Biology Quiz: Cellular Respiration and Fermentation

Fermentation

• Occurs in the absence of oxygen
• Pyruvic acid is metabolized
• Alcoholic Fermentation
  • Performed by Saccharomyces (yeast)
  • Produces: 2 ethanol + 2 CO2 + 2 ATP
  • Used in beer production
• Lactic Acid Fermentation
  • Performed by Streptococcus, Lactobacillus, and Bacillus
  • Produces: 2 lactate + 2 ATP
  • Used in yogurt production

Krebs Cycle

• Occurs in the presence of oxygen
• Also known as the TCA cycle or citric acid cycle
• Products:
  • Oxygen (waste)
  • NADH (electron carriers, major product)
  • FADH
  • ATP
  • It is the pathway that pyruvate enters following glycolysis

Electron Transport Chain (ETC) in Bacteria

• Occurs in the cell membrane
• Oxygen is the final electron acceptor
• Oxygen combines with hydrogen to form H2O (waste product)
• Large amounts of ATP are produced (38-40 ATP)

Calculation of ATP Production

• From 1 glucose molecule: 10 NADH + 2 FADH2 = 30 ATP + 4 ATP = 34 ATP

Oxidative Phosphorylation

• The transfer of electrons from high energy to low energy states
• With each transfer, energy in the form of ATP is captured
• High energy states release energy, which is captured as ATP

Chemiosmosis

• Conversion of ADP to ATP using the ATPase enzyme complex
• Occurs in the cell membrane

Glycolosis

• Occurs in the cytoplasm
• Glucose is converted to pyruvate
• Does not require oxygen
• Produces 2 ATP
• Breakdown of glucose and requires 2 ATP to start

Krebs Cycle

• Occurs in the cytoplasm
• Requires oxygen
• Pyruvate is converted to NADH and FADH2 (electron carriers)
• Produces 2 ATP

Electron Transport Chain

• Occurs in the cell membrane
• Requires oxygen
• Produces ATP
• Produces 34 ATP

Fermentation

• Occurs in the cytoplasm and does not require oxygen
• Lactic Acid Fermentation
  • Pyruvate is converted into lactic acid
  • Performed by Streptococcus, Lactobacillus, and Bacillus
• Alcoholic Fermentation
  • Pyruvate is converted into ethanol and CO2
  • Performed by Saccharomyces (yeast)

Protein Structures

• Peptide linkage: The formation of a peptide bond by removing H2O.
• Primary Structure: A polypeptide strand consisting of a sequence of amino acids.
• Secondary Structure: Alpha helix and pleated sheets.
• Tertiary Structure: A folded structure that combines alpha helixes and pleated sheets.
• Quarternary Structure: The combination of two or more polypeptide chains in folded states.

Binary Fission

• Cell elongation and DNA replication occurs
• Cell wall and plasma membrane begin to constrict
• A cross-wall forms, separating the DNA copies
• Cells separate
• Mother cell produces two daughter cells
• Daughter cells are exact replicas of the mother cell
• Budding is another form of cell division where a small new cell develops at the surface of the parent cell.

4 Phases of Bacterial Growth

• Lag: Preparing for growth, but no growth occurs yet
• Log: Exponential growth, increasing population
• Stationary: Growth and death of cells are equal
• Death: No more nutrients, population declines

Measuring Bacterial Growth (Pure culture only)

• Serial Dilution Method:
  • A concentrated solution of bacteria culture is diluted by a series of 10 folds
  • Colonies in the medium are counted.
  • Example: Diluting a glass of juice with water.
• Standard Plate Count:
  • Culture is added to a medium and allowed to grow
  • Colonies are counted

Other Methods

• Direct Microscopic Counts: Use a counting chamber and can not distinguish dead from alive bacteria
• **Most Probable Number (MPN): ** Used for measuring small amounts of microbes in water quality studies and can't do standard plate counts
• Turbidity: A spectrophotometer is used to measure the cloudiness of a sample.

Factors Affecting Growth

• pH
  • Acidophiles: Extremophiles (not pathogenic), prefer acidic environments
  • Neutrophiles: Prefer neutral pH
  • Alkaliphiles: Prefer alkaline environments
• Temperature
  • Psychrophiles: -10-20°C
  • Psychrotrophs: 0-30°C
  • Mesophiles: 10-50°C (most active, our body temperature)
  • Thermophiles: 40-71°C
  • Hyperthermophiles: 65-110°C
• Oxygen
  • Obligate aerobe: Requires oxygen
  • Facultative anaerobe: Can grow with or without oxygen
  • Obligate anaerobe: Requires the absence of oxygen
• Salinity/Salt:
• Nutrients:
  • Carbon: Ex) glucose
  • Nitrogen: Ex) ammonia, amino acids
  • Sulfur: Ex) sulfur amino acids
  • Phosphorus: Ex) inorganic phosphate
  • Trace elements: Very small amount, used as cofactors for enzymes (micronutrients)
  • Vitamins: Small amounts, used as coenzymes

Culturing Bacteria

• Streak Plate Method: Used to isolate a pure culture
• Types of Media:

In DNA

• Mutations cannot be fixed - permanent
• Mutations will be copied repeatedly
• Large mutations can be fatal

Transfer of Information

• DNA -> RNA -> Protein
• Replication: DNA polymerase: ATGC -> TACA (DNA to DNA)
• Transcription: RNA polymerase: ATGC -> UACG (DNA to RNA)
• Translation: mRNA, tRNA, rRNA: AUG/GCU/UAC/UGA = Met/Ala/Tyr/(stop) (RNA to protein)

Replication (DNA to DNA)

• Leading Strand: Synthesized continuously
• Lagging Strand: Synthesized discontinuously
• Key enzymes:
  • DNA polymerase: Synthesizes complementary DNA
  • RNA polymerase: Synthesizes RNA primers
  • Okazaki fragments: Short DNA fragments
  • DNA ligase: Seals nicks in DNA during synthesis and repair
  • Helicase: Unwinds the double strand of DNA
  • Origin of replication: Location on the chromosome where DNA synthesis starts

Transcription: DNA to RNA

• RNA polymerase is key enzyme
• Uracil replaces Thymine: ATGC -> UACG

Transcription of RNA:

1. RNA polymerase binds with the promoter sequence and opens the DNA double helix.
2. Ribonucleotides (ATP, GTP, CTP, UTP) are assembled into RNA.
3. Ribonucleotides are inserted according to base pairing: G, C, A, U.
4. RNA synthesis proceeds in the 5' to 3’ direction until it reaches the termination sequence, releasing the RNA.

Types of RNA

• Messenger RNA (mRNA): Translates to form a polypeptide
• Transfer RNA (tRNA): Carries amino acids to the growing polypeptide
• Ribosomal RNA (rRNA): Used in building ribosomes (machinery for synthesizing proteins)

Types of Mutations

• Spontaneous Mutation: Occurs naturally in the absence of a mutagen
• Mutagen: An agent that causes mutations
• Base Substitution: A change in one base (point mutation)
• Missense Mutation: Results in a change in the affected amino acid.
• Nonsense Mutation: Results in a stop codon, shortening the protein coded by the gene.

Structural Genes

• Code for proteins (enzymes)
• Example: Represent the output (product) that is created.

Operon

• Control region for structural genes: I P O Z Y A
• Contains regulatory elements: promoter, operator, and genes

Constitutive Genes

• Expressed at a fixed rate
• Always "on"

Inducible Genes

• Increase transcription of genes
• "Turned up" when needed

Repressible Genes

• Decrease transcription of genes
• "Turned off" it there is too much product

Gene Expression - Inducible Operon: Lactose Metabolism

• Example: lactose metabolism
• Key elements:
  • I - P - O - Z - Y - A
  • I: Repressor gene
  • P: Promoter
  • O: Operator
  • Z: β-galactosidase gene
  • Y: Permease gene
  • A: Transacetylase gene

Absence of Lactose

• Repressor protein binds to the promoter region, blocking it
• Prevents the enzyme needed for lactose metabolism from being produced

Presence of Lactose

• Allolactose (inducer) binds to the repressor protein, inactivating it.
• The repressor protein can no longer bind to the promoter region.
• Allows for the production of the enzymes needed for lactose metabolism

Catabolite Repression

• When all glucose is consumed, the microbe will start to use lactose as an energy source.

Gene Expression - Repressible Operon: Tryptophan Synthesis

• Example: tryptophan synthesis.
• Key elements:
  • I - P - O - E - D - C - B - A
  • I: Repressor gene
  • P: Promoter
  • O: Operator
  • E, D, C, B, A: Genes for the enzymes in tryptophan synthesis.

Tryptophan Synthesis - Explanation

• Tryptophan synthesis is on because the cell needs tryptophan to function.
• When there is too much tryptophan it could be detrimental, therefore, the system needs to stop it.
• An active repressor protein is used to repress the synthesis of tryptophan.

Feedback Inhibition

• A type of non-competitive inhibition
• The end product inhibits the first enzyme in the biosynthetic pathway
• End product binds to the enzyme, distorting the active site and preventing it from binding to the substrate.
• This stops the entire pathway.

Bacterial Conjugation

• The transfer of genetic material from one cell to another.
• It requires contact between the donor and recipient cells.
• It transfers much larger quantities of DNA than transformation.
• The transfer occurs in the form of plasmids (extra DNA) that provide benefits like antibiotic resistance.

F Plasmids (Fertility Plasmids)

• Circular, double-stranded DNA molecules.
• Types:
  • F+ cells: Contain F plasmids and make an F pilus (sex pilus).
  • F- cells: Lack F plasmids.
  • F pilus: A conjugation pilus that bridges the donor and recipient cell.
    • The donor cell has the F plasmid (F+)
    • The recipient cell does not (F-)
    • F+ creates and attaches to the F pilus
    • F+ creates a copy of itself
    • The copy is sent to F-
    • F- becomes F+ because it now has the blueprint of the F plasmid

Types of Plasmids:

• **F plasmids/ Fertility plasmids **
• Resistance plasmids: Carry genes that provide resistance to antibiotics
• Virulence plasmids: Carry genes that cause disease (toxin genes)
• Tumor-inducing plasmids: Cause tumor formation in plants.
• Some plasmids contain genes for catabolic enzymes.

Transposons

• Jumping genes
• Mobile genetic sequences
• Can move from one location to another (transposition)
• Contain transposase: An enzyme that allows the transposon to jump and often carries genes like antibiotic resistance.
• Segments of DNA that can move within or between DNA molecules.
• Contain insertion sequences used for cutting and resealing DNA (transposase).
• Complex transposons carry other genes besides the transposase.

Transposon Example:

- ACTTACTG ATCAGTAAGT AT
- TGAATGACTA TA GTCATTCA
- Transposase gene
 - ACTTACTGAT ATCAGTAAGT 
- TGAATGACTA TAGTCATTCA
     - Inverted repeat, Tn5, kanamycin resistance, IS1, IS1

Test your knowledge on cellular respiration and fermentation processes with this quiz. Explore key concepts such as alcoholic fermentation, the Krebs Cycle, and the role of oxygen in energy production. Perfect for biology students looking to reinforce their understanding of these fundamental topics.