Micro Exam 3

What is Oxidative Phosphorylation?

A process by which ATP is synthesized as the result of electron transport driven by the oxidation of a chemical source

What is the chemiosmotic hypothesis?

the most widely accepted hypothesis to explain oxidative phosphorylation. Protons move outward from the mitochondrial matrix as electrons are transported down the chain

How does the chemiostic hypothesis explain proton expulsions role?

Proton expulsion during electron transport results in a formation of a concentration gradient of protons and a charge gradient

How is the proton motive force (PMF) created via oxidative phosphoylation?

The combination of chemical and electrical potential difference creates the PMF, driving ATP synthesis via ATP synthase

What is ATP synthase?

Large protein that uses energy from H+ ions and the PMF down gradient to bind ADP and a phosphate group together to produce ATP

What is the theoritical maximum yield of ATP during aerobic respiration? What is thr actual yield?

Theoritical maximum is 32 ATP, actual is closer to 30 ATP

What are some factors affecting ATP yield?

bacterial ETCs are shorter and have lower P/O ratios, ATP production may vary due to environemental changes, PMF in bacteria and archaea is used for other purposes than ATP production, and precusor metabolites may be used for biosynthesis

What is anaerobic respiration?

An exothermic reaction in which glucose is broken down to release energy in the absence of oxygen, uses another electron carrier than oxygen. Generally yields less energy

dissimilatory nitrate reduction

use of nitrate as a terminal electron acceptor, making it unavailable to cell for assimilation or uptake. Nitrate is converted to Nitrite, which is toxic and unusable

Denitrification

reduction of nitrate to nitrogen gas, skipping nitrite entirely

What is fermentation?

The production of ATP without oxygen. Pyruvate or derivative is used as endogenous electron acceptor. The substrate is only partially oxidized

TRUE or FALSE. Oxidative phosphorylation still occurs during fermentation

False, ATP is formed via substrate level phosphoylation

Homolactic fermenters

organisms that ferment sugars almost completely to lactic acid

heterolactic fermenters

microorganisms that ferment sugars to form lactate and other products such as ethanol and CO2

What is chemolithotrophy?

oxidation of inorganic compounds to yield energy, carried out by chemolithoautotrophs. ATP is synthesized via oxidative phosphorylation

What are the 2 major groups of chemolithotrophs?

sulfur oxidizing mircobes that oxidize hydrogen sulfide, sulfer, and thiosulfate and Nitrifying bacteria that oxidize ammonia to nitrate

What is reverse electron flow?

Performed by chemolithotrophs. Can reverse flow to creat more NADH or create forward flow to produce ATP. In reverse flow protons are taken in while in forward flow protons are pumped out. This creates a flow of energy

What is phototrophy?

Two part process, energy from light is trapped and converted to chemical energy

What is the first part of phototrophy?

Light reaction, light energy is trapped and converted to chemical energy

What is the second part of phototrophy?

Dark reaction, energy produced in the light reactions is used to reduce CO2 and synthesize cell constituents

Photosynthesis

process by which plants and some other organisms use light energy to convert water and carbon dioxide into oxygen and high-energy carbohydrates such as sugars and starches

Chlorophylls

Major light absorning green pigments that give plants their characteristic green color,reacts with sunlight, carbon dioxide and water to form carbohydrates

What differs between different types of chorphylls?

Functional groups

What are accessory pigments?

chlorophyll b, carotenoids, xanthophylls. Transfer light energy to chlorophylls

Antennas

highly organized arrays of chlorophylls and accessory pigments that transfer captured light to special reaction center chlorophyll

What is a photosystem?

An antenna and its associated reaction center chlorophyll

What is anoxygenic photosynthesis?

Photosynthesis that does not produce oxygen when transferring electrons. Only one photosystem is involved, uses bacteriochlorophylls and mechanisms to generate reducing power

What organisms carry out anoxygenic photosynthesis

phototropic green bacteria, phototrophic purple bacteria, and heliobacteria

What type of energy are photons?

electromagnetic energy

Purple Non-Sulfur bacteria

anaerobic bacteria that live in low sulfide conditions; use light for energy but use organic acids from fermentation products of anaerobic bacteria instead of carbon dioxide as carbon source

Green Sulfur bacteria

gram-negative, strictly anaerobic and phototrophic; use reduced sulfur compounds as electron donors for CO2 fixation

What is Bacteriorhodopsin-Based Phototrophy

Type of phototrophy that involves bacteriorhodopsin used by some archaea. Protive motive force is generated without the use of an electron transport chain

What is a bacteriorhodopsin?

a type of membrane protein that functions as a light-driven proton pump

What is anabolism?

the synthesis of complex molecules in living organisms from simpler ones. Uses a carbon source and inorganic molecules to synthesie new organelles and cells

How do antibiotics affect anabolism

inhibit anabolic pathways such as nucleic acid synthesis and protein synthesis

Precursor metabolites

Metabolic intermediates that can be either used to make the subunits of macromolecules or oxidized to generate ATP

Calvin Cycle

a biochemical pathway of photosynthesis in which carbon dioxide is converted into glucose using ATP

Where does the Calvin cycle occur in eukaryotes

stroma of chloroplasts

Where does the calvin cycle occur in cyanobacteria, some nitrifying bacteria, and thiobacilli?

carboxysomes

What are the 3 phases of the Calvin Cycle?

Carboxylation phase, reduction phase, regeneration phase

What occurs in the carboxylation phase of the Calvin cycle?

Rubisco catalyzes the addition of CO2 to ribulose-1,5-biphosphate, forming 2 molecules of 3-phosphoglycerate

What occurs in the reduction and regeneration phases of the Calvin cycle?

3-phosphoglycerate is reduced to glyeraldehyde-3-phosphate, rubisco is regenerated, carbon skeletons are created

What is rubisco?

Rubisco is an enzyme that converts inorganic molecules to organic molecules

What are the 3 major biomolecules of DNA replication

DNA, RNA, proteins

What is the structure of DNA?

double helix structure, linked together by phosphodiester bonds, made up of deoxyribose and the nitrogen base adenine, guanine, cytosine, and thymine

What is the structure of RNA

single stranded, linked together by phosphodiester bonds, made up of ribose and the nitrogen base adenine, guanine, cytosine, and uracil

DNA replication

the process of making a copy of DNA

Steps of DNA replication

2 strands seperate and act as a template for the synthesis of a complementary strand

What type of synthesis is DNA replication?

semi-conservative, each daughter cell obtains one old and one new strand

Parts of the DNA polymerase

beta clamp, alpha subunit, omega subunit, and epsilon subunit

What is the function of the Beta clamp

associates with DNA polymerase III and prevents it from falling of the template strand of DNA

What is the function of the alpha subunit

RNA Polymerase assembly and transcriptional regulation.

What is the function of the omega subunit

helps stabilize the tetrameric core

What is the function of the epsilon subunit?

3' to 5' proofreading

DnaA protein

binds to DnaA boxes within the origin to initiate DNA replication

DnaB protein (helicase)

helicase (5 to 3), breaks hydrogen bonds holding two strands of double helix together, promotes DNA primase activity, involved in primosome assembly

DNA gyrase

Relieves supercoiling of DNA ahead of helicase; separates daughter molecules in final stages of replication

SSB proteins (single stranded binding proteins)

Bind single-stranded DNA after strands are separated by helicases

DnaC protein

Aids DnaA in the recruitment of DNA helicase to the origin

DNA primase

synthesis of RNA primer

DNA polymerease III holoenzyme

complex of about 20 polypeptides, catalzyes most of the DNA synthesis that occurs during DNA replication, has 3 to 5 proofreading activity

DNA polymerease I

removes RNA primers, fills gaps in DNA formed by removal of RNA primers

DNA ligase

enzyme that chemically links DNA fragments together

Tus

termination of replication

Topoisomerase IV

Separation of chromosomes upon completion of DNA replication

What is the pattern of DNA synthesis

bidirectional from a single origin

What is supercoiling?

The two strands in DNA twisted around themselves in a tight manner.

Why does negative supercoiling occur?

Makes it easier for DNA replication to occur

Why does positive supercoiling occur?

How is the origin of replication recognized?

DnaA protein binds to specialized regions rich in AT called AT boxes which are areas that are easier to melt or unbind for replication

What occurs at the replication fork in E. coli

DnaA proteins bind to oriC, DnaB and other helicase seperate strands, SSBs attached, primers are synthesized, leading and lagging strands are synthesized, DNA I removes primers, Okazaki fragments are joined by DNA ligase

How is replication terminated in E coli?

Replication stops when replisome reaches termination site (ter) on DNA

Why are there multiple ter sites?

To increase the likilhood the replisome will reach and recognize one of them

What is a gene?

basic unit of genetic information, segment of DNA that codes for a tRNAm rRNA or polypeptide

in DNA replication, which strand requires an RNA primer?

The lagging strand

Why does the lagging strand require a primer?

Because the polymerase can't just start where it wants, replication in 5 to 3 not 3 to 5

What is a protein coding gene?

A gene that contains the information to synthesize a protein

What is a promoter?

The region of mRNA where RNA polymerase binds and starts transcription

What is the Shine-Dalgarno sequence?

A short conserved nucleotide sequence upstream of the AUG start codon that serves to align the mRNA on the bacterial small ribosomal subunit

Genes that code for tRNA

code fot more than a single tRNA molecule or type of tRNA

Genes that code for rRNA

transcribed as a single large precursor

Transcription elongation

After binding, RNA polymerase unwinds the DNA. A transcription bubble produced which moves with the polymerase as it transcribes mRNA from template strand

What is the difference between Holo and Core enzyme RNA polymerase?

the holo enzyme contains the sigma factor allowing for specific promoter recognition and transcription initiation. The core enzyme handles elongation

How is transcription terminated?

Transcription terminates when the RNA polymerase reaches a sequence called the terminator and falls off of the DNA.

Codon

gentic code word, 3 base pairs long, specifies an amino acid

Start codon

codon that signals to ribosomes to begin translation; codes for the first amino acid in a protein AUG

What is a wobble codon

3rd codon in sequence, less important than 1st or 2nd. Amino acids coded by multiple codons may differ in 3rd position.

Why is the wobble codon important?

decrease the effects and likihood of DNA mutations

What is translation

The process by which ribosomes synthesize proteins using mRNA as a template. It involves the decoding of mRNA codons to assemble amino acids into a polypeptide chain.

Transfer RNA

A type of RNA that carries amino acids to the ribosome during protein synthesis, matching its anticodon with mRNA codons.

Ribosome

A cellular structure composed of ribosomal RNA and proteins, ribosomes are the sites where translation occurs, facilitating the assembly of amino acids into polypeptide chains according to the sequence of mRNA codons.

What is the role of 16S rRNA ribosomal binding sites

bind to the Shine-Dalgarno site on mRNA for protein synthesis initiation and bind protein needed for initiation of translation and aminoacyl-tRNA

WHat is the role of 23S rRNA

ribozyme catalyzes peptide bond formation

How is protein synthesis initiated?

It begins when the initiator codon binds to 16S rRNA in the 30S subunit. The Shine-Dalgarno sequence of mRNA is aligned with 16S rRNA

Elongation cycle

sequential addition of amino acids to growing polypeptide

3 phases of elongation cycle

aminoacyl-tRNA binding, transpeptidation reaction, translocation

Peptidyl site

binds initator tRNA or tRNA attached to growing polypeptide

Aminoacyl site

binds incoming aminoacyl-tRNA

Exit site

briefly binds empty tRNA before it leaves ribosome

3 events of the translocation phase of elongation

peptidyl-tRNA moves from A site to P site, ribosome moves down one codon, empty tRNA leaves P site