Central Dogma and Energetics of Cell Evolution

Central Dogma

Genetic information flow: DNA to RNA to protein.

Baltimore Classification

Virus classification based on genome type and replication.

dsDNA

Double-stranded DNA viruses using host machinery.

ssDNA

Single-stranded DNA viruses converting to dsDNA first.

dsRNA

Requires special enzyme for replication.

+ssRNA

Directly readable by host cell for translation.

-ssRNA

Needs enzyme to convert to readable form.

Retroviruses

Integrate into host DNA using reverse transcriptase.

Satellite Viruses

Depend on helper viruses for replication.

Prokaryotic Genome

Circular genomes primarily composed of protein-coding DNA.

Eukaryotic Genome

Larger, with 0-150 GB size and noncoding DNA.

Organellogenesis

Origin of organelles from engulfed bacteria.

Endosymbiotic Gene Transfer

Gene transfer from organelles to host nucleus.

Energy Maintenance

Required for order, growth, and entropy management.

Phototrophs

Organisms using sunlight for energy.

Chemotrophs

Organisms using chemical compounds for energy.

Chemoorganotrophs

Utilize organic compounds for energy.

Chemolithotrophs

Use inorganic compounds as energy sources.

ATP

Energy currency of cells, couples reactions.

Exponential Growth

Unconstrained growth pattern, rare in nature.

Metabolic Rate

Measured by oxygen consumption in organisms.

Redox Reactions

Involve electron transfer: oxidation and reduction.

Calvin Cycle

Most common carbon fixation pathway in photosynthesis.

Aerobic Respiration

Uses oxygen as terminal electron acceptor.

Anaerobic Respiration

Uses inorganic molecules instead of oxygen.

Winogradsky Column

Microbial ecosystem illustrating metabolic diversity.

dsRNA

Double-stranded RNA viruses with two RNA strands.

+ssRNA

Positive-sense single-stranded RNA viruses, directly translatable.

-ssRNA

Negative-sense single-stranded RNA viruses, require conversion.

Retroviruses

RNA viruses converting RNA to DNA via reverse transcriptase.

Satellite Viruses

Viruses needing a helper virus for replication.

Prokaryotes

Single-celled organisms with circular DNA genomes.

Gene Organization

Prokaryotic genes are fluid and display patterns.

Panegomes

Genomes can be open or closed in prokaryotes.

Organellogenesis

Formation of organelles like mitochondria and chloroplasts.

EGT

Endosymbiotic gene transfer from bacteria to host.

Gene Transfer Ratchet

Nuclear genes more likely to transfer to nucleus.

Eukaryotes

Complex cells with diverse genome sizes and structures.

Eukaryotic Genome Size

Ranges from 0 to 150 GB in diversity.

Noncoding DNA

Majority of eukaryotic DNA is nonfunctional.

Prokaryote vs Eukaryote

Differences in genome structure and scaling.

Onion Test

Demonstrates nonfunctional DNA abundance in eukaryotes.

Cell Energetics

Cells require energy to maintain life and order.

Energy Transformation

Cells convert energy and matter from their environment.

Entropy

Cells increase environmental entropy while maintaining order.

Far-from-equilibrium Systems

Cells maintain different concentrations than surroundings.

Dynamic Steady State

Cells maintain stability amidst constant change.

Energy Sources

Cells extract energy from light or chemical compounds.

Phototrophs

Organisms that extract energy from sunlight.

Chemotrophs

Organisms that extract energy from chemical compounds.

Chemoorganotrophs

Extract energy from organic compounds, derived from phototrophs.

Chemolithotrophs

Extract energy from inorganic compounds.

Energy Definition

Capacity to do work in various forms.

Energy Transduction

Conversion of energy from one form to another.

Chemical Energy

Stored in chemical bonds of molecules.

First Law of Thermodynamics

Energy cannot be created or destroyed.

Cell Growth Energy Requirement

Energy is necessary for cell growth.

Exponential Growth

Unconstrained growth with unlimited resources.

Intrinsic Growth Rate

Natural growth rate of a population.

Resource Constraints

Growth limited by available resources.

Maximum Growth Rate

Achieved briefly under optimal conditions.

Adenosine Triphosphate (ATP)

Energy-transfer molecule in cells.

Energy Currency of Life

ATP is universally used for energy.

High-Energy Bonds

Phosphoanhydride bonds in ATP.

ATP Coupling

Links exergonic and endergonic reactions.

ATP Hydrolysis Energy Release

Energy released during ATP breakdown.

Metabolic Rate

Rate of energy production or use.

Oxygen Consumption Measurement

Common method for metabolic rate assessment.

Specific Respiratory Rate

Higher in rapidly growing cells.

Total Energy Cost

Energy required for cell maintenance and growth.

Construction Costs

One-time energy investment for biosynthesis.

Maintenance Costs

Ongoing energy for cell operation.

Chemostat

Device for continuous cell culture.

Dilution Rate

Rate at which medium is replenished.

Resource Consumption Rate

Calculated from inflow and outflow concentrations.

Dilution rates

Rates affecting cell growth and resource consumption.

Regression analysis

Statistical method to calculate resource costs.

Scaling of ATPs

Cost comparison of cell growth across species.

Chemostats

Controlled environment for studying cell growth costs.

Maximum growth rate

Highest rate at which cells can grow.

Metabolic pathways

Processes determining ATP consumption or production.

Cell volume

Primary factor influencing energetic costs of cells.

Maintenance costs

Lower costs compared to growth costs by two orders.

Cellular feature cost

Measured by growth rate impact upon removal.

Lac operon

Regulates lactose metabolism, affects growth rate.

LacZ gene

Encodes β-galactosidase for lactose cleavage.

Construction costs

Fixed costs for building cellular components.

Maintenance costs

Costs proportional to the length of cell cycle.

Opportunity costs

Potential ATPs lost due to resource allocation.

Deoxyribonucleotide biosynthesis

Requires approximately 52 ATPs per dNTP.

Double-helix unwinding

Costs about 1 ATP per dNTP.

Nucleosome biosynthesis

Requires approximately 190 ATPs per dNTP.

Ribonucleotide biosynthesis

Requires approximately 45 ATPs per NTP.

Chain-elongation

Costs about 2 ATPs per NTP during polymerization.

Relative cost of a gene

Decreases with increasing cell size.

Net selective advantage

Benefit gained from a trait in evolution.

Drift barrier

Inverse of genetic effective population size.

Cellular membranes cost

Comprise 20-30% of a cell's energy budget.

Metabolic diversity

Variety of metabolic processes across organisms.

Metabolic modularity

Combination of metabolic modules for versatility.