mcbr181 exam 3

Enzyme Activity

Enzymes are protein catalysts that accelerate chemical reactions within cells. They facilitate collisions between reactant molecules, enhance proper orientation of reactants, and exclude solvent molecules that may hinder reactions

Enzyme Abilities and Function

Enzymes form an ES (enzyme-substrate) complex, where substrates are converted into products and released. Two models describe enzyme-substrate binding:

1. lock and key

2. induced fit

1. lock and key

2. induced fit

• Lock and Key: Enzymes perfectly match the shape of their substrates.

• Induced Fit: Enzymes adjust their shape slightly upon binding to substrates, enhancing the interaction.

Enzyme Components and Inhibitors

• Active Site: Location where enzyme interacts with substrates. Competitive inhibitors bind here, preventing substrate interaction.

• Allosteric Site: Sites outside active site regulating enzyme activity. Non-competitive inhibitors/activators bind here, affecting substrate binding.

T/F Ribosomes are present in all living cells and made up of tRNA and protein

FALSE

in the lac open, the product of which of the following is involved in regulation of beta-galactoside expression lacY,lacl,lacO,lacA

lacO

In which phase of meiosis do alleles of given gene separate

Anaphase1

When a protein is transferred to a solution with a pH that is much lower than its optimal range what protein structures are affected

Secondary,Tertiary, and Quaternary

Which forces contribute to stability of DNA double helix?

Base stacking interaction with same strand

The human body contains approximately 200 major cell types. They look and function differently from one another because each:

A. Differential expression; expresses a different set of genes at different times

Positive vs. Negative Regulation of Transcription

Positive regulation: A regulatory molecule (activator protein) binds DNA so that transcription can take place

Negative regulation: A regulatory molecule (repressor protein) binds DNA so that transcription can be prevented

The structural genes involved in lactose metabolism are only transcribed when needed when lactose is present T/F?

TRUE

Explain how enzymes recognize their substrates and catalyze chemical reactions.

• Enzyme-Substrate Recognition: Enzymes recognize substrates through specific binding sites on their surface.

• Catalysis: Enzymes lower activation energy, facilitating chemical reactions by bringing substrates together and stabilizing the transition state.

In prokaryotes, gene regulation is simpler than in eukaryotes because

• DNA is not packaged into chromosomes.

• mRNA is not processed.

• There is no nuclear membrane separating the processes of transcription and translation

T/F? Transcriptional regulation can be positive or negative

True

DNA replication: describe how it occues

-two strands of parental duplex seperate to synthesize

-Replication occurs 5’ to 3’ just like transcription.

-3’ (OH) attacks the incoming deoxyribonucleotide triphosphate at the innermost phosphate.

-Catalyzed by DNA polymerase

what is Meselson-Stahl experiment in prokaryotes

Demonstrated semi-conservative DNA replication using heavy isotopes of nitrogen.

• Labeled DNA with different N (nitrogen) isotopes. The heavier form has an extra neutron ( 15N) and was used to label the parent strands.

• After one round of replication in the presence of the lighter form of N, the density of the DNA molecule had intermediate density.

what is Post-Meselson-Stahl experiment in eukaryotes

Demonstrated semi-conservative DNA replication using heavy isotopes of nitrogen.

• Labeled DNA with fluorescent nucleotides.

• After two rounds of replication, one chromatid strongly fluoresces (dark).

Helicase:

catalyzes the unwinding of the parental DNA double helix at the replication fork

Enzyme unwinding DNA double helix ahead of replication fork.

Single-stranded binding proteins:

bind to the single- stranded regions of the parental DNA strands and prevent them from coming back together

Topoisomerases:

relieves the stress of unwinding the DNA double helix at the replication fork.

DNA polymerase:

synthesizes the DNA.

Okazaki Fragment:

Short DNA fragments synthesized on lagging strand during DNA replication.

DNA Ligase:

Enzyme joining Okazaki fragments during DNA replication.

RNA primase:

synthesizes a short piece of RNA complementary to the DNA template

Which of the following is a true statement about the enzymes listed below? Pick the protein-function option with the correct function listed.

A. Primase - Is involved in stabilizing the template DNA when it is unwinding.

B. DNA polymerase - Joins the Okazaki fragments of the lagging strand during DNA replication.

C. RNA primase - Synthesis of RNA primers that are needed to start DNA replication.

D. Helicase - Relieves the stress of unwinding DNA at the replication fork

RNA primase - Synthesis of RNA primers that are needed to start DNA replication.

mutagens: list them and what they do

X-rays

can cause breaks in the sugar-phosphate backbone, in either one strand or both strands.

 

UV light

can cause adjacent pyrimidines to cross-link, which commonly leads to the formation of thymine (T) dimers.

 

Oxidizing agents 

such as hydrogen peroxide can oxidize bases such as guanine which can cause improper base pairing.

Tobacco smoke

can add bulky side groups to the bases, resulting in improper base pairing.

Suppose that a human cell contains a mutated mismatch repair gene that encodes a protein that is similar to MutH. The mutation causes the protein to be non-functional. What is the expected implication for mismatch repair within that cell

A. Mismatch repair will still occur because DNA polymerase is still functional.

B. Mismatch repair will not occur because the mismatched nucleotide will not be recognized.

C. The DNA with the mismatch will be cleaved but the mismatch will not be removed.

D. Mismatch repair will not occur properly because the DNA backbone will not be cleaved.

D. Mismatch repair will not occur properly because the DNA backbone will not be cleaved.

Which of the statements is true regarding telomeres?

A. Telomeres are typically only a few base pairs in size and contain unique sequences.

B. Telomeres are enzymes that repair telomerases, which cap the end of linear chromosomes.

C. Telomeres shorten with every cell division in somatic cells because telomerase is less active.

D. Telomere repeats are added to the same extent in germ cells and somatic cells

C. Telomeres shorten with every cell division in somatic cells because telomerase is less active.

Which of the following is a list of terms that distinguish DNA replication?

A. Deoxyribonucleotide triphosphate, telomerase, translation and hydrogen bond.

B. Semiconservative replication, enhancer, leading strand and start codon.

C. Origin of replication, leading strand, lagging strand and DNA polymerase.

D. Ribonucleotide triphosphate, transcription factor, RNA polymerase and double helix.

C. Origin of replication, leading strand, lagging strand and DNA polymerase.

In replication of a linear double-stranded DNA molecule, one end of each strand becomes shorter in each round of replication why?

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

The point at which DNA synthesis is initiated is called the:

origin of replication

proofreading is a process by which ___ immediately removes and replaces incorrect nucleotides during____.

DNA polymericase; replication

In-frame mutations:A small deletion or insertion that is an exact multiple of 3 nucleotides results in a polypeptide with fewer (in the case of a deletion) or more (in the case of an insertion) amino acids

Example: A deletion of 3 nucleotides eliminates 1 amino acid.

Example: An insertion of 6 nucleotides adds 2 amino acids

You are investigating a mutant eukaryotic cell line that makes mRNAs much longer than the mRNAs from normal cells. Intrigued, you examine the proteins in these cells and note that many of them are also much longer or much shorter than the normal proteins from nonmutant cells. Assuming there is just 1 mutation in the cell line, which of the possibilities is most likely?

A. The poly-A tail has a missense mutation.

B. There is a synonymous mutation in the spliceosome.

C. RNA polymerase has a synonymous mutation.

D. There is a frameshift mutation in the spliceosome

D. There is a frameshift mutation in the spliceosome

The proteins that appear and disappear cyclically are called :

cyclins

Cyclins form a complex with ____ that regulate cell division

CDKs (cyclin-dependent protein kinases)

Cyclins undergo a type of posttranslational modification called ______, which targets them to be rapidly degraded as the cell cycle progresses.

ubiquitination

Cells have many cell-cycle checkpoints, where they can pause the cell cycle if something is not right, before progressing to the next stage. Three major, well-studied checkpoints include:

•(G1) DNA damage checkpoint: checks for damaged DNA before it enters S phase.

•(G2) DNA replication checkpoint: checks for the presence of un-replicated DNA at the end of G2 before the cell enters mitosis.

• (M) Spindle assembly checkpoint: checks for all chromosomes being attached to the spindle before the cell progresses with mitosis.

How should the amount of each of the cyclins change in the following condition? A cell has recently divided, grown in size, and synthesized adequate material for its next cell division. It is currently replicating its DNA.

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

mutations in the development of cancer

Oncogene:

Encode proteins that promote uncontrolled cell growth e.g. mutated form of Ras often called activated Ras

mutations in the development of cancer

Proto-oncogenes:

Encode proteins that are important in cell division that have the potential to become cancerous if mutated (e.g. Ras)

mutations in the development of cancer

Tumor suppressors:

encode proteins whose normal activities inhibit cell division eg. p53

The cancer may be _____, meaning that it is slow growing and non-invasive to surrounding tissue.

Alternatively, it may be ______, which means it grows rapidly and invades surrounding tissues.

benign , malignant

Carcinogenic - ???

Anti-carcinogenic - ??

changes that could promote cancer

changes that could stop cancer

Carcinogenic or anti-C?

A mutation that leads to the hyperactivation (overexpression) of cyclin gene expression -

Carcinogenic because cyclins regulate the cell cycle and are normally cyclical in their expression.

Carcinogenic or anti-C?

A missense mutation in a tumor suppressor gene -

Most likely carcinogenic because missense mutations change the amino acid sequence which could cause the protein to be non-functional.

Carcinogenic or anti-C?

The constitutive expression of DNA polymerase -

Anti-carcinogenic because of the proofreading ability of this enzyme. Also, if there are errors in DNA synthesis (S phase) that aren’t caught by polymerase, there are other mechanisms in place to correct errors before mitosis.

Carcinogenic or anti-C?

Blocking the degradation of p53 so that p53 accumulates in the nucleus -

Anticarcinogenic because p53 is a tumor suppressor gene and the accumulation of this protein will ensure that the cell cycle is regulated.

Which of the following mutations would most likely to lead to the development of malignant cancer?

A. A silent mutation in a proto-oncogene.

B. The constitutive expression of a tumor suppressor gene.

C. A nonsense mutation in a tumor suppressor gene.

D. Down-regulation of the expression of an oncogene.

C. A nonsense mutation in a tumor suppressor gene.

ATP

stores energy in a form that all cells can readily use to perform the work of the cell.

Hydrolysis of ATP drives many reactions in cells.

When chemical reactions occur, bonds between atoms are broken and _____ are formed.

Many chemical reactions in cells are readily ______

-new bonds

-reversible

The reversibility of the reaction is indicated by a double arrow

Gibbs free energy is

if products have more free energy than reactants?? less free energy?? what is positive gibbs free mean?

the amount of energy in a system available to do work

If the products of a reaction have more free energy than the reactants, then ΔG is positive.

If the reactants have more free energy than the products, then ΔG is negative.

Reactions with a positive ΔG require an input of energy and are endergonic

exergonic vs endergonic

Reactions with a negative ΔG release energy and are exergonic.

positive are endergonic non-spontaneous

-exergonic reactions occur spontaneously.

-Spontaneous does NOT mean that a reaction will occur quickly- it means it will occur without a net input of energy .

ATP hydrolysis is an ____ reaction

exergonic

Which of the reactions is most likely to be exergonic?

A. the replication of DNA from free nucleotides

B. the formation of cellulose from individual glucose molecules

C. the synthesis of a phospholipid from glycerol and fatty acids

D. the digestion of protein from food into amino acids

D. the digestion of protein from food into amino acids

Which of the following reactions would you predict could be coupled to ATP synthesis from ADP + Pi (ADP + Pi → ATP + H2 O, ΔG + 7.3 kcal/mol)?

A. creatine phosphate + H2 O → creatine + Pi , ΔG – 10.3 kcal/mol

B. glucose 6-phosphate + H2 O → glucose + Pi , ΔG – 3.3 kcal/mol

C. glucose 1-phosphate + H2 O → glucose + Pi , ΔG – 5.0 kcal/mol

D. glutamic acid + NH3 → glutamine, ΔG + 3.4 kcal/mol

To predict which reaction could be coupled to ATP synthesis from ADP + Pi, we need to find a reaction with a negative ΔG value (exergonic) that is greater than or equal to the ΔG value of ATP synthesis (+7.3 kcal/mol). This ensures that the overall reaction (coupled reaction) has a negative ΔG, allowing it to proceed spontaneously.

option A has a negative ΔG value (-10.3 kcal/mol), indicating an exergonic reaction. Since its magnitude is greater than the ΔG value for ATP synthesis (+7.3 kcal/mol), it can be coupled to ATP synthesis from ADP + Pi.

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 ______.

When their products are needed and their reactants are present, those enzymes are “turned on” by ______

inhibitors,

activators

In cells,_______ function by binding to the enzyme active site,

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

competitive inhibitors,

allosteric regulators

Which of the following do you think would trigger an innate immune response knowing where DNA should normally be stored? (Select all that apply)

A. Intact mitochondria where the mitochondrial DNA is stored

B. E. coli bacteria entering the cell

C. DNA from a dying neighbor cell that is being endocytosed into the cell

D. Nuclear DNA that is in the nucleus

B and C

Kinase is a

Phosphatases are

Transcription factor are

- protein that can add a phosphate group onto another protein

-proteins that removes phosphate groups on other proteins

-proteins that regulate gene transcription

The ΔG for the hydrolysis (lysis with water) of sucrose is -29 kJ/mol. Does this reaction need to be coupled to the hydrolysis of ATP (∆G = -7.3 kcal/mole)?

A. Yes, because this in an endergonic reaction where the energy of the products is more than the energy of the reactants.

B. Yes, because this is an exergonic reaction where the energy of the products is more than the energy of the reactants.

C. No, because this is an exergonic reaction where the energy of the products is less than the energy of the reactants.

D. No, because this is an endergonic reaction where the energy of the products is less than the energy of the reactants.

C. No, because this is an exergonic reaction where the energy of the products is less than the energy of the reactants.

Which of the following statements about enzymes are true?

A. Allosteric inhibitors alter the activity of enzymes by binding to the enzyme’s active site in place of the intended substrate.

B. Enzymes couple chemical reactions that are exergonic (- ΔG) and endergonic (+ ΔG).

C. Reversible inhibitors form covalent bonds with the enzyme.

D. Enzymes increase the rate of reactions by increasing the activation energy.

B. Enzymes couple chemical reactions that are exergonic (- ΔG) and endergonic (+ ΔG)

Which of the following definitions and/or statements is incorrect?

A. A tumor suppressor gene encodes a protein that normally inhibits cell division.

B. Cancer can be difficult to treat because most cancers are caused by multiple mutations.

C. An oncogene encodes a protein that is causing rapid and uncontrolled cell growth.

D. DNA mismatch repair helps to ensure cells don’t proliferate with DNA mutations that are transferred to the next generation.

E. All of the statements or definitions are correct.

all of them correct