BIOL 111 Exam 3 - TAMU

A section of DNA that encodes the instructions needed to make a protein or RNA

5' upstream regulatory sequence, open reading frame (ORF), and downstream regulatory system 3'

Distal control elements (including an enhancer/silencer), proximal control elements, and the promoter TATA box

Specific DNA sequence found in the promoter region

Exons and introns with a Poly-A signal sequence at the end

The terminator and distal control elements which include the enhancer or silencer

Read 5' to 3', Terminator, and Promoter

All genes are controlled by the same operon in between the promoter and operator at the front and the terminator at the back

Cells are governed by a cellular chain of command that dictates the flow of genetic information

DNA (transcription) --> RNA (translation) --> ribosomes

RNA

Cannot leave the nucleus

The process by which DNA directs protein sythesis

Transcription and translation

The synthesis of RNA under the direction of DNA

mRNA

The actual synthesis of the peptide under the direction of mRNA

Operator, one promoter for multiple genes, and operons under control of the same promoter

Each gene encodes for a single enzyme, meaning each gene would influence a specific step in a metabolic pathway

Transcription factors

RNA polymerase reads "termination sequence" which causes RNA polymerase to dissociate from DNA, and the RNA is immediately ready for translation

RNA polymerase reads through a "special termination sequence" known as a Polyadenylation sequence (AAUAAA)

The end of the RNA transcript is then bound by proteins causing the RNA polymerase to dissociate from the DNA

After termination, the RNA needs additional processing

Modifications made in the nucleus prior to translation

5' capping, 3' polyA tail, and intron splicing

When a modified guanine nucleotide is added to an mRNA before leaving the nucleus going through translation

The removal of introns and splicing together of exons in pre-mRNA so it can officially become mRNA

A large ribonucleoprotein complex that removes introns from pre-mRNA

20,000 - 25,000

It is much smaller than the proteome and transcriptome

It occurs only in the cytoplasm and does not require RNA transcript modification

Transcription and translation can occur simultaneously within the cells

The cell uses a DNA template to create a complimentary mRNA, which then carries the genetic information out of the nucleus and into the cytoplasm for protein synthethsis

Both prokaryotic and eukaryotic cells have them

Small ribosomal subunit, large ribosomal subunit, mRNA, tRNA, and peptides

Messenger RNA molecule that serves as the intermediate between DNA and protein synthesis and carries the genetic instructions from a gene to the ribosome

Transfer RNA that is a small, noncoding RNA molecule that delivers the correct amino acid to the ribosome during protein synthesis

From the 5' to the 3' end

The flexibility in base pairing at the third position of a codon during translation, allowing a single tRNA molecule to recognize multiple codons that differ only in that third base

Between 40-60

Initiation, elongation, and termination

The initiation complex forms, where the small ribosomal subunit binds to the mRNA, scanning in the 5' to 3' direction for the start codon, then initiator tRNA binds to the AUG and the large ribosomal subunit joins the complex and the complex recruits another tRNA

The tRNA enters A site (EPA), then transfers to P site where the amino acid forms a peptide bond with the amino acid of the entering tRNA and breaks off from its own tRNA, as the ribosome moves downstream along the mRNA from 5' to 3', and tRNA keeps cycling through on repeat

The ribosome reaches a STOP codon, and a release factor enters A site causing the ribosome to dissociate

UAA, UGA, UAG

UAA

UGA

UAG

There are no tRNAs with anticodons that match them, so there is nothing to translate, which signals termination

The bottom one, also known as the template strand which reads from 3' to 5', as the mRNA is transcribed on top of it reading from 5' to 3'

Genetic code

It is highly conserved (barely changed), redundant, and not ambiguous

One

Multiple codons can code for the same amino acid due to the wobble effect

A change in one bp that does not change the amino acid sequence

A change in 1 bp that results in the substitution/change of only one amino acid (everything else stays the same)

A change in 1 bp that prematurely codes for a STOP codon, changing the function or expression of the gene

The insertion, deletion, or duplication of DNA bases which change the reading frame of the gene

The capacity to do work

Everything

From the sun, which is used for photosynthesis in plants to create O2 that humans use for cellular respiration to create CO2 (it is a never ending cycle)

All of the chemical reactions that take place inside cells through anabolic and catabolic stepwise chemical reactions

Anabolic and catabolic

The building of molecules

The breakdown of molecules

Consists of many biochemical reactions that all require energy transformations, and each step is a separate chemical reaction that is catalyzed by a specific enzyme

Anabolic and catabolic

The synthesis of complex molecules from similar ones that requires an INPUT of energy

The breakdown of complex molecules into similar ones that causes a RELEASE of energy

Stored energy or energy that an object has because of its position relative to other objects, stresses within itself, electrical charge, etc.

The energy of an object's motion

Total amount od energy in the universe is constant and energy cannot be created or destroyed, only transferred or transformed

All energy transfers or transformations are never completely efficient, and every energy transfer increases the entropy of the universe and reduces the amount of usable energy

The study of energy and energy transformations, where the system indicates the matter under study and the surroundings are everything else outside of the system

How the transfer of energy in and among living systems is governed

Open, closed, and isolated

Matter and energy are exchanged between a system and its surroundings (like a mug of coffee)

Where energy is exchanged between a system and its surroundings but not matter (like a mug with a lid on it)

No exchange of matter or energy between a system and its surroundings (like a travel coffee cup)

A decrease in entropy within a cell maintains order (this requires a lot of energy) and causes an overall increase in the entropy of the universe

Living organisms are highly ordered and require constant energy input

Energy that is lost to an unusable form and is commonly associated with states of disorder, randomness, or uncertainty

The energy from a chemical reaction that is available to do work after we account for entropy

The free energy change of a reaction that determines whether a reaction happens spontaneously or nonspontaneously

ΔG = G(final state) - G(starting state)

Exergonic and endergonic

When energy is released, making it catabolic and spontaneous (ΔG is less than 0)

When energy is consumed, making it anabolic and non-spontaneous (ΔG is greater than 0)

Exergonic (fallen jenga blocks aren't going to fall again)

Endergonic (stacked jenga blocks are always at risk of falling)

Exergonic

Endergonic

The initial energy required to start a reaction (every reaction has one)

Endergonic

Exergonic

Molecules, typically proteins, that catalyze biochemical reactions and are highly specific and reusable

Chemical reactants that bind to an enzyme's active site

They catalyze biochemical reactions by lowering the activation energy and speeding up the process

Enzymes

The active site is where the substrate binds and the allosteric site is a separate binding site

When the inhibitor binds to the active site making it to where the substrate can't

When the inhibitor binds to the allosteric site, changing the shape of the active site so the substrate cannot bind

Non-competitive since there is no fight to cover the active site with substrates, the inhibitor can simply go to the allosteric site without any competition

When inducers attach to the allosteric site, which changes the active site shape allowing the substrate to bind

Non-competitive

Occurs when the product of a metabolic pathway shuts down the pathway, usually by inhibiting an upstream enzyme

Very important for regulatory mechanisms in the cell

Glycolisis, Link Reaction, Citric Acid Cycle, and Chemiosmosis

In the cytosol

Within the mitochondria

Composed of one sugar molecule, one adenine, and three phosphate groups

Through phosphorylation of ADP

Process of adding a phosphate group to a molecule

Loss of a phosphate group

2 ATP (actually 4 ATP made, but 2 ATP used up)

2 ATP

Around 32 ATP

Energy is released in breakdown of "fuel" molecules through a series of enzymatic reactions

The loss of electrons during a reaction, which generally results in a decrease of potential energy

A gain of electrons during a reaction, which generally results in an increase of potential energy

Glucose is oxidized to CO2

Oxygen is reduced to water

Glucose

Oxygen

All cells perform glycolisis

In the cytosol outside of the mitochondria

Energy Investment and Energy Payoff

Glucose is phosphorylated twice to make fructose biphosphate, then split into two 3 carbon sugars (DHAP and G-3-P)

The two G-3-P molecules are oxidized into pyruvate which produces 2 NADH and 4 ATP (net 2)

2 pyruvate, 4 ATP, and 2 NADH

The pyruvate is oxidized into acetate and combined with coenzyme A, which releases CO2 (two for both pyruvate)

Twice (once for each pyruvate)

4 CO2, 6 NADH, 2 FADH, 2 ATP

To gather electrons for electron transport chain

Oxaloacetate (regenerated at the end of the cycle)

Oxidative phosphorylation

The NADHs are phosphorylized into NAD+, leaving 2 electrons that go through a protein channel into the intermembrane space, flowing in and out of the sites by CoQ and Cyt c until protein IV where oxygen is oxidized turning into H2O, and then H+ ions go down the proton gradient of ATP Synthase, phosphorylating ADP to create ATP

1 NADH, 1 H+, and Acetyl CoA

Regenerate supply of NAD+ (what keeps glycolisis running)

Pyruvate --> Lactate

Pyruvate --> acetaldehyde --> EtOH (ethanol)

It begins to turn off or slow down