BIO 100 Study Guide: Exam 3

Glycolysis

What it is: The breakdown of a 6-carbon glucose molecule into two 3-carbon pyruvate molecules.

Location: Cell cytoplasm (cytosol).

Output: A net gain of 2 ATP and 2 NADH (no oxygen required).

Pyruvate Oxidation

What it is: The conversion of pyruvate into a 2-carbon molecule called acetyl-CoA, releasing carbon dioxide (\(\text{CO}_{2}\)).

Location: Mitochondrial matrix in eukaryotes (cytoplasm in prokaryotes).

Output: Acetyl-CoA, \(\text{CO}_{2}\), and NADH (requires oxygen indirectly).

Citric Acid Cycle (Krebs Cycle / TCA Cycle)

What it is: A closed loop of chemical reactions where acetyl-CoA combines with a 4-carbon molecule to cycle through steps that strip high-energy electrons and release \(\text{CO}_{2}\).

Location: Mitochondrial matrix (eukaryotes) or cytoplasm (prokaryotes).

Output per glucose: CO2, 2 ATP/GTP, 6 NADH, and 2 FADH2

Oxidative Phosphorylation

What it is: The final stage where electron carriers NADH and FADH2 drop off electrons down an electron transport chain, driving a proton gradient that powers ATP synthase. Oxygen acts as the final electron acceptor, combining with protons to form water.

Location: Inner mitochondrial membrane (eukaryotes) or plasma membrane (prokaryotes).

Output: vast majority of cellular ATP (26-28) and H2O

Substrate-Level Phosphorylation

A direct metabolic reaction that produces ATP (or GTP) by transferring a phosphate group directly from a reactive intermediate substrate to ADP, without using a proton gradient or an electron transport chain.

Occurs during glycolysis and the citric acid cycle.

Oxidation and Reduction (Redox Reactions)

Oxidation: The loss of electrons (often paired with losing hydrogen atoms or gaining oxygen). Mnemonic: OIL (Oxidation Is Loss).

Reduction: The gain of electrons (often paired with gaining hydrogen atoms or losing oxygen). Mnemonic: RIG (Reduction Is Gain).

In cellular respiration, glucose is oxidized to CO2 while oxygen is reduced to H2O

ATP

primary cellular energy currency, breaking its high-energy phosphate bonds power cellular work

NADH

A high-energy electron carrier produced mainly during glycolysis, pyruvate oxidation, and the citric acid cycle; delivers electrons to the electron transport chain to make ATP

NADPH

similar to NADH but primarily used as a reducing agent in anabolic (biosynthetic) reactions and photosynthesis/antioxidant pathways rather than fueling standard cellular respiration ATP production.

Lactic Acid Fermentation

Pyruvate is directly reduced by NADH to lactate (lactic acid). Used by human muscle cells during heavy exercise and by certain bacteria (e.g., in yogurt-making).

Alcohol (Ethanol) Fermentation

Pyruvate is converted into acetaldehyde, releasing CO2 and is then reduced into ethanol and NAD+ Used by yeast and some plant tissues.

Oxygenic (Aerobic) Respiration

Uses molecular oxygen O2 as the final electron acceptor at the end of the electron transport chain, producing water and high yields of ATP.

Anoxygenic (Anaerobic) Respiration

Uses an inorganic molecule other than oxygen (such as sulfate SO2/4 nitrate NO3, or sulfur S as the final electron acceptor. Common in certain bacteria and archaea living in oxygen-depleted environments.

Eukaryotes

Glycolysis happens in the cytoplasm.

Pyruvate oxidation and the citric acid cycle happen inside the mitochondrial matrix.

Oxidative phosphorylation happens across the inner mitochondrial membrane

Prokaryotes

Lacking mitochondria, all stages (glycolysis, pyruvate oxidation, citric acid cycle) happen in the cytoplasm.

The electron transport chain and oxidative phosphorylation happen across the cell's plasma membrane.

Often yields a slightly different net total of ATP because they do not have to shuttle electrons across mitochondrial membranes.

Electron Transport Chain

What it is: A series of protein complexes and organic molecules embedded in a membrane that pass high-energy electrons from one carrier to the next.

How it produces ATP (Chemiosmosis):

1. NADH and FADH2 drop off high-energy electrons at the chain.

2. As electrons move down the chain, they release energy.

3. Protein complexes use that energy to pump protons H across the membrane, creating a strong proton (concentration and electrical) gradient.

4. Protons flow back across the membrane down their concentration gradient through a specialized enzyme called ATP synthase.

5. The spinning action of ATP synthase forces ADP and inorganic phosphate together to synthesize ATP.

Required for Photosynthesis to occur

sunlight, carbon dioxide, water, and pigments and enzymes

Organisms

Land plants, algae, various protists, and cyanobacteria (plus certain other prokaryotes like purple and green sulfur bacteria)

Photoautotroph

An organism that uses light energy as an energy source to synthesize organic compounds (food) from inorganic carbon sources like carbon dioxide

Chemical equation of photosynthesis

6CO2 + 6H2O + light energy —> C6H12O6 +6O2

Chlorophyll

The primary green pigment molecule in the thylakoid membranes that absorbs blue and red wavelengths of light and reflects green. It plays a direct role in converting light energy into chemical energy

Carotenoid

Accessory pigments (red, orange, or yellow) that absorb wavelengths of light not well-absorbed by chlorophyll and help protect the plant by dissipating excess light energy

Light energy harvesting

When a photon of light strikes an antenna pigment molecule in a photosystem, the energy is passed (resonance energy transfer) from pigment to pigment until it reaches a special pair of chlorophyll \(a\) molecules in the reaction center, exciting an electron to a higher energy level

Light reactions

Where: In the thylakoid membranes of chloroplasts.

What happens: Light energy excites electrons, driving a flow of electrons through photosystems. This process generates ATP and NADPH and splits water

Why/How oxygen gas is made

Oxygen is produced during Photosystem II when water molecules (\(H_{2}O\)) are split (photolysis) to replace the electrons lost by chlorophyll (\(P680\)). Oxygen is a byproduct of this oxidation-reduction step

The Z-scheme

The classic diagram (resembling a "Z" or an "N" sideways) represents the path of non-cyclic electron flow through Photosystem II (PSII), the electron transport chain, and Photosystem I (PSI). Electrons move from water up to a high-energy state in PSII, drop through the chain to PSI, and are boosted again to reduce NADP+ to NADPH

Cyclic Electron Transport

An alternative pathway where electrons from Photosystem I are cycled back to the cytochrome b6f complex instead of moving on to reduce NADP+. This pumps extra protons across the thylakoid membrane to produce ATP, without making NADPH or O2, helping the cell balance its ATP-to-NADPH ratio

Calvin Cycle

Where: In the stroma of the chloroplast.

What happens: Uses the ATP and NADPH produced during the light reactions to fix atmospheric CO2 (via the enzyme Rubisco) through carbon fixation, reduction, and regeneration phases to assemble carbohydrate molecules like G3P and glucose

DNA Replication

The entire genome must be precisely copied so that each new daughter cell receives a complete set of genetic instructions

Cell Mass & Organelle Duplication

The parent cell must generate enough cytoplasm, duplicate its organelles, and accumulate metabolic energy to sustain two separate living entities

Binary Fission

cell type: prokaryotes

nuclear envelope: no nucleus exists

spindle apparatus: absent; uses actin-like proteins to pull DNA

Mitosis

cell type: eukaryotes

nuclear envelope: completely breaks down and reforms

spindle apparatus: present; complex microtubule spindle arrays

Intermediate Mitosis

cell type: primitive eukaryotes

nuclear envelope: remains intact throughout divisions

spindle apparatus: present, but forms inside the nucleus or passes through nuclear tunnels

Replication

DNA polymerases cannot start synthesizing a DNA strand from scratch; they require specific initiator proteins to recognize a starting point, unwind the double helix, and bind the replication machinery. Starting at an origin ensures that the entire genome is copied exactly once per cell cycle

Anchoring

Without physical anchoring, there is no spatial framework to pull the duplicated genetic material to opposite ends of the cell, leading to catastrophic errors in chromosome distribution

karyotype

individual's complete collection of chromosomes, structurally isolated, stained, and digitally organized by size, shape, and banding patterns to identify genetic disorders or chromosomal mutations

Homologous Pair

Two structurally identical chromosomes (one maternal, one paternal) that carry the same genes at the same locations, though they may have different variations (alleles) of those genes.

Sister Chromatid

Two identical copies of a single chromosome formed by DNA replication, physically bonded together at a shared centromere until they are pulled apart

Interphase

G1 Phase (First Gap): The cell grows physically larger, duplicates organelles, and accumulates molecular building blocks.

S Phase (Synthesis): The cell synthesizes a complete copy of the nuclear DNA and duplicates the centrosome

G2 Phase (Second Gap): The cell grows more, produces proteins needed for division, and double-checks the duplicated DNA for errors.

Mitosis

Prophase: Chromatin condenses into visible chromosomes. The nuclear envelope breaks down, and the mitotic spindle begins to form.

Metaphase: Chromosomes align along the center of the cell (metaphase plate). Spindle fibers securely attach to the kinetochores of each chromosome.

Anaphase: Sister chromatids are pulled apart by the spindle fibers and travel to opposite poles of the cell.

Telophase: Chromosomes reach opposite poles and begin to decondense back into loose chromatin. New nuclear envelopes reform around each set of separated DNA.

Cyclin-Dependent Kinases

Constant, baseline enzymes present throughout the cell cycle that remain inactive until bound to a specific partner protein.

Cyclins

Regulatory proteins whose internal concentrations cyclically fluctuate depending on the specific phase of the cell cycle.

Mitosis

Purpose: Growth, tissue repair, regeneration, and asexual reproduction.

Location: Occurs in somatic (body) cells.

Divisions: One nuclear and cytoplasmic division (PMAT once).

Product: Two daughter cells that are genetically identical to each other and to the parent cell.

Ploploidy: Maintains the same chromosome number (e.g., diploid to diploid).

Homologous pairing / Crossing over: Does not occur

Meiosis

Purpose: Sexual reproduction and the production of gametes (sperm and egg).

Location: Occurs in germ cells (testes and ovaries).

Divisions: Two consecutive nuclear divisions known as Meiosis I and Meiosis II (PMAT twice).

Product: Four daughter cells that are genetically unique.

Ploploidy: Reduces the chromosome number by half (e.g., diploid to haploid).

Homologous pairing / Crossing over: Occurs extensively during Prophase I

diploid (2n)

cell contains two complete sets of chromosomes (one set from the mother, one set from the father). In humans, this is 2×23=46 total chromosomes.

haploid (n)

cell contains only one complete set of chromosomes (23 in humans)

Crossing over

What it is: The physical exchange of genetic material between non-sister chromatids of homologous chromosomes.

When it happens: During Prophase I of meiosis.

How it works: Homologous chromosomes pair up tightly in a process called synapsis to form a tetrad (or bivalent). Non-sister chromatids break and recombine, swapping segments of DNA. This creates recombinant chromosomes with new, unique combinations of maternal and paternal alleles

Independent of Assortments

What it is: The random and independent alignment and separation of maternal and paternal chromosome pairs during cell division.

When it happens: During Metaphase I and Anaphase I of meiosis (as well as random alignment in Metaphase II).

How it works: As homologous pairs line up at the cell's equator in Metaphase I, the orientation of each pair (which side faces which pole) is completely random and independent of every other pair. Consequently, the mix of maternal and paternal chromosomes that ends up in each resulting gamete is shuffled in millions of possible combinations ( 2n, where n=23 in humans).

Meiosis I

Prophase I: Chromosomes condense, nuclear envelope breaks down, homologous chromosomes undergo synapsis, and crossing over occurs.

Metaphase I: Paired homologous chromosomes (tetrads) align randomly along the cell's equatorial plane (independent assortment).

Anaphase I: Homologous chromosomes are pulled apart to opposite poles of the cell; sister chromatids remain attached at their centromeres.

Telophase I & Cytokinesis: Nuclear membranes may reform briefly, and the cell divides into two haploid daughter cells (each with duplicated chromosomes)

Meiosis II

Prophase II: Chromosomes condense again in the two new haploid cells, and new spindle fibers form.

Metaphase II: Chromosomes line up individually along the equator in a single-file line (similar to mitotic metaphase).

Anaphase II: Sister chromatids are pulled apart toward opposite poles, becoming individual chromosomes.

Telophase II & Cytokinesis: Nuclear envelopes reform around the separated sets of chromosomes, and the cells divide, resulting in a total of four genetically unique haploid gametes