exam 4 + exam 5 mcb 181

You are examining a human pedigree for a trait. You notice that the trait appears in every generation, is equally likely to occur in males and females, and about half of the offspring are affected when one parent is affected. The trait is most likely:

dominant

with independent assortment, the ratio of phenotypes in the F2 generation of a cross between true-breeding strains (AA bbX aa BB) can be described as 9:3:3:1 when A and B are dominant over a and b. to what phenotype do the "#"s in the ratio refer?

dominant for one trait and recessive for the other

How do most cancers arise?

from a series of mutations that arise in the descendants of a single somatic cell

addition or subtraction of nucleotide

generated by small insertions of deletions

Of the molecules, which has the greatest chemical potential energy?

glucose

During the process of PCR, what plays the role in the test tube that helicase plays in the cell?

heat

A _________ expresses a gene or genes that direct production of the signaling molecule, and the _______________ expresses a gene or genes that direct production of the _________________.

signaling cell; responding cell; receptor protein

replication begins at many places at once

site where replication begins called the origin of replication & happen in several places along chromosome

plasmid

small piece of DNA many bacteria have

point mutation (nonsense mutation)

smaller protein ends due to stop codon

the Z scheme is a model for the interpretation of:

the changes in the energy level of electrons as they pass through the photosynthetic electron transport chain

Glycolysis turned on when ATP levels are _______ = activation

low levels

The pH in the intermembrane space of the mitochondria should be _____ compared with the matrix, due to the _____ concentration of protons in the intermembrane space.

lower; higher

Genes that are located in the same chromosome and are close together:

may not assort independently from each other.

A simplified overall equation for respiration is as follows: C6H12O6 + 6O2 → 6CO2 + 6H2O + energy In this reaction, we can say that _____ is reduced and _____ is oxidized.

oxygen; glucose

Which of the reactions would you predict could be coupled to ATP synthesis from ADP + Pi (ADP + Pi → ATP + H2O ΔG = +7 kcal/mol)?

phosphoenolpyruvate + H2O → pyruvate + Pi , ΔG - 14.8 kcal/mol two pyruvates for every 1 glucose molecule

which of choices is an example of kinetic energy?

photon of light

In the lac operon, the repressor prevents transcription

operator (Lac O)

How do mutations arise?

Mutations arise randomly and independent of other mutations in the cell.

Which elements (other than N) could have been used to mark DNA for this experiment?

-carbon & oxygen

UV radiation from the sun increases the rate of spontaneous mutation in most organisms. In the original Lederberg experiment, what would have been a possible consequence of exposing the master plate to UV radiation?

The number of surviving colonies on replica plates exposed to antibiotics likely would have increased.

pH is a measure of the acidity of a solution and equals the negative logarithm of the proton concentration. If the proton concentration decreased on the inside of the vesicle, what would happen to the pH measured on the outside of the vesicle?

The pH would decrease outside of the vesicle.

when chemical reactions occur the _______ but the _______.

atoms retain their identities; arrangement of bonds changes

Monod found that, when lactose was removed from the growth medium, the amount of b-galactosidase in the culture remained constant for 30 minutes or more. How can this result be explained?

b-galactosidase is stable and does not break down for at least 30 minutes.

many cellular processes represent work that requires expenditure energy. Which of the actions is not a cellular process that requires the cell to expend energy?

diffusion of water into cells

DNA wrapped around proteins called _______

histones

In replication of a linear double-stranded DNA molecule, one end of each strand becomes shorter in each round of replication. This happens because:

the RNA primer cannot be replaced at the very end of a lagging DNA strand.

Which process provides an eventual carbon source for glycolysis?

the calvin cycle

A recessive X-linked trait can be expressed in both males and females.

true

Which molecule is initially oxidized to provide electrons for the photosynthetic electron transport chain?

-water (H2O)

PRC cycle step 2:

1. In the final step, extension, the solution is heated to the optimal temperature for DNA polymerase and each primer is elongated/extended with the deoxynucleoside triphosphates.

Enzymes catalyze reactions by reducing the activation energy

1. When the activation energy is low, the reaction is faster. 2. Enzymes are able to reduce the activation energy by stabilizing the transition state. 3. The rate of the reaction increases because the activation energy is reduced.

how to repair?

-recognize damage -recognize which strand has correct sequence -repair

At the beginning of the experiment, the percent 16O2 in the test tubes was

99.8%

In which compartment does pyruvate oxidation take place?

A

Other than cyclins, the levels of most proteins that the researchers observed most resembled which graph?

A

Where are photosystems II and I of the photosynthetic electron transport chain located?

A

What is the hypothesis for Racker and Stoeckenius's experiment?

A proton gradient is required for ATP synthase to synthesize ATP.

Which of the statements best summarizes the function of G protein-coupled receptors?

A signal present on the outside of the cell leads to a change on the inside of the cell.

Which component pictured here does not participate in the flow of electrons?

ATP synthase

No controls are described for the experiment. What would be a useful negative control for the experiment?

All of the answer options are correct.

RNA primase lays down an RNA primer to start DNA replication. If a mutation occurs that blocks the function of RNA primase, which synthesis of which strand is affected, and why?

Both strands are affected because all DNA polymerase can only add new nucleotides to a 3′-OH present at the end of the RNA primer.

peptide bonds

Covalent bonds form between amino acid monomers

Which energy change labeled by a lower case letter (a-e) is the ∆G of the reaction?

D

Why is the transporter in the figure considered to be an example of "secondary transport"?

It is driven by the proton gradient that was created by energy from ATP.

Post-replication Mismatch Repair

MutS, MutL, and MutH form a multiprotein mispair recognition and removal system that works on the newly synthesized DNA strand.

mutation definition

Mutation: Any heritable change in the genetic material

_____ bind to the active site of an enzyme.

Substrates and some types of inhibitors

alternative splicing

The same primary transcript can be spliced in different ways to yield different proteins, a phenomenon

What would be a useful negative control for the experiment?

all of answers correct

Oncogene

cancer-causing gene (e.g. activated Ras)

Which molecule is the end product of glycolysis?

pyruvate

Some viruses with an RNA genome require a virus-encoded reverse transcriptase.

true

potenital energy

stored energy -depends on position of object relative to its surrounding or on objects structure

the chemical modification to DNA and histones could affect the binding of ribosomes to mRNA to initiate translation

false

Based on your interpretation of this model of phosphofructokinase-1 (PFK-1) activity, which of the following would increase PFK-1 activity?

increased concentration of AMP

Based on your interpretation of this model of phosphofructokinase-1 (PFK-1) activity, which of the following would decrease PFK-1 activity?

increased concentration of citrate

Adrenaline is produced by the adrenal gland and secreted into the bloodstream in response to fear, etc. In the liver, it influences fuel (glucose) availability by stimulating the breakdown of glycogen to form glucose Suppose you are a research scientist studying the fight-or-flight response in cultured liver cells. You inject these cells with cAMP. What outcome would you predict?

increased glucose production from glycogen

transition state

intermediate, highly unstable stage between two reactants & products in which old bonds are breaking & new ones are forming

Before this experiment was performed, Kurt Stern had already shown that the enzyme catalase forms a complex with its substrate. Therefore, this current set of experiments:

investigated a different enzyme and substrate.

polymerase chain reaction (PCR)

is a way to amplify specific DNA sequence to give you a larger sample that can be used either in recombinant DNA or be used to analyze in sequence in techniques such as genetic testing or forensic

s molecules move down their concentration gradient, from a more ordered state to a less ordered state, entropy:

is increasing.

A loss of function mutation in which labeled sequence in the diagram would likely result in continuous production of the enzymes from the lac operon?

lacI

Which gene in the diagram here codes for a repressor protein that binds to the operator site when lactose is not present?

lacI

A folding domain of a polypeptide chain has a primary structure containing 5 phenylalanine residues, where F represents the side chain of phenylalanine. Consider the possible folding orientations. If this domain folds in one of the two orientations shown, which is more likely, the one on the left or the one on the right?

left one

Hemoglobin

made up of four subunits: two copies of polypeptide depicted in magenta & two copies of polypeptide depicted blue

universal code within DNA

means once human DNA apart of bacterial model it still can be replicated, transcribed and translated bc code is same between two organisms

identify organelle A and the processes that take place there.

mitochondrion; citric acid cycle, oxidative phosphorylation

When cells communicate by the signaling process, one cell produces a _________________ that must be received by the ___________ on or in the responding cell.

signaling molecule; signal receptor

Which of the choices would be most likely to lead to the development of cancer?

the activation of an oncogene and the inactivation of a tumor suppressor gene

reuqirements of the cell

-A way to encode/transmit informationA membrane separating the inside of the cell from the outside -ENERGY

characteristics of enzymes

-Allow chemical reactions to occur at the rate needed for cells to survive and thrive -Specific -Unchanged by the chemical reaction -Generally proteins (but can be nucleic acid) -Have optimal pH, temperature, and ionic strength -Can be regulated C

secondary structure

-Secondary structure results from hydrogen bonding between backbone groups -Alpha helices are common secondary structures in proteins -Beta sheets are common secondary structures in proteins

telomere

-The ends of eukaryotic chromosome are capped by a repeating nucleotide sequence called the telomere -The synthesis of telomeres is catalyzed by an enzyme called telomerase

Instability Elements Control mRNA Half-Life

-The half-life of mRNAs is often controlled by instability elements. -These are specific sequences of nucleotides (e.g., AUUU repeats) which can be recognized by special proteins that target the mRNA for rapid degradation.

chemical reactions part 2

-involves conversion reactants to products -proceed through transition state that has large amount of energy

What happens if protein structure comes apart?

1. If a protein loses its structures, it also loses its function. 2. Proteins can be denatured (unfolded) by chemical treatment (e.g. change in pH, high salt) or high temperatures and lose their function. 3. If the optimal conditions are returned, the protein can refold and regain its function

Repairing point mutations in a small region of DNA

1. Occurs after proofreading by DNA polymerase during active DNA replication 2. Post-replication mismatch repair: a single mispaired base is repaired by removing and replacing a DNA segment. 3. Base excision repair: the incorrect base and its sugar are excised from the strand, then replaced. 4. Nucleotide excision repair: recognizes multiple mismatched bases in a region

Linear DNA After Each Round of Replication

1. On the leading strand: a. Only one primer is required to start synthesis. b. Replication continues to the end. c. The strand is replaced by DNA when the last fragment of the lagging strand at the opposite fork of the replication bubble catches up to it. 2. On the lagging strand: a. Multiple RNA primers are required. b. The final primer is added about 100 nucleotides from the 3' end of the template. c. When it is removed, the new daughter strand is shortened by about 100 nucleotides.

Enzymes

1. RNA primase= catalyzes the synthesis of RNA primer thats required for DNA synthesis to occur -only synthesizes short fragments of RNA 2. DNA polymerase= catalyzing synthesis of DNA in template dependent manner (going to match up A to T & C to G base pairs) and going to catalyze synthesis of phosphodiester bond so have covalent bonds forming longer DNA molecule needs RNA primer so extends primer out **synthesis occurring from 3' hydroxyl at end to ass next incoming nucleotide**

DNA repair systems must:

1. Recognize DNA damage or mutation 2. Recognize which strand has the correct sequence and which one needs to be repaired 3. Repair DNA to restore normal sequence and DNA structure

DNA Synthesis by DNA Polymerase Requires a Primer

1. Synthesis of the primer is catalyzed by an enzyme called RNA primase 2. RNA primase synthesizes a short piece of RNA complementary to the DNA template. 3. Once the primer has been synthesized, the DNA polymerase takes over and elongates the primer, adding successive DNA nucleotides to the 3' end of the growing strand.

how many different types of aminoacyl tRNA synthetases are there?

20

The researchers found that the level of ATP produced in the light is 594 units and the level produced in the dark is 23 units. Approximately how much more ATP is produced in the light compared to the amount produced in the dark?

25 times

Why are studies in yeast mentioned in the Background section?

Cell division is well conserved across many organisms.

The enzyme responsible for proofreading a growing DNA strand and for replacing mismatched nucleotides is

DNA polymerase

Which of the following sequences accurately represents the flow of electrons through living organisms?

H2O → photosynthesis → carbohydrate → cellular respiration → H2O

In the overall reactions of photosynthesis, the electrons from _____ are used to reduce _____.

H2O; CO2

Phosphofructokinase is an allosteric enzyme in the pathway that breaks down glucose to produce ATP. Regulation of glycolysis is directly related to the level of ATP and citrate. If ATP or citrate levels are high, phosphofructokinase is inhibited. What will happen to this enzyme when ATP levels drop?

Phosphofructokinase is activated

Which of the answer choices is most likely to result in a nonfunctional polypeptide?

a nonsense mutation

three ways to illustrate tertiary structure

a. Ball-and-stick model: shows the atoms in the amino acid chain b. Ribbon model: emphasizes the alpha helices and the beta sheets c. Space-filling model: shows the shape and contour of the folded protein

Failure to recover a specific band in a gel made after PCR can be attributed to:

all of these correct

What cellular process(es) is/are responsible for the increase in protein content associated with the gap phases of the cell cycle?

both transcription and translation

Chemicals called uncouplers can make membranes permeable to small molecules and ions. What effect might uncouplers have on photosynthesis?

decreased ATP production because the proton gradient would decrease

RNA polymerase with transcription does not have proofreading subunit

error can happen in RNA synthesis (errors propagated in all proteins translated from RNA, but will NOT be passed down to next generation)

Processes and molecules that affect the lifespan of mRNA molecules in the cytoplasm can be important regulators of gene expression. An example of this:

example: -mRNAs for casein (a milk protein) can have different lifespans in different cell types. ->In mammary glands of non-lactating female mice, the half-life of casein mRNA is ~1 hour. ->In mammary glands of lactating female mice, the half-life of casein mRNA is ~28.5 hrs.

hat is the name for the enzyme activity that DNA polymerase has when it removes an improperly paired base from the end of the growing strand?

exonuclease activity

During transcription of a given protein-coding gene, both strands are used as template.

false

G protein-coupled receptors are found:

on the cell surface.

What is the dependent variable in the graph?

the concentration of protons outside of the vesicles, as measured by pH

"Turning off" or inactivating the X chromosome in cells of female mammals involves production of noncoding RNA by the Xist gene found in the X chromosome inactivation center (XIC) of the X chromosome. True or False?

true

A daughter strand of DNA produced during chromosome replication can be composed of leading and lagging strands from different replication bubbles.

true

A daughter strand of DNA produced during chromosome replication can be composed of leading and lagging strands from different replication bubbles. T or F?

true

DNA replication

Double-stranded DNA molecule in the parental cell duplicates and gives rise to two double-stranded daughter DNA molecules that are identical to each other, except for rare mutations that may have taken place.

Which of the statements is true about exergonic reactions?

Exergonic reactions are catabolic.

When chlorophyll in solution returns to its ground state via energy release, it is ready to absorb another photon. How is this different in the reaction center chlorophyll in the chloroplast?

In the chloroplast the reaction center chlorophyll must obtain a replacement electron.

Why is no hypothesis stated?

Not all experiments are hypothesis-driven.

When an appropriate signal binds to a G protein-coupled receptor, what is the best description of how the information is passed across the plasma membrane?

Signal binding causes a conformational change in the cytoplasmic portion of receptor protein.

Which of the statements best describes the effect of having the S allele, which is associated with sickle cell anemia?

The effect depends on whether the allele occurs in its homozygous or heterozygous form, and the environment (i.e., whether malaria is present).

what gives cells identities?

type of genes from zygote that are expressed in each one, differential gene expression

which of the following are covalent bonds found in the DNA double helix?

all bonds in DNA double helix are covalent

in eukaryotic cells what types of RNA are transcribed from DNA?

mRNA only

when chemical reactions occur the ______ but the ________

pairing of atoms that share electron pair changes; individual atomic nuclei stay the same

If a mutation occurs such that photosystem I no longer functions as efficiently as it should, which of the answer choices would be most directly affected?

the rate at which NADPH is produced

Identify compound B.

ATP

point mutations

Point mutations are changes in a single nucleotide

Which of the choices could be a proto-oncogene?

all of these choices are correct

Cyclin-CDK Complexes

• Cyclins form a complex with CDKs (cyclin-dependent protein kinases) to form enzymes that regulate process through cell division. • Cyclins are rapidly degraded as the cell cycle progresses • CDK alone are inactive

Example: Mutations (polymorphisms) in hemoglobin genes

• Polymorphism refers to any genetic difference among individuals that is present in multiple individuals in a population • Polymorphisms can be harmful, be beneficial, or have a neutral effect on an individual's phenotype. -HbA= does not have sickle-cell anemia but, they have resistant to malaria -HbS= polymorphism, a DTA mutation; produces hemoglobin & people can have sickle-cell anemia but they have more resistant to malaria -HbC= produces hemoglobin more likely associated with anemia but less likely to be susceptible to malaria

One of your friends is arguing that viruses are alive. What information would you provide to convince him that viruses can't be considered alive?

-Viruses cannot carry out metabolic reactions on their own.

Molecules that can move freely across the membrane can also move across the membrane by going through channels.

False

Identify compound A.

NADPH

Which of the statements is true regarding a basic amino acid?

The positively charged R group of a basic amino acid could bind DNA.

In the example illustrated here, a substance is moved _______ its concentration gradient using the energy of ______________.

against; an electrochemical gradient

The language of DNA is converted to the language of RNA during the process known as:

transcription

Which of the following mutations will stimulate transcription of lacZ and lacY when glucose levels are high and lactose is present?

-A and B -A mutation in CRP gene that produces a CRP protein that binds the CRPcAMP site in the presence and the absence of cAMP -A mutation in lacO prevents the repressor from binding.

chemical reactions

-When chemical reactions occur, bonds between atoms are broken and new bonds are formed. The reversibility of the reaction is indicated by a double arrow -Many chemical reactions in cells are readily reversible.

Under conditions of low iron concentration in the cell, the IRE-BP is ____________ to the transferrin receptor mRNA and the transferrin receptor protein is ______________.

-bound; produced -biological effect= iron is imported into cell

conservative

-replicate DNA molecule and this DNA molecule comes together new one is formed -1st stage= heavy + light

You attach fluorescent dye to nucleotides. Double-stranded DNA molecules with both strands labeled red fluoresce dark red (B), those with one strand labeled red and unlabeled fluoresce light red (C). If both strands are unlabeled the molecule does not fluoresce (A). In a cell grown for many generations in the presence of fluorescent nucleotide, which pattern of fluorescence shown in Figure 2 would you expect to see in a pair of homologous chromosomes?

1

In-frame deletions can also be harmful

1. A small deletion or insertion that is an exact multiple of three nucleotides results in a polypeptide with as many fewer (in the case of a deletion) or more (in the case of an insertion) amino acids as there are codons deleted or inserted. 2. Examples: a.A deletion of three nucleotides eliminates one amino acid. 3. An insertion of six nucleotides adds two amino acids. 4. The mutant CFTR protein is a result of an inframe deletion of three nucleotides that code for PHE at amino acid 508. 5. The resulting protein does not fold properly.

active site of enzyme

1. An enzyme's active site is extremely small compared to the enzyme itself. 2. The active-site amino acids may be spaced far apart in the primary sequence of the enzyme, but when the protein is folded, they come together to form the active site. 3. Enzymes active site is specific for both the substrate and the type of reaction that is catalyzed.

cAMP complex is a positive regulator of the lac operon

1. CRP-cAMP provides another level of control over transcription that is more sensitive to the nutritional needs of the cell than the level of control provided by the presence or absence of lactose. 2. When more than one type of energy source is available in the environment, certain sources are used before others (i.e., glucose > lactose > glycerol).

Checkpoints

1. Cells have many cell-cycle checkpoints, where they can pause the cell cycle if something is not right, before progressing to the next stage. 2 .Three major, well-studied checkpoints include: a. DNA replication checkpoint: checks for the presence of unreplicated DNA at the end of G2 before the cell enters mitosis b. DNA damage checkpoint: checks for damaged DNA before it enters S phase c. Spindle assembly checkpoint: checks for all chromosomes being attached to the spindle before the cell progresses with mitosis

Chromatin can be remodeled by chemical modification of the histones

1. Chemical modification usually occurs on the histone tails that protrude from the histone proteins of the nucleosome. 2. Individual amino acids in the tails can be modified by the addition (or removal) of different chemical groups, including methyl and acetyl. 3. The pattern of modifications of the histone tails is thought to constitute a histone code that affects chromatin structure and gene transcription.

A new nucleotide can only be added to the _____ end of a growing DNA strand. DNA therefore always grows in the _____ direction.

3'; 5' to 3'

Which of the statements is true of allosteric inhibitors of an enzyme?

Allosteric inhibitors decrease enzyme activity.

what is most common mechanism of translational regulation that affects the initiation process.

Base sequence recognized by binding protein can block ribosome.

Where does the Calvin cycle take place?

C

If oxygen is unavailable, predict what will happen to the citric acid cycle.

It will stop because the supplies of NAD+ and FAD will become depleted.

coupled reactions

Non-spontaneous reactions are often coupled to spontaneous reactions: Coupled Reactions

A mutation leads to a change in amino acid from serine, an amino acid with a polar side chain, to alanine, an amino acid with a non-polar side chain Do you think that the following levels of protein structure change? If so how and why? If not, why not.

Primary Structure: no change in this structure with this specific type of mutation. Secondary Structure: the this structure also won't change beta sheets and alpha helices are formed with main chain hydrogen bond interactions, not the side-chain interactions. Tertiary Structure: will change because of the polar side chain is mutated to non-polar side chain amino acid which deletes the previous side-chain interactions of serine. Quaternary Structure: this structure will also change because the tertiary structure is changing.

A protein you work on has a very important glutamic acid (glutamate) residue in the site where it binds to its substrate. This helps it to bind the substrate and catalyze a chemical reaction. Which of the following amino-acid substitutions would likely have the least impact on the function of this protein?

Replacing that glutamate with an aspartate

Termination of signals and signaling pathways is critical to proper cell function. Ras is a GTPase, meaning that it can turn itself off by hydrolyzing its bound GTP to form GDP. When Ras is bound to GDP, it is inactive. What would be the result if Ras lost this GTPase activity due to a mutation in the ras gene?

The "go" signal for cell division would be always on.

Kangaroo rats live in the deserts of the southwestern United States. Kangaroo rats have many adaptations to minimize water loss. They obtain a small amount of water from seeds that they eat. However, the rest of the water they obtain is from cellular respiration.

This could be true, as water is produced in cellular respiration.

the antibotic rifamycin inhibits prokaryotic RNA polymerase. what is the biological effect of rifamycin?

Translation is blocked in prokaryotic cells

The image illustrates our understanding of how typical cell membranes are structured. Which line is pointing at a protein? Which arrow is pointing at a cholesterol? Which arrow is pointing at the hydrophilic head group of a phospholipid? Which of the types of molecules depicted in the figure is amphipathic?

Which line is pointing at a protein? LINE A Which arrow is pointing at a cholesterol? LINE D Which arrow is pointing at the hydrophilic head group of a phospholipid? LINE B Which of the types of molecules depicted in the figure is amphipathic? integral membrane proteins, cholesterol, and phospholipids

The inversion of a promoter sequence will:

block transcripition

The nonmutant allele of the BRCA1 gene helps to suppress tumor formation in women who are heterozygous for the mutation. Women heterozygous for BRCA1 nevertheless have a 50% to 70% chance of developing breast cancer before age 70, and the usual reason is that the nonmutant allele is lost or inactivated in a lineage of cells. One possible mechanism for such "loss of heterozygosity" is:

a somatic mutation in a breast cell inactivates the nonmutant BRCA1 allele.

Which of the steps does not result in an amplification of the signal information?

activation of adenylyl cyclase by active G protein

active telomerase versus telomerase unactivated

active telomerase: -shortening & continue dividing can go into crisis (then stop dividing) -reactivated continue dividing telomerase not activated: - losing end of chromosome until reach short telomerase - HTERT cell goes into sequence and occurs with aging -tHERT immobilization (cancer)

although they share, different cell types look & function differently from one another why?

because each type of cell expresses different sets of genes. regulation of gene expression assures that the right genes are expressed at the right time

In response to seasonal changes in temperature, many organisms must alter the composition of their plasma membranes to maintain the proper degree of fluidity. Which change in the fatty acids of phospholipids would be most effective in maintaining membrane fluidity in a colder environment?

a decrease in phospholipid fatty acid side chain length and a decrease in side chain saturation

Genetically engineered organisms are known as transgenic organisms or genetically modified organisms (examples)

a. Sheep that produce a human protein in their milk to treat emphysema b. Chickens that produce eggs containing human antibodies to help fight bacteria c. Salmon with increased growth hormone for rapid growth d. Crops like corn, canola, and cotton that have been engineered to resist insect pests

peptide bonds formation

a. The carboxyl group of one amino acid reacts with the amino group of another amino acid. b. A molecule of water is released via a dehydration (condensation) synthesis reaction. 2. The free amino group is at the amino end of the peptide, and the carboxyl group is at the carboxyl end.

In the example of adrenaline signaling, which steps represent an amplification of the signal?

activated receptor activates G proteins, activated adenylyl cyclase produces cAMP, active protein kinase A phosphorylates target proteins

a cell in prophase I of meiosis has _______ as much DNA as each of the daughter cells following cytokinesis of meiosis II

four times

At the end of the experiment, the amount of 16O2 was

greater in the test tube supplied with C18O2

At the end of the experiment, the amount of 16O2 was what?

greater in the test tube supplied with C18O2.

At the end of the experiment, the amount of 18O2 was

greater in the test tube supplied with H218O.

At the end of the experiment, the amount of O2 in the test tubes was

greater than at the beginning of the experiment.

When lactose is removed from the growth medium, the cells continued to divide by using other nutrients that are present. The amount of b-galactosidase in the culture remains constant for 30 minutes or more. What happens to the amount of b-galactosidase per cell?

it decrease by half with each cell division

Which of the statements about the lactose operon is incorrect?

lacO is a gene sequence coding for the operator.

In the graph, what does the y-axis plot?

level of fluorescence in the bleached area of the cell

The beaker in the illustration contains two solutions of salt with different concentrations (measured by molarity, M). The two solutions are separated by a membrane that is permeable to both salt and water. What will occur in this container?

net diffusion of water from A to B and of salt from B to A

The photosynthetic reaction center becomes ________ when it passes its __________ to the ______________, which is thus ______

oxidized; excited electron; electron acceptor; reduced

Which molecule is the final electron acceptor for the mitochondrial electron transport chain?

oxygen -> O2

women with mutations in BRCA1 gene have 50% lifetime risk of ovarian cancer, the increased risk of ovarian cancer is an example of:

phenotype

Signal molecules that are _______ usually have their corresponding receptor ______________ of the cell.

polar; on the surface

A virus achieves host specificity through _____ on the surface of the capsid or envelope, which bind to the host cell.

proteins

After application of the laser, the bleached spot slowly regains fluorescence over time, so the researchers were able to conclude that:

proteins move in the plane of the membrane.

When light is absorbed by chlorophyll that has been extracted into a solvent solution, it _________ releases the energy in the form of ____________.

rapidly; heat and light

Translational Regulation: Regions on the mRNA have specific functions

refer to diagram

Refer to the drawing of mRNA shown. Choose the letter that best fits the description. The 3' UTR corresponds to:

region D

RNA processing in eukaryotes includes

removal of nueclootide cap to the 5' end and a poly (A) tail to the 3' end of newly transcribed RNA

What is the process of "proofreading" by DNA polymerase?

removing an improperly paired base and replacing it with the proper one

In replica plating, the geometrical arrangement of bacterial colonies on the agar surface of an agar plate 1 is:

reproduced exactly on agar plate 2

To move a specific molecule across a membrane, carrier proteins:

require that the molecule specific to the carrier bind and cause a change in conformation.

In double-stranded DNA, the amount of A equals that of T and the amount of C equals that of G because:

the strands have complementary sequences of bases.

How is DNA replication during PCR similar to DNA replication in cells?

-As you know, cells replicate their DNA before they divide, and in doing so, double the amount of the cell's DNA. PCR essentially mimics cellular DNA replication in the test tube, repeatedly copying the target DNA over and over, to produce large quantities of the desired DNA -PCR requires a DNA polymerase enzyme that makes new strands of DNA, using existing strands as templates

-The sequence of amino acids dictates how proteins fold in three dimensions

-Based on sequence of amino acids and the order of the R groups, the proteins will fold in a particular way. another.

Epigenome

-DNA & histones covered with chemical tags -these tags react to signals from outside world (diet/stress) -it adjusts specific genes in our genomic landscape in response to changing environment

What influences proteins' final folding?

-Most protein folding is driven primarily by hydrophobic interactions: hydrophobic side chains cluster together in the center of the protein, avoiding the surrounding water. Backbone and side chain interactions help to maintain the basic structure. -Most proteins can fold into their proper shapes spontaneously in water at pH 7, although in cells, there are often proteins (chaperones) that help the process along

facilitated diffusion

-The solute movement occurs from higher concentration of solute compartment to the lower concentration of solute compartment across semipermeable membrane. -The facilitated transport doesn't require energy. It transports the molecules which is water soluble such as monosaccharides, lipid, gonadal hormones, gases and water. -The facilitated transport is mediated via the channel or carrier proteins.

active transport

-The solute movement occurs from lower concentration of solute compartment to the higher concentration of solute compartment across semipermeable membrane. -The active transport requires the chemical energy. It transports the large protein molecules, ions, complex sugars and the cell. -The active transport is carrier mediated and pump mediated.

How is DNA replication during PCR different to DNA replication in cells?

-contrast to cellular DNA replication, which amplifies all of a cell's DNA during a replication cycle, PCR does targeted amplification to replicate only a segment of DNA bounded by the two primers that determine where DNA polymerase begins replication. -Machinery involved : DNA replication is carried out at body temperature (37C in humans) with the help of a complex machinery. for example, helicase unwinds dsDNA, single-strand-binding-proteins stabilize these unwound strands, etc. The PCR reaction utilizes temperature cycles (with extremes of 70-90C) to cause denaturation and annealing of DNA strands. -Type of polymerase : There are many DNA polymerases in eukaryotes. In PCR, thermostable DNA polymerases derived from bacteria or archaea are used (eg. Taq polymerase) -Length of DNA : Whole genomic DNA is routinely replicated in the body. in the PCR reaction, the polymerase used has a much shorter half-life, and is only efficient for much smaller fragments of DNA

biotechnology can:

-determine genetic risk factors (genetic testing) -identify DNA at crime scene investigations (forensic- DNA profiling) - Express genes from one organism in another (recombinant DNA, gene therapy, genetic engineering)

nucleotide excision repair part 2

-recognizing a regions wheres theres damaged bases: if they're covalently attached to one another or something strange happening its easy to recognize which one has correct and which doesn't have damage -other strand chemical modifications or covalent bonds where don't belong to recognize damage -enzymes come in & catalyze cleavage of phosphodiester backbone and removal of that region then damage is repaired

Epigenome details:

-shapes physical structure of genome -tightly wraps inactive genes, making them unreadable -relaxes active genes, making them easily accessible -flexible

Place each of the following events into the correct stage of cell signaling.

1) Adrenaline binds the extracellular domain of a G protein-coupled receptor. 2) A G protein catalyzes the hydrolysis of GTP to GDP and Pi. 3) Activation of protein kinase A (PKA) 4) Changes in gene expression 5) Receptor kinase dimerizes after binding insulin 6) Inactivation of a receptor kinase by protein phosphates.

nonsense mutations:

1. A point mutation called a nonsense mutation can change an amino acid to a stop codon that terminates translation. 2. When the stop codon is encountered, translation stops, resulting in a truncated polypeptide. 3. Nearly all truncated proteins are nonfunctional and unstable **end result: protein length would be shorter since a stop codon is coded further ahead**

PRC cycle step 3

1. After sufficient time to allow new DNA synthesis, the solution is heated again and again and the cycle is repeated over and over, usually for 25−35 cycles. 2. The first round amplifies the target DNA into two copies, followed by 4, 8, 16, 64, 128, 256, 512, and 1024.

Epigenetic- over and above inheritance

1. Epigenetic effects are due changes that do not change the DNA sequence but do affect gene expression 2. These changes sometimes cause changes in gene expression. 3. They can be inherited, but are often reversible and responsive to changes in the environment. 4. Epigenetic changes include chromatin remodeling, histone modifications, and DNA methylation

DNA Damage Checkpoint (G1/S)

1. When DNA is damaged by radiation, a specific protein kinase is activated that phosphorylates the p53 protein. a. Under normal conditions, p53 is exported from the nucleus at very low levels. b. When phosphorylated, p53 is prevented from being exported and its levels in the nucleus rise. 2. As p53 levels rise, p53 activates the transcription of a gene that expresses a CDK inhibitor protein. 3. This inhibitor binds to and blocks the activity of the G1/S cyclin-CDK complex. 4. This arrests the cell at the G1/S transition, giving the cell time to repair the DNA damage.

eukaryotic gene regulation can take place:

1. through chemical modification of chromatin or histones 2. during transcription 3. during RNA processing 4. during translation

process of mutation

1."Heritable" means that the mutation is stable and, therefore, is passed on through cell division. 2.Spontaneous and random mutations occur all the time during DNA replication and environmental influences can cause mutations by damaging DNA 3.Mistakes/mutations in replication lead to alterations in the nucleotide sequence in the DNA, and these alterations are passed on to daughter cells when the cell divides.

Adenosine Triphosphate (ATP)

1.ATP stores energy in a form that all cells can readily use to perform the work of the cell. 2.Hydrolysis of ATP drives many reactions in cells.

For a gene to be transcribed, the DNA must be accessible:

1.Eukaryotic DNA is packaged as chromatin, a complex of DNA, RNA, and proteins that gives chromosomes their structure. 2.When the chromatin is coiled, the proteins that carry out transcription cannot access the DNA. 3.The chromatin must unravel to allow space for transcriptional enzymes and proteins to work. 4.This is accomplished by chromatin remodeling. 5.During chromosome remodeling, the nucleosomes are repositioned to expose different stretches of DNA.

In which order does one molecule of glucose undergoing cellular respiration go through processes 1-4? 1. glycolysis 2. oxidative phosphorylation 3. pyruvate oxidation 4. citric acid cycle

1>3>4>2 -glycolysis -pyruvate oxidation -citric acid cycle -oxidative phosphorylation

A loss-of-function mutation is one in which the function of a gene is completely knocked out or obliterated. Frameshift mutations never result in the loss-of-function of a gene. T or F?

A loss-of-function mutation is one in which the function of a gene is completely knocked out or obliterated. Frameshift mutations never result in the loss-of-function of a gene.

Amino acid substitution

A mutation that results in replacement of the correct amino acid with an incorrect amino acid

What features of DNA make it possible to make recombinant DNA in the lab?

A. Two double helices from different sources can be ligated together. B. Restriction enzymes cut DNA from all species. C. The genetic code is the same for all organisms. D. All of these choices are correct.

Which two molecules are produced by the photosynthetic electron transport chain and used in the Calvin cycle?

ATP, NADPH

In Experiment 1, why is the percentage of 18O in CO2 equal to 0.2% at the start of the experiment?

About 0.2% of the oxygen atoms in the atmosphere, including those in CO2, are naturally 18O.

You find a way to attach either a red or green fluorescent dye to nucleotides. Double-stranded DNA molecules with both strands labeled red fluoresce red, those with both strands labeled green fluoresce green, and those with one strand labeled red and the other green fluoresce yellow. You grow human cells in the presence of "red" nucleotides until both DNA strands of all chromosomes fluoresce red. You then allow one round of DNA replication in the presence of "green" nucleotides.What pattern of fluorescence do you expect to see in the sister chromatids of each chromosome?

Both chromatids will be yellow.

Biotechnology= DNA manipulation

By exploiting the structure and physical properties of DNA or principles of DNA replication, scientists are able to isolate, identify, and sequence DNA fragments

Carriers can move certain molecules across a membrane. Which of the answer choices is not a property of carriers?

Carriers can transfer any molecule as long as it is not larger than the diameter of the carrier.

Shown here is a representation of a centrifuge tube that is similar to that used in the Meselson-Stahl experiment to determine the type of DNA replication that occurs in bacteria. The positions where DNA of various types migrate are shown as horizontal lines. Heavy is double-stranded DNA in which both strands carry the heavy isotope of nitrogen (15N). Light is double-stranded DNA in which both strands carry the light isotope of nitrogen (14N). Half-heavy is double-stranded DNA in which one strand carries 14N and the other carries 15N. Suppose that, as in the Meselson-Stahl experiment, E. coli is grown for many generations in heavy nitrogen (15N). Which test tube best represents the position(s) that this DNA would be expected to migrate to?

E (heavy)

What effect does each successive mutation have on the colon cells in the example?

It causes them to divide more rapidly than normal cells.

If the researchers added a transmembrane protein channel that allows protons to freely pass through it, what result would you predict?

Less ATP would be produced when the light is on because protons would bypass the ATP synthase.

The small red dots in the simulation could represent which of the answer choices?

O2

As described in the text, radiation and chemicals in the environment can induce mutations in cells. Why do the random mutations induced by the environment NOT violate or negate the results of the Lederberg's experiments?

Radiation or chemical mutations are extremely unlikely to induce a mutation that protects an organism from that radiation or chemical.

Another experiment that asks the same question - "Do proteins move in the plane of the membrane?" - relies on a technique called FLIP, or Fluorescence Loss in Photobleaching. This technique is similar to FRAP, but a laser acts continuously over a long period of time. Based on the conclusion of the FRAP experiment, what results would you expect to see in a FLIP experiment?

The entire cell will become bleached over time.

In 1937, two German biochemists published a paper proposing these reactions as part of glucose oxidation: citrate →isocitrate →α-ketoglutarate →succinate →fumarate →malate →oxaloacetate. Adding succinate, fumarate, or malate to thin slices of tissue increased oxygen consumption, supporting the hypothesis that these molecules are intermediates in the process. However, they were puzzled by the observation that these intermediates were still present in the reaction mixture at the end of the experiment. They had thought that intermediates would be consumed as they were converted to the next molecule in the pathway. What explains the observation that these intermediates were still present?

The pathway is a cycle, constantly regenerating intermediates as glucose is broken down.

Synonymous mutation:

The protein would not change since it would have the same amino acids.

Which of the answer choices could result if a plant cell is exposed to a toxin that causes the outer chloroplast membrane to be less permeable to H2O?

There would be a decrease in the amount of O2 produced

Which statement about DNA replication is true?

When DNA polymerase reaches a primer from prior DNA synthesis, the primer is removed and replaced with DNA.

Very low concentrations of detergent make membranes leaky to small molecules and ions without damaging proteins. In isolated mitochondria exposed to detergent, the molecules of the electron transport chain and of ATP synthase remain intact. Do you expect the citric acid cycle to continue in the presence of low concentrations of detergent?

Yes, because all enzymes and electron carriers remain intact and NADH and FADH2 continue to be oxidized so the citric acid cycle can continue

Which of the answer choices would be the best analogy for an electrochemical gradient across a cellular membrane?

a battery

In the image, an active transport proton pump drives protons out of the cell using energy from ATP. Under some circumstances pumps like this can be run in reverse. If this pump could be reversed, what would be the result in the cytoplasm?

a decrease in pH and an increase in ATP

Select the correct label for compound A.

acetyl-CoA

The defining characteristics of active transport are that this category of transport moves substances _________ their concentration gradient and requires ___________.

against; energy

Which force can contribute to a protein's tertiary structure?

all of these answers are correct

The transformation step in creating bacteria genetically engineered to produce human proteins involves:

bacteria taking up the recombinant DNA in the form of the vectors.

In the replica plating experiments, bacterial colonies from a master plate were reproduced using a disk of sterilized velvet, a silken fabric with a dense pile consisting of upright loops of yarn. Why is velvet a better choice for replica plating than plain cloth fabric?

bacterial cells stick to its pile

Another experiment that asks the same question - "Do proteins move in the plane of the membrane?" - relies on a technique called FLIP, or Fluorescence Loss in Photobleaching. This technique is similar to FRAP, but a laser acts continuously over a long period of time. In a FLIP experiment and a FRAP experiment, the role of the laser is to:

bleach an area of the membrane

You find a way to attach either a red or green fluorescent dye to nucleotides. Double-stranded DNA molecules with both strands labeled red fluoresce red, those with both strands labeled green fluoresce green, and those with one strand labeled red and the other green fluoresce yellow. You grow human cells in the presence of "red" nucleotides until both DNA strands of all chromosomes fluoresce red. You then allow one round of DNA replication in the presence of "green" nucleotides. What pattern of fluorescence do you expect to see in the sister chromatids of each chromosome?

both chromatids yellow

The transition state is that portion of the progress of a chemical reaction with a large amount of energy found in _______ reactions.

both endergonic and exergonic

how do enzymes accelerate chemical reactions?

by reducing activation energy of reaction

Epigenetic mechanisms of gene regulation _____ inherited by daughter cells and are _____.

can be; often reversible and responsive to environmental change

Histone modification:

can change over time in response to environmental cues, allowing genes to be turned on or off as needed.

Identify compound C.

carbohydrates

During ______, large molecules are broken down and energy is released.

catabolism

Enzymes in your gastrointestinal tract digest your lunch. These chemical reactions are categorized as:

catabolism

example of potential energy

cell membrane can block movement of ions from 1 side to other, storing potential energy that is released if transmembrane chanel is opened

X inactivation: chromosome level gene regulation

cells with inactivated x chromosome are only expressing genes from ONE parent

In the Meselson-Stahl experiment, was the DNA circular or linear?

circular

A research group has discovered an organism with cells that contain a previously undescribed organelle. Researchers perform some tests on the isolated organelle to see if it is involved in any major metabolic reactions. To do this, they incubate these organelles for a period of time and determine changes in the amount of various substances in the suspending solution. The results follow. Based on this analysis, which metabolic process would you conclude could be taking place in this organelle?

citric acid cycle

Which process is correctly paired with the cellular location in which it takes place?

citric acid cycle: mitochondrial matrix

If researchers want to investigate whether phospholipids move in the plane of membrane they could:

conduct the same experiment but attach a fluorescent dye to the phospholipids instead of proteins

If the researchers want to investigate whether phospholipids move in the plane of the membrane, they could:

conduct the same experiment but attach a fluorescent dye to the phospholipids instead of the proteins.

one cell mutation

continue to divide have mutation in tumor suppressor, while having second mutation requires oncogene cells grow -> can end up with benign -> 2nd tumor suppressor gene now cells grow malignant cells -> ends up with cancer

Which of the following reactions would you predict could be coupled to ATP synthesis from ADP + Pi (ADP + Pi → ATP + H2O, ΔG + 7.3 kcal/mol)?

creatine phosphate + H2O → creatine + Pi , ΔG - 10.3 kcal/mol

CDKs active=

cyclin present, then cell progresses through cell cycle the cyclin that is specific to different cell cycle phases are degraded in the cell

Ferritin is the cytoplasmic iron storage protein that sequesters excess iron when cellular iron levels are too high. The transferrin receptor is a protein that transports iron from the bloodstream into the cell when iron levels are too low. Based on this information, a decrease in a cell's iron levels should _____ ferritin levels and ____ transferrin receptor levels in the cell.

decrease; increase

Positive regulation- "turning genes on"

diagram

What combination of reactions is an example of energetic coupling in a cell? Equation 1: ATP + H2O → ADP + Pi ΔG1 = -7 kcal/mol Equation 2: phosphoenolpyruvate + H2O → pyruvate + Pi ΔG2 = -14.8 Kcal/mol Equation 3: glucose + Pi → glucose-6-phosphate + H2OΔG3 = +3.3 kcal/mol Equation 4: ADP + Pi → ATP + H2OΔG3 = +7 kcal/mol

equations 1 and 3

Which of these equations is/are endergonic? Equation 1: ATP + H2O → ADP + Pi ΔG1 = -7 kcal/mol Equation 2: phosphoenolpyruvate + H2O → pyruvate + Pi ΔG2 = -14.8 Kcal/mol Equation 3: glucose +Pi → glucose-6-phosphate + H2O ΔG3 = +3.3 kcal/mol Equation 4: ADP + Pi → ATP + H2O ΔG3 = +7 kcal/mol

equations 3 and 4

All cancers are caused by viruses.

false

Gene regulation can occur only during transcription and translation.

false

annealing step

going to require primers and going to require nucleotides to fill in and DNA polymerase (extension)

Based on what you know of ATP's chemistry, which of the substances is most likely to have similar functions in energy-management processes?

guanosine nucleotide triphosphate

A human cell with a total of 23 chromosomes is:

haploid

bacterial protein (shown as a spacefilling model)

has a cavity that can bind with a small molecule (shown as a balland-stick model in the center).

In chemical reactions, most of the entropy increase occurs as:

heat

If you could attach fluorescent marker tags to the enzyme that transfers the acetyl group from acetyl CoA to oxaloacetate, and then detect that fluorescence with a powerful microscope, in which part of a cell would you predict to observe the fluorescence?

in the mitochondrial matrix

Humans with hypohidrotic ectodermal dysplasia have defects in the formation and function of their sweat glands. Males with the condition have reduced ability to sweat over their entire body. Females with the condition lose the ability to sweat only in patches of skin. Where must the gene that encodes this trait be located?

in the x chromosome

When Ruben and his colleagues designed this experiment, they were aware of earlier studies demonstrating that oxygen atoms can be exchanged between water and dissolved carbon dioxide. For this reason, at the end of the experiment, they measured not only the percentage of 18O in O2, but also the percentage of 18O in H2O and CO2. The table below gives their results. If Experiment 2 were allowed to run for a longer amount of time, the %18O2 would be expected to:

increase.

Due to the pumping action of the electron transport chain, protons have a high concentration in the _____ and a low concentration in the _____.

intermembrane space; mitochondrial matrix

lips and water do not mix because the lipids are _______ and water is ______.

lips and water do not mix because the lipids are nonpolar and water is polar.

frameshift mutations

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

In the Background section, it is noted that inhibition of protein synthesis blocks cell division in sea urchins. This observation implies that:

new proteins must be made for cell division to occur.

A single gene on the X chromosome in cats has two alleles. One produces orange fur and the other produces black fur. In a cross between an orange female and a black male cat, which types of offspring are possible?

orange male and calico female

At some point in their life cycle, all cells have a _____, whereas not all cells have a(n) _____.

plasma membrane; nuclear membrane

The researchers noticed that when the light is turned on, the amount of ATP is higher than when the light is turned off. This relationship between the presence of light and the synthesis of ATP could be described as a

positive correlation

denaturation step

requires heat to disrupt the hydrogen bonds between the two DNA strands

cyclin first observed in sea urchin embryos

single cell -> 2 cells -> 4 cells * refer to graph * cyclin protein are seen

Based on the results presented in the graph and table, the researchers

supported their initial hypothesis.

Diffusion is best described as the random movement of molecules influenced by:

the thermal energy of the environment and energy transferred from molecular collisions in the cell.

At equilibrium, there will be no net movement of molecules across the cell membrane.

true

Different organisms have different rates of mutations

viruses have high rate of mutation (bd they do not have proofreading mechanisms)

Many antibiotics, such as tetracycline, act on ribosomes and block translation in bacteria, but not eukaryotes. If the researchers added tetracycline to the sea urchins embryos, the researchers:

would have seen the same results.

Enzymes increase reaction rates of the reactions they catalyze in two primary ways:

-Enzymes physically align reactants in the orientations needed for reactions to proceed. -Enzymes stabilize the transition states of reactants through temporary chemical interactions.

Which of the following statements about the citric acid cycle in the context of cellular respiration is true?

The citric acid cycle produces electron donors NADH and FADH2 which serve as an electron source for the electron transport chain.

Proteins Involved in Replication

- DNA polymerase - RNA primase - DNA ligase • Helicase: catalyzes the unwinding the parental double helix at the replication fork • Single-stranded binding proteins: bind to the single-stranded regions of the parental strands and prevent them from coming back together • Topoisomerases: catalyzes the unwinding the double helix at the replication fork

during replication if added to sequence from insertion (frameshift mutation) will change very codon in mRNA and every amino acid after that will be different

**same thing happens in deletion**

Observation leading to the discovery of the lac operon

- Bacteria E.coli only produces the enzyme B-galactosidase when lactose is in the media - Jacob and Monod measured Bgalactosidase activity when lactose is added and then removed. Hypotheses: - Enzyme is always produced but breaks down in absence of lactose - Enzyme is only produced in the presence of lactose

Free-Energy Change & Activation Energy

-Even exergonic reactions don't always proceed very quickly on their own because they have to get over an energy barrier in order to proceed. -This is because in order to get from reactants to products, the reacting atoms have to go through a transition state that actually has higher free energy than the reactants. This is called the activation energy.

example of coupled reactions: Digestion of Sucrose

-Hydrolysis of the glycosidic bond releases two monosaccharides: glucose and fructose -The total overall reaction is EXERGONIC -Outside living organisms, sucrose breakdown occurs VERY SLOWLY

example of gene regulation (iron metabloism)

-Iron is essential: humans use ~20 mg/day to make new red blood cells. -Too much free iron is toxic. -Cells can safely store iron by binding it to a protein called ferritin. -Iron can be safely transported to cells in the bloodstream when bound to a protein called transferrin. -Transferrin-bound iron is taken into the cells by binding to a cell surface protein called the transferrin receptor.

Nucleotide excision repair

-Nucleotide excision repair recognizes multiple mismatched bases in a region of the DNA. -Can remove bulky lesions caused by UV light or other mutatgens

missense mutation

-One amino acid will change. This could have beneficial, harmful, or neutral effects on the protein. -substituting one amino acid for another (changing protein sequence)

Regulating enzymes: Covalent modification

-Reversible example: phosphorylation (adding a phosphate to a particular amino acid in an enzyme) -Irreversible example: cleaving peptide bonds in the enzyme

You are interested in studying human ß-globin and decide to produce the protein in bacterial cells. The ß-globin gene is a relatively simple gene with a single intron. You insert the entire gene, including the gene's promoter, in a plasmid and transform the recombinant plasmid into E. coli. You are disappointed to discover that your bacterial culture does not produce the correct protein.What are some possible explanations? Select all that apply.

-The bacterial cell produces the protein, but the protein is rapidly degraded. -The bacterial cell does not recognize the eukaryote promoter. -The bacterial cell cannot splice introns.

example of alternative splicing

-The insulin receptor produced in skeletal muscle is 12 amino acids shorter than the one in the liver, and has a high affinity for insulin. -This difference allows muscle cells to absorb enough glucose to fulfill energy needs.

What would the expected effect be on a PCR reaction if the primers used were slightly shorter and more variable than the intended oligonucleotide sequences?

-The reaction would yield a mixture of nonspecific products -primers annealing all along DNA= less specific sequences

enzyme activity is regulated. BUT, Enzymes in cells are not always active.

-When the products of a type of enzyme's reaction build up or are not needed in the cell, those enzymes are "turned off" by inhibitors. -When their products are needed and their reactants are present, those enzymes are "turned on" by activators. -Cells use several different strategies to accomplish enzyme regulation. -Enzyme inhibitors are used clinically to treat many disorders

In Monod's experiment, the b-galactosidase enzyme appeared almost immediately when lactose was added to a growing culture. Which explanation is consistent with this finding?

-all above are correct

Under conditions of low iron concentration in the cell, the IRE-BP is ____________ to the ferritin mRNA and the ferritin protein is ______________.

-bound; not produced -biological effect= iron is available to the cell

lose or gain 3 nucleotides in a row these small deletions or insertions then will not shift frame but will cause single amino acid go be added in case of insertion of deletion

-example: cystitis fibrosis -3= missing entire amino acid -transcription= missing entire codon -proteins unstable no longer can go in membrane results in cystitis fibrosis phenotype (missing protein)

Which type of repair is a backup for the DNA polymerase proofreading function?

-mismatch repair -the mutLS system

experimental evidence (semi-conservative)

-nitrogen radioactive label= 1 more neutron than normal nitrogen (DNA will be heavier) -heavy-to-light ratio can be distinguished in centrifuge -light DNA= does not have radioactive nitrogen -take out replicate 1 cycle= DNA heavy+light nitrogen band -2nd round= 1/2 molecules light & 1/2 mixed (semi-conservative)

how does food contain energy?

-organic molecules (carbohydrates, fats, proteins) contains chemical energy (form of potential energy) -carbon-carbon bonds & carbon-hydrogen bonds -these covalent bonds weak which require a lot of energy to stay intact, so organic molecules store large amount potential energy due to their chemical structure

You are comparing the structure of a channel protein that transports polar molecules across the plasma membrane to an enzyme that is in the cytoplasm. What type of amino acid side chains (i.e., polar or nonpolar) do you expect to be in the following positions:

-outside of the channel, interacting with the hydrophobic region of the lipid bilayer:Amino acids side chain are hydrophobic ( non polar ) -the outside of the cytoplasmic enzyme:Amino acids side chain are hydrophilic ( polar ) -the center of the channel where solutes pass:Amino acids side chain are polar due to the interaction of water -the center of the cytoplasmic enzyme: Amino acids side chain are non polar

Role of Tumor Suppressors: Example p53

-p53 is a tumor-suppressor protein. -DNA damage causes p53 phosphorylation and prevents its degradation. -Accumulation of p53 in the nucleus produces cell cycle inhibitors.

Exact mechanism of DNA replication depends upon the genome structure

-prokaryotes: DNA replicated in circular chromosomes only need 1 origin of replication; the replication forks will go in both directions until circular chromosomes are replicated -no end and eventually replicate the entire molecules

tertiary structure

-results from interactions between side groups (R) -3D shape of polypeptide, usually made of several secondary structure elements. -The tertiary structure is determined by the spatial distribution of the hydrophilic and hydrophobic R groups along the molecule as well as by the chemical bonds and interactions that form between the R groups.

Sickle-cell anemia is due to a single amino-acid replacement

-single glutamate to be replaced by a valine in one of the polypeptides that makes up the hemoglobin protein. Half of the hemoglobin molecules in his body have this substitution. -valine sits where gluatmate acid should be and makes hemoglobin molceules stick together forming long fiber disort shape of red blood cells

Proteins function:

-structure (keratin, collagen, elastin) -catalyse (enzymes) -carries & transport (membrane channels) -receptors & binding (defense) -contraction (actin & myosin) -signaling (hormones) -storage (bean seed proteins) -immune response (immunoglobulin/antibodies)

quaterny structure

-structure results from interactions of polypeptide subunits

Which of the reactions is most likely to be exergonic?

-the digestion of protein from food into amino acids -larger complex molecule -> smaller molecules

Under conditions of high iron concentration in the cell, the IRE-BP is ____________ to the transferrin receptor mRNA and the transferrin receptor protein is ______________.

-unbound; not produced -biological effect= iron is NOT imported in the cell

Under conditions of high iron concentration in the cell, the IRE-BP is ____________ to the ferritin mRNA and the ferritin protein is ______________.

-unbound; produced -biological effect= iron sequestered in ferritin

A beaker is divided by a membrane that is permeable to water and glucose, but not to sucrose. Equal volumes of solutions are added to side A and B with the initial concentrations as shown below. Initially, the liquid levels on both sides are the same.After the system described above reaches equilibrium, what will be the concentration of glucose on side B?

0.75 M

Select the arrow(s) that represent the direction(s) in which: 1. protons are pumped when coupled to electron transfer 2. protons flow through ATP synthase to power ATP synthesis

1 - A; 2 - B

Cyclins are synthesized and degraded at specific points in the cell cycle

1. Cyclins were discovered in sea urchin embryos 2. Scientists added radioactive methionine (an amino acid) to eggs, which became incorporated into any newly synthesized proteins. 3. The eggs were then fertilized and allowed to develop. 4. Samples of the rapidly dividing embryos were taken every 10 minutes and run on a gel to visualize the levels of different proteins. 5. Although most protein bands became darker as cell division proceeded, the level of one protein band oscillated, increasing in intensity and then decreasing with each cell cycle, as shown in the graph.

Eukaryotic Genome Organization

1. DNA in the nucleus of eukaryotes is packaged differently from that of bacteria. 2. Eukaryotic genomes are spread across several chromosomes. 3. Eukaryotic chromosomes are linear. Each one must be replicated. 4. The ends of chromosomes are capped by repetitive DNA sequences called telomeres. -chromosomes linear -structure of chromosome: ends have repeated sequences (telomeres) -caps are repetitive non-coding DNA sequences means they are NOT coding proteins or functional RNAs and there to help replication at end of chromosome

enzymes bind substrates at the active site

1. Enzymes have a 3D structure that brings together particular amino acids to form the active site. 2. The enzyme active site binds the substrate and converts it to the product. 3. The interactions between the substrate and the active site are weak noncovalent interactions or transient covalent bonds that stabilize the transition state and decrease the activation energy required for the reaction

Cell Cycle

1. G1 phase: The first "gap" phase, where the size and protein content of the cell increases in preparation for the S phase. During this phase, many regulatory proteins are made and activated. 2. S phase: The "synthesis" phase, where the entire DNA content in the nucleus of the cell is replicated. 3. G2 phase: The second "gap phase," where the cell prepares for mitosis and cytokinesis. 4. G0 phase: Distinguished from the G1 phase because there is no active preparation taking place for cell division. This phase is present in cell types that do not actively divide.

Hypertonic versus Hypotonic

1. If a red blood cell is placed in a hypertonic solution (one with a higher solute concentration than that inside the cell), water will leave the cell by osmosis and the cell will shrink. 2. If a red blood cell is placed in a hypotonic solution (one with a lower solute concentration than that inside the cell), water will move into the cell by osmosis and the cell will burst. 3. Cells solve the problem of water movement by using active transport to keep the intracellular fluid isotonic (at the same solute concentration as exists outside the cell). A solution with the same concentration as the solute concentration as the cell is referred to as isotonic.

Proofreading assures the fidelity of DNA replication

1. If improper hydrogen bonds form, DNA polymerase can correct errors because it detects the mispairing. 2. If an error is detected, DNA polymerase activates a cleavage function and catalyzes the removal the incorrect nucleotide and addition of the correct one in its place.

continued experiment 1

1. In a second experiment, radioactively labeled β-thiogalactoside is added to compartment 1 and enzyme is added to compartment 2. 2. Over time, the level of radioactivity is greater in compartment 2 than in compartment 1. 3. These results can be explained if the substrate diffuses from compartment 1 to compartment 2, forms a complex with the enzyme, and is not released. 4. In other words, the β-thiogalactoside and the enzyme form a complex.

Passing mutations onto the next generation

1. In single-celled organisms, mutations are 2. In multicellular organisms, somatic mutations are passed only to the daughter cells in that area and are not transferred to future generations. 3. Mutations in germ cells are passed to new offspring. 4. In mammals, the rate of mutation per nucleotide per replication in somatic cells is much greater than the corresponding rate in germ cells.

Presence of Glucose

1. In the presence of glucose: a. cAMP levels are low. b. The cAMP-CRP complex does not form. c. CRP does not bind the lactose operon. 2. As a result, even in the presence of lactose, the lactose operon is not transcribed to high levels. 3. E. coli preferentially utilizes glucose when both glucose and lactose are present; it utilizes lactose only when glucose is depleted.

Regulating Metabolic Pathway

1. In the synthesis of isoleucine from threonine, five reactions take place. 2. Once enough isoleucine is made, its production is shut down by the product isoleucine binding to the first enzyme in the pathway, threonine dehydratase. 3. The binding of isoleucine causes the enzyme's shape to shape, inhibiting its function. 4. The enzyme threonine dehydratase is an example of an allosteric enzyme, an enzyme that is activated or inhibited when binding to another molecule changes its shape. 5. The process in which the final product inhibits the first step of the reaction is known as negative feedback or feedback inhibition.

Regulation of the Cell Cycle

1. Mitotic cell division occurs during the growth of a multicellular organism, wound healing, or in the maintenance of actively dividing tissues such as the skin or lining of the intestine. 2. Cell division cannot occur all the time because uncontrolled division is dangerous and can lead to cancer. 3. Progression through the cell cycle is controlled by proteins that appear and disappear in a cyclical fashion, and by several enzymes that become active and inactive, also in cycles. 4. The proteins that appear and disappear cyclically are called cyclins.

Multiple-Mutation Model for Cancer Development

1. Most human cancers require more than the over-activation of one oncogene or the inactivation of a single tumor suppressor. 2. When several different cell-cycle regulators fail, it is likely that cancer will develop. 3. The cancer may be benign, meaning that it is slow growing and non-invasive to surrounding tissue. 4.Alternatively, it may be malignant, which means it grows rapidly and invades surrounding tissues. 5.The gradual accumulation of mutations in multiple genes over a period of years can be correlated with the stepwise progression of the cancer from benign to malignant forms.

Mutations from DNA Damage

1. Mutations are typically spontaneous and are caused by mutagens. 2. X-rays can cause breaks in the sugar-phosphate backbone, in either one strand or both strands. 3. UV light can cause adjacent pyrimidines to cross-link, which most commonly leads to the formation of thymine dimers. 4. Tobacco smoke can add bulky side groups to the bases, resulting in improper base pairing.

cycle of polymerase chain reaction

1. One method for making copies of a piece of DNA is the polymerase chain reaction (PCR), which allows a targeted region of DNA to be replicated and amplified into as many copies as are desired. 2. The PCR reaction is a DNA synthesis reaction that requires the same basic components used by the cell to replicate its DNA

DNA Editing

1. One of the newest and most exciting ways to edit DNA is CRISPR: clustered regularly interspaced short palindromic repeats. 2. The first step is to transform a cell with a plasmid containing sequences that code for a CRISPR RNA as well as the CRISPR -associated protein Cas9. 3. The RNA contains a region engineered to have bases complementary to any DNA molecule in the cell to be altered, known as the target DNA. 4. When the RNA undergoes base pairing with the target DNA, Cas9 cleaves the target DNA. 5. An editing template DNA is introduced to the cell by a plasmid and contains a sequence of interest to replace the degraded sequence of the target DNA, flanked by sequences complementary to the target. 6. The result is that the sequence has been altered according to the sequence present in the editing template.

PRC cycle step 1:

1. PCR creates new DNA fragments in a cycle of three steps: denaturation, annealing, and extension. 2. Denaturation involves heating the solution containing the components needed for PCR to a temperature just short of boiling to break the hydrogen bonds between the complementary bases, separating, or denaturing, the two strands of DNA. 3. The second step, annealing, begins as the solution is cooled. 4. Because of the great excess of primer molecules the two primers bind to their complementary sequence on the DNA template rather than the two strands of DNA coming back together.

amino acid structure

1. Proteins and polymers are made of monomers called amino acids. 2. Amino acids consist of a central carbon atom (α carbon). 3. The central carbon atom is covalently bonded to amino and carboxyl functional groups, a hydrogen, and a side chain or R group. 4. The R groups make each amino acid unique and are responsible for the chemical and physical properties of each amino acid monomer

exergonic reactions

1. Reactions with a negative ΔG release energy and are exergonic. 2. These reactions occur spontaneously. 3. Spontaneous does NOT mean that a reaction will occur quickly- it means it will occur without a net input of energy.

Recombinant DNA Allows Genes from One Organism to Be Expressed in a Different Organism

1. Recombinant DNA technology recombines DNA molecules from two (or more) different sources into a single molecule. 2. This method requires a fragment of double-stranded DNA that serves as the donor. 3. The donor fragment may be a protein coding gene, a regulatory part of a gene, or any DNA segment of interest. 4. Also required is a vector sequence into which the donor fragment will be inserted. 5. The vector is the carrier of the donor fragment; it must have the ability to be maintained in the new cell. 6. This technology involves cutting DNA (both donor and vector) with the same restriction enzyme so that the donor DNA and the vector DNA have complementary ends. 7. The resulting fragments (donor DNA and vector) are mixed together and joined by DNA ligase, resulting in the recombinant DNA molecule.

Insertions or deletions

1. Small insertions or deletions involve several nucleotides. 2. Frameshift mutations are caused by the insertion or deletion of one or two bases, resulting in disruption/shifting of the reading frame.

Cyclin-CDK Complexes Control Progression Through the Cell Cycle

1. The G1/S cyclin-CDK complex is active at the end of G1. a. It prepares the cell for S phase. b. For example, it promotes the expression of histone proteins needed for packaging the newly replicated DNA strands. 2. The S cyclin-CDK complex is involved in the initiation of DNA synthesis. a. It activates protein complexes involved in DNA replication that contain enzymes necessary for DNA synthesis. 3. The M cyclin-CDK complex initiates events associated with mitosis.

Structure of the 20 amino acids

1. The R groups allow the 20 amino acids to be grouped easily based on the following characteristics: a. How they interact with water (hydrophilic or hydrophobic) b. Whether they are basic or acidic c. Whether they are polar or non-polar 2. These properties are very important because they influence how a protein folds and its three-dimensional shape. 3. Shape = function.

Experimental Demonstration of the Enzyme/Substrate Complex

1. The enzyme β-galactosidase catalyzes the cleavage of the glycosidic bond that links galactose to glucose in the disaccharide lactose. 2. Lactose belongs to a family of molecules called β-galactosides: it contains a galactose unit attached to the rest of the molecule by a glycosidic bond. 3. In a related compound called βthiogalactoside, the oxygen atom in the glycosidic bond is replaced by sulfur. 4. The enzyme β-galactosidase binds βthiogalactoside but cannot cleave or release it.

Somatic Mutation and Cancer Example: Colon Cancer

1. The figure shows three key mutations that have been implicated in the origin of invasive colon cancer. 2. Each mutation occurs randomly, but if a mutation in the Ras gene occurs in a cell that is derived from one in which the APC gene has been mutated, that cell's progeny will form a polyp. 3. Another chance mutation in the cell having mutations in both the APC and Ras genes could lead to malignant cancer.

Primers are removed and fragments joined together:

1. The lagging strand has many of these short RNA primers 2. When the growing fragment comes into contact with the primer, a different DNA polymerase complex takes over, the removal of the RNA primer and synthesis DNA. 3. When the replacement is complete, an enzyme called DNA ligase catalyzes the joining of fragments together. -molecule comes in & forms last phosphodiester bond to put together 2 fragments called Okazaki fragments -to put these 2 Okazaki fragments together and synthesize that of phosphodiester bond -synthesized into one continuous covalently attached strand of DNA

Replication occurs on both strands

1. The leading strand has its 3' end pointing toward the replication fork; it is synthesized as one long, continuous polymer as the parental strand is unwound. 2. The lagging strand has its 3' end pointed away from the replication fork; it is synthesized in short, discontinuous pieces.

primary structure of protein

1. The primary structure is the amino acid sequence. 2. It can be represented by a series of three-letter or one-word abbreviations. 3. They are listed starting at the amino end (N-terminus) and going toward the carboxyl end (C-terminus).

Analyzing Mutations in the Lac operon: Constitutive Mutations

1. The ways in which the repressor and the operator work were originally determined by studying mutants of the lac operon and the repressor. a. lacI mutants do not produce functional repressor, so lacZ and lacY are expressed in the presence and absence of lactose. b.Operons mutant for lacO prevent the repressor protein from binding, so lacZ and lacY are expressed in the presence and absence of lactose. 2. Mutations of these types are called constitutive, because the proteins are produced continuously no matter what. 3. Some mutations will be constitutive while others will lead to no expression of lacZ and lacY. You can use the diagram of the lac operon to make prediction as to whether or expression of lacZ and lacY are "turned on" or "turned off" under different conditions.

Demonstration of the Enzyme/Substrate Complex: Experiment 1

1. To show the formation of an enzyme/substrate complex, a container is separated into two compartments by a semipermeable membrane. 2. The membrane is permeable to β-galactoside and βthiogalactoside, but not permeable to the enzyme. 3. In the first beaker, radioactively labeled βthiogalactoside is added to compartment 1, and its movement is followed by measuring the level of radioactivity in the two compartments. 4. Over time, the level of radioactivity becomes the same in the two compartments.

Why proteins final folding is important?

1. Ultimately, the primary structure determines the secondary and tertiary structures of a protein 2. The tertiary structure determines the protein's function: the contours and distribution of charge on the outside of the molecule and the presence of pockets that might bind with smaller molecules on the inside all play a role in the protein's function.

why do point mutations matter?

1. When the amino acid sequence is changed due to the mutation, the protein may fold incorrectly, causing it to no longer function. This is a nonsynonymous or missense mutation. 2. The disease sicklecell anemia results from nonsynonymous mutation.

absence of glucose

1. absence of glucose a. cAMP levels are high. b. cAMP binds to CRP, changing the shape of CRP. c. CRP binds DNA and activates transcription. 2. If lactose is present, the repressor cannot bind and the lactose operon is induced. 3. If lactose is not present, the repressor is bound and the lactose operon is not transcribed, even in the presence of the cAMP-CRP complex.

3 amplification steps:

1. double-stranded DNA is denatured 2. (annealing) specific DNA primers going to allow you to amplify sequence that interested in are annealed to the 2 strands of denatured DNA and finally each of thee are extended; allows target specific regions in DNA 3. extension: DNA polymerase syntheses new DNA strands (complementary to template duplex strands) by extending primers in a 5' to 3' direction

endergonic reactions

1.The difference in Gibbs free energy between the reactants and the products of a chemical reaction is written as ΔG. 2. If the products of a reaction have more free energy than the reactants, then ΔG is positive. 3. If the reactants have more free energy than the products, then ΔG is negative. 4. Reactions with a positive ΔG require an input of energy and are endergonic.

Reversable methylation of DNA is another mechanism of epigenetic control:

1.The most common chemical modification to DNA is the addition of a methyl group to the base cytosine. 2.CpG sites are often clustered near the promoter of the gene; these clusters are called CpG islands. 3.Methylation of a CpG island can change over time or in response to environmental cues, providing a way to turn genes on or off. 4.Repression of a gene is often accompanied by heavy methylation of a nearby island.

You attach fluorescent dye to nucleotides. Double-stranded DNA molecules with both strands labeled red fluoresce dark red (B), those with one strand labeled red and unlabeled fluoresce light red (C). If both strands are unlabeled the molecule does not fluoresce (A). In a cell grown for several generations in the presence of fluorescent nucleotide, and then moved to grow in a medium containing only normal, nonfluorescent nucleotides for exactly two rounds of DNA replication, which pattern of fluorescence in Figure 2 would you expect to see in a pair of homologous chromosomes?

2

In order to answer this question, you will need to read and understand the content in the Extension and Application Information section in the interactive How Do You Know figure. In a cell grown for several generations in the presence of fluorescent nucleotide, and then moved to grow in a medium containing only normal, nonfluorescent nucleotides for exactly three rounds of DNA replication which pattern of fluorescence shown in Figure 2 would you expect to see in a pair of homologous chromosomes?

2, 5, 6

The diagram shown here is part of an RNA transcript containing four open reading frames (M, H, K, and L) and three introns (1, 2, 3). The sites labeled d1-d3 are nucleotides immediately before each intron on the 5′ side and those labeled a1-a3 are nucleotides immediately after each intron on the 3′ side. Splicing out an intron involves a spliceosome facilitating the cleavage of the DNA at the d and a sites at either end of the intron.

3

The oligonucleotide primers used in the polymerase chain reaction are typically 20-30 nucleotides in length or longer; however, for purposes of this question, assume that 6 nucleotides is long enough. Suppose you wish to amplify the fragment shown (the raised dots indicate several kilobases of DNA sequence not shown). You decide to design primers corresponding to the regions that are underlined. What primer sequences would you use? 5'-ATGCTGAAACTTCTC···GGGATGAAATCAGTTT-3' 3'-TACGACTTTGAAGAG···CCCTACTTTAGTCAAA-5'

5'-TGAAAC-3' and 5'-CTGATT-3'

You attach fluorescent dye to nucleotides. Double-stranded DNA molecules with both strands labeled red fluoresce dark red (B), those with one strand labeled red and unlabeled fluoresce light red (C). If both strands are unlabeled the molecule does not fluoresce (A). In a cell grown in the absence of fluorescent nucleotide, which pattern of fluorescence shown in Figure 2 would you expect to see in a pair of homologous chromosomes?

6

As a cat pounces on a mouse, its muscles consume 10 units of potential energy (which the cat previously gained from the food it consumed). However, the pounce itself only required 4 units of kinetic energy. How many units of energy were dissipated as heat?

6 units

You attach fluorescent dye to nucleotides. Double-stranded DNA molecules with both strands labeled red fluoresce dark red (B), those with one strand labeled red and unlabeled fluoresce light red (C). If both strands are unlabeled the molecule does not fluoresce (A). In a cell grown for many generations in the presence of fluorescent nucleotide, and then moved to grow in a medium containing only normal, nonfluorescent nucleotides for exactly one round of DNA replication, which pattern of fluorescence shown in Figure 2 would you expect to see in a pair of homologous chromosomes?

8

Gibbs Free Energy (ΔG)

= amount of energy in a system available to do work

Why does the level of fluorescence decrease dramatically in the middle of the experiment?

A laser bleaches an area of the membrane.

Certain mutations in a gene for a regulated protein that stimulates cell division could result in uncontrolled cell divisions. Mutations that over activate Ras are an example. Which of the mutations would not likely cause Ras to be overactive?

A one-base-pair deletion early in the ras gene

A cell has been exposed to high doses of X-rays, and its DNA is damaged. Which of the statements should be true of this cell?

A. G1/S cyclins should be at high levels and activating cyclin-dependent kinases. B. p53 should be phosphorylated and binding to DNA.

The enzyme lysozyme catalyzes the hydrolysis of glycosidic bonds of peptidoglycans, a molecule found in the cell wall of some bacteria. Consider the three-dimensional model of the tertiary structure enzyme lysozyme (A) and a map of the primary structure of lysozyme showing the location amino acids that participate in binding and catalysis at the active site (B) and answer the following questions.

A. Peptidoglycan has β-(1,4)-glycosidic bond. whereas glycogen has α-1,4-glycosidic bonds and at branches it has α-1,6-glycosidic bonds. Thus, lysozyme can cleave only peptidoglycan glycosidic bond and not the glycogen glycosidic bond. B. Changing a glutamic acid that is negatively charged amino acid to a lysine (positively charged amino acid) can affect the substrate binding as the substrate interactions conferred by glutamic acid like salt-bridge interactions can't be produced with lysine.

A chemical compound would increase the mutation rate if it inhibited:

A. mismatch repair. B. nucleotide excision repair. C. base excision repair. D. All of these choices are correct.

colon cancer

APC gene mutation -> cause small benign poly to occur in colon (growth of cells continue growing) -all daughter cells will carry this mutation as division occurs if gains second mutation in oncogene (Ras) ever subsequent cell that divides from lineage will have both APC & Ras mutations causing larger benign polyps -if 3rd mutation occurs: another tumor suppressor will get p53 mutation & every cell that divides from that will get all 3

Mutations arise in which order in the colon cancer example shown in the animation?

APC, Ras, p53

example of exergonic reactions

ATP hydrolysis is an exergonic reaction ∆G = -7.3 kcal/mole

If plants are exposed to a toxin that makes the thylakoid membrane leaky to protons, what would you predict about the rate of ATP production by the chloroplasts?

ATP production will decrease.

Monod discovered that the amount of b-galactosidase enzyme produced per minute reached a maximum at a certain level of lactose and could not be increased by adding even more lactose. Which explanation is consistent with this finding?

All of the answer options are correct.

The strands in a double helix of DNA are:

All of these choices are correct.

Which of the statements represents a change in a proto-oncogene protein that would cause it to become an oncogene?

All of these choices are correct.

Why is pyruvate imported from the cytoplasm into the mitochondrial matrix?

Although pyruvate is made in the cytoplasm, the product of its oxidation, acetyl-CoA, is a substrate for the citric acid cycle, which is located in the mitochondrial matrix.

Why does the primary active transport of molecules across a membrane need to be coupled to ATP hydrolysis?

An input of energy is needed to allow the movement of molecules from an area of low concentration to one of higher concentration.

Which of the answer choices occurs in the E site of the ribosome during translation?

An uncharged tRNA is ejected from this site as the ribosome slides to the next codon

the human body contains approximately 200 major cell types. they look & function differently from one another because each:

expresses a different set of genes

point mutation

B) synonymous: -change DNA sequence (mRNA with different sequence) -protein sequence (amino acid sequence the same) silent mutation C) non-synonymous: - change DNA sequence -> encode new amino acid - AT -> TA -changes second codon in transcription GAG to GUG -which encodes different amino acid ( valine ) -changes DNA which leads to new amino acid sequence -results in sickle-cell anemia & resistance to malaria -missense mutation

You isolate a mutant that produces the repressor protein but also produces B-galactosidase whether or not lactose is present. In which gene would you expect to find that mutation to be and why?

B. In the mutant, lac repressor is produced from the Lac I gene. Lac Z expresses this mutant because lac oppressor will not be able to bind to operator. So the mutant will be present in Lac O gene as well. The repressor will not be able to bind to operator which means it will not be able to turn off the lac operon.

In an experiment, a radioactively labeled CO2 is added to a growing plant cell, and radioactive acetyl-CoA is produced and collected. In what order does the molecule of CO2 pass through the indicated cellular locations as it is converted into acetyl- CoA?

B>A>C chloroplast > cytoplasm > mitochondria

Which of the strands use a template for DNA replication?

Both strands use a template during DNA replication.

similarities between facilitated diffusion and active transport

Both use proteins to help transport their materials and particles from in or out of the cell. Both of their main functions are to move substances across the cell membrane.

breaking the ionic bonds between amino acid side chains would affect the secondary structure of a protein

false

In the figure, during photosynthesis, where will protons accumulate? Select from the boxed red letters.

C

In the figure, which area would you predict to have the lowest pH during daylight? Select from the boxed red letters.

C

The diagram shown represents the four stages of aerobic cellular respiration as four simple boxes. Many of the "inputs" and "outputs" are shown as arrows. Open arrows (→) represent "energy management molecules" (ATP and electron carriers), and closed arrows (→) represent other inputs and outputs, such as substrates and products. Use this diagram to answer the questions. Which arrow in the diagram shown could represent ATP?

C

Where are protein complexes I through IV of the electron transport chain located?

C

Which shows inhibition by an allosteric inhibitor?

C

Suppose that, as in the Meselson-Stahl experiment, E. coli is grown for many generations in heavy nitrogen (15N). After the E. coli is shifted to grow in light nitrogen (14N) for additional generations. Select the test tube that best corresponds to the positions that DNA would be expected to migrate to in this situation: Everything is just like the original experiment (the bacteria is grown for many generations in 15N and then switched to light 14N) and DNA replication is semi-conservative and the culture is grown in light media for two generations.

C (half-heavy to light)

You isolate a mutant strain with a mutation in lacP (promotor) that prevents RNA polymerase from binding. When would expect this strain to produce B-galactosidase: all the time, only in the presence of lactose, or never? Explain your reasoning

C. If you isolate a mutant strain with a mutation in lacP (promotor) that prevents RNA polymerase from binding I would expect this strain to NOT produce B-galactosidase. If lac operon is on, lactose should be present. But, since the promoter is mutated; the RNA polymerase will not be able to bind to promoter to initiate transcription of Lac Z gene.

Two petri dishes of radish seeds are prepared as follows: A disk of absorbent, but otherwise inert, filter paper is placed in the bottom of each dish. Next, 5 mL of distilled water are added to each disk. Then, 2 grams of dry radish seeds are spread over each moist disk. One dish is put in a dark cupboard, and the other is put on a sunny windowsill. The investigator checks the dishes daily and adds water equally as needed. Seeds in both treatments germinate within 2 days. At the end of 10 days, the plant material on each petri plate is dried and weighed. The results are: What is the most likely explanation for why the dark-grown seedlings lost biomass?

Cellular respiration in the cells of the seedlings consumed the starch and oils present in the seeds as sources of energy.

Which one of the statements describes an event that takes place during gene regulation at the level of the chromosome?

Chromatin is remodeled and nucleosomes are repositioned, thereby making specific regions of the DNA available for transcription.

Which of these pairs of gels could result from a nonsense mutation in exon 2? Why?

D

second subunit= proofreading DNA replication

DNA polymerase proofreading: There would increase genetic variation. This could lead to harmful, beneficial, or neutral phenotypes depending on the environment. Since DNA polymerase is missing, this would lead to more nucleotide pair mistakes to be copied.

In bacteria, operons allow groups of genes to be controlled together. Lac operon is an example

E. coli can metabolize lactose. Two genes involved in lactose metabolism are only transcribed when needed -B-galactosidase is an enzyme that catalyzes the breakdown of the sugar lactose into glucose and galactose -Lactose permease is an enzyme the facilitates the import of lactose from the media into the cell

The activation of multiple kinases by phosphorylation is a common theme in cell signaling pathways ("phosphorylation cascades"). Why might phosphorylation cascades be useful?

Each activated kinase can in turn activate multiple targets, allowing the signal to be amplified.

Before CoVID-19 pandemic, Remdesivir was developed as an antiviral drug for to treat Ebola virus. Based on this observation, what can you say about Ebola virus?

Ebola must have an RNA genome that replicates using an RNA dependent RNA polymerase

Which of the answer choices correctly describes the movement of water across a selectively permeable membrane during osmosis?

Either of these descriptions is correct and equivalent.

What hypothesis did this experiment test?

Enzymes form complexes with substrates.

Single nucleotide insertion or deletion:

Everything after the single nucleotide will result in different amino acids.

If DNA repair mechanisms were perfect, which of the answer choices would most likely result?

Evolution as we know it would stop because mutations are the only source of new genetic variation.

example of biological phenomena, identify the signal and the response.

Example: Follicle-stimulating hormone stimulates a cell to secrete growth factors. -Signal: Follicle-stimulating hormone -Response: growth factor secretion Insulin levels in the blood lead to glucose being imported into fat cells. -Signal:Insulin hormone -Response: glucose being imported into fat cells A growth factor stimulates the synthesis of proteins needed for a cell to grow. -Signal: growth factor -Response: cell to grow after protein synthesis. An undifferentiated cell becomes a glial cell after coming in contact with a neuron expressing the Delta protein. -Signal: Neuron expressing the delta protein -Response: An undifferentiated cell becomes a glial cell

Compare and contrast active transport and facilitated diffusion in terms of the size and chemical properties of the solutes crossing the membrane and the source of energy.

Facilitated diffusion is a passive process & does not require energy. Active transport uses carrier proteins. Energy is used to change the shape of the carrier protein. Facilitated diffusion uses both gated channel proteins & carrier proteins in transport. In facilitated diffusion the molecules moved are polar molecules & larger ions. In active transport the molecules move against their gradient coupled to the hydrolysis of ATP.

How should each of the cyclins change in the following conditions?

G1/S cyclins should be low, S cyclins should be high, and M cyclins should be low

When a G protein-coupled receptor binds a signal molecule, it activates a G protein. The active G protein is bound to a molecule of _______, and in its active state can _________.

GTP; activate another target protein

How is denaturing proteins similar and/or different from denaturing nucleic acids?

Heat can denature both proteins and nucleic acid secondary structure (e.g. double helix) because each held together by non-covalent interactions

Why isn't MPF always active in rapidly dividing sea urchin embryos?

The activity of MPF depends on cyclin, and cyclin levels rise and fall as the cell progresses through the cell cycle.

Base excision repair

In base excision repair, an enzyme specialized to remove one particular base acts to remove that base when that base is in the wrong place. In this example, uracil (instead of cytosine) is found in the DNA strand. The incorrect base and its sugar are excised from the strand, then replaced.

Chlorophyll molecules in chloroplasts normally only fluoresce a very small amount compared to chlorophyll that has been extracted into a solvent solution. Which of the following is the best explanation for this difference?

In chloroplasts, the molecules are held close together and oriented to allow transfer of excitation energy between molecules.

In replica plating, why is it important that the velvet be pressed onto the control plate (no antibiotic) prior to being pressed onto the selective plate (containing antibiotic)?

It avoids contact with antibiotic.

If a mutation caused the G protein to become permanently bound to GTP, what result can be predicted?

It constantly signals its pathway to be "on."

Which is more fit - antibiotic-resistant bacteria or antibiotic-sensitive bacteria?

It depends on whether antibiotic is present or not.

The emperor penguins of Antarctica live on a diet of fish and crustaceans obtained from the cold Antarctic seawaters. During their annual breeding cycle, however, they migrate across the frozen continent to their breeding grounds 50 miles away from the sea (and 50 miles away from their source of food). For over two months, the male emperor penguins care for and incubate eggs, while the females return to the sea to feed. During this time, a male penguin can lose up to 50% of its biomass (by dry weight). Where does this biomass go?

It is converted to CO2 and H2O and then released.

for a rare x-linked recessive trait, an unaffected father and unaffected mother can have affected sons

false

If the researchers replaced the bacterial proton pump with a proton pump that was activated only by ATP, what result would you predict?

Less ATP would be produced when the light is on because no proton gradient would be available to produce ATP.

The secondary sex ratio of newborns in the United States is 105 males : 100 females. Which of the answer choices is the accepted hypothesis to explain why this observed ratio doesn't this match the 1:1 predicted primary sex ratio?

Males and females have different survival rates between conception and birth.

What are the main hypotheses of this experiment?

Mutations are either spontaneous, without regard to survival, or are directed by the environment to improve survival.

If one follows the respiratory energy transfers and transformations sequentially from glucose through glycolysis, pyruvate oxidation, and the citric acid cycle, but before the electron transport chain and oxidative phosphorylation, most of the free energy captured from the original glucose molecule is found in:

NADH

Which example represents the reduced forms of the two major electron carriers (i.e. the form that will bring electrons to the electron transport chain)?

NADH and FADH2

Very low concentrations of detergent make membranes leaky to small molecules and ions without damaging proteins. In isolated mitochondria exposed to detergent, the molecules of the electron transport chain and of ATP synthase remain intact. Do you expect ATP synthesis to continue in the presence of low concentrations of detergent?

No, because with a leaky membrane, the proton gradient cannot be maintained.

Cancer can be caused by mutations. Genetic analysis of a tumor found in a patient shows that the cell proliferation was triggered by a somatic mutation in the MYC gene, causing this gene to be inappropriately activated. The patient is concerned about passing this cancer on to the children she plans to have in the future. Should she be concerned?

No, she should not worry about her children because this did not occur in a germ-line cell.

The function of a protein is dependent upon the shape into which the chain of amino acids folds. Many noncovalent interactions are responsible for maintaining the protein's shape. Assume you have isolated a protein from an organism in its proper shape, and you have treated it with an enzyme that selectively targets and breaks only the peptide bonds in the proteins. Would the protein retain its shape under these conditions?

No; while the noncovalent bonds determine the shape of a protein, the peptide bonds are required to hold the amino acids together.

Given the results of Experiment 1, what can you infer about the amount of oxygen in the test tubes at the beginning of the experiment relative to the amount of oxygen produced by photosynthesis?

The amount of oxygen at the beginning of the experiment is much less than the amount of oxygen produced by photosynthesis.

While many proteins move freely in the plane of the membrane, there are some proteins that are confined to specific places or regions of the membrane. If a membrane protein that is confined to a specific membrane region were labeled in a FRAP experiment, what result would you predict?

The bleached spot will not recover fluorescence over time.

Histone proteins are rich in the basic amino acids that are positively-charged under normal cellular conditions. How does this feature of histones' structure relate to histones' biological function?

Positively-charged amino acid R groups on histones are attracted to negatively-charged phosphodiester backbone of DNA holding DNA wrapped around histones in place.

Why did the researchers choose sea urchin embryos to study cell division?

Sea urchin embryo cells divide rapidly by mitosis.

three nucleotide deletion

Shorter protein and it would have the amino acids "skipped" (I have a hard time explaining this one)

If you used replica plating to make 50 replicas all on antibiotic-covered plates, what would you expect to see?

Some bacteria may already have a mutation conferring antibiotic resistance. The physical location of these bacteria will be identical on all 50 plates.

Active β-galactosidase enzyme is observed only in E. coli growing in the presence of lactose.One hypothesis is that the enzyme is always being produced but is produced in an unstable form that breaks down rapidly in the absence of lactose (hypothesis 1).A second hypothesis is that the enzyme is stable but is produced only in the presence of lactose (hypothesis 2).An experiment was performed to test these hypotheses. A culture of growing cells was exposed to lactose, which was later removed. The amount of β-galactosidase present in the culture during the course of the experiment was measured. The data are shown in the graph. Which one of the statements is a conclusion that can be obtained from these experimental data?

Synthesis of β-galactosidase is turned on when lactose is added and turned off when lactose is removed, in support of hypothesis 2.

A container is divided into two compartments by a membrane that is fully permeable to water and small ions. Water is added to one side of the membrane (side A), and a 5% solution of sodium chloride (NaCl) is added to the other (side B). If allowed to reach equilibrium, which of the answer choices would you predict?

The NaCl concentration on side A and side B will each be 2.5%.

nondisjunction can only occur in the sex chromosome and not the autosomes

false

Although the phospholipid molecules can be in constant lateral movement, they very rarely flip from one side of the bilayer to the other. Which of the answer choices could explain this?

The head groups are repelled by the hydrophobic membrane interior.

Suppose you add fluorescent ribonucleotides to a cell undergoing DNA replication so that the RNA primers used in DNA synthesis glow when viewed with a fluorescent microscope. You notice that, near each replication fork, one strand glows more than the other. Which strand glows more, and why?

The lagging strand glows more because its RNA primer is nearer the replication fork.

In the experiment that showed membrane fluidity, what was the purpose of shining a laser on the membrane?

The laser light destroys the dye fluorescence.

A loss-of-function mutation is one in which the function of a gene is completely knocked out or obliterated. Frameshift mutations never result in the loss-of-function of a gene.

false

Scientists often try to answer the same question using different techniques to gain confidence in their interpretations and conclusions. In a related experiment, a mouse cell and human cell were fused to create a single hybrid cell. The mouse and human cells were labeled with different antibodies (proteins) that bind to membrane proteins. Based on the conclusion of the FRAP experiment, what would you expect to see in this experiment?

The mouse and human proteins would slowly mix over time in the hybrid cell.

When a specific colony (identified through replica plating as being antibiotic resistant) is pulled from the original parent plate and used to inoculate a liquid culture, what happens when that liquid culture is then spread over an antibiotic plate?

The new plate will be covered with bacteria because all of the cells are antibiotic resistant.

After several weeks of no rain during the summer, you observe that leaves of some plants are wilted. Which of the answer choices would you expect to observe at the cellular level with respect to photosynthesis?

The rate of the reduction of chlorophyll molecules will be decreased.

You strip off all proteins on the cell surface by using a protease (an enzyme that destroys proteins). Now, when you add a specific signaling molecule, the cell still responds. What is the most reasonable explanation of this?

The receptor for this signal is inside the cell, and the signaling molecule is nonpolar and can diffuse into the cell.

Why regulate gene expression?

The regulation of gene expression conserves energy and space. It would require a significant amount of energy for an organism to express every gene at all times, so it is more energy efficient to turn on the genes only when they are required.

Which does not occur after an incorrect base is removed by DNA polymerase?

The template and daughter strands are separated by helicase activity.

A container is divided into two compartments by a membrane that is fully permeable to water but not to larger molecules. Water is added to one side of the membrane (side A), and an equal volume of a 5% solution of glucose is added to the other (side B). What would you predict will happen?

The water level on side B will increase and on side A will decrease.

A beaker is divided by a membrane that is permeable to water and glucose, but not to sucrose. Equal volumes of solutions are added to side A and B with the initial concentrations as shown below. Initially, the liquid levels on both sides are the same.After the system described above reaches equilibrium, what can you predict about the water levels?

The water will be higher on side A than on side B.

If a molecule can freely cross the membrane, then at equilibrium there will be no further movement of molecules across the membrane.

false

A researcher is evaluating the expression of p53 in cells she is culturing in the laboratory. She notices that in a small group of cells, high levels of phosphorylated p53 occur in the nuclei. What can she deduce about these cells?

These cells likely contain damaged DNA.

When p53 becomes mutant in cells already mutant for APC and Ras, what occurs?

These cells survive despite DNA damage and divide extremely rapidly.

Protein denaturation

Under changes in temperature or pH, or exposition to chemicals or UV, H bonds and interactions between R groups may be disrupted, causing the protein to lose its three-dimensional structure and turn back into an unstructured string of amino acids: Denatured proteins are usually non-functional. (can be reversed)

Most protein folding is driven primarily by hydrophobic interactions: hydrophobic side chains cluster together in the center of the protein, avoiding the surrounding water. Backbone and side chain interactions help to maintain the basic structure?

Valine

Which of the statements is an accurate description of events leading to the lytic pathway following viral infection in a bacterium?

When bacterial cells are grown in favorable conditions, proteases degrade cII and cro represses cI transcription, which leads to the expression of all genes needed for synthesis of phage components and lysis.

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

false

A mutation takes place in a protein-coding gene that changes one codon resulting in a single amino acid replacement. Which type of replacement is most likely to result in a disruption of protein structure and function?

a hydrophobic amino acid to a hydrophilic amino acid

Proteins produced from the Xist RNA transcripts coats the X chromosome to inactivate it. True or false?

false

Small regulatory RNAs regulate gene expression in either of two ways:

a. Binding to transcripts and blocking translation b. Binding to transcripts and causing degradation -Two types of small regulatory RNAs are microRNAs and small interfering RNAs.

Telomerase activity differs from one cell type to the next.

a. It is fully active in germ cells (sex cells) that produce eggs or sperm and in stem cells that always dividing b. It is almost inactive in adult somatic cells. In these cells, mitotic division can occur only about 50 times before the telomeres become so short that the cells stop dividing. (telomerase inactive: can only keep dividing until telomeres gone)

Kurt Stern used spectral analysis to test whether the enzyme forms a complex with its substrate by shining a white light on the reaction as it took place. Different molecules absorb different wavelengths of light. The maximum absorption of a wavelength by each molecule is called the absorption peak. By analyzing the patterns of absorption peaks as the reaction proceeded, Stern could determine whether or not a complex was formed. What do you predict Stern observed as the reaction proceeded?

all of answers correct

When a single antibiotic was present in the selective medium, the number of antibiotic-resistant bacteria observed was about 1 in 109 bacterial cells. If the selective medium contained two different antibiotics, no resistant cells were observed. Why?

all of answers correct

Which of the events is a possible function of a protein-folding domain?

all of these choices are correct

In cells, ___________ regulate enzymes by binding outside the active site.

allosteric regulators (noncovalent)

What would happen to the variation between organisms in a population if their DNA polymerase did not have a proofreading function?

amount of variation would increase

which of choices is an example of potential energy?

an electrochemical gradient across the cell membrane

Analyzing: In a metabolic pathway, a series of enzymatic reactions catalyzes the conversion of molecule A to molecule E. Several intermediate steps are involved in which the product of one reaction becomes the substrate for the next. The graph illustrates the changes of free energy that occur at each step in the pathway. Overall, this _____, based on the changes in free energy that take place as A is converted to E.

anabolic pathway

What feature of double-stranded DNA makes it necessary to have a leading strand and a lagging strand during replication?

antiparallel orientation of the strands

Which labeled arrow in the figure represents the activation energy (EA)?

arrow B

Which labeled arrow in the figure represents the change in free energy of the reaction (G)?

arrow E

Which arrow in this figure best depicts the proton pumping that is driven by the electron transport chain of photosynthesis?

arrow b

If you added an enzyme that catalyzes the reaction shown, you would predict that ____ would be reduced but ____ would remain the same.

arrow b; arrow e

Which arrow in the figure best depicts the flow of protons in powering the formation of ATP?

arrow d

At which checkpoint would a cell become arrested if a chromosome was not properly aligned in the spindle?

at a checkpoint early in the mitotic phase

Simple diffusion of a molecule down its concentration gradient requires an input of energy to the system.

false

The model of clustering genes into operons is commonly found in both prokaryotes and eukaryotes. true or false?

false

In the lac operon diagrammed here, which coding sequence(s) code for the enzymes required to effectively use lactose as a source of energy?

both lacZ and lacY

The repressor of lactose operon binds to the operator in the presence of lactose.

false

all RNAs are translated into proteins

false

In the figure, the boxed red letter ___ is in the thylakoid lumen, and the boxed red letter ___ is in the stroma of the chloroplast.

c; a

Which phase of the Calvin cycle does not require ATP?

carboxylation

In a related experiment, scientists studied catalase, which is an enzyme that catalyzes the reaction: In this experiment, we would expect an ES complex to be formed between:

catalase and hydrogen peroxide (enzyme) + (substrate) = ES complex

In a related experiment, Kurt Stern studied catalase, which is an enzyme that catalyzes the reaction: 2H2O2→2H2O+O2 Hydrogen peroxide Water Oxygen In this experiment, we would expect a complex to be formed between:

catalase and hydrogen peroxide.

Identify organelle A and the process(es) occurring there.

chloroplast; photosynthesis, the Calvin cycle

Genes that are _____ do not assort independently and are said to be _____.

close to each other in the same chromosome; linked

in cells, _____ function by binding to the enzyme active site

competitive inhibitors (noncovalent)

Which of the statements is true regarding telomeres?

contain repeated base sequences

although lifestyle choices cannot generally change our genomes, they can change our genetic code

false

pH is a measure of the acidity of a solution and equals the negative logarithm of the proton concentration. When the light is on and the proton pump is activated, the pH:

decreases inside the vesicle and increases outside of the vesicle.

Negative regulation "Turning genes off"

diagram

what does a "energy barrier" represent?

difference in energy between the transition state and reactions= activation energy

In the test tubes shown in the figure, what do the bands represent?

double-stranded DNA

semi-conservative

each new DNA molecule had backbone of one of the parents

Tumor suppressors:

encode proteins whose normal activities inhibit cell division (e.g. p53)

In this figure the solid blue curve plots free energy of a reaction against progress of that reaction. This reaction is:

endergonic

The synthesis of ATP from ADP and Pi is a(n) _____ reaction with ____ ΔG.

endergonic; a positive

kinetic energy

energy of motion

hydrolysis of sucrose

exergonic reactions

The phenotype of an individual results from an interaction between:

genotype and the envrionment

Telomerase is fully active in _____ and _____ cells, but almost completely inactive in _____ cells.

germ; stem; somatic

The accompanying table gives hypothetical data on the average length of telomeres among groups of people that differ in the lifestyle variables of stress, level of vigorous exercise, and daily caloric intake. To test the hypothesis that "high levels of stress have an effect on average length of telomeres," which groups would you compare?

group 2 & 3

The accompanying table gives hypothetical data on the average length of telomeres among groups of people that differ in the lifestyle variables of stress, level of vigorous exercise, and daily caloric intake. To test the hypothesis that "high levels of stress have an effect on average length of telomeres," which groups would you compare?

group 2 and group 3

late chemical energy is inversely related to height of energy barrier:

higher energy barrier, slower reaction lower energy barrier, faster reaction

Secondary structures are stabilized by which type of interaction?

hydrogen bonding

Which force can contribute to a protein's secondary structure?

hydrogen bonding

Suppose that three critical amino acids in the active site of a specific enzyme are arginine, lysine, and histidine. Which of the characteristics would you predict the substrate to possess, in order to bind the active site of this enzyme?

hydrophilic, with a negative charge

Which force contributes to the stability of a DNA double helix?

hydrophobic interactions of bases in the same strand and hydrogen bonding between bases in opposite strands

A _______ substance could contain __________ bonds which cause it not to interact with water.

hydrophobic; nonpolar covalent

Molecules that are _____________ and _____________ are able to move across the cell membrane via simple diffusion.

hydrophobic; small

The experiment was designed to distinguish among which of the following alternative hypotheses? Hypothesis 1: Water (H2O) is the source of the O2 released in photosynthesis. Hypothesis 2: Carbon dioxide (CO2) is the source of the O2 released in photosynthesis. Hypothesis 3: Both H2O and CO2 release O2 in photosynthesis. Hypothesis 4: O2 released during photosynthesis is derived from something other than H2O or CO2

hypotheses 1, 2, 3, and 4

The results of the experiment are consistent with which of the following alternative hypotheses? Hypothesis 1: Water (H2O) is the source of the O2 released in photosynthesis.Hypothesis 2: Carbon dioxide (CO2) is the source of the O2 released in photosynthesis.Hypothesis 3: Both H2O and CO2 release O2 in photosynthesis.Hypothesis 4: O2 released during photosynthesis is derived from something other than H2O or CO2.

hypothesis 1

enzymes

in cell, energy barrier is reduced by chemical catalysts ______.

A receptor that is inside the cell would require a __________ signal molecule that can ____________________ the plasma membrane.

nonpolar; pass through

Proto-oncogenes:

normal genes important in cell division that have the potential to become cancerous if mutated (e.g. Ras)

A) non-mutant strand

original DNA strand transcribed & translated & gene product expressed normally

In the Calvin cycle, NADPH is:

oxidized

enzymes catalyze ______ & ________

reactions & coupled reactions

One example of a cellular response to a signal is the triggering of cell division. If a mutation occurred in the gene for the signal receptor in this pathway that caused the receptor to reject binding of the signal, what response can be predicted?

the cells do not divide

In the gel, the amount of protein can be determined by:

the intensity of the band

On which strand is DNA synthesis discontinuous, occurring in fragments that are later connected?

the lagging strand

On which strand are new nucleotides being added in the same direction as the replication fork is opening?

the leading strand

What is the independent variable in the graph?

the presence or absence of light

The reactions of the Calvin cycle used to be referred to as the "dark reactions" of photosynthesis, implying that light was not required for this pathway to incorporate CO2 into carbohydrate. However, in the absence of light, the Calvin cycle shuts down. Which parts of the Calvin cycle would be impacted first by the absence of light energy?

the reduction of 3-phosphoglycerate

What is the first thing to occur in DNA replication?

the strands of the DNA double helix are separated

In a given reaction, which of the choices has the highest amount of free energy?

the transition state when the reaction is not catalyzed by an enzyme

In the gel, proteins migrate different distances based on:

their size and charge.

Why did the researchers attach a fluorescent dye to the membrane proteins?

to be able to visualize the proteins in the plane of the membrane

As your text notes, in XX females the dosage of X-linked genes is twice what it is in XY males. However, the level of expression of X-linked genes is about the same in both males and females. In mammals this dosage compensation is the result of X-inactivation in females. T or F?

true

If a mutation is not repaired, then it is passed down to all daughter cells in the cell lineage.

true

In the mammalian developing female (XX) embryo, a random inactivation of either the maternally derived X chromosome or the paternally derived X chromosome results in all the cells from subsequent cell divisions expressing only genes on the active X chromosome. True or False?

true

Same genotype can result in multiple phenotype. Same phenotype can be encoded by multiple genotypes

true

The histone proteins are among the most slowly evolving proteins. For example, a histone protein called histone H4 in cows and peas differs by only 2 amino acids among a total of about 100. A reason why histone proteins evolve so slowly is their function: These proteins bind with the negatively charged phosphate groups in double-stranded DNA, so the proteins must be rich in the basic amino acids lysine and arginine. Therefore, these amino acids cannot be replaced without disrupting the histone's structure and function. true or false

true

The histone proteins are among the most slowly evolving proteins. For example, a histone protein called histone H4 in cows and peas differs by only 2 amino acids among a total of about 100. A reason why histone proteins evolve so slowly is their function: These proteins bind with the negatively charged phosphate groups in double-stranded DNA, so the proteins must be rich in the basic amino acids lysine and arginine. Therefore, these amino acids cannot be replaced without disrupting the histone's structure and function. true or false?

true

cell division can not occur at all times

true

hydrogen bonds are covalent bonds. true or false?

true

one mutation on own cannot cause cancer

true

ow frequently is an improper base incorporated into the growing daughter strand?

very rarely

Which of the following is a product (as opposed to a substrate) of at least one of the processes of cellular respiration?

water

Ricin is a toxin found in castor beans that acts on ribosomes and blocks translation in eukaryotes. If the researchers added ricin to the sea urchins embryos, the researchers:

would have blocked cell division.

Suppose that cyclin does not contain the amino acid methionine. If this were the case, the researchers:

would not have observed cyclical levels of any proteins.

Experimental evidence that DNA replication is semi-conservative hypotheses

• Hypothesis 1: DNA replication is semiconservative (new molecule will have one parent strand and one newly synthesized strand) • Hypothesis 2L DNA replication is conservative (one DNA molecule will have two parental strands and the other has two newly synthesized strands)

Details of the DNA synthesis reaction

• Replication Occurs 5' to 3' • Requires a free 3' hydroxyl group • Catalyzed by DNA polymerase • Coupled to the hydrolysis of dNTP