1002B Final Study

Eyespot Structure

Eyespot Structure

The eyespot, also known as stigma or paraflagellar body, is a specialized organelle in flagellated cells like Chlamydomonas, containing photoreceptor pigments sensitive to light.

Eyespot Function

The eyespot enables organisms to detect light direction, crucial for phototaxis - movement toward or away from light.

Channelrhodopsin

A light-sensitive ion channel in Chlamydomonas' eyespot, allowing ion passage upon light activation, influencing cell behavior.

Voltage-gated Na Channel

Found in neurons, it triggers action potentials by allowing sodium influx at a specific membrane potential threshold.

Action Potential Generation

Involves resting state (polarized membrane), depolarization (sodium influx), and repolarization (potassium efflux).

Channelrhodopsin & Photoisomerization

Channelrhodopsin's retinal pigment undergoes photoisomerization upon light absorption, leading to opsin conformational changes.

Channelrhodopsin vs human eye

Both contain retinal pigment but differ in function (ion channel vs. visual signal) and location

Optogenetics

Modifying neurons to express light-sensitive proteins like Chlamydomonas' channelrhodopsin for light-controlled neuronal activity studies.

Phototaxis Loss

Mutation affecting eyespot or channelrhodopsin can lead to loss of phototactic ability, causing cells to move away from light.

Chlamydomonas Structural Features

Includes chloroplast, flagella, nucleus, vacuole, and cell wall in a single cell.

Macronutrient vs micronutrients

Macronutrients (e.g., carbon) are needed in large amounts, while micronutrients (e.g., iron) are required in smaller quantities.

Phosphate & Iron Importance

Phosphate for DNA, RNA, ATP; iron for chlorophyll, hemoglobin, electron transport, and enzyme function.

Growth & Doubling Time

Chlamydomonas population doubles every 10 hours under optimal conditions at 25°C.

Cilia Structure

Composed of microtubules in a 9+2 pattern, involved in cell motility and signaling, with mutations causing ciliopathies.

Motile vs non-motile

Motile flagella aid movement (e.g., Chlamydomonas), while non-motile flagella are for sensory reception.

Quaternary structure

Arrangement of multiple polypeptide subunits, stabilized by the same interactions as tertiary structure.

Free energy (ΔG)

The energy available to do work in a system; spontaneous reactions have a negative ΔG.

Enzymes

Proteins that lower the activation energy barrier for reactions, increasing their rate.

Exothermic reactions

Release energy to the surroundings.

Endothermic reactions

Absorb energy from the surroundings.

Energy funneling model

Proteins fold by lowering their free energy progressively to a stable structure.

Primary structure

Sequence of amino acids in a polypeptide chain.

Secondary structure

Regular repeating patterns like alpha helices and beta sheets.

Tertiary structure

Three-dimensional folding of a polypeptide chain.

Closed system

Allows energy exchange but not matter.

Open system

Allows both energy and matter exchange.

Isolated system

Cannot exchange energy or matter with surroundings.

First Law of Thermodynamics

Energy cannot be created or destroyed, only changed in form.

Second Law of Thermodynamics

Total entropy of an isolated system increases over time.

Photosynthesis

Process using sunlight to synthesize food from CO2 and water.

Endergonic

Reaction requiring energy input to proceed.

Redox reaction

Chemical reaction involving oxidation and reduction.

Calvin cycle

Uses ATP and NADPH to fix CO2 and produce sugars.

Electron transport chain

Transports electrons to generate a proton gradient.

Redox potential

Determines electron gain or loss tendency.

Anoxygenic photosynthesis

Photosynthesis in bacteria that does not produce oxygen as a byproduct.

Oxygenic photosynthesis

Photosynthesis in plants and algae that releases oxygen as a byproduct.

Evolutionary advantage of oxygenic photosynthesis

Production of oxygen leading to the oxygenation of the atmosphere, enabling the evolution of aerobic organisms.

Basics of Measuring Respiration in Isolated Mitochondria

Procedure involving isolated mitochondria, a respiration chamber, substrates, and cofactors to measure oxygen consumption.

NADH Addition

Stimulates oxygen consumption by providing electrons to the electron transport chain.

ADP & Pi Addition

Promotes ATP synthesis, activating the electron transport chain for ATP production.

Uncoupler Addition

Disrupts the proton gradient, increasing oxygen consumption to maintain the gradient.

Respiratory Control

Regulation of mitochondrial respiration by ADP availability and ATP demand.

Autotrophic Metabolism

Organisms synthesizing organic molecules from inorganic sources, like plants using photosynthesis.

G3P Exported from Chloroplast

Serves as an energy and carbon source in cellular respiration and biosynthetic pathways.

Mixotrophic Metabolism

Ability to use both organic and inorganic sources for growth, as seen in Chlamydomonas.

Gas Exchange in Respiration and Photosynthesis

Respiration consumes O2 and produces CO2, while photosynthesis consumes CO2 and produces O2.

Underestimation of Rates in Whole Chlamy Cells

O2 production or CO2 fixation rates underestimated due to concurrent respiration.

Light Response Curve

Shows light-limited and light-saturated regions affecting photosynthetic rate.

Rate of Reaction vs Enzyme Concentration

Initial linear increase in reaction rate with enzyme concentration saturation.

Competitive Inhibitor

Competes with substrate for enzyme binding, affecting Km but not Vmax.

Non-competitive (Allosteric) Regulation

Binds to enzyme at a site other than the active site, reducing Vmax without affecting Km.

Three Domains of Life

Bacteria, Archaea, and Eukarya with distinct characteristics.

LUCA (Last Universal Common Ancestor)

Hypothetical organism from which all life on Earth descended.

Evolution of Life

From simple anaerobic to complex aerobic organisms, influenced by oxygenic photosynthesis.

Great Oxygenation Event

Rise of oxygen in the atmosphere enabling the evolution of complex organisms.

Endosymbiosis

Theory of mitochondria and chloroplasts originating from engulfed prokaryotic cells.

Signal Peptide and Protein Targeting

Directs proteins to organelles like mitochondria and chloroplasts.

Mode of Action of Major Antibiotics

Inhibit cell wall synthesis, protein synthesis, disrupt cell membrane, or nucleic acid synthesis.

Mitochondria Are Prokaryotic

Originated from an endosymbiotic event, retaining characteristics of prokaryotic ancestors.

Horizontal Gene Transfer (HGT)

Transfer of genetic material between unrelated organisms.

Bacterial Conjugation

Transfer of genetic material through direct cell-to-cell contact.

Major Mechanisms of Resistance

Efflux pumps and downregulation of porin proteins.

Comparison of Prokaryotic and Eukaryotic Transcription and Translation

Differences in location, machinery, and regulation of gene expression.

RNA Polymerases

Enzymes (I, II, III) responsible for transcribing DNA into RNA during transcription.

Transcription Initiation

The process of starting RNA synthesis, involving promoter recognition and initiation complex formation.

Elongation

The phase of transcription where RNA polymerase adds nucleotides to the growing RNA strand.

Termination

The conclusion of transcription, marked by the release of RNA from the DNA template.

Introns

Non-coding segments of DNA that are removed during RNA processing in eukaryotes.

RNA Processing

Modifications to pre-mRNA, including splicing, capping, and polyadenylation, before translation.

Complementary Base Pairing

Specific hydrogen bonding between nucleotide bases in DNA and RNA.

Central Dogma

The flow of genetic information from DNA to RNA to protein, with exceptions for non-coding RNAs.

Ribosomes

Cellular structures where translation occurs, composed of rRNA and proteins.

tRNA

Transfer RNA molecules that transport amino acids to the ribosome during translation.

Denaturation

Heating DNA to separate strands for PCR.

Annealing

Cooling to allow primers to bind in PCR.

Extension

DNA polymerase adds nucleotides in PCR.

RT-PCR

Converts RNA to cDNA for amplification.

cDNA

DNA from mRNA lacking introns.

Gene Expression

Measuring mRNA levels.

CRISPR-Cas System

Bacteria defense against foreign DNA.

NHEJ (Non-Homologous End Joining)

Direct DNA repair with mutations.

HDR

Precise DNA repair using a template.

Base Editing

Changing single DNA bases precisely.

Immunotherapy

Enhancing immune response with CRISPR.

Epigenetics

Changes in gene expression without DNA alteration.

Genome

Complete DNA set in an organism.

Epigenome

Patterns of modifications regulating gene activity.

DNA Methylation

Addition of methyl groups to DNA.

Histone Modifications

Alterations affecting gene expression.

Heterochromatin

Dense, inactive DNA regions.

Euchromatin

Less condensed, active DNA regions.

Transgenerational Inheritance

Passing epigenetic changes to offspring.

Epigenetic Therapy

Modifying epigenetic marks for treatment.

Epigenetic Clock

Correlation between age and DNA methylation.