BIS2A MT 3

Lecture 17-20

What is chlorophyll and where is it found in plant cells?

• A pigment responsible for the green color seen in many plants

• Electrons can be “excited” to different energy levels

• Found in the chloroplasts of plant cells

What is the primary pigment in plants?

Chlorophyll a

How do different types of chlorophylls (a, b, etc) affect absorption?

• Each chlorophyll has a different functional group attached on the end of their molecule

• Each variant absorbs light at different wavelengths and are more efficient than others

What are cartenoids, what type of molecule are they, and what is their function?

• Accompanied with chlorophyll to help collect excess light to prevent damage and assist in photosynthesis

• Commonly found in fruits/vegetables

• All have a lipid structure

• Examples: B-carotene, y-carotene, lycopene

Where does photosynthesis occur in plant and bacterial cells?

• Plants: chloroplasts

• Bacteria: the plasma membrane

What is cyclic photophosphorylation, what is produced, and where is it found?

• Electrons cycle back to the original pigment

• Only ATP is produced

• Found in some bacteria

Where does the electron originate from and end up in cyclic photophosphorylation?

Originate and ends back up in chlorophyll; it returns to the original pigment

What is noncyclic photophosphorylation, what is produced, and where does it occur?

• Electrons leave the system entirely; electrons are donated to NADP+ to create NADPH

• Requires an external electron donor to operate (water)

• Produces both ATP and NADPH

• Occurs in oxygenic photosynthesis

What photosystem does cyclic photophosphorylation occur in?

• Photosystem I

What photosystem does noncyclic photophosphorylation occur in?

• Photosystem I and II

What is oxygenic photosynthesis, who uses it, and what does it use/produce?

• Used in plants, algae, and cyanobacteria

• Uses sunlight to convert water + carbon dioxide (electron donors) to produce oxygen

What is anoxygenic photosynthesis, who uses it, and what does it use/produce?

• Utilized by some bacteria

• Doesn’t use water as an electron donor; uses other compounds like H2S

• Does not produce oxygen

What is a photosystem?

A protein-pigment complex that absorbs light and excites electrons

Which photosystem acts first in light-dependent reactions?

• Photosystem II first, then photosystem I

What is the function of photosystem II?

• Splits water to extract electrons

• Releases oxygen

• Provides electrons that are then transferred through he ETC

What is the function of photosystem I?

• Accepts electrons transferred through the ETC from photosytem II

• Re-excites electrons using another photo

• Electron are transferred to NADP+ to form NADPH

What is the Z-scheme?

• Shows electron flow and stepwise energy increase of electrons

• Light-dependent reactions

What are the 6 main steps of the Z-scheme?

1. Photosystem II absorbs light; electrons excited

2. ETC moves the electrons and H+ ions across the membrane

3. Photosytem I accepts electrons and absorbs light; electrons are re-excited

4. Electrons reduce NADP+ to NADPH

5. ATP synthases uses PMF to generate ATP

Where process does photophosphorylation occur in?

Photosynthesis

What is the calvin cycle also known as and where does it occur?

• Light-independent cycle

• Occurs in the stroma of the chloroplasts

What products does the calvin cycle produce?

ATP and NADPH

What is the key enzyme of the calvin cycle?

• Ribulose-1,5-biphosphate carboxylase-oxygenase (RuBisCo)

• Incorporates CO2 into plants during photosynthesis

• Catalyzes the first step of carbon fixation

What is carbon fixation?

• The process of taking carbons from inorganic molecules (like CO2) and using them to generate organic molecules (like glucose)

What are the inputs of the Calvin cycle?

• ATP, NADPH, CO2, H2O, and ribulose-1,5-biphosphate (RuBP)

What is the main product of the calvin cycle?

• Glucose (after six turns)

What is the pentose phosphate pathway and its functions? (PPP)

• Metabolic pathway parallel to glycolysis

• Generates NADPH for anabolic reactions, pentose phosphates (sugar intermediates) for DNA/RNA production

• Works alongside glycolysis and TCA cycle as part of central carbon metabolism

What are the two phases of the PPP?

1. Oxidative phase (generates NADPH)

2. Non-oxidative phase (sugar rearrangement)

What are the inputs and output of the oxidative phase in PPP?

• Inputs: glucose-6-phosphate (G6P)

• Outputs: Ribulose-5-phosphate (R5P) for nucleotide synthesis, NADPH for anabolic reactions, CO2 as a byproduct

What are the inputs and outputs of the non-oxidative phase of PPP?

• Inputs: Rearranges sugars into different carbon lengths (3,4,5,6,7 carbons)

• Outputs: fructose-6-phosphate (F6P) + glyceraldehyde-3-phosphate (G3P) to reenter glycolysis, pentose-phosphates for nucleotide biosynthesis, erythrose-4-phosphate for amino acid synthesis, sedoheptulose-7-phosphate for bacterial outer membranes

What is DNA (deoxyribonucleic acid)?

• Stores genetic information

• Composed of two antiparallel strands in a double helix

• Contains A, T, C, G base pairs

How can you identify a deoxyribose in DNA?

It doesn’t have an OH group on 2’ carbon

What is RNA?

• Involved in protein synthesis and other functions

• Single-stranded

• Has A, U, C, G base pairs

How can you identify a ribose in DNA?

• The ribose has an OH group on the 2’ position

Which base pairs are pyrimidines? CaTs are from PYRamids

Cytosine, Thymine, Uracil

Which base pairs are purines? AnGels are PURE

Adenine and Guanine

What are the components of a nucleotide?

Phosphate groups, ribose or deoxyribose, and nitrogenous base

What carbon are the phosphate groups attached to in a nucleotide?

5’ carbon

What carbon is the nitrogenous base attached to in a nucleotide?

1’

What carbon are the OH groups attached to in a nucleotide?

• Deoxyribose: 3’ carbon

• Ribose: 2’ and 3’ carbon

What does a DNA double helix consist of and what are they held together by?

• Has two antiparallel strands (5’ to 3’ direction) and are complementary joined together

• Strands are held together by hydrogen bonds between nitrogenous bases

How many hydrogen bonds does it take to pair A with T?

2

How many hydrogen bonds does it take to pair C with G?

3

What direction does DNA read?

5’ to 3’

What is the name of a bond that connects two nucleotides and what atoms are involved?

• Phosphodiester bond

• Oxygen are phosphorus

What is the origin of replication?

• Sequence element on the DNA that recruits the replication machinery

• Assembly site; tells the machinery where to start

What is the helicase?

Uses ATP hydrolysis to separate parent DNA strand

What is topoisomerase?

• Enzyme that uses ATP hydrolysis and favorable functional groups associations to help the helicase unwind DNA

• Functions outside the replication fork

• Resolves supercoiling in DNA

What is DNA polymerase III?

• Synthesizes daughter DNA strands

What direction does DNA polymerase III move along the template strand?

3’ to 5’ direction

What direction does DNA polymerase III synthesize the daughter strand?

5’ to 3’ direction

What is ligase?

Connects okazaki fragments

What is primase?

Generates and places RNA primers to inform DNA polymerase III of where to begin synthesizing daughter strands

What is telomerase?

• Lengthens telomeres and places RNA primers on shortened daughter strands; DNA polymerase III will then places complementary bases

• Contains an RNA sequence and acts as template for telomeric DNA sequences

What does DNA polymerase I do?

Removes RNA primers and replaces them with DNA nucleotides

How can nucleoside triphosphates release energy?

Cleaving the phosphate groups on the 5’ end can release energy via hydrolysis

When joining two nuclei acid monomers, what is the exergonic reaction?

The hydrolysis of the phosphoanhydride bond between the alpha and beta phosphate groups

When joining two nucleic acid monomers, what is the endergonic reaction?

• Joins the 3 -OH group on the existing nucleotide chain and the -P on the alpha phosphate attached to the 5’ carbon to generate the phosphodiester bond

What is required to attach new nucleotides together?

• A free 3’ -OH group

What are okazaki fragments?

• Newly synthesized DNA on the lagging strand

What is the leading strand and what direction does it follow?

• The new DNA strand synthesized continuously by DNA polymerase III

• Follows 5’ to 3’ direction towards the replication fork

What is the lagging strand and what direction does it follow?

• Strand synthesized discontinuously in short Okazaki fragments

• Follows 5’ to 3’ direction away from the replication fork

What does DNA ligase do and does it require ATP?

• Connects the 5’ -PO4 and 3’ -OH groups together in the backbone between the two Okasaki fragments

• Yes, it requires ATP

What bond does ligase form?

A phosphodiester bond

What are the steps of leading strand replication?

1. Helicase goes in and unzips DNA

2. Topoisomerase cuts the backbone to prevent supercoiling

3. Single-strand binding proteins bind to DNA to prevent it from joining back together

4. Primase generates an RNA primer

5. DNA polymerase III builds off the primer and follows the helicase

6. Leading strand is constructed 5’ to 3’ continuously

7. DNA polymerase I replaces RNA primer with DNA nucleotides

What are the steps of lagging strand replication?

1. While the leading strand is being made, another DNA polymerase III finds an open spot where it can build 5’ to 3’ on the other parent strand

2. Primase makes an RNA primer at an open spot

3. DNA polymerase III builds off the primer until it reaches the end of the strand or reaches the previous Okasaki fragment

4. DNA polymerase I removes RNA primers from one fragments and replaces them DNA nucleotides

5. Ligases, with the help of ATP, connects the 5’ -PO4 and 3’ -OH groups together in the backbone between the two fragments

What is a genome and where is it stored?

• The complete collection of heritable genetic information in an organism

• Stored in DNA (sometimes RNA)

How do genomes change over time?

• Mutations

• Genome rearrangements (insertion, deletion, duplication, etc)

What is a chromosome?

A long DNA molecule with part or all of an organisms genetic material.

What are the 3 steps of DNA replication?

1. Initiation: DNA strands separate

2. Elongation: New DNA strands synthesized

3. Termination: Replication process ends

How are DNA strands proofread and corrected?

• DNA polymerases detect and corrects errors immediately during replication

• Exonuclease activity removes incorrect nucleotides

What is mismatch repair and when does it occur?

• Recognizes incorrect base pairings and replaces the incorrect nucleotide

• Occurs after replication

What is nucleotide excision repair?

• Repairs larger DNA damage

• Enzymes remove a damaged segment and replace it with the correct sequence