BIMM120 Week 4

discussion
 Quick Reminders

Homework 1 Due next Tuesday

Midterm next Thursday!

My office hours are Wednesdays

11am-12pm at MOM if you have questions
or want to study

Contact me: g2chang@ucsd.edu

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 Lecture 4
Bacterial/Archaeal Molecular Biology
Shared molecular features between
archaea and bacteria

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 Genome structures

‐ Most have a singular

circular chromosome
(some have two)

‐ Lack introns

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 DNA processing

‐ DNA gyrase: introduces negative supercoils into DNA

‐ Prevents DNA from overwinding
‐ Reverse gyrase: introduces positive supercoils into DNA
‐ Present in thermophiles
‐ Restriction endonucleases: double stranded DNA degrading
enzymes to protect cells from foreign DNA

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 transcription

Sigma factors Polycistronic mRNA Repressor Proteins

‐ Bacterial proteins ‐ Bacterial and ‐ Transcription of
required for RNA archaeal gene bacterial and
synthesis (not in structure is often archaeal genes can
Archaea or Eukarya) organized into be blocked by
‐ Mediate recognition operons proteins that bind to
and binding of RNA ‐ Can encode more the promoter →
polymerase than one polypeptide interferes with RNA
separately within the polymerase binding
same RNA molecule and processing

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 Translation

‐ rRNA genes: 5S, 16S, 23S

‐ Bacterial rRNA genes are arranged as operons
‐ Archaeal rRNA genes are scattered throughout the
genome

‐ 70S ribosomes: bacterial and archaeal ribosomes are

composed of 30S and 50S subunits
‐ 80S ribosomes in Eukarya

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 Lecture 5
Microbial Differentiation, Regulation, and Sensing
 “
Cells do what they need to do
when they need to do it!

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 Major modes of Regulation
‐ No control
‐ Constitutive expression

‐ Transcriptional control
‐ Gene on/off
‐ No mRNA synthesis

‐ Translational control
‐ Product activity
‐ do/don’t translate

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 Transcriptional control is mediated by DNA-binding proteins

‐ Typically homodimers
‐ Highly sequence-specific
‐ Recognition occurs due to structure of DNA

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 Transcriptional control
Negative control elements
‐ Repression
‐ Arginine example: repressed
when arginine is present
‐ Anabolic process: constructive
‐ Induction
‐ Lactose example: lack lactose
= lack transcription
‐ Catabolic process: destructive
‐
Positive control elements
‐ Activator proteins
‐ Promote binding of RNA
polymerase to DNA
‐ Maltose catabolism: RNA
pol binds when maltotriose
is bound (no repressor
present)

Regulator proteins can act at the level of single genes, operons or regulons
(a group of genes and/or operons involved in a concerted function)

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 Post-transcriptional control

‐ Antisense RNAs
‐ Small non-coding RNAs bind to mRNA and
marks it for degradation
‐ Riboswitches
‐ mRNA self-regulation
‐ Influence secondary structure of mRNA to
prevent translation

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 Two-component regulatory systems

‐ Sensor Kinase (component 1)

‐ Binds signal, autophosphorylates and transfer phosphoryl group to
component 2
‐ Response regulator (component 2)
‐ Phosphorylation results in active state, allowing DNA binding and
transcriptional control; can activate or repress
‐ Example: EnvZ/OmpR
‐ EnvZ = sensor kinase; OmpR =response regulator; OmpC = smaller pore
outer membrane porin protein; OmpF = larger pore outer membrane porin
protein

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 EnvZ/OmpR Osmoregulation system
HyperOsmotic (seawater) - want to HypoOsmotic (freshwater) - want
have low permeability more diffusion in to get diluted
nutrients
1. EnvZ phosphorylated
2. ompF repressed and ompC 1. EnvZ unphosphorylated
activated 2. ompF is de-repressed and ompC
3. OmpF decreases and OmpC is un-activated
increases 3. OmpF increases and OmpC
decreases

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 Quorum sensing
‐ Density-dependent cell-to-cell signaling
‐ Make products that are useful when there are lots of cells
together (light, toxins, exopolysaccharide)
‐ Autoinducers : species-specific signaling molecules
‐ Help sense when other cells are nearby → positive
feedback
‐ Ex: Acyl homoserine lactones (AHLs)
‐ Bioluminescence: lux gene expression
‐ AHL→ LuxR (DNA-binding activator protein) → light →
LuxI (AHL synthase)

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 Chemotaxis
Sensing and responding to
attractants/repellants via
motility

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 Chemotaxis
Step 1: Response to Step 2: Controlling Step 3: Adaptation
chemical signals flagellar rotation ‐ CheB = response regulator
‐ CheA = sensor kinase ‐ CheY-P = clockwise de-methylase
‐ CheY = Response rotation (tumble) ‐ CheR = methylase
Regulator ‐ CheY = CCW (run) ‐ CheA = sensor kinase
‐ Transducer (MCPs): ‐ CheZ ‐ Repellants: de-methylated
sensor dephosphorylates MCPs (CheB active):
‐ Repellants: more CheY tumble→ run
phosphorylation ‐ Attractants: methylated
‐ Attractants: less MCPs (CheB inactive): run→
phosphorylation tumble

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 Lecture 6
Genomics of Bacteria and Archaea
 Genome and genomics

Genome: the entire complement of genetic information

of an organism
‐ Can tell us organism’s identity, evolutionary history,
and metabolic potential
Genomics: field of study involving the sequencing,
analysis and comparison of genomes

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How to get genome

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 How do we decode this and extract useful information?

1. Identify genes
a. Find open reading frames (orf) for protein-coding
genes
2. Annotation
a. Assign functional roles to genes
b. Identified genes are compared to genes of known
function when possible
3. Metabolism
a. Reconstruct the metabolism of the organism based on
its gene content and functional attributes
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 The “-omics” and systems biology
Transcriptomics Proteomics Metabolomics
‐ Global analysis of ‐ Genome wide
gene expression analysis of protein
patterns expression and
‐ Methods: RNA regulation
(cDNA) sequencing ‐ Methods: liquid
and DNA microarrays chromatography-ma
ss spec and 2D
polyacrylamide gel
electrophoresis
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‐ Analysis of small
molecules and
metabolic
intermediates
‐ Methods: mass
spectrometry-based
identification of small
molecules