short answers 2

• 1. Factors affecting enzyme function; what are the factors; how do they affect enzyme activity?

  Temperature:-every enzyme has it's optimum temperature-too hot → denature, too cold → slow down molecular motion and reducing collisions between enzymes and substrates.
• pH:

  -every enzyme has its optimum pH

  -changes can alter the ionization state of amino acid residues in the enzyme's active site, affecting substrate binding and catalytic activity

  -extreme pH levels can denature
• Concentration of the substrate:

  -increasing substrate concentration can initially increase enzyme activity as more substrates are available for binding

  -At saturation, enzyme activity levels out as all enzyme molecules are bound to substrates
• Enzyme inhibitors:

  -competitive inhibitors directly bind to the active site of the enzyme, preventing the substrate from entering and being converted to product (reaction stops)

  -non-competitive inhibitors bind to another site on the enzyme (allosteric site) causing a change in the shape of the active site into which the substrate can no longer fit.
• 2. Culture media: types? What differentiates them- selective, differential, enriched.

  Chemically defined media:exact composition is known
• Complex media:

  -nutrients from yeast, animal and plant extracts (some variation between batches naturally results)
• Selective:

  -has chemicals to prevent the growth of unwanted bacteria

  -(ex. EMB- dye suppresses the growth of Gram positive bacteria)
• Differential:

  -has chemicals that makes it easier to distinguish between colony types on the same plate visually.

  -(ex. EMB- E. coli appears as dark purple colonies with metallic green)
• Enriched:

  -has specific nutrients and environmental conditions that favor growth of a particular species (while partially suppressing others) that is rare to find in the sample.

  -(ex. Chocolate agar used to grow Neisseria spp)
• 3. Growth-binary fission: population dynamics; log, lag, stationary, death phases.

  Definition:-How bacterial cells divide, involves duplicating one chromosome

  -Bacteria divide by binary fission every 20-30 minutes
• Lag phase:

  no to very little growth
• Log phase:

  rapid, explosive cell division (growth)
• Stationary phase:

  reproductive rate (growth) equals death rate
• Death phase:

  rapid decline in population due to greater death
• 4. Translation:

  Genetic code:-a triplet code, where each three-nucleotide sequence on the mRNA (codon) specifies a particular amino acid or serves as a start or stop signal.

  -There are 64 possible codons, encoding for 20 amino acids and three stop codons
• Start and stop codons:

  -The start codon AUG initiates translation and serves as the starting point for protein synthesis.

  -Stop codons signal the termination of translation, UAG, UGA, UAA
• Redundancy of the code:

  -The genetic code is redundant, meaning that multiple codons can code for the same amino acid.

  -This redundancy provides flexibility to the genetic code, helping to minimize the impact of mutations.
• Roles of:

  mRNA

  -(messenger RNA) carries the genetic information from DNA to the ribosome

  -where it serves as a template for protein synthesis.
• rRNA

  -(ribosomal RNA) is a structural component of ribosomes, where protein synthesis occurs.
• tRNA

  -(transfer RNA) molecules carry specific amino acids to the ribosome, where they recognize and base pair with complementary codons on the mRNA through their anticodon sequences.
• 5. Recombination: definitions, purpose; types- conjugation, transformation, transduction, transposition.

  Recombination:-any process that produces new combinations of existing genes in an individual cell

  -More likely to bring about beneficial combinations

  -Always involves a gene donor and a gene recipient
• Types:

  1. Conjugation:

  -Transfer of DNA througha mating type of process involving direct contact between bacteria that are joined by a sex pilus.

  -Sex pilus of donor cell makes contact with recipient cell → transfers DNA → recipient becomes new donor
• 2. Transformation:

  - DNA fragments (from dead cells) can be picked up by living cells and incorporated into their genomes.

  -No direct contact, works best when cells are starving and when donor and recipient are closely related
• 3. Transduction:

  - host DNA carried from host → host by a virus (bacteriphage)

  - Transfer of DNA from one bacteria to another through bacteriphage infection
• 4. Transposition:

  -DNA moves from one part of the genome to another, they have special sequences at both ends

  -It makes a circle of itself by connecting the ends with the special sequences and can jump around and insert / incorporate somewhere else.
• 6. DNA replication:

  the process by which a cell makes an identical copy of its DNA.
• 1. Initiation:

  -begins at specific sites on the DNA molecule called origins of replication.

  -Enzymes called helicases unwind and separate the double helix, forming a replication bubble with two replication forks.
• 2. Primer Binding:

  -Primase synthesizes a short RNA primer complementary to the DNA template strand.

  -This primer provides a starting point for DNA synthesis.
• 3. DNA Synthesis (Elongation):

  -DNA polymerase adds nucleotides to the growing DNA strand, following the base-pairing rules.

  -It synthesizes the new strand in the 5' to 3' direction.

  -The leading strand is synthesized continuously in the direction of the replication fork

  -the lagging strand is synthesized discontinuously in short fragments called Okazaki fragments.
• 4. Proofreading:

  -DNA polymerase has proofreading capabilities, allowing it to correct errors in nucleotide incorporation.
• 5. Primer Removal and Gap Filling:

  -Once the DNA polymerase reaches the end of the template or encounters the RNA primer, another enzyme called exonuclease removes the RNA primer.

  -DNA polymerase then fills in the gap left behind with DNA nucleotides.
• 6. Ligation:

  -DNA ligase seals the spaces between the Okazaki fragments on the lagging strand and joins the newly synthesized DNA fragments into a continuous strand.