Test 2 bio

What are the four classes of large biological molecules all living things are made up of?

• Carbohydrates

• Lipids

• Protein

• Nucleic Acids

Macromolecules

large molecules composed of thousands of covalently bonded atoms

polymers, built from monomers

polymer

a long molecule consisting of many similar building blocks

– Carbohydrates

– Proteins

– Nucleic acids

monomers

small building-block molecules

dehydration reaction

occurs when two monomers bond together through the loss of a water molecule

An enzyme reaction linking monomers through the loss of hydrogen from one monomer and hydroxide from the other monomer to form a bond whose name varies by macromolecule group

C – glycosidic linkage

L – ester linkage

P – peptide bond

N – phosphodiester linkage

hydrolysis

Polymers are disassembled to monomers by by this process, a reaction that is essentially the reverse of the dehydration reaction

An enzyme reaction using water thereby adding hydrogen to one side and hydroxide to the other side of a bond within a polymer resulting in smaller molecules or monomers.

Carbohydrates and it’s Building Block

The body's primary source of energy and the brain's preferred energy source.

include sugars and the polymers of sugars

macromolecules are polysaccharides, polymers composed of many sugar building blocks

Glucose & Monosaccharides (simple sugars)

Lipids and it’s Building Block

Help control what goes in and out of your cells.

Fatty acids, glycerol

Proteins and it’s Building Block

Structural support, biochemical catalysts, hormones, enzymes, building blocks, and initiators of cellular death.

Amino acids

Nucleic acids and it’s Building Block

Storage and expression of genomic information.

Nucleotides

Monosaccharides

glucose, fructose, galactose (simple sugars)

molecular formulas that are usually multiples of CH2O

– The location of the carbonyl group

– The number of carbons in the carbon skeleton

disaccharide

formed when a dehydration reaction joins two monosaccharides

Polysaccharides

• polymers of sugars have storage and structural roles

• The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages

Types of Polysaccharides

Starch, Glycogen, Cellulose, and Chitin

Starch

• a storage polysaccharide of plants, consists entirely of glucose monomers

• Plants store surplus starch as granules within chloroplasts and other plastids

• The simplest form of starch is amylose

Glycogen

a storage polysaccharide in animals

Humans and other vertebrates store glycogen mainly in liver and muscle cells

Cellulose

• a major component of the tough wall of plant cells

• Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ

• The difference is based on two ring forms for glucose: alpha and beta

  human food passes through the digestive tract as insoluble fiber

• Some microbes use enzymes to digest cellulose

• Many herbivores, from cows to termites, have symbiotic relationships with these microbes

Chitin

• another structural polysaccharide, is found in the exoskeleton of arthropods (crunch!)

• also provides structural support for the cell walls of many fungi

Adenosine Triphosphate (ATP)

a compound produced and used in living systems because it holds potential energy in its bonded phosphate groups

What happens when ATP interacts with another molecule?

it transfers a phosphate group to the other molecule. This destabilizes the other molecule allowing work to be done.

Phosphorylation

the transfer of the 3rd phosphate group of ATP to another molecule allows for the performing of chemical, mechanical, or transport work.

Which phosphate group is lost during phosphorylation?

The last group or 3rd group

How is ATP made?

ADP + Pi → ATP

How is ATP used?

ATP → ADP + Pi
...with the help of enzymes
and electrochemical
gradients

Substrate level phosphorylation of ADP to ATP

With the use of an enzyme, individual ADP molecules are phosphorylated back to ATP.

One at a time!

Oxidative phosphorylation of ADP to ATP

With the use of an enzyme called ATP synthase, an electrochemical gradient across a membrane draws protons near the ATP synthase. The spinning of ATP synthase phosphorylates many ADP simultaneously.

Multiple at a time!

What are all the Bioenergetics?

Energy, Free energy

Chemical energy < - > Potential energy

Kinetic energy < - > Heat (thermal energy)

Energy

can cause change and is not matter

Chemical energy

potential energy available for release in a chemical reaction

Goes with potential energy

Potential energy

energy that matter possesses because of its location or structure

Goes with Chemical energy

Kinetic energy

energy associated with motion

Goes with Heat (thermal energy)

Heat (thermal energy)

kinetic energy associated with random movement of atoms or molecules

Goes with Kinetic energy

Free energy

is the energy of a system available to do work

What are the Laws of Thermodynamics?

First law – Conservation of energy

Second law – Entropy

First law – Conservation of energy

Energy can be transferred and transformed, but it cannot be created or destroyed

Second law – Entropy

Every energy transfer or transformation generates some unusable energy This increases the entropy (disorder) of the universe

What are the two types of Free energy (G)?

exergonic reaction and endergonic reaction

exergonic reaction

proceeds with a net release of free energy (- ∆ G) and is spontaneous

endergonic reaction

absorbs free energy (+∆ G ) from its surroundings and is nonspontaneous

How is “energy” associated with ATP?

Phosphorylation couples an endergonic reaction with the breakdown of ATP (exergonic), the change in free energy can be driven to a negative value resulting in an exergonic reaction.

Where does photosynthesis occur in Eukaryotes?

Plants → leaves using tens of thousands of
chloroplasts
Plant like Protists → cytoplasm containing chloroplasts

Where does photosynthesis occur in Prokaryotes?

Some bacteria only → possibly cell membrane
and cytoplasm of the bacteria

What are the parts of a Leaf?

cuticle, upper epidermis, palisade mesophyll, spongy mesophyll, lower epidermis, stoma, Bundle-sheath cells, Xylem & phloem

Chloroplast Structure:

Within the cells of the leaf

• Outer membrane

• Inner membrane

• Thylakoid membrane, folded to form thylakoids

• Thylakoids are arranged in stacks called grana.

Chlorophyll and other pigments involved in photosynthesis are embedded in the thylakoid membrane.

What are Pigments?

• Molecules that absorb light energy.

• Different ones absorb light of different wavelengths.

What are the major photosynthetic pigments?

• Chlorophyll A

• Chlorophyll B

• Carotenoids

  Xanthophyll Carotenes

what is net overall equation for photosynthesis?

6 CO2 + 6 H2O → light → C6H12O6 + 6 O2

What happens to 6H2O in photosynthesis?

It splits during the light reactions to replace electrons lost from Photosystem II

What happens to 6CO2 in photosynthesis?

Provides the carbon to produce organic compounds during the Calvin Cycle

What happens to light in photosynthesis?

Excites electrons during the light reactions

What happens to 6O2 in photosynthesis?

Produced as a byproduct of the splitting of water during the light reactions

What happens to C6H12O6 in photosynthesis?

The organic compound ultimately produced during the Calvin Cycle

How could the rate of photosynthesis be measured?

Could be measured by using the:

• Decrease in environmental CO2 (in a closed system)

• Increase in environmental O2 (in a closed system)

• Increase in glucose (perhaps measured using radioactive carbon)

Is photosynthesis an endergonic or exergonic reaction?

endergonic

What 2 stages does Photosynthesis occurs?

Phase 1: Light Reactions

Phase 2: Calvin Cycle

What are the 2 versions for Light Reaction?

Non-Cyclic Electron Flow and Cyclic Electron Flow

Non-Cyclic Electron Flow

• 2 photosystems (PS II & PS I) are used.

• Water is split through photolysis to replace the “lost” electron.

• Oxygen is released.

• NADPH is produced.

• ATP is produced.

Cyclic Electron Flow

• a process that occurs during photosynthesis, specifically in the light reactions, and helps produce ATP.

• Only 1 photosystem (PS I) is used.

• Water is not split to replace electrons – the electron is “recycled” back to the photosystem.

• Oxygen is not released.

• NADPH is not produced: useful when the plant needs more ATP than NADPH for the Calvin Cycle.

• ATP is produced.

Step 1- The Light Reactions: Non-Cyclic Electron Flow

Photosystem II [a group of pigment molecules] absorbs the energy in a photon [a particle of light], exciting an electron to a higher energy level.

Thus, PSII is now 1 electron SHORT of what it needs.

Step 2- The Light Reactions: Non-Cyclic Electron Flow

This electron is replaced by photolysis – the splitting of water using light.

O2 is released as a byproduct.

Step 3- The Light Reactions: Non-Cyclic Electron Flow

The excited electron travels down the electron transport chain, made of increasingly electronegative cytochromes, “losing energy” as it goes. This energy is used to build a concentration gradient of protons [chemiosmosis].

Step 4- The Light Reactions: Non-Cyclic Electron Flow

At the same time, Photosystem I [another group of pigment molecules] also absorbs light energy, exciting one of ITS electrons to a higher energy level.

Step 5- The Light Reactions: Non-Cyclic Electron Flow

The electron lost from Photosystem I is replaced by the electron that was excited and subsequently lost from Photosystem II.

Step 6- The Light Reactions: Non-Cyclic Electron Flow

The excited electron from Photosystem I travels down another electron transport chain, “losing energy” as it goes, and ultimately REDUCES NADP+ to NADPH [an electron carrier].

What happens to photosynthesis based on light intensity?

As light intensity increases, so too does the rate of photosynthesis.

Step 1- Cyclic Electron Flow

Photon Absorption: Light energy is absorbed by chlorophyll in the thylakoid membranes of chloroplasts.

Step 2- Cyclic Electron Flow

Electron Excitation: This light energy excites electrons, which are then transferred to a primary electron acceptor.

Step 3- Cyclic Electron Flow

Electron Transport Chain: The excited electrons move through a series of proteins in the electron transport chain.

Step 4- Cyclic Electron Flow

ATP Production: As electrons move through the chain, they release energy, which is used to pump hydrogen ions (H+) into the thylakoid lumen. This creates a gradient.

Step 5- Cyclic Electron Flow

ATP Synthase: Hydrogen ions flow back into the stroma through an enzyme called ATP synthase, driving the production of ATP from ADP and inorganic phosphate.

Step 6- Cyclic Electron Flow

Recycling of Electrons: Instead of moving to NADP+ to form NADPH, the electrons return to the chlorophyll, allowing the process to continue.

Calvin Cycle

a process that plants use to convert carbon dioxide into glucose, which they can use for energy.

This cycle happens in the chloroplasts of plant cells and does not require light directly, though it relies on products from the light-dependent reactions.

Step 1- Calvin Cycle

Carbon Fixation: Carbon dioxide from the air enters the plant through small openings called stomata. It combines with a 5-carbon sugar called ribulose bisphosphate (RuBP) to form a 6-carbon compound.

Step 2- Calvin Cycle

Split the 6-Carbon Compound: The 6-carbon compound quickly breaks down into two 3-carbon molecules called 3-phosphoglycerate (3-PGA).

Step 3- Calvin Cycle

Energy Input: Energy from ATP and NADPH (produced during the light-dependent reactions of photosynthesis) is used to convert 3-PGA into another 3-carbon molecule called glyceraldehyde-3-phosphate (G3P).

Step 4- Calvin Cycle

Glucose Formation: Some G3P molecules exit the cycle and are used to form glucose and other carbohydrates.

Step 5- Calvin Cycle

Regeneration of RuBP: The remaining G3P molecules are rearranged using ATP to regenerate RuBP, allowing the cycle to continue.

Why is there a change in photosynthesis based on light intensity?

• This occurs due to increased excitation of electrons in the photosystems.

• However, the photosystems will eventually become saturated.

• Above this limiting level, no further increase in photosynthetic rate will occur.

What happens to photosynthesis based on Temperature?

The effect of temperature on the rate of photosynthesis is linked to the action of enzymes.

As the temperature increases up to a certain point, the rate of photosynthesis increases.

Why is there a change in photosynthesis based on Temperature?

• Molecules are moving faster & colliding with enzymes more frequently, facilitating chemical reactions.

• However, at temperatures higher than this point, the rate of photosynthesis decreases.

• Enzymes are denatured.

What happens to photosynthesis based on Oxygen concentration?

As the concentration of oxygen increases, the rate of photosynthesis decreases.

Why is there a change in photosynthesis based on Oxygen concentration?

This occurs due to the phenomenon of photorespiration.

Photorespiration

• occurs when Rubisco (RuBP carboxylase) joins oxygen to RuBP in the first step of the Calvin Cycle rather than carbon dioxide.

• is a negative process for photosynthetic organisms.

• Whichever compound (O2 or CO2) is present in higher concentration will be joined by Rubisco to RuBP.

• Photorespiration prevents the synthesis of glucose AND utilizes the plant’s ATP.

What happens when in Photorespiration when Rubisco joins CO2?

More CO2 → Rubisco joins CO2 to RuBP → Photosynthesis occurs; glucose is produced

What happens when in Photorespiration when Rubisco joins O2?

More O2 → Rubisco joins O2 to RuBP → Photorespiration occurs; glucose is NOT produced

what happens when plants are under water stress?

their stomata close to prevent water loss through transpiration

However, this also limits gas exchange.

How does gas exchange get limited when plants are under water stress?

O2 is still being produced (through the light reactions). Thus, the concentration of O2 is increasing.

CO2 is not entering the leaf since the stomata are closed. The concentration of CO2 is decreasing.

When and how has photorespiration been prevented in some plants species?

Plant species that live in hot, dry climates (where photorespiration is an especially big problem) have developed mechanisms through natural selection to prevent photorespiration.

A mutation occurs, which may increase or decrease an organism’s chance of survival.

• C4 plants

• CAM plants

C 3 “normal” Plants (Preventing Photorespiration)

• Perform the light reactions and the Calvin Cycle in the mesophyll cells of the leaves.

• The bundle sheath cells of C3 plants do not contain chloroplasts

C 4 Plants- corn, sugar cane, sorghum (Preventing Photorespiration)

• In this process, CO2 is transferred from the mesophyll cells into the bundle-sheath cells, which are impermeable to CO2.

• The bundle-sheath cells of C4 plants do contain chloroplasts.

How do C4 plants work?

• PEP carboxylase adds carbon dioxide to PEP, a 3-carbon compound, in the mesophyll cells.

  This produces a 4-carbon compound (which is why it’s known as C4 photosynthesis).

• This 4-carbon molecule then moves into the bundle-sheath cells via plasmodesmata.

• In the bundle sheath cells, the CO2 is released and the Calvin Cycle begins.

If the Hatch-Slack pathway helps to prevent photorespiration, why wouldn’t ALL plants have this adaptation?

1. This biochemical pathway is unique to certain plants that evolved from ancestors with a beneficial mutation. Organisms cannot choose their pathways; they are shaped by their evolutionary history.

2. C4 plants use the Hatch-Slack pathway, which requires extra ATP for converting pyruvate to PEP, in addition to what’s needed for the Calvin cycle. While C3 plants don’t have this extra energy cost, for C4 plants, the benefits of using this pathway to avoid photorespiration in dry environments make the additional ATP worth it.

CAM Plants (Preventing Photorespiration)

• Plants that use CAM photosynthesis include succulent plants (like cacti) and pineapples.

• In CAM (crassulacean acid metabolism) photosynthesis, plants open their stomata at night to obtain CO2 and release O2.

  • This prevents them from drying out by keeping their stomata closed during the hottest & driest part of the day.

• When the stomata are opened at night, the CO2 is converted to an organic acid (via the C4 pathway) and stored overnight.

• During the day – when light is present to drive the Light Reactions to power the Calvin Cycle – carbon dioxide is released from the organic acid and used in the Calvin Cycle to produce organic compounds.

  • Remember: Even though the CO2 is taken in at night, the Calvin Cycle cannot occur because the Light Reactions can’t occur in the dark!

Avoiding Photorespiration in Both C4 and CAM plants

• C4 plants perform the Calvin Cycle in the bundle-sheath cells.

• CAM plants open their stomata at night and store the CO2 until morning.

Cell Respiration Equation

C6H12O6 + 6 O2 → 6 H2O + 6 CO2 + ATP

What is the first part of cell respiration?

Glycolysis

Glycolysis Equation

C6H12O6 + 2 ATP → 2 pyruvate + 2NADH + 2 ATP (net)

Where does cell respiration take place?

cytoplasm of the cell outside mitochondria

Glycolysis purpose

convert glucose into a pyruvate; a molecule which can be transported into the mitochondria

What must occur before the second step of cell respiration?

Conversion of pyruvate (C3H3O3) into Acetyl CoA (C23 H38 N7 O17 P3 S) must occur