Module 3 Energy and Biological Building Blocks

photoautotrophs

use light as an energy source to produce organic compounds

chemoautotrophs

use environmental inorganic compounds as an energy source to produce organic compounds

heterotrophs

must obtain energy and carbon by consuming other organism or organic matter

photosynthesis

the process used by plants, algae, and certain bacteria to turn sunlight, water, and carbon dioxide into sugar (food) and oxygen

sunlight + 6H2O + 6CO2 → C6H12O6 (glucose) + 6O2

chemosynthesis

uses energy from chemical reactions to build sugars out of smaller molecules

properties of light

the amount of energy in light is inversely proportional to its wavelength

how photosynthesis harvests light energy

photosynthetic pigments with different absorption peaks collect solar energy

reflect unabsorbed wavelengths → we see different colors

chlorophyll a

the primary photosynthetic pigment in plants, algae, cyanobacteria

chlorophyll b

an accessory pigment that broadens light harvesting in plants, green algae and a few cyanobacteria

carotenoids

masked by chlorophyll

anthocyanin

pigment made in the fall

where photosynthesis takes place

most photosynthesis takes place in the ground tissue cells of leaves called the mesophyll cells

mesophyll cells

contain many chloroplasts where photosynthesis occurs

chloroplast morphology

chloroplast: double membraned organelles descended from cyanobacteria that are found in plants

stroma: the space inside the inner membrane of the chloroplast, site of chemical reactions that produce biomass in photosynthesis

thylakoid membranes: stacked into grana and are a key component for energy production of photosynthesis

photosystems

complexes of proteins and pigments (chlorophylls and carotenoids) that harvest light energy to generate high energy electrons

2 types

1. photosystem 1

2. photosystem 2

Light reactions (photosynthesis part 1)

uses light to produce ATP

1. light excited electrons in photosystem 2, water is split releasing O2, protons and electrons

2. electrons travel down an electron transport chain to photosystem 1, this releases energy to pump H+ into the thylakoid lumen, building a gradient and generates NADPH

3. H+ flow down the gradient back into the stroma, passing through ATP synthase which drives ATP production

summary

• Converts sunlight (lightnenergy) into ATP (chemical energy)

• Splits water and releases oxygen

• Products of the light reactions (ATP and NADPH) are released into the stroma

calvin cycle (photosynthesis part 2)

Converts CO2 to biomass (glucose)

summary

• Fixation changes CO2 into biomass

• Reduction uses products of the light reactions (ATP and NADPH) to store energy in glucose

• Regeneration uses energy from ATP to maintain pool of RuBP

1. Carbon Fixation

• enzyme called RuBisCo exists in stroma

• RuBP is a five carbon sugar produced by the calvin cycle

• RuBisCo combines CO2 gas with RuBP to “fix” it into a solid but unstable six carbon sugar

• six carbon sugar splits into two three carbon molecules - 3PGA

2. Reduction

• ATP and NADPH turn low energy 3PGA into high energy G3P

• takes 2 G3P to generate 1 glucose molecule

• calvin cycle must turn 2x to generate 1 glucose molecule and regenerate RuBP

3. Regeneration

• of the 6 G3P molecules 1 is used to form glucose

• ATP used to rearrange 5 remaining G3P into 3 RuBP molecules

• maintains pool of RuBP to continue cycle of CO2 fixation

C3 photosynthesis

• CO2 fixation produces 3 carbon molecule

• this is the ancestral form of photosynthesis and most common

• the C3 pathway is driven by RuBisCo enzyme

• only works well in cool, humid environments

RuBisCo

• drives C3 photosynthesis

• RuBisCo is slow but plentiful

• RuBisCo makes mistakes (will us O2 instead of CO2)

photorespiration (C2 cycle)

process in plants where the enzyme RuBisCo mistakenly uses O2 instead of CO2 during photosynthesis

• leads to 20-50% reduction in efficently

• if O2 is used it makes 3PGA and 2-phosphoglycolate which is useless and toxic to plants

• 2-phosphoglycolate can then be made back into 3PGA

waste product of photosynthesis

O2 and builds up inside the leaf

stomata

pores of the dermal tissue of plant leaves

CO2 in, water and O2 out

different → open pores allow water to evaporate out

guard cells

open and close the stomata to allow gas exchange

C4 photosynthesis

• physically separate carbon fixation from calvin cycle in different cells

  • carbon fixation → mesophyll cells

  • calvin cycle → bundle sheath cells

C4 mesophyll cells → carbon fixation

• enzyme called PEPC exists in stroma, had higher attraction to CO2 than O2

• PEP is a three carbon sugar

• PEPC combines CO2 gas with PEP to “fix” it into malate a four carbon sugar

• malate actively pumped into bundle sheath cells

C4 bundle sheath cells → calvin cycle

• malate split apart

  • 1 carbon enters regular calvin cycle (with RuBisCo) → glucose

  • 3 carbons → pyruvate

• pyruvate diffuses into the mesophyll cell and the ATP is used to regenerate PEP

• physically separating steps isolates RuBisCo from O2

• common in grasses like corn and sugarcane adapted to hot, sunny environments

CAM photosynthesis

• carbon fixation from calvin cycle in mesophyll cells is separated in time

• carbon fixation occurs at night

  • 4 carbon molecule stored in vacuoles

• calvin cycle occurs during the day

• typical of dessert plants like cacti and succulents

metabolism

the chemical reactions that occur in a living organism

• obtain energy from food by converting glucose to ATP for use in cellular processes

• convert biomass of food into biological building block (macromolecules)

• excrete metabolic wastes

anabolic processes

build larger molecules from smaller ones

• require energy

catabolic processes

break down larger molecules into smaller ones

• release energy

how do you measure metabolic activity

the amount of oxygen use dup (or carbon dioxide produced)

• gas exchange use is more easily measured

basal metabolic rate (BMR)

the rate at which an animal consumes oxygen while at rest, no digestion of food, no physical, thermal or psychological stress, normal temperature conditions

• minimal resting lifestyle

maximum metabolic rate (MMR)

the maximal rate at which oxygen can be transported from the environment to the tissue mitochondria

• induced by activity/stress

metabolic rate and enviroment

• BMR and max MMR are fundamental physiological parameters providing the floor and ceiling in aerobic energy metabolism

• it takes more energy to maintain metabolic function at environmental extremes

• as environmental conditions change BMR and MMR will change to different extents

aerobic scope

capacity of an organism to increase its aerobic rate above maintenance level

• aerobic scope = MMR - BMR

• it determines how much excess energy is available for growth and reproduction

glucose

six carbon sugar that stores energy in chemical bonds

• all multicelluar eukaryotes store glucose and oxidize it to provide chemical energy in the form of ATP

• once glucose is in a cell it may be used for cellular respiration or fermentation

• the site of these processes is in the mitochondria

mitochondrial morphology

double membraned organelles that are descended from bacteria that underwent endosymbiosis found in all eukaryotes

mitochondrial matrix: the space inside the inner membrane of the mitochondrion, the site of aerobic respiration

cristae: inner membrane folds, increase surface area for energy reactions to occur

cellular respiration

breaks sugar down to generate ATP

C6H12O6 + 6O2 + ADP + P → 6H2O + 6CO2 + ATP + heat

1. glycolosis

• “breaking sugar” in cytosol

• glucose breaks down into

  • 2 pyrivate (3 carbon molecules)

  • 2 ATP

  • 2 NADH

• if there is oxygen

  • pyruvate enters mitochondrion → aerobic respiration

  • goes to link reaction

• if there is NO oxygen

  • pyruvate remains in cytosol → fermentation (anaerobic)

  • regenerates NAD+ from NADH

  • allows glycolysis to continue

  • end products: lactate (animals), ethanol and CO2 (yeast)

2. Link reaction (only if oxygen is present)

• in mitochondrial matrix

• end products: acetyl CoA (2 carbons), NADH, CO2

3. citric acid cycle

• multi-step cycle

• stores energy in reduced molecules

  • 3 NADH, FADH2, ATP (all going to the electron transport chain)

• waste product: 2 CO2

4. electron transport chain

1. NADH and FADH2 donate electrons to the ETC on the inner mitochondrial membrane

2. electrons travel down an electron transport chain releasing energy to pump H+ into the inner membrane space, building a proton gradient

3. oxygen (1/2 of an O2 molecule) is the final electron acceptor → forms water

4. protons flow down gradient through ATP synthase rotor, from high to low concentration, proton flow drives rotation in ATP synthase and converts ADP + Pi to ATP

cellular respiration simple summary

• glycolysis (cytosol)

  • 1 glucose → 2 pyruvate + 2 ATP + 2 NADH

• if no O2: fermentation (cytosol)

  • 2 pyruvate + 2 NADH → lactate + 2 NAD+

• if O2: link reaction (mitochondrial matrix)

  • 2 pyruvate → 2 acetyl CoA + 2 NADH + 2 CO2

• citric acid cycle (mitochondrial matrix)

  • 2 acetyl CoA → 6 NaDH + 2 FADH2 + 2 ATP + 4 CO2

• electron transport chain and ATP synthesis (inner mitochondrial membrane)

  • NADH and FADH2 donate electrons to establish proton gradient

  • O2 final electron acceptor

  • ATP synthase → 28 ATP

why is breakdown required

it is difficult for macromolecules (large and complex molecules) to enter a cell → break them down into micro molecules that can

primary producers

make biomass from environmental CO2

ex. photoautotrophs (photosynthesis) and chemoautotrophs (chemosynthesis)

food web

a graphical representation of the flow of energy through an ecosystem

trophic level

an organisms position in a food web

animal body plans arranged around gut used for internal digestion & absorption

ingestion: acquire and mechanically process food, taken in through the mouth to the gut

• many specialized structures exist to allow animals to acquire and mechanically process food

• mechanical breakdown increases surface area from chemical digestion to occur

digestion: chemically (and mechanically) process food in the gut

• tissues secrete digestive enzymes to breakdown macromolecules and the gut may house microbes to help break down of complex molecules

• gut has high surface area to maximize absorption

allows breakdown of macromolecules to micromolecules → required for growth, development, and biological functions.

herbivores (primary consumer)

consume primary producers

suspension/filter feeders (primary consumer)

consume food particles taken out of the water column

passive filter feeders

strain suspended matter from environment

active filter feeders

create water current to strain matter

carnivores (secondary consumer)

consume other consumers

omnivores (secondary consumer)

consume both primary producers and other consumers

defense mechanisms

chemical

• produce chemicals to make tissues toxic or unpalatable

• consume and repurpose chemical defenses from food

behavioral

• move away from predator

physical

• avoid predation

  • crypsis allows animals to blind in with surroundings and hide

  • aposematism: bright colors act as warning of chemical defenses

• deter predation → spines

parasites (secondary consumer)

organisms that live on or inside another organism at the expense of the host

detritivores

consume organic waste and decaying matter, helping to return nutrients to the biosphere

deposit feeder (detritivore)

consume organic matter found on and within the substrate (the material that forms the floor of the enviroment)

fungi body plans maximize surface area for absorption via hyphae

fungi can secrete enzymes to externally break down macromolecules for absorption

• many are decomposers: break down dead matter and release nutrients back to the biosphere, especially on land

• fungi are the only organisms able to break down lignin, a plant material found in woody plants

• many fungi form symbiotic relationship with other organisms to obtain energy and nutrients

• ex. lichens are a symbiosis of fungi and algae/cyanobacteria

nutrients

the raw materials organisms use to build structures and supply chemical reactions

macronutrients

elements required in large amounts for growth and development

ex. C, N, P, K, O, Mg

micronutrients

elements required in trace amounts for vital biochemical functions

ex. Fe, Cu, Ni, Zn, Mn, Cl

decomposers

key to breaking down complex molecules and returning nutrients to environment in forms that other organisms can use

ex. detritivores, fungi, microbes

microbiology

the study of microscopic organisms such as bacteria, viruses, fungi, protozoa, and algae

microbiome

the collective genomes of all microbes in an environment

microbiota

the community of microorganisms themselves

microbes

tiny living organisms, they are found everywhere, many are crucial for human health, digestion, and the environment

• gut biomes → microbes help animal digestion

• fewer than 1% are pathogenic

• the rest form the invisible infrastructure of life: breaking down organic matter, recycling nutrients, and sustaining both our own physiology and global ecosystems.

limiting nutrient

nutrients that limit the growth, abundance, or distribution of a population of organisms in an ecosystem due to their scarcity

• phosphorus (P) and nitrogen(N) are common limiting nutrients in both soil and aquatic systems, and sometimes iron (Fe)

law of the minimum

productivity dictated not by total resources available, but by the scarcest resource (limiting factor)

nitrogen cycle

although N2 is abundant it cannot be used for growth by living organisms

N2 gas is “fixed” by microorganisms to form nitrogen compounds that are used by other organisms to sustain life

summary

• nitrogen Fixation: specialized microbes convert nitrogen gas into inorganic forms organisms can use

• ammonification: decomposers convert organic N compounds to Ammonia

• nitrification: 2-step process where nitrifying bacteria convert Ammonia to Nitrate

nitrogen cycle: nitrogen fixation

Specialized microbes convert nitrogen gas (N2) to Ammonia

(NH3) or Ammonium (NH4+) in soil

• Energy intensive process – requires ATP

• Some plants have a symbiotic relationship with nitrogen-fixing bacteria in root nodules

• Plants can take-up ammonium directly, but too much can damage cells and movement in soil is limited

nitrogen cycle: ammonification

• Dead organisms contain organic N (proteins, etc.)

• Decomposers use enzymes to break-down organic N in dead matter → inorganic Ammonia (NH3) and Ammonium (NH4+)

• Plants can take-up ammonium directly, but too much can damage cells and movement in soil is limited

nitrogen cycle: nitrification

• Nitrifying bacteria convert Ammonia (NH3) → Nitrite (NO2-) → Nitrate (NO3-)

• 2-step process:

  • Nitrosomonas converts Ammonia (NH3) → Nitrite (NO2-)

  • Nitrobacter converts Nitrite (NO2-) → Nitrate (NO3-)

• Nitrate preferred by most plants, can move more readily in the soil, but may be returned to atmosphere by de-nitrifying bacteria

spatial subsidy

a resource (nutrients, prey, detritus) gets transported from one habitat to another, increasing the productivity of the organisms living there