Microbiology Chapter 8 & 11

Vocabulary

Potential Energy

stores inactive energy

kinetic energy

movement

Protons

positive charge

neutrons

no charge

ion

if atoms lose or gains electrons

covalents

sharing electrons

hydrogen bonds

(not true bonds) F, O, H, N

Catabolic

large breaks down to small molecules(hydrolysis) exergonic

Anabolic

small molecules make large molecules (dehydration synthesis) endergonic

Activation energy

minimum amount of energy to start a chemical reaction

Brownian movement

slight vibration, energy transferred when particles collide

Reaction rate

depends on collision rate (increase speed= increase temp)

Enzymes

biological catalysts, determines organism’s metabolic pathways

substrate

molecules on which enzymes act

active site

region that interacts with the substrate (enzyme substrate complex)

ENZYMES WORK BY LOWERING ACTIVATION ENERGY OF CHEMICAL REACTIONS

Apoenzyme

protein portion- inactive, non-functional, activated by a cofactor

Cofactor

activator, non-protein component

some form bridge between enzyme and substrate

Coenzyme

cofactor that is an organic molecule

(apofactor+ cofactor)= holoenzyme (whole/active)

competitive inhibitors

shape structure similar to substrate, enters active site- compete with substrate, but no products

non-competitive/ allosteric inhibitions

molecule does not bind to active site but to the allosteric site, and active site changes shape, can/ cannot bind substrate (binding can activate or inactive enzyme)

Feedback inhibition

(metabolic pathways) - prevents cell from wasting resources by making more of substance than it needs

Ribozymes

enzymes made from RNA, biological catalysts, active sites, remove sections/splices

metabolism

sum total of all chemical reactions in a cell

Oxidation

loss of electrons, often releases energy

Reduction

molecule gains one or more electrons

Phosphorylation

adding a phosphate to a molecule

Substrate level phosphorylation

a phosphate group taken from another phosphorylated molecule

Oxidative Phosphorylation

electron carries deliver electrons to ETC, adp—atp chemiosmosis

Photophosphorylation

conversion of light—- ATP & NADPH

Glycolysis aka Embden- Meyerhof Pathway

cytosol, glucose converts to pyruvate, with/wo O2

end product of glycolysis- 2 ATP, 2NADH, 2 Pyruvic acid

Transition Step of glucose→ pyruvate acid

2 CO2, 2 NADH, 2 Acetyl CoA

Kreb Cycle

4CO2, 6NADH, 2ATP, 2FADH2 - mitochondria

ETC

electrochemical gradient, 36 ATP

chemiosmosis

across electrchemical gradient, H+ pass through ATP synthase, 1NADH: 2.5 ATP

1FADH2: 1.5ATP

Fermentation

anaerobic, NAD+ regenerated so glycolysis can continue (Homolactic-lactic acid)(Hemolactic-others as well)

Protein Metabolism

protein-amino acid-transamination/deamination

transamination- transfer amino group

deamination- removal of an amino group

DNA

double helix, bounded, ATCG, long length, long life

RNA

single stranded, UACG, short length, short life

chromosome

made of DNA tightly wound around histone proteins (1 single copy = haploid) (2 copy=diploid)

Chromatin

arms/legs of the chromosome, Euchromatin=active Heterochromatin=inactive

Gene

DNA instructions

Allele

form of a gene

Genotype

actual alleles of genes in a genome

Phenotype

expression of those genes (traits)

genome

all genetic information in a cell

homologous

term for 2 like chromosomes

Primase

synthesizes RNA primer

Topoisomerase

uncoils DNA

Helicase

separates 2 strands(unzips strands exposing the replication fork)

DNA polymerase III

adds nucleotides to the 3’, proofreads, adds new bases

DNA polymerase I

replaces RNA primer with DNA nucleotides

DNA ligase

joins Okazaki fragments on lagging strand

Bidirectional Replication

2 sets of enzymes, 2 replication forks, 2 leading and 2 lagging strand

Semiconservative

DNA- each new DNA contains 1 old and 1 new strand

Different types of RNA molecules

RNA primer- used in DNA replication

mRNA- protein synthesis, made in transcription, read during translation

rRNA- used in translation in protein synthesis

tRNA- used in translation in protein synthesis

Regulatory RNA- alter gene expression by interacting with DNA

Transcription

DNA—→ RNA

makes mRNA (contains codons)

Translation

mRNA+tRNA+rRNA—> new protein (contains anticodons)

3 steps for transcription

Initiation- RNA polymerase binds to a promoter recognizes by sigma factor of RNA polymerase

Elongation- 10 nucleotides of promoter, RNA polymerase (adds more)

Termination- terminator, sequence ends

redundant codons

one amino acid coded more than once

sense codons

code for amino acids

nonsense codons

do not code for amino acids (stop codons end protein synthesis)

Introns

non-coding regions, removed, spliced

Exons

coding regions, spliced together (expressed)

Vertical gene transfer

gene passed from organisms to its offspring, prokaryotes & eukaryotes(prophase I meiosis)

Horizontal gene transfer

gene transferred within same generation

Horizontal Gene Transfer (1.Transformation)

naked DNA transfer from 1 bacterium to another (competence required)

Horizontal Gene Transfer (2.Transduction)

DNA transfer by virus from one cell to other

generalized; random gene

specialized; specific gene transfer, bacterial toxins

Horizontal Gene Transfer (3.Conjugation)

transfer of genes on plasmids

requires direct cell to cell

Plasmids

self replicating circle pieces of DNA

dissimilation plasmids- enzymes of catabolism of rare molecules

toxin/production plasmids- like e.coli

bacteriocins- toxins that kill other bacteria

resistance factors- resistance for antibiotics

Horizontal Gene Transfer (4. Transposons and Transposition)

small DNA segments from 1 location on DNA to another within same chromosome, can be carried between cells on plasmids and viruses

What is the Electron Transport Chain (ETC) in mitochondria?

The Electron Transport Chain (ETC) is a sequence of protein complexes and electron carriers situated in the inner mitochondrial membrane. It transfers electrons from NADH and FADH2 through redox reactions, resulting in the generation of ATP during oxidative phosphorylation. The process creates a proton gradient, which is essential for ATP synthesis. (36 ATP)

What are the four steps of cellular respiration?

The four steps of cellular respiration are Glycolysis, Transition Step, Kreb Cycle, and the Electron Transport Chain (ETC).

Comparison of Active Site and Allosteric Site

The active site is the location where substrates bind and reactions occur, while the allosteric site is a separate site that regulates the enzyme's activity through conformational changes. A key distinction is that binding to the allosteric site affects the enzyme's shape and function without participating in the reaction directly.

what happens when cell does not want to proceed with glycolysis?

Another term for glycolysis, a series of reactions that convert glucose to pyruvate in the cytosol, yielding 2 ATP and 2 NADH (EMP). A metabolic pathway parallel to glycolysis that generates NADPH and ribose 5-phosphate for nucleotide synthesis. (PPP)

why do cells need ATP?

Cells need ATP because it serves as the primary energy currency, providing the energy required for various biochemical processes, such as muscle contraction, active transport, and biosynthetic reactions.

Why is fermentation in bacteria slower compared to aerobic respiration?

Fermentation is slower because it relies on substrate-level phosphorylation for ATP generation, which produces significantly less ATP (2 ATP per glucose) compared to aerobic respiration, which utilizes the electron transport chain to generate a much larger yield of ATP (up to 36 ATP per glucose). Aerobic

Role in Protein Synthesis

Protein synthesis involves transcription (where DNA is converted to RNA) and translation (where RNA is used to assemble amino acids into proteins), essential for cellular functions and growth.

Importance of 3' to 5' Direction in DNA Synthesis

The 3' to 5' direction is crucial for DNA polymerase function during replication, as it synthesizes new DNA strands by adding nucleotides to the 3' end of the existing strand which directly

Applications of Yeast Fermentation in Biotechnology

Yeast fermentation is essential for producing alcoholic beverages like beer and wine, enhancing food products like bread, and generating bioethanol as a renewable energy source.