midterm 2 cram Flashcards

1
Q

gene transfer in bacteria and archaea

foreign DNA can enter a prokaryotic cell in 3 ways (TTC)

A

transformation: competent cells (can take up free DNA) incorporate free DNA into recipient cell and bring genetic change

transduction: DNA from environment captured by pili; one DNA strange usually degraded, other strand passes through cytoplasmic membrane and into cell via a multi-protein competence system
- bacteriophage infections happen here!
- virus DNA package into virions, just can bind cells and inject DNA
- in lytic pathway, phage DNA replicated, use host resources, then viruses lyse host cell and are released to infect new cell
- in lysogenic pathway, viral DNA integrated into host DNA (prophage). this can be induced triggering the lytic cycle
- temperate phages mean they can operate via lytic or lysogenic pathway

2 types of transduction:
transduction recap: virus (phage) transfers DNA from one cell to another
Generalized transduction
- lytic cycle, host cle DNA is accidentally pacakged into a viral particle
- DNA injected into new cell
Specialized transduction
- when a prophage is induced, DNA is excised from genome and packaged into phage particles
- DNA can then be injected into a new cell by that phage particle

conjugation
- HGT requiring cell-cellcontact
mediated by conjugative plasmids
donor cell uses a conjugative pilus to grab a recipient cell
specific DNA is replicated and transferred from donor to recipient using type 4 secretion system

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2
Q

genetic recombination

A

physical exchange of DNA between elements
homologous recombination is important
- important DNA repair mechanie used to repair double strand breaks
- HGT
- foreign DNA with homology to a region of host chromosome can be inserted into genome in place of - or in addition to - the native DNA
sequence
- HR is also important for genome rearrangements – deletions,
duplications, inversions of segments of genomic DNA

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3
Q

Transposable elements

A

mobile genetic elements found in almost all
species. Contain transposase gene (and often extra DNA too) flanked
by inverted repeats.
Transposase enzymes are able to:
-Recognize inverted repeats of DNA sequences
-Cleave that DNA to free “transposable element”
-Cleave another DNA (e.g. chromosomal DNA)
-Insert the transposable element into that DNA
-Wow! That’s one impressive enzyme!!!
-This process called “transposition”.

  • Many transposable elements are conservative (cut and paste) – move
    from one place to another. Others work via a replicative mechanism –
    transposon remains and a copy is produced & inserted elsewhere
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4
Q

Evolution via horizontal gene transfer

A

Much acquired DNA will not be evolutionarily useful and will ultimately
be lost. For example:
o Transposon or recombination-mediated processes
o Random processes/errors during DNA replication or DNA repair
o Genes that provide a selective advantage will be maintained and can
outcompete parental strains that lack this new DNA

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5
Q

Gene names and protein names

A

Gene names, by convention are 4 letters. First 3 letters describe function
– 4th letter designates a specific gene.
Gene names are italicized – first three letters lower case, end with upper
case letter (btuC)

Protein names are the same, but start with an upper-case letter and are
NOT italicized (BtuC).

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6
Q

mutations

A

Spontaneous mutations: Relies on natural mutations that arise by
random processes (see last lecture!). Need large numbers of bacteria
& powerful methods to isolate mutants of interest.

Induced mutations: Expose your organism to agents that increase
mutation rate. E.g. UV light, or various chemicals that interact with
DNA.

Transposon insertion mutations: Introduce a transposon that
inserts randomly into the genome of your organism (e.g. by
transformation or conjugation). Generally disrupts whatever gene it
inserts into. Transposon carries antibiotic resistance gene to isolate
bacteria with a Tn insertion. (See next slide)

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7
Q

Transposon mutagenesis

A
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8
Q

Isolating interesting mutants

A

In some instances, mutants of interest can be isolated by selection –
mutant grows, parent doesn’t
E.g. antibiotic
resistance.
Selection is highly efficient – can identify single mutant with a desired
phenotype out of millions (or more) of cells

auxotroph mutants. Mutants that require a specific nutrient to
grow.

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9
Q

Transposon INsertion site sequencing (INseq)

A

Make a large library of transposon (Tn) mutants - lots of different
bacteria, each with one random Tn insertion.

Sequence the Tn insertion sites - the DNA immediately beside when
the transposon landed. Tells you frequency of each Tn mutant in your
library. Millions of DNA sequence reads (input population)

Expose mutant library to some challenge. Can be anything. E.g. grow
in a medium that lacks a key nutrient. Sequence insertion sites again
(output population)

Comparing input/output populations tells you which genes important
for surviving that challenge (e.g. enzymes that make the key nutrient).

Transposon Insertion Sequencing (INSeq) is a high-throughput technique used to identify essential genes and gene functions in bacterial genomes. This method combines transposon mutagenesis (where transposons are inserted randomly across the genome) with next-generation sequencing to analyze the location and frequency of transposon insertions across a bacterial population. Here’s an overview of how it works and why it’s useful:

Key Steps in INSeq:
Transposon Mutagenesis:

A large population of bacterial cells is generated, each containing a transposon inserted at a random location in the genome.
Transposons disrupt genes upon insertion, meaning that if a transposon inserts into an essential gene, the cell may not survive, reducing the frequency of insertions in essential genes in the final dataset.
Growth and Selection:

The population of transposon-mutant bacteria is grown under specific conditions (e.g., in the presence of a stressor, nutrient limitation, or antibiotic) to identify genes important for survival or adaptation under those conditions.
Cells with transposon insertions in non-essential genes will survive, while insertions in genes essential for the selected condition will result in the loss of those cells.
DNA Extraction and Sequencing:

After selection, DNA is extracted from the surviving bacteria, and regions flanking the transposon insertion sites are amplified and sequenced.
By sequencing these regions, researchers determine the precise locations of transposon insertions across the genome.
Data Analysis:

Sequencing data are analyzed to identify “gaps” in insertion sites, which may indicate essential genes (regions with few or no insertions) or non-essential genes (regions with high transposon insertion frequencies).

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10
Q

DNA sequencing – First complete genome

A

Craig Venter was a major name in DNA
sequencing. Used “Shotgun sequencing”
– sequence random bits of DNA, let
computers figure out how it all fits
together.
Faster/more efficient than more
structured approach used originally

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11
Q

DNA sequencing - Sanger

A

Developed by Fredrick Sanger in 1970s – Nobel prize (one of his two!)
o Based on DNA polymerase building a complementary strand using: (i)
mostly normal dNTPs and (ii) rare special dNTPs that lack a 3’OH
and therefore cannot be elongated further
o Special “ddNTPs” each labelled a
different way (different fluorophores)
o Build DNAs of different lengths, each
terminated with a labelled ddNTP
o Determine sequence based on identity of
terminating residues (e.g. – 26 nt
sequence terminated with a “T”, 27 nt
sequence terminated with a “G”, etc.)

Sanger sequencing, also known as chain-termination sequencing, is a method developed by Frederick Sanger in 1977 to determine the nucleotide sequence of DNA. This technique was the gold standard for DNA sequencing for decades and remains widely used for smaller-scale sequencing tasks, such as verifying specific genes or cloning.

How Sanger Sequencing Works
DNA Replication Setup:

Sanger sequencing relies on the principles of DNA replication. The process begins by denaturing (unwinding) the DNA double strand and then synthesizing a complementary strand using a DNA polymerase enzyme.
A single-stranded DNA template, a primer, DNA polymerase, and four standard nucleotides (dATP, dTTP, dCTP, and dGTP) are required, as well as a small proportion of modified nucleotides called dideoxynucleotides (ddNTPs).
Dideoxynucleotides (ddNTPs):

The key to Sanger sequencing is the use of ddNTPs. These nucleotides lack a hydroxyl group at the 3’ carbon, meaning they cannot form a phosphodiester bond with the next nucleotide. When a ddNTP is incorporated into the growing DNA chain, it terminates synthesis at that position.
Each of the four ddNTPs (ddATP, ddTTP, ddCTP, ddGTP) is labeled with a different fluorescent dye, allowing the termination points to be identified by color.
Chain Termination and Fragment Generation:

During DNA synthesis, the polymerase randomly incorporates either a standard nucleotide or a ddNTP. This random incorporation results in a collection of DNA fragments of varying lengths, each ending at a point where a ddNTP was added.
The sequence length of each fragment corresponds to the position of that nucleotide in the template.
Separation and Detection:

The fragments are then separated by capillary electrophoresis, where shorter fragments move faster and longer fragments move slower through a gel or capillary.
A laser detects the fluorescently labeled ddNTPs at the end of each fragment, and the sequence of colors detected corresponds to the DNA sequence.
Data Output:

The data is displayed as a chromatogram, where each peak represents a nucleotide in the DNA sequence. By reading the chromatogram, researchers can determine the precise sequence of the DNA.

What genes are present/absent & the sequences of each gene
o Metabolic capabilities of an organism
o Virulence genes, antibiotic resistance genes, etc
o Unusual mutations that account for unusual phenotypes
o Discover new genes that might be of medical/industrial interest
o etc…
Provides DNA blueprint required for many studies/analyses
o Genetics approaches (e.g. making mutations to genes)
o Transcriptomics, qPCR, etc – studies of RNA expression
o Proteomics – studies of proteins
o INseq (Tn-seq)

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12
Q

Metagenomics

A

Metagenomics is the study of the complete genetic content of an environmental sample

This approach allows scientists to analyze the genetic diversity and functional potential of entire microbial communities, including bacteria, viruses, fungi, and other microorganisms, in complex environments like soil, ocean water, human gut, or even air.

Key Aspects of Metagenomics
Environmental Sampling:

Instead of isolating and culturing individual organisms, metagenomics collects all DNA from an environmental sample.
DNA is extracted directly from the sample, capturing genetic material from all the organisms present.
DNA Sequencing:

Extracted DNA is sequenced using high-throughput sequencing methods (e.g., Illumina, PacBio) to obtain millions of DNA fragments.
Sequencing strategies include shotgun metagenomics (sequencing all DNA present) or amplicon sequencing (targeting specific genes, like the 16S rRNA gene in bacteria, to identify species diversity).
Bioinformatics Analysis:

Powerful bioinformatics tools are used to assemble the DNA sequences, identify organisms (taxonomic analysis), and predict gene functions.
Metagenomic data analysis can provide insights into microbial community structure, gene abundance, metabolic pathways, and potential interactions between organisms.
Applications of Metagenomics
Environmental Microbiology:

Metagenomics is widely used to study microbial diversity and ecosystem functions in natural environments, such as oceans, soil, and extreme habitats.
It helps in understanding nutrient cycling, decomposition, and ecosystem health.
Human Health:

In the human microbiome, metagenomics reveals the composition of microbial communities in different body sites, such as the gut, skin, and mouth, and their roles in health and disease.
Metagenomics has linked certain microbial profiles to conditions like obesity, inflammatory diseases, and mental health issues.
Biotechnology and Industry:

By identifying novel enzymes and metabolic pathways, metagenomics has enabled the discovery of new biocatalysts for applications in drug development, biofuel production, and agriculture.
Environmental cleanup efforts, like bioremediation, benefit from metagenomics, as it helps identify microbes capable of degrading pollutants.
Antibiotic Resistance:

Metagenomic studies can track the spread of antibiotic resistance genes in different environments, helping to monitor and manage public health risks.
Advantages of Metagenomics
Culture-Independent: It enables the study of microorganisms that cannot be easily cultured in the lab, which is the vast majority of microbes.
Comprehensive View: Provides a holistic understanding of microbial ecosystems, capturing all genetic material, including viruses and rare species.
Functional Insight: Metagenomics reveals not only what organisms are present but also the genes and metabolic functions they contribute to their environment.

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13
Q

Transcriptomics: RNA-seq

A

RNA can be converted to DNA using a process called reverse
transcription

Why Convert RNA to cDNA?:

DNA is more stable than RNA, making it easier to handle and sequence.
The reverse transcription step enables researchers to study the full range of RNA in the cell, including both coding and non-coding RNA molecules, by leveraging sequencing technologies optimized for DNA.
Reverse transcription is, therefore, a critical step in RNA-seq, enabling the study of gene expression and transcript structure from the RNA present in cells at any given time.

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14
Q

Proteomics

A

mass spectrometry!!!! to identify proteins/protein levels

Proteomics seeks to identify, quantify, and characterize proteins to understand their functions, interactions, and roles in cellular processes.

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15
Q

Transcription initiation:
Promoters

A

Transcriptional initiation is guided by DNA sequences called promoters - DNA sequences bound by factors that promote
transcriptional initiation.

Reside upstream of (before) genes.

Whether or not a sequence acts as a promotor & if promoter is active
is dictated by binding of sigma factors (next slide) & regulatory
proteins (future lectures) to the promoter region.

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16
Q

Transcriptional initiation:
Sigma factors

A

Transcription uses an enzyme called RNA polymerase

A special subunit of RNA polymerase called a sigma factor binds DNA
as an essential step in initiating transcription

Bacteria encode multiple different sigma factors that are produced under
different conditions. They recognize different sequences (promoters) –
see next slide.

The housekeeping (most commonly used/most important) sigma factor is called or �70 (or RpoD) – it recognizes two sequences upstream of the transcriptional start site.

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17
Q

Transcription in bacteria: A bit more detail

A

RNA polymerase core enzyme made up of 5
subunits: ⍺ (2 copies), β, β’, ω. Holoenzyme
also includes � (sigma) subunit (sigma factor)
o Sigma factor binds promoter region, then
dissociates from core enzyme
o Core enzyme unwinds DNA to expose template
- forms transcription bubble
o Using NTPs (ATP, CTP, GTP, UTP) as
substrates and the template strand as guide, the RNA chain is built one nucleotide at a time
o Ultimately, RNA polymerase will encounter a transcriptional terminator (see next slide) and will dissociate from the template & release the RNA

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18
Q

Termination of transcription

A

Transcription will (generally) continue until RNA polymerase (RNAP)
encounters a transcriptional terminator. RNAP then dissociates from
DNA, stops making RNA & releases transcript

Intrinsic (rho-independent) terminators form when RNA hairpin structures form, followed by a string of “U” residues. U residues act as pause signal for RNAP – formation of hairpin forces RNAP off template.

Rho-dependent terminators: A protein called Rho binds RNA as it is being transcribed and causes RNA polymerase to dissociate after it encounters certain sequences

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19
Q

Types of transcripts

A

There are 3 major classes of RNAs
Messenger RNA (mRNA) – converted to protein via translation
Transfer RNA (tRNA) – functional RNAs, used in translation process
Ribosomal RNA (rRNA) - functional RNAs, used in translation process

mRNAs contain both Open reading frames (ORFs) and untranslated regions (UTRs). ORFs are translated to protein, UTRs are parts of the mRNA transcript that are not translated into protein

mRNAs that encode multiple ORFs are polycistronic. Such genes are arranged in an operon. Genes in an operon are cotranscribed.

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20
Q

In a simple mRNA encoding a single open reading frame (ORF):

A

5’UTR – everything from first transcribed residue (+1) through the start codon of gene. Contains ribosome binding site (RBS), more?

ORF – Start codon (e.g. AUG) through stop codon (e.g. UAA)

3’ UTR – everything from the stop codon of the gene through the final transcribed residue. Often contains transcriptional terminator sequences

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21
Q

Some ways transcription is different in eukaryotes

A

Location:
Eukaryotes: Transcription occurs in the nucleus, where DNA is separated from the cytoplasm by a nuclear membrane. After transcription, the mRNA undergoes processing and is transported out of the nucleus for translation in the cytoplasm.
Prokaryotes: Transcription occurs in the cytoplasm since they lack a nucleus, allowing transcription and translation to occur simultaneously.

RNA Polymerases:
Eukaryotes: Have three main RNA polymerases (RNA Polymerase I, II, and III), each dedicated to transcribing different types of RNA:
RNA Polymerase I synthesizes rRNA (ribosomal RNA).
RNA Polymerase II synthesizes mRNA (messenger RNA).
RNA Polymerase III synthesizes tRNA (transfer RNA) and other small RNAs.
Prokaryotes: Use a single RNA polymerase to transcribe all types of RNA.

Promoters and Transcription Factors:
Eukaryotes: Promoters are complex and often include a TATA box along with other regulatory sequences. Transcription initiation requires general transcription factors (TFs)!!!!! and specific activator proteins !!!!! that help RNA polymerase bind to the promoter.
Prokaryotes: Promoters are simpler, typically with -10 and -35 regions recognized by sigma factors!!!!!. These sigma factors are the main initiation proteins, binding RNA polymerase to the promoter directly.

mRNA Processing:
Eukaryotes: The primary mRNA transcript (pre-mRNA) undergoes extensive processing:
5’ Capping: A modified guanine nucleotide is added to the 5’ end for stability and recognition.
3’ Polyadenylation: A poly-A tail is added to the 3’ end to protect mRNA from degradation.
Splicing: Introns (non-coding sequences) are removed, and exons (coding sequences) are joined together to produce a mature mRNA.
Prokaryotes: mRNA is typically not processed, as prokaryotic genes lack introns. Transcription and translation can occur simultaneously.

Regulation Complexity:
Eukaryotes: Gene expression regulation is complex and occurs at multiple levels (epigenetic, transcriptional, post-transcriptional). Transcription can be influenced by DNA packaging (chromatin structure) and modifications like histone acetylation and methylation.
Prokaryotes: Regulation is generally simpler, primarily at the transcriptional level, often via operons (gene clusters with a single promoter). Gene expression is regulated by repressors, activators, and sigma factors.

Termination:
Eukaryotes: Termination is less defined; transcription may continue well past the end of the gene, and the transcript is cleaved at a specific site, followed by polyadenylation.
Prokaryotes: Termination is more straightforward and occurs by two main mechanisms: Rho-dependent and Rho-independent termination, where the RNA forms a structure that signals transcription to stop.

mRNA Longevity:
Eukaryotes: mRNA is generally more stable, with some transcripts lasting hours or even days, thanks to 5’ caps and poly-A tails.
Prokaryotes: mRNA is typically less stable and degrades rapidly (within minutes), allowing prokaryotes to quickly adjust gene expression in response to environmental changes.

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22
Q

Transcription in Archaea

A

RNA Polymerase:
Archaea: Have a single RNA polymerase that closely resembles eukaryotic RNA polymerase II in structure and function, containing multiple subunits.
Similarity to Eukaryotes: Archaeal RNA polymerase is more complex than bacterial RNA polymerase and includes homologous subunits to those found in eukaryotic RNA polymerase II.
Similarity to Bacteria: Like bacteria, Archaea have only one type of RNA polymerase responsible for transcribing all types of RNA (mRNA, tRNA, and rRNA).
2. Promoters and Transcription Factors:
Promoter Structure: Archaeal promoters often contain TATA boxes and BRE (B recognition element) sequences, similar to eukaryotes.
Transcription Factors: Instead of bacterial sigma factors, Archaea use transcription factors TBP (TATA-binding protein) and TFB (transcription factor B), which are homologous to the eukaryotic transcription factors involved in recruiting RNA polymerase to the promoter.
Similarity to Eukaryotes: These transcription factors bind to the promoter in a manner similar to eukaryotic transcription initiation, where TBP binds to the TATA box and TFB binds to the BRE sequence.
3. mRNA Processing:
Lack of Extensive Processing: Archaeal mRNA generally does not undergo extensive processing like eukaryotic mRNA does. There is usually no 5’ capping, polyadenylation, or splicing since Archaea lack introns in most genes.
Exception: Some Archaea have introns in tRNA and rRNA genes, which are spliced out, but this is far less common than in eukaryotes.
4. Transcription Regulation:
Regulatory Proteins: Archaea use regulatory proteins, such as repressors and activators, similar to bacteria, to control gene expression.
Similar to Bacteria: Many regulatory mechanisms in Archaea resemble bacterial mechanisms, with transcriptional repressors and activators binding directly to DNA to either inhibit or enhance transcription.
Unique to Archaea: Some Archaea have regulatory proteins that are specific to their domain, with functions adapted to extreme environments (e.g., high temperatures, acidic conditions).
5. Transcription Termination:
Mechanisms: Archaeal transcription termination is less well understood but may involve sequences or structures similar to those in bacteria. Evidence suggests that some Archaea have termination sequences resembling the Rho-independent termination of bacteria.
Similarity to Eukaryotes and Bacteria: Archaea do not have a distinct Rho factor like bacteria; termination often relies on intrinsic mechanisms encoded in the DNA sequence.

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23
Q

Protein folding/chaperones

A

Functions: initial folding, re-folding denatured proteins, helping
subunits in multimeric proteins come together, etc.

There are RNA chaperones that help RNAs adopt the correct
structure.

Special chaperones are activated in response to high or low temperatures
(heat shock / cold shock proteins) to assist with protein/RNA folding

In E. coli DnaJ/DnaK & GroEL/GroES are major chaperones that assist in protein folding – essential proteins for the cell to survive. Amongst the most abundant proteins in the cell

Use energy from ATP hydrolysis
to enable unfolded or unstable
conformations to re-fold in a
controlled fashion (precise
mechanisms complex & debated)

24
Q

Protein secretion in prokaryotes

A

Tat pathway (not shown) secretes pre-folded proteins across membrane
o The Sec secretion system recognizes a signal sequence in the first ~20
amino acids of protein - translocates unfolded protein before it folds
In Sec pathway, proteins are either:
1) Passed across cytoplasmic membrane (SecA pathway)
2) Recognized by RNA/protein complex – signal recognition particle - and
inserted into the cytoplasmic membrane (SRP pathway).
Both pathways:
1) Pass the unfolded protein through a membrane channel - Sec YEG
translocon
2) Require ATP for energy
3) Signal sequence is cleaved following translocation

All proteins are synthesized by ribosomes in the cytoplasm, but many
proteins are required in other locations (e.g. cytoplasmic membrane,
periplasm, outer membrane, outside of cell)

use translocase systems that transport proteins across (and into) the
cytoplasmic membrane.

Most translocated proteins contain a signal sequence at the N-terminus
(within first ~25 amino acids) that targets the protein to a particular
secretion system – often removed after translocation.
The Sec secretion system (see next slide) & twin arginine translocase
(Tat) are ubiquitous in prokaryotes

Protein Secretion in Gram-Positive Bacteria
Structure: Gram-positive bacteria have a single cell membrane and a thick peptidoglycan cell wall.
Secretion Systems:
Sec Pathway (Sec-dependent): This is the most common pathway, transporting proteins across the cell membrane in an unfolded state.
Signal Peptide: Proteins destined for secretion contain an N-terminal signal peptide that directs them to the Sec translocon complex.
Mechanism: After transport, the signal peptide is cleaved, and the protein folds into its functional form outside the membrane.

Tat Pathway (Twin-arginine translocation): This pathway transports folded proteins, which is especially important for proteins that require cofactors inserted in the cytoplasm before export.
Signal Sequence: The Tat signal sequence contains a twin-arginine motif (RR) that directs proteins to the Tat translocase.

25
Q

Regulating transcriptional initiation

A

regulating transcriptional initiation is most common/important

control whether or not RNA polymerase binds a promoter and initiates transcription (more accurately, the rate at which that occurs).

Largely accomplished by DNA-binding regulatory proteins called transcription factors

Sensing is key! You need to know which genes to turn on and off and when – must be able to detect cues from your environment/cellular status

26
Q

DNA-binding regulatory proteins

A

Many regulatory proteins are DNA-binding proteins

Have DNA-binding domains that usually bind the major groove of DNA helix

DNA binding proteins often recognize a
consensus sequence

Often DNA sequences with direct or
inverted repeats are bound by homodimers
- one monomer binds each repeat &
dimerization required. Ensures specificity

27
Q

Activators and repressors

A

Transcription factors that promote transcription are called activators
and those that inhibit transcription are called repressors. Some transcription factors both (activator of one gene, repressor of another)

Activators often work by binding DNA at promoter & recruiting RNA polymerase (sigma factor) to begin transcription. Gene
under “positive control”

Repressors bind DNA & (often) prevent RNAP DNA binding or transcriptional initiation after it binds. Sequence bound by
repressor often called operator. Gene under “negative control”

28
Q

Allosteric regulatory proteins

A

Some transcription factors are regulated allosterically – binding of an
effector - usually a small molecule – that activates or inactivates the protein.
Often works by altering whether it binds DNA

Inducers = effectors that “turn on” ACTIVATOR proteins or that inactivate
repressor

Corepressors = effectors that
activate REPRESSOR proteins

An inducible system is one
that is off by default, but can
be turned on

A repressible
system is one that is on by
default, but can be turned off.

A single gene is often
controlled by both inducible
and repressible systems.

29
Q

Example of a repressible system:
Arginine biosynthesis

A

ArgR is a repressor protein that controls the expression of an arginine biosynthesis operon

When arginine is present, it acts as a co-repressor. (effectors that activate repressor proteins)

When arginine levels are low, ArgR isn’t bound by arginine, doesn’t bind DNA – genes are expressed and arginine is synthesized by cell

When arginine levels are high, it binds ArgR, enabling ArgR to bind the operator & prevent transcription of this operon

Role in Arginine Biosynthesis Regulation
ArgR is a negative regulator of genes involved in arginine synthesis. When arginine levels are sufficient in the cell, ArgR binds to arginine, allowing it to repress transcription of genes needed for synthesizing more arginine.
Genes Regulated by ArgR: ArgR typically controls the arg operon, which includes genes encoding enzymes for arginine biosynthesis. The binding of ArgR to operator sequences in the promoter regions of these genes blocks transcription when arginine is abundant.
2. Mechanism of Action
Arginine as a Corepressor: ArgR binds to arginine, which then allows the ArgR-arginine complex to bind to specific DNA sequences (operators) near arginine biosynthesis genes.
Binding to DNA: Once bound to arginine, ArgR undergoes a conformational change that enables it to bind to DNA more effectively. This binding to the operator sequences prevents RNA polymerase from accessing the promoter and thus blocks transcription.
Repression in Arginine Excess: By repressing the arginine biosynthesis pathway in response to high intracellular arginine levels, ArgR conserves cellular resources, preventing unnecessary synthesis of arginine.

30
Q

The (classic!) lac operon

A

Lactose is a good energy source for many bacteria

Machinery for breaking down lactose is encoded by the lac operon (requires both:
lactose AND low glucose levels)

Expressing these genes in absence of lactose not useful – to prevent this, LacI repressor protein binds lac Operator, prevents transcription

When lactose is available, a lactose isomer called allolactose!!! binds LacI!! & inactivates it (allolactose = inducer)

Inducible system - catabolic systems are often inducible

Glucose regulation is indirect
(cAMP is direct inducer)
In the presence of glucose,
production of cAMP is inhibited.
Low cAMP levels in cell

For lac operon to be expressed, also
requires CRP (cAMP receptor
protein) to bind cAMP. cAMPbound CRP binds promoter region
& recruits RNA polymerase

The regulation of the lac operon involves two main mechanisms: repression by the lac repressor and activation by cAMP-CRP (catabolite activator protein):

Repression by the Lac Repressor:

In the absence of lactose, the lac repressor (produced by the lacI gene) binds to the operator region (O), preventing RNA polymerase from transcribing the operon. This repression conserves energy by preventing the synthesis of enzymes for lactose metabolism when lactose is not available.
When lactose is present, it is converted into allolactose, which acts as an inducer. Allolactose binds to the lac repressor, causing a conformational change that reduces its affinity for the operator. This leads to the release of the repressor from the operator, allowing RNA polymerase to transcribe the lac operon genes.
Activation by cAMP-CRP:

The lac operon is also subject to positive regulation. When glucose levels are low, the intracellular concentration of cAMP increases. cAMP binds to CRP (catabolite activator protein), forming the cAMP-CRP complex.
This complex binds to a site near the lac promoter and enhances the binding of RNA polymerase, increasing the transcription of the lac operon. Conversely, when glucose is abundant, cAMP levels drop, reducing the activation of the lac operon.

Summary of Lac Operon Regulation
Absence of Lactose:

The lac repressor binds to the operator, blocking transcription.
No enzymes for lactose metabolism are produced.
Presence of Lactose:

Allolactose binds to the lac repressor, leading to its dissociation from the operator.
RNA polymerase can now transcribe the lac operon genes.
Glucose Availability:

High glucose → low cAMP → reduced transcription of the lac operon.
Low glucose → high cAMP → cAMP-CRP complex promotes transcription.

31
Q

cAMP: example of a signaling molecule

A

Cyclic AMP (cAMP) is an example of a
signaling molecule or second messenger

In bacteria, nucleotide-based molecules are
extensively used for this: cAMP, (p)ppGpp,
cyclic-di-GMP and more!

Produced in response to some signal(s) – they then regulate multiple different processes in the cell – impact the activity of multiple different regulatory (or non-regulatory) proteins

E.g. ppGpp produced in response to amino
acid starvation. ppGpp shuts down protein
synthesis & induces amino acid biosynthesis in a process that is called stringent response

32
Q

Quorum sensing

A

a form of cell-to-cell communication that enables bacteria to coordinate their behavior based on population density. This process allows bacteria to monitor their surroundings and regulate gene expression collectively, enabling behaviors that are beneficial at high cell densities, such as biofilm formation, virulence factor production, and bioluminescence. Here’s a detailed overview of quorum sensing, including its mechanisms, components, and implications in microbial communities:

Key Features of Quorum Sensing
Cell Density-Dependent Communication:

Quorum sensing relies on the production and detection of signaling molecules called autoinducers. As the bacterial population grows, the concentration of these signaling molecules increases in the environment.

When the concentration of autoinducers reaches a certain threshold, it triggers a change in gene expression in the bacterial population. This coordinated response allows the community to behave collectively rather than as individual cells.

**Used to coordinate group behaviours like biofilm formation, virulence,
etc. Only useful to carry out these activities at high cell densities

Basic idea: Produce autoinducer (small molecule), it diffuses away.
Doesn’t accumulate except at high density. Detect high density – know
you’re in a group – activate group behaviours

Different autoinducers exist. Acyl homoserine lactones (AHL) common
in Gram-negative bacteria – different versions of AHL in different
species.
o Quorum sensing is a form of chemical communication. It is used by
bacteria, archaea and eukaryotic microbes

33
Q

Two-component regulatory systems

A

Two-component regulatory systems (TCS) are essential signaling mechanisms used by bacteria (and some archaea) to sense and respond to changes in their environment. These systems allow cells to detect environmental signals and trigger appropriate responses, enabling them to adapt to varying conditions, such as nutrient availability, stress, or changes in temperature. Here’s an overview of the components, mechanism, and significance of two-component regulatory systems:

Components of Two-Component Regulatory Systems
Sensor Kinase:

The sensor kinase is a membrane-bound protein that detects environmental signals (e.g., changes in osmolarity, pH, temperature, or the presence of specific molecules).
Upon sensing a stimulus, the sensor kinase undergoes autophosphorylation, where a phosphate group from ATP is transferred to a specific histidine residue in the kinase.
Response Regulator:

The response regulator is a cytoplasmic protein that receives the phosphate group from the sensor kinase.
Upon phosphorylation, the response regulator typically undergoes a conformational change that activates its ability to regulate gene expression, often through binding to DNA and promoting or inhibiting transcription of target genes.
Mechanism of Action
Signal Detection:

The sensor kinase detects a specific environmental signal through its sensory domain. Different sensor kinases are tuned to different stimuli.
Autophosphorylation:

Upon detecting a stimulus, the sensor kinase autophosphorylates, transferring a phosphate group from ATP to a conserved histidine residue in the kinase.
Phosphotransfer to Response Regulator:

The phosphorylated sensor kinase transfers the phosphate group to a conserved aspartate residue in the response regulator.
Regulation of Gene Expression:

The phosphorylated response regulator can then interact with target genes, typically affecting transcription. This can involve:
Activation of transcription by promoting RNA polymerase binding to the promoter.
Repression of transcription by blocking RNA polymerase access to the promoter.
Dephosphorylation:

To reset the system, the phosphate group can be removed from the response regulator, often through the action of specific phosphatases or through spontaneous hydrolysis, allowing the system to respond to new signals.

34
Q

Transcriptional regulation in Archaea

A

Despite differences in transcription
mechanisms (see lecture 4-1),
transcriptional regulatory systems in
Archaea often analogous with bacterial
systems
o Activators/repressors bind DNA to
affect recruitment of RNA polymerase
o Two-component regulatory systems
also present in Archaea…but not as
common as in bacteria
o More complex regulation is observed in
Eukarya

35
Q

Regulation at the level of RNA

A

Transcriptional attenuation is regulation that involves terminating
mRNA synthesis before gene(s) are transcribed

The stability of mRNAs can be controlled – how long before they are
degraded (longer lifetime, more translation, more protein produced)

Translation efficiency can be controlled – usually whether or not
RBS is free to be bound by the ribosome RBS structure

36
Q

RBS

A

Ribosome binding sites (RBS) are essential sequences in mRNA that help initiate translation, the process of protein synthesis. Located just upstream of the start codon (AUG), these sequences help recruit the ribosome to the mRNA, aligning it correctly to ensure that translation begins at the right location.

In bacteria, the most well-known RBS is the Shine-Dalgarno sequence, which is complementary to a segment of the 16S rRNA within the small ribosomal subunit. This pairing helps position the ribosome directly at the start codon, enhancing translation efficiency.

In eukaryotes, ribosome binding doesn’t involve a Shine-Dalgarno sequence. Instead, the ribosome binds to the 5’ cap of the mRNA and scans until it finds the first AUG start codon.

37
Q

mRNA lifetime effects protein levels

A

Bacterial transcripts do not last long – lifetime (half-life) spans from
seconds to ~an hour. How long an mRNA lasts affects how many
protein molecules will be made from that transcript

All cells contain multiple ribonucleases
(RNases) that degrade mRNAs

Different mRNAs can have very
different half-lives

Regulatory proteins/RNAs can bind
to mRNA and impact its half-life

38
Q

RNA structures that “shut off ” gene expression

A

During transcription, the formation of rho-independent (intrinsic) transcriptional terminators before a gene’s transcription is complete leads to transcriptional attenuation.

For translation to initiate, the ribosome binding site (RBS) of the gene needs to be “free” to bind ribosome, not involved in base-pairing

Formation of stem-loop structures in mRNA can shut off gene expression if they: (i) involve the RBS, or (ii) involving the formation of a transcriptional terminator upstream of a gene. This can be regulated.

39
Q

transcriptional attentuation and rho-independent (intrinsic)

A

Transcriptional attenuation and rho-independent (intrinsic) termination are mechanisms that bacteria use to regulate gene expression and terminate transcription.

  1. Transcriptional Attenuation
    Transcriptional attenuation is a regulatory mechanism that halts transcription prematurely based on the cell’s metabolic needs. It’s commonly found in operons controlling amino acid biosynthesis, like the trp (tryptophan) operon in E. coli.

Mechanism: In this process, a leader sequence in the mRNA has regions that can form alternative secondary structures. Depending on the concentration of specific molecules (like charged tRNAs), the leader sequence can form either a terminator or anti-terminator structure.
When amino acids are plentiful, a terminator hairpin forms, causing RNA polymerase to stop transcription early.
When amino acids are scarce, an anti-terminator structure forms instead, allowing transcription to proceed and produce the full-length mRNA.
2. Rho-Independent (Intrinsic) Termination
Rho-independent, or intrinsic termination, is a transcription termination mechanism that does not require the rho protein.

Mechanism: This type of termination relies on specific sequences in the mRNA that form a stable hairpin structure followed by a string of uracil (U) residues.
As RNA polymerase transcribes this region, the hairpin structure destabilizes the RNA-DNA hybrid within the polymerase.
The string of uracils further weakens the interaction, causing RNA polymerase to release the mRNA and detach from the DNA, ending transcription.
In summary:

Attenuation is a regulatory control that adjusts transcription levels based on metabolic conditions, often involving alternative secondary structures in mRNA.
Rho-independent termination is a sequence-dependent termination mechanism that uses mRNA structure to stop transcription without the need for additional proteins.

40
Q

rho-independent vs rho dependent transcription

A

Rho-Independent Termination
Rho-independent termination, also called intrinsic termination, is a termination process that does not require any additional protein factors, like the rho protein.

Mechanism: It relies on specific sequences in the mRNA:
A GC-rich hairpin structure followed by a poly-U tail (string of uracils).
When RNA polymerase transcribes this region, the hairpin structure destabilizes the interaction between the RNA and DNA, and the weak bonds in the poly-U tail allow the mRNA to detach from the DNA template.
Result: The RNA polymerase pauses and then releases the mRNA, ending transcription.
2. Rho-Dependent Termination
Rho-dependent termination is a different form of transcription termination that requires the rho protein, a helicase that tracks along the mRNA.

Mechanism:
Rho binds to a specific site on the mRNA called the rut site (rho utilization site), typically a sequence rich in cytosine and poor in guanine.
Once bound, rho moves along the mRNA toward RNA polymerase by using ATP for energy.
When rho catches up to RNA polymerase (often stalled at a pause site), it unwinds the RNA-DNA hybrid, causing RNA polymerase to release the mRNA.
Result: Transcription is terminated when rho disrupts the RNA-DNA complex.
3. Attenuation (often misunderstood as “rho-dependent attenuation”)
Attenuation is a regulatory mechanism, not a termination mechanism, though it can prevent transcription from completing under certain conditions.

Mechanism:
Operons such as the trp operon use attenuation to sense the cell’s amino acid levels.
This involves a leader sequence with regions that form alternative RNA structures, either a terminator or an anti-terminator.
Attenuation is independent of rho; it relies instead on translation dynamics and the availability of charged tRNA molecules to form different structures, controlling whether transcription terminates prematurely.

41
Q

sRNAs

A

All cells encode regulatory RNAs – noncoding RNA whose function is to regulate gene expression

Bacterial sRNAs (~50-300 nt long) generally exert effects by base-pairing to target mRNA(s). Base-pairing with sRNA affects RBS availability and/or RNase targeting, thereby controlling how much protein gets made

sRNAs (small RNAs) are short, non-coding RNA molecules typically found in bacteria and some archaea, and they play crucial roles in regulating gene expression. They are generally about 50-500 nucleotides long and can influence gene expression at both the transcriptional and post-transcriptional levels.

Key Roles and Mechanisms of sRNAs:
Post-Transcriptional Regulation (most common)

mRNA Stability: sRNAs can bind to mRNAs, either protecting them from degradation or promoting it by making them accessible to RNases.
Translation Inhibition or Activation: Many sRNAs bind near the ribosome binding site (RBS) on mRNAs. This binding can block ribosome access, preventing translation, or expose the RBS, enhancing translation.
Examples:
MicF sRNA in E. coli binds to the ompF mRNA, inhibiting its translation under stress.
RybB sRNA regulates multiple mRNAs related to membrane proteins during envelope stress in bacteria.
Transcriptional Regulation

While less common, some sRNAs can interact with DNA-binding proteins or transcription factors, influencing the transcription of specific genes.
Example: sRNAs can bind and sequester proteins like Hfq, which is an RNA chaperone that stabilizes interactions between sRNAs and target mRNAs.
Protein Sequestration

Some sRNAs bind directly to regulatory proteins, affecting their activity and altering gene expression indirectly.
Example: CsrB sRNA in E. coli binds to the CsrA protein, preventing it from regulating mRNAs involved in metabolism and motility.
Stress Response and Environmental Adaptation

sRNAs play critical roles in responding to environmental stress, such as changes in temperature, osmolarity, or nutrient availability. They allow bacteria to adjust their physiology rapidly by upregulating or downregulating specific genes.
Example: DsrA sRNA in E. coli is involved in cold shock response and can activate rpoS, a sigma factor that induces stress-response genes.
Pathogenesis in Bacteria

In pathogenic bacteria, sRNAs help regulate genes related to virulence, allowing pathogens to adapt to host environments and evade the immune response.
sRNA Chaperones
Some sRNAs require protein chaperones, such as Hfq, to stabilize their structure and facilitate binding to their target mRNAs. Hfq assists in many sRNA-mRNA interactions, enhancing the regulatory function of sRNAs in bacteria.

Summary
sRNAs are versatile, non-coding regulatory RNAs primarily acting at the post-transcriptional level to regulate gene expression. By binding to mRNAs or proteins, they help fine-tune bacterial responses to environmental changes, stress, and other regulatory needs.

42
Q

sRNAs - Hfq

A

Many sRNAs have limited sequence complementarity to target mRNAs
(perhaps only a ~ 5-11 nt stretch base pairs)

An RNA chaperone (and more!) called Hfq is usually essential for
mediating this regulation

Binds to both RNAs (sRNA and mRNA) to stabilize their interaction - in some cases also appears to recruit RNases to mediate degradation

43
Q

Riboswitches

A

Riboswitches are ligand-binding RNAs

binding allows riboswitches to sense their environment

Riboswitches reside in the 5’UTR of certain
bacterial mRNAs – regulate expression of
downstream gene(s) on same mRNA

Ligand binding changes RNA structure in
5’UTR – this change induces or represses
expression of downstream genes

Riboswitches have been found in all 3
domains of life, but mostly identified/
characterized in bacteria

Very different from sRNAs

Riboswitches are segments of RNA, typically located in the 5′ untranslated regions (UTRs) of bacterial mRNAs, that regulate gene expression by directly binding small molecules. They act as molecular “switches” that control transcription, translation, or mRNA stability based on the presence of specific metabolites or ions, allowing bacteria to adjust gene expression rapidly in response to changing environmental conditions.

Structure and Function of Riboswitches
Riboswitches have two primary regions:

Aptamer Domain: This is the “sensor” part of the riboswitch that directly binds to a specific small molecule (ligand) with high specificity. Binding of the ligand induces a conformational change in the riboswitch structure.
Expression Platform: This is the “response” part of the riboswitch that undergoes structural changes in response to ligand binding, influencing gene expression by affecting transcription, translation, or mRNA stability.
Mechanisms of Riboswitch Regulation
Riboswitches regulate gene expression at two main levels:

  1. Transcriptional Control
    Mechanism: When the ligand binds to the aptamer domain during transcription, it triggers a structural shift in the expression platform, typically forming a transcriptional terminator (a stem-loop structure followed by a poly-U tail). This terminator causes RNA polymerase to detach, stopping transcription prematurely.
    Example: The B. subtilis rib operon riboswitch binds FMN (flavin mononucleotide). When FMN is abundant, the riboswitch terminates transcription, reducing the production of riboflavin biosynthesis enzymes.
  2. Translational Control
    Mechanism: In this case, ligand binding alters the riboswitch structure to either expose or occlude the ribosome binding site (RBS), affecting the translation of the downstream gene.
    Example: The E. coli thiM riboswitch binds thiamine pyrophosphate (TPP). When TPP levels are high, the riboswitch structure changes to block the RBS, preventing ribosome binding and thus translation of thiM mRNA.
    Types of Ligands Recognized by Riboswitches
    Riboswitches can bind a variety of small molecules, including:

Amino acids (e.g., lysine riboswitch)
Vitamins and cofactors (e.g., TPP, FMN, and cobalamin riboswitches)
Metal ions (e.g., magnesium-binding riboswitches)
Nucleotides (e.g., purine riboswitches that bind guanine or adenine)
Biological Significance of Riboswitches
Metabolic Regulation: Riboswitches allow bacteria to conserve resources by downregulating biosynthesis pathways when sufficient metabolites are available.
Environmental Adaptation: Riboswitches enable bacteria to respond rapidly to changes in nutrient availability, stress, or metabolic needs, contributing to bacterial survival and competitiveness.
Antibiotic Targets: Some riboswitches are unique to bacteria and essential for their survival, making them attractive targets for developing antibiotics that could disrupt bacterial metabolic pathways.
Summary
Riboswitches are RNA elements that bind small molecules to regulate gene expression at the transcriptional or translational level. By acting as direct sensors of cellular metabolites, they help bacteria fine-tune gene expression based on the immediate biochemical environment, providing a versatile means of regulating metabolic pathways efficiently and responsively.

44
Q

extra info on riboswitches

A
45
Q

Post-translational regulation
(regulating protein levels/activity)

A

An enzyme within a given biosynthetic pathway is sometimes inhibited by
the end product of that pathway – feedback inhibition

Activity of proteins can also be regulated by protein-protein interactions (one protein binds another to control its activity

Protein activity can be changed via post-translational modifications – a chemical moiety such as a phosphate group is added to a specific amino acid residue of a protein (changes activity, or turns it “on”/“off ”)

Proteolytic Cleavage

Mechanism: Specific cleavage of a protein by proteases can activate or inactivate it. This irreversible modification often converts an inactive precursor protein into an active form.
Effect: Proteolytic cleavage can activate enzymes (e.g., digestive enzymes), hormones, or signaling proteins.
Example: Proinsulin is cleaved to form active insulin, and caspases are activated by cleavage in response to apoptotic signals.

Phosphorylation

Mechanism: Phosphate groups are added to specific amino acids, typically serine, threonine, or tyrosine, through the action of kinases, and removed by phosphatases.
Effect: Phosphorylation can change a protein’s activity (activating or inactivating it), alter its stability, or affect its interaction with other proteins. This mechanism is particularly important in signal transduction pathways, like the MAP kinase pathway.
Example: In response to growth signals, phosphorylation activates kinases involved in cell cycle progression.

46
Q

Protein degradation/turnover

A

Like RNA, protein can also be degraded and their building blocks recycled.
This is accomplished by enzymes called proteases

Proteases are essential for clearing away and recycling misfolded proteins

In other cases proteolysis can be very specific and regulated mechanism to
clear away specific proteins in the cell

47
Q

Overview of (some) regulatory mechanisms

A
48
Q

Enzymes are catalysts. They lower the
activation energy of a reaction

A

Enzymes work by lowering the activation energy of a reaction

They do NOT change the energetics (ΔG) or the equilibrium of the reaction

By lowering the activation energy, enzymes increase the rate of a reaction – in some cases by many, many orders of magnitude

49
Q

How do enzymes increase reaction rates &
lower activation energies??

A

Local concentrations of substrates are increased at the active site
of the enzyme & are oriented properly for the reaction to take
place

Many enzymes alter the electronic distribution of the
substrate(s), which enhances reactivity

Stabilization of transition states of the reaction

Some enzymes use of coenzymes or prosthetic groups – some of
which employ metallic elements (E.g. - Fe, Mg, Zn, Co…) that can
help with challenging chemistry

50
Q

Controlling enzyme activity:
Competitive inhibitors

A

Competitive inhibitors of an enzyme “fit” in the same active site as the substrates – inhibit substrate binding (and thus the reaction)

Competitive inhibitors are molecules that inhibit enzyme activity by competing with the substrate for binding to the active site of the enzyme. This type of inhibition is reversible and is a common way to regulate enzyme activity in metabolic pathways.

Mechanism of Competitive Inhibition
Binding Site: Competitive inhibitors have a structure similar to the enzyme’s natural substrate, allowing them to fit into the enzyme’s active site.
Competition with Substrate: By occupying the active site, the inhibitor prevents the substrate from binding. However, if the concentration of the substrate is high enough, it can outcompete the inhibitor for binding to the enzyme.
Reversibility: Because competitive inhibitors do not permanently alter the enzyme, increasing the substrate concentration can overcome the inhibition, allowing normal enzyme activity to resume.

51
Q

Controlling enzyme activity:
Allosteric activators/inhibitors

A

Allosteric regulation of an enzyme: Catalytic activity of an enzyme controlled by a molecule (“effector”) that binds the enzyme
at a location other than the active site.

Allosteric activators and inhibitors are molecules that regulate enzyme activity by binding to a site on the enzyme other than the active site, called the allosteric site. This binding induces conformational changes in the enzyme, altering its activity either positively (allosteric activation) or negatively (allosteric inhibition). Allosteric regulation plays a crucial role in finely tuning enzyme activity, especially in complex metabolic pathways.

Mechanism of Allosteric Regulation
Allosteric Site: Allosteric regulators bind to a specific site on the enzyme that is separate from the active site. This binding does not directly block the substrate from binding to the enzyme.
Conformational Changes: Binding of an allosteric regulator induces a structural change in the enzyme that can either enhance or inhibit its catalytic activity.
Cooperative Binding: Many allosteric enzymes exhibit cooperative binding, meaning that binding of a regulator (or substrate) to one subunit can affect the activity of other subunits. This is common in enzymes with quaternary structures, like hemoglobin.
Types of Allosteric Regulation
Allosteric Activators

Effect: Allosteric activators increase enzyme activity. Binding of an activator stabilizes the enzyme’s active form, making it easier for the substrate to bind or enhancing the enzyme’s catalytic efficiency.
Example: ADP acts as an allosteric activator for phosphofructokinase (PFK), a key enzyme in glycolysis. When ADP levels are high (indicating low energy), it binds to PFK, increasing its activity and thus enhancing the glycolytic pathway to produce more ATP.
Allosteric Inhibitors

Effect: Allosteric inhibitors reduce enzyme activity. They stabilize an inactive or less active form of the enzyme, making it more difficult for the substrate to bind or decreasing the enzyme’s catalytic efficiency.
Example: ATP acts as an allosteric inhibitor of phosphofructokinase (PFK). When ATP levels are high, it binds to PFK at the allosteric site, reducing the enzyme’s activity and slowing glycolysis, thus preventing excessive ATP production when energy levels are already sufficient.

52
Q

Feedback inhibition:
Common strategy to control metabolic pathways

A
53
Q

autotrophs vs heterotrophs

A

Autotrophs: take more energy
Definition: Autotrophs are organisms that can produce their own food from inorganic sources. They synthesize complex organic compounds (like glucose) from simple molecules (such as carbon dioxide) and use energy from either sunlight or chemical reactions.
Types:
Photoautotrophs: Use sunlight as their energy source and carry out photosynthesis. They convert carbon dioxide and water into glucose and oxygen using sunlight. Examples include plants, algae, and cyanobacteria.
Chemoautotrophs: Obtain energy by oxidizing inorganic compounds (like hydrogen sulfide, ammonia, or ferrous ions) rather than sunlight. Examples include some bacteria and archaea, often found in extreme environments like deep-sea hydrothermal vents.
Primary producers – very important – synthesize the organic
molecules that heterotrophs (like us) use
Most chemolithotrophs and phototrophs

Chemolithotrophs are organisms that obtain energy by oxidizing inorganic molecules, such as hydrogen, ammonia, nitrite, sulfur, or ferrous iron. Unlike phototrophs that rely on sunlight, chemolithotrophs use chemical reactions as their energy source, making them key players in ecosystems where sunlight is unavailable, such as deep-sea hydrothermal vents, soil, and certain subsurface environments.

Heterotrophs
Definition: Heterotrophs are organisms that cannot synthesize their own food from inorganic sources. Instead, they obtain organic compounds (and therefore carbon and energy) by consuming other organisms or organic matter.
Types:
Herbivores: Eat plants or other autotrophs to obtain energy.
Carnivores: Feed on other animals.
Omnivores: Consume both plants and animals.
Decomposers: Break down dead organic material, recycling nutrients back into the ecosystem. Examples include fungi and some bacteria.

54
Q

Gibbs free energy

A

ΔG0 is the free energy change of a reaction under standard conditions.

Can be calculated based on nature of reactants/products.

55
Q

Redox tower

A

Redox couples with more negative
values (top of table) have a stronger
tendency to act as electron donors (to
be oxidized)

Redox couples with more positive
values (bottom of table) have a strong
tendency to act as electron acceptors
(to be reduced)

Glucose is a great electron donor, O2 is
phenomenal electron acceptor

bigger differences in redox potential produce more energy

56
Q

cool summary

A
57
Q

DNA base pairs

A

C/T are pyrimidines (6 membered rings)

A/G are purines (fused 5/6
membered rings)

A/T base pair has a weaker interaction with 2
hydrogen bonds

C/G base pair has a stronger interaction with 3
hydrogen bond