Chapter 4 Gene Expression: 3D Animation, LS7A Midterm 2 Learning Objectives + Chapter 3 Quiz 1, 2, 3

Provide the complementary sequences of a given sequence of DNA

- antiparallel -nucleic acids synthesized by addition of nucleotides to 3' end -ex: 5'-ATGGGCATGCATGTGCA-3' 3'-TACCCGTACGTACACGT-5'

Explain how the Calvin Cycle transforms carbon dioxide into sugar and where the energy for this transformation comes from

- carboxylation - CO2 added to 5 carbon molecule RuBP, catalyzed by rubisco, forms 3-PGA -reduction - energy and electrons transferred to compound formed in step 1, uses NADPH and ATP, forms triose phosphate, either exits to become carbohydrate or used for regeneration -regeneration of RuBP, also requires ATP -energy comes from light dependent reactions in photosynthetic election transport chain, in which light captured and transformed into chemical energy (ATP and NADPH)

Describe the role of the components of the endomembrane system as they relate to cellular function

- nuclear envelope - defines boundary of nucleus, 2 membranes, nuclear pores - allow molecules to move into and out of nuclei, essential for nucleus to communicate with rest of cell -ER - produces and transports many lipids and proteins of cell, rough ER - synthesizes transmembrane proteins, proteins that end up in interior of organelles and proteins destined for secretion, smooth ER - fatty acid and phospholipid biosynthesis -Golgi - further modifies proteins and lipids produced by ER, acts as sorting station as move to final destination, site of synthesis of carbohydrates -lysosomes - degrade macromolecules -plasma membrane - determine what comes into and out of cell -vesicles - transport materials in and out of cells, exocytosis (stuff goes out of cell), endocytosis (stuff comes into cell)

State the function of eukaryotic mRNA modifications

-3 types of chemical modifications in RNA processing -5' cap added to 5' end - essential for translation, allows ribosome to recognize mRNA, stabilize transcript -polyA tail added to 3' end - important role in export of mRNA to cytoplasm, keeps it from degrading, stabilize transcript -RNA splicing - removal of noncoding introns and splicing together of exons, catalyzed by complex of RNA protein called splicosome

Describe the structure and function of ATP synthase

-ATP synthase converts energy of the proton gradient into energy of ATP -huge molecular complex embedded in the inner membrane of mitochondria -3 to 4 protons converts a molecule of ADP and Pi into a molecule of ATP -protons that have accumulated in the intermembrane space enter the Fo complex and exit from it into the matrix. The energy they give up as they travel down their concentration gradient rotates Fo and its stalk. Induces repeating conformational changes in the head proteins that enable them to convert ADP and Pi into ATP.

Describe how gel electrophoresis separates nucleic acid fragments based on size

-DNA samples loaded into wells at one end of gel -electric current applied to pull them through gel -DNA fragments negatively charged, so move towards positive electrode -since all DNA fragments have some amount of charge per mass, small fragments move through gel faster than large ones -when gel stained, DNA fragments can be seen as bands, representing group of same sized fragments -can see how many different DNA fragments present and how large they are relative to one another

Discuss the role of tRNA in the process of translation

-carry amino acids to mRNA for translation -anitcodon - base pair with corresponding codon -enzymes called aminoacyl tRNA sythetases connect specific amino acids to specific tRNA -enzymes actually translate codon sequence to specific amino acid -tRNA with no amino acid attached - uncharged -tRNA with amino acid attached - charged

Explain how light energy reaches photosystem reaction centers and what happens when it gets there

-chlorophyll molecules in thylakoid membrane function as antenna: energy transferred between them until transferred to specially configured pair of chlorophyll molecules known as reaction center -light hits antenna chlorophyll molecule -> excites electron -> excites electron in next chlorophyll -> continues until reaction center -> transfers excited electron to electron acceptor molecule -> reaction center oxidized and adjacent molecule reduced

Describe the process of splicing and the role of the spliceosome in eukaryotic gene expression

-coding sequences (exons) and noncoding sequences (introns) in RNA -RNA splicing or removal of introns catalyzed by complex of RNA and protein called spliceosome -spliceosome brings specific site in intron into proximity with 5' end of intron (5' splice site) -proximity enables reaction that cuts RNA at 5' splice site and cleaved end connects back on itself forming loop and tail called lariat -spliceosome brings 5' splice site close to 3' splice site and clears bond that holds lariat to transcript and attaches ends of exons together -lariat released and broken down -alternative splicing - primary transcripts from same gene spliced in different ways to yield different mRNAs and different protein products

Define the "denatured" as it relates to protein structure

-denaturation - unfolding of protein by chemical treatment or high temperature, disrupts ionic bonds holding tertiary structure together, proteins lose functional ability -can lead to inappropriate aggregation which may prevent proper folding - proteins called chaperones help protect slow folding or denatured proteins -can be renatured

Describe the role of Rubisco in the process of photosynthesis

-first step of Calvin cycle, CO2 added to 5 carbon sugar RuBP -rubisco catalyzes reaction

Discuss the central dogma of molecular biology

-genetic information flows from DNA to RNA to protein

Discuss what happens to matter and energy through the different stages of cellular respiration: glycolysis, pyruvate oxidation, the citric acid cycle, and ETC/oxidative phosphorylation

-glucose holds chemical potential energy in covalent bonds, energy released in series of reactions and captured in chemical form -some reactions generate ATP directly by substrate-level phosphorylation (glycolysis), others are redox reactions that transfer energy to the electron carriers NADH and FADH2 (ETC) -donate electrons to electron transport chain, uses energy stored in electron carriers to pump protons across the inner membrane of the mitochondria (energy of reduced electron carriers transformed into energy stored in proton electrochemical gradient) - ATP synthase converts energy of proton gradient to rotational energy, which drives the synthesis of ATP -The cell now has a form of energy that it can use in many ways to perform work.

Identify where the different stages of cellular respiration occur in the eukaryotic cell

-glycolysis - cytoplasm -pyruvate oxidation - mitochondrial matrix -the citric acid cycle - mitochondrial matrix -ETC/oxidative phosphorylation - inner membrane and matrix

Explain the major events that occur during initiation, elongation, and termination of translation

-initiation - initiator AUG codon recognized and Met established as first amino acid -initiation factos bind to mRNA (at 5' cap in eukaryotes) and recruit small subunit of ribosome and tRNA charged with Met, moves along mRNA until first AUG, establishes reading frame -large subunit joins complex and initiation factors released -next tRNA joins at A site -bond connecting Met to its tRNA transferred to amino group of next amino acid in line -ribosome shifts one codon -uncharged tRNA shifts to E site and released, peptide bearing tRNA shifts to P site -elongation - successive amino acids added one by one to growing chain -continues process of adding amino acids -formation of peptide bonds requires energy - elongation factors, bound to GTP molecules, break high energy bonds -termination - addition of amino acids stops and completed polypeptide chain released -encounters stop codon (UAA, UAG, UGA), no corresponding tRNA, protein release factor binds to A site

Label a diagram of the lac operon and state the function of each component

-lacI - structural gene for repressor protein, lacI+ is working, lacI- is not -CRP cAMP binding site - positive regulation of transcription -promoter - initiates transcription -lacO - where repressor binds, negative regulation, lacO+ is working, lacOc is constitutive (continuous) -lacZ - codes for B-galactosidase, cleaves lactose molecule into glucose and galactose, lacZ+ is working, lacZ- is not -lacY - codes for protein lactose permease, transports lactose from external medium into cell, lacY+ is working, lacY- is not

Recognize that not all proteins are translated on the RER

-not all proteins translated on RER -some translated on free ribosomes in cytoplasm

Define and relate the terms operon, polycistronic mRNA, and structural gene

-operon - promoter, operator, structural genes that are transcribed into single mRNA called polycistronic mRNA -structural gene - code for sequence of amino acids making up primary structure of each protein -polycistronic mRNA - group of functionally related genes located next to one another along bacterial DNA and share promoter, the coding sequences of structural genes transcribed from promoter transcribed together into single molecule of mRNA

Identify where the different stages of photosynthesis take place

-prokaryotes - photosynthetic electron transport chain in membranes within cytoplasm or in plasma membrane -eukaryotes - chloroplasts -light dependent reactions - thylakoid membrane, mvmt of molecules between stroma and lumen -Calvin cycle - stroma

Compare and contrast transcription in prokaryotes and eukaryotes

-prokaryotes - transcription and translation occur in cytoplasm, transcript immediately available for protein synthesis -eukaryotes - two processes separated by nuclear envelope, transcription occurs in nucleus and translation occurs in cytoplasm, allows for additional levels of gene regulation, transcript chemically modified and then transported to nucleus -however processes similar

Compare and contrast translation in prokaryotes and eukaryotes

-prokaryotes - translation occurs as soon as mRNA comes off DNA template, both transcription and translation occur in cytoplasm -eukaryotes - two processes separated by nuclear envelope, transcription occurs in nucleus, translation occurs in cytoplasm, eukaryotic ribosomes larger -in both, ribosome consists of small and large subunit

Define the role of promoters and terminators in the transcription of eukaryotic and prokaryotic genes

-promoters - region where RNA polymerase and associated proteins bind to DNA duplex to begin transcription -promoter recognition facilitated by sigma factors -general transcription factors bind to promoter region and transcriptional activator proteins bind to enhancers -recruit mediator complex which recruits RNA polymerase -DNA looped - brought into close proximity with RNA polymerase, transcription begins -terminators - signal for transcription to end

Explain the mechanism of protein trafficking and its role in protein localization inside or outside the cell

-protein sorting - process by which proteins end up where they need to be to perform function, directs proteins to cytosol, lumen of organelles, membrane of endomembrane system, or out of cell -proteins produced on free ribosomes in cytosol and membrane bound ribosomes on rough ER -produced on free ribosomes - sorted after translation, have signal sequences that allow to be sorted -several types of sequences -no sequence - remain in cytosol -sequence at amino ends - mitochondria or chloroplasts -sequence internal - nuclear signal sequence called nuclear localization signal, enable proteins to move through nuclear envelope -proteins produced on rough ER - sorted as translated -remain in ER lumen - SRP (protein synthesis begins in cytosol, SRP binds to growing polypeptide chain and to ribosome, translation pauses, SRP binds to receptor, translation resumes through membrane, signal sequence cleaved) -remain in membrane (transmembrane) - contain signal anchor sequence

Explain how the process of cellular respiration can be regulated by inhibiting or activating PFK

-reaction 3 of glycolysis -"committed" step, subject to tight control -reaction catalyzed by the enzyme PFK-1, that regulates the rate of glycolysis -allosteric enzyme with many activators and inhibitors -ADP and AMP are activators -ATP and citrate are inhibitors -when ADP and AMP are abundant, bind to enzyme and causes enzyme's shape to change, activates enzyme, increasing the rate of glycolysis and the synthesis of ATP -when ATP abundant, binds to same site on the enzyme, but binding inhibits enzyme's catalytic activity, glycolysis and the rate of ATP production slow down

Identify proteins and small molecules that regulate expression of the lac operon

-repressor protein - binds with operator and prevents transcription -inducer - lactose acts as inducer, binds with repressor to prevent it from binding operator -CRP-cAMP binds to binding site and activates transcription

Describe how the lac repressor and CRP regulate expression of the lac operon

-repressor protein binds with operator and prevents transcription but not in presence of lactose -CRP-cAMP complex - positive regulator of lac operon -glucose preferred as energy source to lactose - CRP-cAMP complex regulates which compounds utilized -low glucose - high cAMP - CRP-cAMP complex binds to site near promoter, activates transcription -high glucose - low cAMP - complex does not bind, transcription not induced to high levels even in presence of lactose -cAMP binds to CRP - changes shape of CRP so can bind at site near operator - cAMP is allosteric activator of CRP binding

Describe the structure and function of the ribosome

-ribosome - complex structure of RNA and protein that bind with mRNA and are site of translation -consists of small and large subunit -eukaryotic ribosome larger than prokaryotic -large subunit has 3 binding sites for molecules of transfer RNA (A, P and E site) -major role of ribosome - ensure that sequence of mRNA read in successive non overlapping groups of 3 nucleotides

Relate the metabolism of different molecules (i.e., sugars and fats) to the process of cellular respiration

-sugars other than glucose contribute to glycolysis -disaccharides (maltose, lactose and sucrose) and monosaccharides (fructose, mannose and galactose) -disaccharides hydrolyzed into monosaccharides -hydrolysis of some monosaccharides produces glucose molecules that directly enter glycolyisis. -other monosaccharides also enter glycolysis, not as glucose, converted into intermediates of glycolysis that come later -triacylglycerols are broken down to glycerol and fatty acids -the fatty acids shortened by a series of reactions that sequentially remove two carbon units from their ends (beta-oxidation) -end product is acetyl-CoA, which feeds the citric acid cycle Carbohydrates in diet produce a variety of sugars; hydrolysis of some disaccharides produces glucose molecules that directly enter glycolysis. They are converted into intermediates of glycolysis that come later in the pathway FATTY ACIDS AND PROTEINS: Lipids are a good source of energy → butter, oils, ice cream, etc Triacylglycerol are broken down inside cells and then shorted by beta oxidationOxidation of fatty acids produces a large amount of ATP but cannot be used by all tissues of the body

Describe how Southern blots allow specific genes or DNA sequences to be visualized on a gel

-used to verify presence or absence of specific nucleotide sequence in DNA from different sources and to identify size of restriction fragment that contains sequence -DNA isolated from each source -DNA restriction fragments loaded on gel and separated by electrophoresis, smaller fragments migrate faster -transferred from gel to nylon filter -radioactively labeled acid probe added, binds to complementary DNA segments -detect position of radioactive probe by covering with x ray film -after development radioactive probe becomes visible

Glycolysis

1st step of cellular respiration glucose—a six-carbon sugar—undergoes a series of chemical transformations. In the end, it gets converted into two molecules of pyruvate, a three-carbon organic molecule. In these reactions, ATP is made, and NAD+ is converted to NADH

Arrange the steps in RNA splicing in order from earliest to latest. 1 - exon ends are covalently joined together 2 - components of the spliceosome bind conserved regions in the intron and bring them together in close proximity 3 - acceptor splice site is cut. 4 - donor splice site is cut and the end of the intron is joined covalently to the branch site

2, 4, 3, 1

Pyruvate Oxidation

2nd step of cellular respiration Each pyruvate from glycolysis goes into the mitochondrial matrix—the innermost compartment of mitochondria. There, it's converted into a two-carbon molecule bound to Coenzyme A, known as acetyl CoA. CO2 is released and NADH is generated.

In a DNA strand, successive nucleotides are linked by:

3'-5' phosphodiester bonds

A template strand of DNA is read in the _____ direction in order to direct synthesis of RNA in the _____ direction.

3'-5'; 5'-3'

Citric Acid Cycle

3rd step of cellular respiration The acetyl CoA made in the last step combines with a four-carbon molecule and goes through a cycle of reactions, ultimately regenerating the four-carbon starting molecule. 1 pyruvate (3 carbon) oxidized to 3 CO2 ACoA completely oxidized to electron carriers 4 NADH, 1 FADH2, and 1 GTP (or ATP) are produced

The regions on a DNA helix where the strands must be separated so processes like transcription can start often have an A-T pair bias, that is, there are more A-T pairs than G-C pairs. What might you suggest as the basis for this bias? A., G-C pairs have fewer H-bonds to break, so it requires less energy. B., A-T pairs have fewer H-bonds to break, so it requires less energy. C., The strands are farther apart and easier to split at A-T pairs. D., The strands are farther apart and easier to split at G-C pairs.

A-T pairs have fewer H-bonds to break, so it requires less energy.

The information carried by DNA is in the _______BLANK and their ___________BLANK. A., bases; sequence B., phosphates; phosphodiester bonds C., deoxyribose; phosphodiester bonds D., sugar-phosphate backbone; hydrogen bonds

A., bases; sequence

Compare and contrast the major and minor groove and the information they provide

Backbones are closer on one side of the helix than the other Major groove = occurs where backbones are far apart, easier for certain proteins to interact with bases on the major groove bc backbones are not in the way (serves as a point to regulate transcription, translation, or alter its structure Minor groove = occurs when they are close together, less info bc too small for amino acid side chains in proteins to fit in and interact with bases there

Predict how changes to the DNA sequence of a gene and/or the function of proteins involved in transcription and mRNA processing will alter the final products of transcription

Change to DNA sequence Exons/introns - if in the exons, it has a considerable effect as it might bring another amino acid that will change the conformation and shape of the protein; if in the introns, has no effect 5' cap - if a change in the 5 cap, it is possible that mRNA will degrade or the ribosome won't be able to bind and translate Promoter - if change in the promoter, it is possible that transcription will not start Terminator - possible that it won't stopChange to proteins DNA helicase - DNA strands cannot be taken apart and RNA cannot be made RNA polymerase - if changed, won't be transcribed Change in mRNA processing5' cap - if a change in the 5 cap, it is possible that mRNA will degrade or the ribosome won't be able to bind and translate Poly A tail - possible that it won't be exported out into the cytoplasm, also degradation

In which aspect of DNA structure are hydrogen bonds important? A., 5'C to phosphate bond B., 3'C to phosphate bond C., base-to-deoxyribose bond D., base-to-base pairing

D., base-to-base pairing

Compare and contrast the structures of DNA and RNA

DNA is double stranded, RNA is single stranded and can fold back onto itself Sugar in RNA is ribose, while in DNA it is deoxyribose RNA is much shorterUracil base in RNA replaces thymine in DNA

Describe the structure and organization of DNA

DNA is made out of nucleotides, which consist of three components: a 5-C sugar, a base, and one or more phosphate groups Bases can be double ring structures called purines (adenine or guanine) or single ring structures called pyrimidines (cytosine and thymine) These nucleotides are strung together by phosphodiester bond (covalent bonds); has a 5' end (phosphate) and a 3' end (hydroxyl) DNA wraps like a double helix, each side held together by hydrogen bonds There is a major groove and a minor groove, which serve as points of recognition for the cellStrands are antiparallel to each other 3H bonds for C and G 2H bonds for A and T

What is the central dogma?

DNA is transcribed into RNA, which is translated into protein.

Relate the process of photosynthesis to the process of cellular respiration

Differences: Photosynthesis produces carbohydrates, while cellular respiration breaks down those carbohydrates to make ATPPhotosynthesis occurs in the chloroplast, while cellular respiration occurs in the mitochondria Similarities Uses the same ETC chain to pump protons and transfer electronsPumps protons from stroma to thylakoid lumen (mito matrix to intermembrane space) and diffusion back down produces ATP

Muscle cells make different proteins than nerve cells because they have different sequences of DNA.

False

Interpret results from gel electrophoresis experiments and how mutation may affect the products of transcription and their migration distances on a gel

If mRNA is longer, it will not go as far down the gel If intron site isn't spliced out If termination is mutated at a later point If mRNA is shorter, it will go farther down the gelIf exon site is spliced out Addition of RhoIf termination end is mutated at an earlier point Possible if 5' cap/promoter sequence is mutated that transcription will not occur at all and there will be no fragments in the gel

Evaluate how changes in one metabolic pathway (i.e., fatty acid synthesis) will affect the products, reactants, and reaction rates of other integrated metabolic pathways

If there is too much ATP, the broken down carbohydrates either get stored as branched glycogen or as fats (fatty acid synthesis)

Predict how introducing changes in one stage of cellular respiration (e.g., altering the activity of an enzyme) will affect components both upstream and downstream of the change.

If you stop a carrier complex from working, such as cyt b, the reduced forms will build up and the rest of the rxn cannot follow through If you make mitochondria membrane extremely leaky, then H+ gradient is not as effective and not enough ATP will be produced, driving the cell to produce more ATP

Where does the expression of a protein begin? a. In the nucleolus b. In the cytoplasm c. In the nucleus

In the nucleus

Connect redox reactions to the energy transformations that occur throughout cellular respiration

Oxidation reactions that produce CO2 are coupled with reduction of electron carrier NAD+ to NADH Energy released is moved to NADH Lots of energy stored in the bonds between the carbon and hydrogen atoms in glucose. redox reactions basically transfer this bond energy in the form of electrons from glucose to molecules called electron carriers An electron carrier is basically a molecule that transports electrons during cellular respiration. By using electron carriers, energy harvested from glucose can be temporarily stored until the cell can convert the energy into ATP.

Predict how introducing changes in one stage of photosynthesis (e.g., altering the activity of an enzyme) will affect the production of NADPH, ATP, and sugar

Photosystem II Requires: light, electrons from the splitting of water Measured by: amount of water left, O2 being produced If disturbed: Protons being diffused into lumen will decrease and electrons that will be transported to cytochrome complex will decrease. O2 will decrease and H20 will increase. Ex: chloroplasts are unable to split water// something binds to chlorophyll and changes its absorption spectrum Photosystem I: Requires: light, electrons from PSII Measured by: NADPH being produced, NADP+ left If disturbed: NADPH will decrease and protons diffused into lumen will decrease Ex: Takes electrons away from ETC (we need e to produce NADPH) ATP Synthase Requires: flow of protons Measured by: amount of ATP being produced If disturbed: Amount of ATP will decrease and will not provide as much energy that reduces CO2 into G3P Ex: disrupts proton flow across thylakoid membrane (makes it permeable to H+ flow) Calvin Cycle Requires: NADPH, CO2, ATP, and Rubisco Measured by: NADP+ produced, CO2 left, G3P produced (direct product) If disturbed: Amount of G3P will decrease. CO2 and NADPH will accumulate. Ex: Inactivates the enzyme that produces G3P which prevents sugars from being built A lack of NADPH in the Calvin Cycle will slow down the reduction process, as molecules will not be able to break down into G3P. Remember that the reduction of 3-PGA requires substantial amounts of ATP and NADPH. If photosystem II loses the ability to split water, there will not be enough electrons that can move through the ETC. This results in a lack of ATP and NADPH needed for the Calvin Cycle If a mutation caused photosystem I to function at only 10 percent of its normal capacity, NADP+ reductase activity would decrease. Think of it as a machine; if one part of the machine stops working, the others slow down as well. A partial inhibition of NADP+ reductase decreases the rate of G3P production. Hint: We know the NADP+ reductase reduces NADP+ to NADPH. If there are not enough NADPH molecules, NADP+ will build up and will not be able to break down into G3P.

Discuss what a plant cell can do with the products of photosynthesis once they are produced

Plants can only transfer carbohydrates from the chloroplasts to the cytosol, where they can be used as energy storage or starting points of synthesis for other moleculesTo get energy, they must break down the carbohydrates to form ATP with mitochondria (this is why plants have both chloroplasts and mitochondria!!)

Discuss the four levels of protein structure and relate them to the function of a protein

Primary - sequence of amino acids in a protein (these are connected by peptide bonds and determines how a protein folds). It is connected by covalent bonds Secondary - local interactions between stretches of amino acid in a structure; result from H bonding in the polypeptide backbone; divided into two types (alpha helix and beta sheets) Tertiary - longer range interactions between secondary structures that support overall 3d shape of polypeptide; determined by interactions of hydrophilic and hydrophobic R groups and ionic, hydrogen, and van der Waals interactions that form between them as well Quaternary - formed by individual polypeptides that interact with each other

Why is it that the primary transcript in prokaryotes can immediately serve as mRNA while in eukaryotes it undergoes elaborate multistep processing? (Select all that apply.) Primary transcripts in eukaryotes contain introns that have to be removed. A 5′ cap is added to the prokaryotic primary transcript allowing the ribosome to start translation immediately. All of these choices are correct. General transcription factors in eukaryotes are unable to enter the nucleus. Prokaryotes do not have a nuclear envelope and the ribosome can start translation even before transcription ends.

Primary transcripts in eukaryotes contain introns that have to be removed. Prokaryotes do not have a nuclear envelope and the ribosome can start translation even before transcription ends.

Which one of the following statements about RNA is INCORRECT?

RNA is usually found in double-stranded form, just like DNA.

Which of the following reads the nucleotide sequence of a gene and synthesizes the corresponding primary transcript? a. DNA polymerase b. Ribosome c. RNA polymerase

RNA polymerase

Which one of the following CORRECTLY lists the components necessary for eukaryotic transcription?

RNA polymerase, general transcription factors, DNA, and RNA nucleotides

Relate the movement of electrons through the electron transport chain to the production of ATP by ATP synthase

Redox reactions that transfer energy to the electron carriers NADH and FADH2. These electron carriers donate electrons to the electron transport chain, which uses the energy stored in the electron carriers to pump protons across the inner membrane of the mitochondria. In other words, the energy of the reduced electron carriers is transformed into energy stored in a proton electrochemical gradient. ATP synthase then converts the energy of the proton gradient to rotational energy, which drives the synthesis of ATP.

Oxidative Phosphorylation

The NADH and FADH2 made in other steps deposit their electrons in the electron transport chain, turning back into their "empty" forms (NAD+ and FAD). As electrons move down the chain, energy is released and used to pump protons out of the matrix, forming a gradient. Protons flow back into the matrix through an enzyme called ATP synthase, making ATP. At the end of the electron transport chain, oxygen accepts electrons and takes up protons to form water.

Which of the following do you think best describes the way that base pairing stabilizes the double helix of DNA? A., Shapes of complementary bases fit together like lock and key. B., The arrangement of atoms allows precise hydrogen bonding. C., Bases can pair as long as there are enough electronegative atoms. D., Bases can pair as long as there are enough hydrogen atoms.

The arrangement of atoms allows precise hydrogen bonding.

Which of the following is true about the structure of a double-stranded DNA molecule?

The diameter of a DNA molecule is the same along its entire length due to the specific complementary base pairing of the DNA nucleotides.

Compare and contrast the generation of ATP in the presence or absence of oxygen

The production of ATP is much greater in the presence of oxygen: 34-38 ATP are produced per glucose molecule. In the absence of oxygen, the net yield of ATP produced is 2 per glucose molecule. -energetic gain small in comparison to aerobic respiration due to lactic acid and ethanol, not fully oxidized and still contain a large amount of chemical energy in their bonds. Fermentation converts carbohydrates into lactic acid or alcohol: ethanol fermentation: pyruvate from glucose metabolism is broken into ethanol and carbon dioxide Lactic acid fermentation: glucose is converted into cellular energy (ATP) and lactic acid.

Evaluate how transcription factors bind to promoter sequence and their effect on transcription

Transcription factors help initiate transcription by binding to promoter and stimulating movement of RNA polymerase down the RNA strand

Whichever DNA strand is transcribed, the RNA polymerase reads the template strand from 3′ to 5′.

True

Connect redox reactions to energy transformations that occur throughout photosynthesis

Two parts of photosynthesis: light dependent reactions and the Calvin Cycle Light dependent rxns involve the splitting of water (oxidation) to produce reduced NADPH and ATP. (Oxygen is used as a byproduct due to the oxidation of water.) Involve using light energy to split water and excite chlorophyll antennas which bring electrons to the reaction centers of each photosystemAs e flows from photosystem II to photosystem I through cytochromes, protons are pumped from stroma into thylakoid lumen The electrons in photosystem I are then shuttled to a NADP reductase, which reduces NADP+ to NADPH These will, in turn, be used in the Calvin Cycle to power the reduction of CO2 into a higher energy and more complex carbohydrate molecule that the cell can later use to power processes in cellular respiration. First, CO2 is incorporated into a 5C molecule Energy is added by the reduction from NADPH and ATP NADPH provides the 2 electrons ATP provides the phosphate groups This forms a G3P molecule (triose phosphate groups)

Transcription is the process by which:

a section of DNA is used as information to generate an RNA molecule.

Transcription continues until:

a terminator sequence is encountered.

The primary transcript is _________ to the DNA template strand. a. complementary b. antiparallel c. identical d. a, and b e. a, b, and c

a, and b (complementary and antiparallel)

The protein shown being synthesized during the animation is: a. myosin b. RNA polymerase II c. a histone protein d. chaperone e. actin

actin

An intron is:

an RNA sequence that is removed during the processing of an RNA molecule in the nucleus.

When we consider the orientations of the two strands of DNA that make up a double helix, we see that they are: A., parallel. B., antiparallel. C., mirror images.

antiparallel.

Which one of the following represents an actual Watson-Crick base pair with the LARGEST number of hydrogen bonds?

cytosine and guanine

Alternative splicing allows for:

different polypeptides to be made from a single gene.

Alternative splicing means that:

different spliced forms contain different combinations of exons.

In eukaryotes, activator proteins bind to _____; generalized transcription factors bind to _____.

enhancers; promoters

True or False: mature mRNAs are exported through a nuclear pore complex in a linear fashion, and remain linear throughout the process of translation. a. b.

false

A template DNA strand contains the sequence 3'-ATGCTGAC-5'. This strand is transcribed:

from left to right

The cap that is added to the RNA during processing: (Select all that apply.) is needed for ribosomes to attach to messenger RNA. aids in the accuracy of translation of the messenger RNA into protein. helps prevent formation of complex three-dimensional structures in the messenger RNA. helps prevent rapid breakdown of the messenger RNA.

is needed for ribosomes to attach to messenger RNA. helps prevent rapid breakdown of the messenger RNA.

Determine the product of transcription given the DNA sequence of a gene

mRNA should be complementary and antiparallel to DNA; almost the same but replace thymine with uracil

Which one of the following types of RNAs carries information for making a single type of protein?

messenger RNA

For each of the following organelles or structures, check the corresponding box if the organelle or structure is named or discussed in the animation. (Note that you only get one chance on this question, so make sure you watch the animation carefully before answering.)

mitochondria nucleus ribosomes

Which one of the following mRNA processing events does not occur in the nucleus of human cells? a. 5' cap addition b. excision of introns c. poly-A tail additions d. splicing of exons e. none of the above are correct. all of the events described above occur in the nucleus of human cells

none of the above are correct. all of the events described above occur in the nucleus of human cells

In double-stranded DNA, the sugar-phosphate backbones are:

on the outside, separated by grooves of unequal size.

In a double-stranded DNA molecule, the strands are said to be antiparallel because:

one strand runs 5' to 3' and the other 3' to 5'.

We identify nucleic acid strand orientation on the basis of important chemical functional groups. These are the _________BLANK group attached to the 5' carbon atom of the sugar portion of a nucleotide and the __________BLANK group attached to the ___BLANK carbon atom. A., nitrogenous base; phosphate; 3' B., phosphate; hydroxyl; 3' C., hydroxyl; phosphate; 3' D., amino; phosphate; 2' E., phosphodiester; nitrogenous base; 2'

phosphate; hydroxyl; 3'

In eukaryotes, where do general transcription initiation factors bind?

promoter

Label the promoter, transcription start site, exons, introns, and polyA signal sequence on a model of a eukaryotic gene

promoter -> transcription start site - > exon -> intron -> exon -> intron -> exon -> polyA signal sequence

Label the promoter, transcription start site, and terminator on a gene model

promoter -> transcription start site - > terminator

Translation is the process by which:

ribosomes synthesize protein from information in an RNA molecule.

Non-protein coding genes are typically found in: a. mitochondria b. the endoplasmic reticulum c. the nucleolus d. the cytoplasm e. areas of the nucleus other than the nucleolus

the nucleolus

Does protein expression begin with transcription or translation? a. translation b. transcription

transcription

Which of the following types of RNA molecule delivers amino acids to the ribosomes? a. messenger RNA b. transfer RNA c. ribosomal RNA

transfer RNA