BIO 1801 -Exam 3

Major groups that can photosynthesize:

Algae/protists, plants, and bacteria

Photosynthesis

The use of sunlight to manufacture carbohydrates. It converts electromagnetic energy to chemical energy

Autotrophs (self-feeders)

Organisms that make organic molecules from inorganic ones

Heterotrophs (different-feeders)

Must consume organic molecules

Reactants for Photosynthesis

Sunlight, carbon dioxide, and water

Product of Photosynthesis

Oxygen

Chloroplasts

Organelles in plants and algae that carry out photosynthesis

Chlorophyll

Main pigment in chloroplasts (green)

Physical location of chloroplasts:

In the leaves in the mesophyll

Through the stomata, carbon dioxide enters and oxygen exits the leaf, CO2 from atmosphere goes in through the stomata

How do gases get in/out of mesophyll?

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Light Dependent Reactions

Produce O2, ATP, and NADPH. Water is split to form O2, its electrons are excited by light energy, pump protons into the lumen, high-energy electrons are transferred to the electron carrier NADP+, forming NADPH, ATP is produced by chemiosmosis

Calvin Cycle

Reactions produce sugar from CO2, electrons from NADPH and ATP are used to reduce CO2

Thylakoid membranes

Where are photosynthetic pigments located?

Red and blue

What colors do chloroplasts absorbs?

Green

What color do chloroplasts reflect?

Visible Light

The electromagnetic radiation that humans can see

Shorter

Which wavelength has more energy, shorter or longer?

Carotenoids

Absorb blue and green light, reflect and transmit yellow, orange, and red light

Pigments

Molecules that absorb and reflect light energy

Chromatography

A technique for separating molecules

Absorption Spectrum

Wavelengths of light absorbed by that pigment

Action Spectrum

Rate of photosynthesis at each wavelength

Blue and Red Photons

What photons are most effective at driving photosynthesis?

Carotenoids and Xanthophylls - protect chlorophylls from damage by stabilizing free radicals

Which part of a pigment absorbs light?

One energy level

Red photons bump an electron up…

Two energy levels

Blue photons bump an electron up…

Not absorbed

Green photons are intermediate, so they are…

Antenna Complex

Composed of 200-300 chlorophyll and accessory pigment molecules. Energy is transferred from one molecules to the next until it reaches the reaction center

Reaction Center

Energy finally transferred to a specialized chlorophyll. Transfers an excited electron to an electron acceptor

Photosystem II

Comes first, excited electrons passed to ETC, ETC pumps protons into thylakoid lumen (drives ATP Synthase), reaction center splits water (oxidized), generates O2 and more protons in lumen, replaces electrons in reaction center

Manganese Cluster

Oxidation of water yields oxygen gas - this is the only protein complex that can oxidize water into atmosphere

Photosystem I

Electrons from ETC are re-excited, passed to NADP+ reductase, NADP+ is reduced to form NADPH (terminal electron acceptor)

Z Scheme

A model of how photosystems I and II interact: PS II energy pumps protons, produces ATP, PS I energy excites electrons to produce NADPH

Noncyclic Electron Flow

Electrons pass from water to NADP+ in a linear fashion

Cyclic Phosphorylation

Electron cycling releases energy to transport H+ into lumen driving synthesis of ATP

Carbon Fixation

Add inorganic carbon to an organic compound

3 Steps of the Calvin Cycle

Fixation, Reduction, Regeneration

Fixation

CO2 attached to a five-carbon compound called ribulose biphosphate (RuBP - 5C +1CO2)

Reduction

The 3PGA are phosphorylated by ATP and reduced by NADPH

Regeneration

The remaining G3P is used in reactions that use ATP to regenerate RuBP

CAM Plants

Open stomata at night and fix CO2, release CO2 and run Calvin Cycle during the day when stomata is closed

Redox Reaction

Glucose is oxidized into carbon dioxide, oxygen is reduced into water because O2 is highly electronegative to accept the electrons

Mitochondria

Primary role is to make ATP, outer and inner membrane, contain their own DNA- divide by binary fission

Aerobic Cellular Respiration

When we breathe, oxygen enters the lungs, diffuses into our blood stream (circulatory system) to carry the oxygen to cells used for cellular respiration

Glycolysis (when glucose is oxidized)

Glucose (6C) is broken down into two pyruvate

Pyruvate Processing (when glucose is oxidized)

Pyruvate (3C) is oxidized to form acetyl CoA (2C) + CO2

Citric Acid Cycle (when glucose is oxidized)

Acetyl CoA is oxidized fully to CO2

Electron Transport and Oxidative Phosphorylation (when glucose is oxidized)

Electron transport chain produces proton gradient that is used to make ATP

Feedback Inhibition (allosteric)

How is Glycolysis regulated?

Electron Transport Chain

Used to pump protons across the mitochondrial inner membrane into the intermembrane space - forms a strong electrochemical gradient

Oxidative Phosphorylation

Most of the ATP made during cellular respiration is made by…

First carbohydrates, then fats, then proteins

For ATP production cells use…

Long fatty acid chains can make lots of Acetyl CoA groups for Krebs Cycle

Why do fats store more energy?

Aerobic Respiration

All eukaryotes and many prokaryotes use oxygen as the terminal electron acceptor for the ETC

Anaerobic Respiration

Some prokaryotes use other electron acceptors

Soil and intestinal bacteria (Nitrate), wetlands and thermal bacteria (Sulfate), Methanogen bacteria (CO2)

Other molecules that are electron acceptors…

Oxygen

Most effective electron acceptor (highest electronegativity)

Fermentation

A metabolic pathway that regenerates NAD+ from NADH- electrons from NADH are transferred to pyruvate and enables ATP production from glycolysis only

Lactic Acid Fermentation

Muscle cells deprived of oxygen convert to…

Alcohol Fermentation

Some yeast cells can perform…

Fermentation

Alternative to cellular respiration

Facultative Anaerobes

Can switch between fermentation and aerobic respiration

Deoxyribonucleic Acid (DNA)

Stores genetic information in modern cells

Ribonucleic Acid

Used to build proteins, decodes this information into instructions for linking together a specific sequence of amino acids to form a polypeptide chain

Nucleic Acid

A polymer of nucleotide monomers, has a central five-carbon sugar (ribose), a phosphate group, and a nitrogenous base

Deoxyribonucleotides

The monomers of DNA - lacks O at the 2’ carbon

Ribonucleotides

Monomers of RNA

Phosphodiester Linkage

Occurs between nucleotides- phosphate group on the 5’ carbon of one nucleotide bonds to the 3’ carbon of another

5’ phosphate group → 3’ hydroxyl group

Nucleic Acid Direction

\# of purines = # of pyrimidines, equal number of T’s and A’s; equal number of C’s and G’s

Chargaff established…

Rosalind Franklin “dark lady of DNA”

Studied DNA, the way it revealed the helix structure, dark portion at the top and bottom reveals the feature is repeated over and over

Two strands are held together by hydrogen bonds between pyrimidines and purines, complementary base pairing, DNA strands are antiparallel, DNA strands form a double helix

James Watson and Francis Crick determined that…

Complementary base pairing

A and T, C and G

Antiparallel

One strand runs 3’ → 5’ , the other runs 5’ → 3‘

Double helix

The sugar-phosphate backbone faces the exterior

Ball and Stick

Model Watson and Crick used to solve the structure of DNA

Tertiary Structure of DNA

Forms a more compact three-dimensional structures in cells, it wraps around proteins, compacting DNA

RNA

Contains ribose instead of deoxyribose, more reactive, much less stable, contains uracil instead of thymine

RNA Tertiary Structure

Forms when secondary structures fold into more complex shapes

RNA can function as a Catalytic Molecule

Highly versatile, an information-containing molecule, capable of self-replication, capable of catalyzing reactions: ribozymes

Sugar/phosphate backbone and an exposed series of nitrogen-containing bases

Each strand of DNA has…

Hydroxyl Group

3’ end has an exposed…

Phosphate Group

5’ end has an exposed…

3’ side

New bases are only added to…

Double Helix

Two DNA strands hydrogen bonded form a…

Parental Strands

Serve as a template for replication producing daughter strands

Semiconservative replication

Parent strands separate and each is copied, new double helix is half parents half daughter

DNA Polymerases

Enzymes that catalyze DNA synthesis, can add new nucleotides only to the 3’ end of a growing DNA chain

5’ → 3’

Daughter produced…

3’ → 5’

Parent read…

Origin of Replucation

Double helix separates at a specific sequence

Replication bubble with two replication forks

Replication forms…

One replication bubble

In replication, bacteria forms…

Many on each chromosome

In replication, eukaryotic forms…

Bidirectional replication

Replication bubbles grow in both directions

DNA helicase

Breaks hydrogen bonds between the two DNA strands to separate them

Single-strand DNA binding proteins

Attach to the separated strands to prevent them from closing

Topoisomerase

Relieves tension from unwinding the DNA helix

Primase

An enzyme that makes primers

DNA polymerase

Works only in the 5’ → 3’ direction on a single-stranded template, requires a primer with 3’ end to extend from