biol112 final exam

How do nutrients act as signal molecules in operon regulation?

Nutrients can act as inducers or repressors, influencing the transcription of operons by binding to repressor proteins or allowing RNA polymerase recruitment.

What is the role of inducers in operon regulation?

Inducers bind to repressor proteins, causing them to change shape and preventing them from binding to the operator, thus allowing transcription to occur.

What happens when a repressor binds to the operator?

When a repressor binds to the operator, it prevents RNA polymerase from initiating transcription.

What are the two levels at which gene expression can be regulated?

Gene expression can be regulated at the transcriptional level (synthesis of mRNA) and post-transcriptional level (synthesis of proteins and their modifications).

What are housekeeping genes?

Housekeeping genes are constitutively expressed genes that are always needed for basic cellular functions, such as RNA polymerase subunits and ribosome components.

What is the difference between basal level transcription and constitutive transcription?

Basal level transcription refers to operons that are rarely expressed, while constitutive transcription refers to operons that are expressed at high levels.

What are the structural components of a bacterial operon?

A bacterial operon consists of the promoter, operator, and coding sequences for genes, with the promoter initiating transcription and the operator being the binding site for regulatory proteins.

What is the role of the promoter in an operon?

The promoter is the site where transcription is initiated, determined by its strength and the binding of regulatory proteins.

What is the function of the operator in operon regulation?

The operator is the binding site for repressor proteins, which can inhibit transcription when bound.

How does the CRP-cAMP complex regulate the lactose operon?

The CRP-cAMP complex acts as a positive regulator that binds near the promoter to activate transcription when glucose levels are low.

What distinguishes strong promoters from weak promoters?

Strong promoters can bind RNA polymerase effectively without an activator, while weak promoters require an activator for effective transcription.

What is the effect of signal molecules on positively regulated operons?

The presence of signal molecules increases transcription levels in positively regulated operons, while their absence decreases transcription.

What happens if there are mutations in the lac operon regulatory elements?

Mutations in the lacI gene can lead to expression of lac genes regardless of lactose presence, while mutations in the lacO can prevent repressor binding, also leading to constant expression.

How does the lac operon demonstrate negative regulation?

In the absence of lactose, the lacI protein binds to the lac operon, repressing transcription; when lactose is present, it induces a conformational change in lacI, allowing transcription to proceed.

What is the mechanism of the mal operon?

The mal operon is positively regulated; when maltose is present, it binds to the malt protein, which then binds to the malPQ operator to initiate transcription.

What is the significance of differential gene expression in multicellular organisms?

Differential gene expression allows for the development of specialized cell types and the ability to respond to environmental changes.

What is the role of post-translational modifications in gene expression?

Post-translational modifications can alter protein function and activity after synthesis, impacting how proteins contribute to cellular processes.

How does environmental regulation affect gene expression?

Environmentally regulated genes have expression linked to environmental conditions, such as nutrient availability, allowing cells to adapt to changing surroundings.

What is the function of the coding sequence in an operon?

The coding sequence contains the genetic information that is translated into proteins, preceded by a ribosome binding site for translation initiation.

How does the presence of glucose affect cAMP levels and operon regulation?

High glucose levels lead to low cAMP levels, preventing the CRP-cAMP complex from binding to the promoter, thus reducing transcription.

What is the impact of an activator in positive transcriptional regulation?

An activator binds to DNA near the promoter to facilitate RNA polymerase recruitment and increase transcription levels.

What is the relationship between transcription factors and gene expression?

Transcription factors can either enhance (activators) or inhibit (repressors) gene expression by binding to specific DNA regions.

What is the role of ribosome binding sites in operon structure?

Ribosome binding sites are crucial for initiating translation at each coding sequence within the operon.

How do mutations in regulatory genes affect operon function?

Mutations in regulatory genes can lead to the loss of functional repressors or activators, resulting in altered gene expression patterns.

Genotype

hereditary genetic information of a cell or organism within the genome

Phenotype

an organisms observable characteristics or traits from the resulting expression of the genotype

Point mutation

mutation where a base pair is replaced with another, incorrect base pair

Missense mutation

mutation where the mRNA sequence is altered and so is the amino acid sequence as the change in codons coded for different amino acids

Nonsense mutation

mutation in which a premature stop codon is found and polypeptide chain is terminated early, becoming unfunctional and unstable

Silent mutation

mutation where the mRNA sequence is changed, but the codon changed does not alter the amino acid sequence as the both original and altered codon code for the same amino acid

Indel mutation

when nucleotides are deleted or inserted resulting in a frameshift and change in reading frame - usually abolishes protein function

Semi conservative DNA replication

each cell will have a parental template strand that is based paired with a newly synthesized daughter strand

Bacteria replication

one origin of replication - circular chromosome

Eukaryotes replication

multiple origins of replication - multiple and long chromosomes

DNA Polymerase

reads template sequence and links nucleotides together from 5' to 3'

RNA primer

needs to start from RNA primer 3' -OH

Activated monomers

provide energy for the reaction - removal releases energy due to their instability

Separating the DNA strand

DNA is separated at the replication fork into single strands using helicase to unwind and break the hydrogen bonds between the bases

Single stranded binding proteins

keeps single stranded DNA apart and prevents the strands from rewinding/folding - stabilizes the open ends

Topoisomerase

relaxes the stress on the unwinding helix

Primase

RNA Polymerase needs to make a RNA primer before DNA Polymerase can add nucleotides for synthesis

Leading strand

synthesized towards and with the replication fork

Lagging strand

synthesized away from replication fork in fragments and gaps are noticeable

DNA Polymerase 1

removes RNA primers and replaces them with DNA

DNA ligase

joins the fragments together

Okazaki fragment

short pieces of the lagging strand (daughter strand) that are joined together later

What is the role of ΔH and ΔS in the Gibbs Free Energy (ΔG) equation?

ΔH represents enthalpy (heat content), while ΔS represents entropy (disorder). A negative ΔG indicates a catabolic reaction that releases energy, while a positive ΔG indicates an anabolic reaction that requires energy.

What characterizes catabolic reactions?

Catabolic reactions break down large molecules into smaller ones, releasing energy. They are spontaneous and exergonic.

What characterizes anabolic reactions?

Anabolic reactions synthesize larger molecules from smaller ones using energy. They are not spontaneous and are endergonic.

What types of nutrients are required for cellular metabolism?

Reduced carbon compounds that can be oxidized to release energy, which is used to generate ATP.

How do high energy phosphate bonds in ATP contribute to its role as an energy carrier?

The bonds linking phosphate groups have high potential energy. When these bonds are broken, energy is released, facilitating reactions like anabolic polymerization.

Where does glycolysis occur in bacterial and eukaryotic cells?

Glycolysis takes place in the cytoplasm/cytosol for both bacteria and eukaryotes.

What are the inputs and outputs of the glycolytic pathway?

Inputs: glucose, NAD+, ADP. Outputs: two molecules of pyruvate, two molecules of NADH, and a net gain of two ATP.

What is substrate level phosphorylation in glycolysis?

It is the process where an enzyme transfers a phosphate from a phosphorylated molecule to ADP to generate ATP, though it is not very efficient.

What is the function of NADH produced during glycolysis?

NADH acts as a high energy electron carrier, donating electrons and being oxidized in subsequent reactions.

What happens to reduced carbon compounds during cellular respiration?

They are oxidized, releasing energy that is harnessed as high energy intermediates.

What defines oxidation and reduction in redox reactions?

Oxidation is the loss of electrons (losing H and gaining O), while reduction is the gain of electrons (gaining H and losing O).

What is the relationship between the number of CH and CO bonds in organic molecules and their energy state?

More reduced organic molecules have more CH bonds and fewer CO bonds, indicating higher potential energy.

Provide an example of a highly reduced organic compound.

Methane or fatty acid chains.

What characterizes more oxidized organic compounds?

More oxidized compounds have more CO bonds and fewer CH bonds, indicating lower potential energy.

What is the significance of the high energy intermediates formed during oxidation?

They are more strongly bonded, have less potential energy, and are more oxidized than their reduced counterparts.

What is the net ATP yield from glycolysis?

The net yield from glycolysis is two molecules of ATP.

How does ATP hydrolysis contribute to exergonic reactions?

Hydrolysis of ATP releases energy that helps drive reactions forward, allowing them to proceed spontaneously.

What is the fate of NADH produced in glycolysis?

NADH can be used as an electron carrier in cellular respiration or fermentation processes.

What is the importance of ATP in anabolic reactions?

ATP provides the necessary energy for synthesizing larger molecules from smaller ones.

Explain the concept of energetic coupling in metabolism.

Energetic coupling refers to the use of energy released from exergonic reactions to drive endergonic reactions.

What is the role of ADP in ATP synthesis during glycolysis?

ADP is phosphorylated to form ATP during substrate level phosphorylation.

What is the primary function of glycolysis in cellular metabolism?

Glycolysis breaks down glucose to produce energy in the form of ATP and high energy electron carriers.

ΔH and ΔS in Gibbs Free Energy

ΔH represents enthalpy (heat content), while ΔS represents entropy (disorder). A negative ΔG indicates a catabolic reaction that releases energy, while a positive ΔG indicates an anabolic reaction that requires energy.

Catabolic reactions

Catabolic reactions break down large molecules into smaller ones, releasing energy. They are spontaneous and exergonic.

Anabolic reactions

Anabolic reactions synthesize larger molecules from smaller ones using energy. They are not spontaneous and are endergonic.

Nutrients for cellular metabolism

Reduced carbon compounds that can be oxidized to release energy, which is used to generate ATP.

High energy phosphate bonds in ATP

The bonds linking phosphate groups have high potential energy. When these bonds are broken, energy is released, facilitating reactions like anabolic polymerization.

Location of glycolysis

Glycolysis takes place in the cytoplasm/cytosol for both bacteria and eukaryotes.

Inputs and outputs of glycolysis

Inputs: glucose, NAD+, ADP. Outputs: two molecules of pyruvate, two molecules of NADH, and a net gain of two ATP.

Substrate level phosphorylation in glycolysis

It is the process where an enzyme transfers a phosphate from a phosphorylated molecule to ADP to generate ATP, though it is not very efficient.

Function of NADH in glycolysis

NADH acts as a high energy electron carrier, donating electrons and being oxidized in subsequent reactions.

Reduced carbon compounds during cellular respiration

They are oxidized, releasing energy that is harnessed as high energy intermediates.

Oxidation and reduction in redox reactions

Oxidation is the loss of electrons (losing H and gaining O), while reduction is the gain of electrons (gaining H and losing O).

CH and CO bonds in organic molecules

More reduced organic molecules have more CH bonds and fewer CO bonds, indicating higher potential energy.

Example of a highly reduced organic compound

Methane or fatty acid chains.

Characteristics of more oxidized organic compounds

More oxidized compounds have more CO bonds and fewer CH bonds, indicating lower potential energy.

Significance of high energy intermediates

They are more strongly bonded, have less potential energy, and are more oxidized than their reduced counterparts.

Net ATP yield from glycolysis

The net yield from glycolysis is two molecules of ATP.

ATP hydrolysis and exergonic reactions

Hydrolysis of ATP releases energy that helps drive reactions forward, allowing them to proceed spontaneously.

Fate of NADH in glycolysis

NADH can be used as an electron carrier in cellular respiration or fermentation processes.

Importance of ATP in anabolic reactions

ATP provides the necessary energy for synthesizing larger molecules from smaller ones.

Energetic coupling in metabolism

Energetic coupling refers to the use of energy released from exergonic reactions to drive endergonic reactions.

Role of ADP in ATP synthesis

ADP is phosphorylated to form ATP during substrate level phosphorylation.

Primary function of glycolysis

Glycolysis breaks down glucose to produce energy in the form of ATP and high energy electron carriers.

Where do photophosphorylation and the Calvin cycle occur in chloroplasts?

Photophosphorylation occurs in the thylakoid membrane, while the Calvin cycle occurs in the stroma.

What is the source of electrons in photophosphorylation?

Electrons originate from water, which is oxidized by light energy.

What role does light play in generating the proton gradient during photophosphorylation?

Light energy is used to energize electrons, which helps create a proton gradient by moving protons from the stroma into the lumen.

Trace the path of electrons from water to NADPH in oxygenic photosynthesis. What are the key steps?

1. Light energy is absorbed by PSII, oxidizing water to produce O2 and protons. 2. Electrons move through the transport chain, creating a proton gradient. 3. Light energy is absorbed by PSI, re-energizing electrons to reduce NADP+ to NADPH.

What are the electron donor and acceptor in the process of photophosphorylation?

The electron donor is H2O and the electron acceptor is NADP+.

Compare photophosphorylation and oxidative phosphorylation in terms of electron donors and products. What are the key differences?

Photophosphorylation uses H2O as the electron donor and produces ATP in the presence of light. Oxidative phosphorylation uses NADH and FADH2 as electron donors and produces ATP in the presence of oxygen.

What are the three key steps in polymerase chain reactions (PCR)?

1. Denaturation: heating separates DNA strands. 2. Annealing: primers bind to template strands. 3. Extension: DNA polymerase synthesizes new DNA strands.

What components are needed to start a PCR amplification experiment?

DNA template, four deoxynucleoside triphosphates (dNTPs), DNA polymerase (Taq), and DNA primers.

What is the role of deoxyribonucleoside triphosphates (dNTPs) in DNA synthesis?

dNTPs are the monomers used to build new DNA strands.

Identify the structural end of a DNA molecule where dNTPs are added during DNA synthesis.

dNTPs are added at the 3' end of the growing DNA strand.