structures; make unit conversions; micron-nanometer-Angstrom)

Micron (micrometer) = 10^-6 meters 1 Micron (micrometer) = 1000 nanometers (nm) 10 nanometers (nm) = 1 Angstrom (Å) At 0.1-5.0 µm in diameter, prokaryotic cells are significantly smaller. Eukaryotic cells have diameters ranging from 10-100 µm. Organelles allow eukaryotic cells to carry out more functions than prokaryotic cells can. This allows eukaryotic cells to have greater cell specificity than prokaryotic cells. Ribosomes, the organelle where proteins are made, are the only organelles in prokaryotic cells.

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

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

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 monosaccharides that take on different functions depending on linkages and folding. i.e. nutritional like glycogen, starch or structural like cellulose, chitin, and GAGS Most sugars have the general formula (CH2O)n The sugars of importance in cellular metabolism have values of n that range from 3 to 7: •three carbons (trioses) •four carbons (tetroses) •five carbons (pentoses) •six carbons (hexoses) •seven carbons (heptoses) Each carbon atom is linked to a single hydroxyl group, except for one that bears a carbonyl (C=O) group. -carbonyl group located at internal position, ketose. -carbonyl is located at one end, aldose.

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.

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)

*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 maintain 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.

Compare and contrast prokaryotes, plant cells, and animal cells in terms of energy sources and means of fixing energy

Plants cells produce energy from sunlight through the process of photosynthesis Animal cells fix energy via cellular respiration Most prokaryotes use light energy to remove CO2 & fix it into organic molecules

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 Carbon dioxide reduced in photosynthesis In catabolism reduced carbon atoms can be oxidized, releasing energy to do work The more hydrogen atoms that can be stripped from a "fuel" molecule, the more ATP that ultimately can be produced.

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(KcsAusedforbacteria)

Identify the primary driving force underlying primary, secondary, tertiary and quaternary structure formation

Primary and Secondary Structures: Main driving force is hydrogen bonding Tertiary and Quaternary: Main driving force is hydrophobic effect

Differentiate primary cell culture versus a secondary cell culture or a cell line; choose the best type of cell culture given an experimental goal(i.e., what is the advantage of a cell line over a primary culture or vice versa?)

Primary culture - sample of cells taken directly from the organism Secondary culture - the reproduced cells from the primary culture Cell line - Cells that have been modified to reproduce indefinitely The advantages of a cell line over a primary or secondary culture is that they are cost effective and easy to use, and there are no ethical concerns about the source of cells. Cell lines might not representative of normal cells.

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 General transcription factors (TFs) 1. Protein that binds to a eukaryotic promoter near the transcription start site and is a part of the basal transcription apparatus that indicates transcription 2. 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 Required for transcription: 1. Transcriptional activator proteins (TAPs)- 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. 5.. Stimulate assembly of basal transcription apparatus to increase transcription levels Remember that TFs and TAPs are specific to eukaryotes

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

Categorize ETC/ATP synthase, glycolysis, Kreb's /TCA/CAC Cycle, respiration-linked ATP synthesis, ATP synthase, glucose conversion to pyruvate, breakdown/synthesis of glycogen, glucose breakdown/synthesis, acetyl CoA oxidation, carbon dioxide release and reduction of oxygen as being primarily associated with Stage I, II or III of metabolism(Fig. 3.22)

Stage I: - breakdown/synthesis of glycogen Stage II: - glucose conversion to pyruvate - glucose breakdown/synthesis Stage III: - Kreb's /TCA/CAC Cycle - respiration-linked ATP synthesis - carbon dioxide release and reduction of oxygen - ATP synthase - acetyl CoA oxidation

If given the namesglucose-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

Stage II: glucose-6-phosphate, fructose-1,6-bisphosphate, and phosphoenolpyruvate acetyl CoA is between stage II and III (gets produced in stage II but oxidized in Stage III) Stage III: citric acid, succinate, or ETC Complexes are in the inner mitochondrial membrane Acetyl coA is a reduced carbon that helps create citrate

Distinguish the structures of starch, glycogen, and cellulose; distinguish chitin and glycosaminoglycans from glycogen/starch/cellulose

Starch is a plant product made of both branched and unbranched glucose polymers. Ex: Amylose (unbranched) and amylopectin (branched) Glycogen is an animal product made of branched glucose polymers. Cellulose: plant product made of unbranched polymer of glucose Chitin: component of invertebrate exoskeleton made of acetylated glucosamine polymer GAGs (glycosaminoglycans) : polymer of dimers of modified monosaccharide and found in extracellular space.

Identify sucrose and lactose as disaccharides joined by glycosidic bond

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

Describe the features of water that make it especially well suited as the 'solvent of life'; 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.

The "Solvent of Life" Features: 1. Both covalent O-H bonds are highly polarized 2. It is asymmetric, both H atoms are on one side (nonlinear) 3. All three atoms readily form H-bonds

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

The 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

Relate the structure of an ion channel to the flow of ions through it using the Kcs A 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 Offer 3 examples of the ways in

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.

Relate the terms activation energy (free energy of activation), transition state, enzyme catalyst and active site.

The initial energy input, which is later paid back as the reaction proceeds, is called the activation energy and is abbreviated E(A) In order for the reaction to take place, some or all of the chemical bonds in the reactants must be broken so that new bonds (those of the products) can form. To get the bonds into a state that allows them to break, the molecule must be contorted into an unstable state called the transition state. This creates the initial energy input, or the activation energy. Enzyme catalysts lower the activation energy (but do not affect free energy of reactants and products) The part of the enzyme where the substrate binds is called the active site (this is where the catalysis occurs)

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 model organism studies have also indicated that caloric restriction may increase the production of reactive oxygen.

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 solubility 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 phospholipids. 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

Distinguish between equilibrium conditions and the cell's steady state with regard to chemical reactions. Use ATP hydrolysis as an example of the steady state principle.

The main difference between equilibrium and steady state is that equilibrium is a state in which the rate of the forward reaction equals the rate of the backward reaction steady state is the stage of a chemical reaction that has a constant concentration of an intermediate. (ATP hydrolysis is a process that is used to power other reactions. It does not reach equilibrium, therefore it is an example of the steady state principle)

Distinguish between protein amino acid sequence and protein amino acid composition and the ways the two are notated.

The protein sequence of amino acid are what make up the essentials of the protein. The amino acid composition determines the properties of said protein. Sequence is notated by using the one/three letter code, while composition is notated by their side chain characters.

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 bend in the chain that interferes with the well ordered structure which would favor membrane fluidity and lower Tm

Explain how cDNA is synthesized

The synthesis of DNA from an RNA template, via reverse transcription, produces complementary DNA (cDNA). - - Reverse transcriptases (RTs) use an RNA template and a short primer complementary to the 3' end of the RNA to direct the synthesis of the first strand cDNA - Once the DNA-RNA hybrid is formed, the RNA is nicked by treatment with RNaseH - DNA polymerase I is added to digest the RNA and replace it with DNA

List the two types of secondary structures and explain why they form

The two types are alpha helixes & beta pleated sheet. Form due to hydrogen bonding between carbonyl and amino groups in the peptide backbone.

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

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 conformation; such channels are said to be gated. The opening and closing of the gates are subject to complex physiologic regulation and can be induced by a variety of factors depending on the particular channel.

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 positive 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 structure of a virus and compare/contrast viruses with prokaryotic/eukaryotic cells; If given a description, categorize a unit as prokaryotic vs eukaryotic vs viral

Viruses contain a plasma membrane, cell wall, RNA or DNA, and a protein capsule which encases the nucleic acid. Outside the cell, the Viruses are much, much smaller than prokaryotes. Prokaryotic and Eukaryotic cells are both alive, while viruses are not. Viruses cannot procreate w/o hijacking other cells. Viruses have very few organelles, similar to the prokaryotic cells.

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 When ATP is abundant: ATP used to drive the synthesis of glucose, glycogen in anabolic pathways 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. when ATP levels 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. When glucose is high: After a meal, various food materials (such as proteins) were carried to the liver where they were chemically converted to glucose and stored as glycogen When glucose is low: 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. balance between glycogen formation and glycogen breakdown in the liver is the prime determinant in maintaining the relatively constant ( homeostatic ) level of glucose in the blood.

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

Identify polar and nonpolar regions within members of the lipid class of macromolecules

Within the lipid class of macromolecules, there are lipids that are amphipathic. The head will usually be polar and placed externally in order to interact with cytosol. Nonpolar regions are within the center of the lipid, as they would be facing away from the cytosol

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 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 histidine's hydrogen --> positions histidine in the correct orientation to interact with serine. The partial negative nitrogen interacts with the H of serine.

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

any 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

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 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) containing 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

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 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.