Biological Molecules

Lipids

phospholipids- major component of cell membranes

fats- function is energy storage^

steriods

Carbohydrates- fuel and building material

include sugars and polymers of sugars

creating glucose in ring formation as well as linear

alpha isomer the OH group on the bottom of the structure^

Nucleic Acids

deoxyribonucleic acid (DNA) : provides direcrions for its own replication

mRNA: messenger RNA which controls protein synthesis

Transcription (information in the DNA is used to make mRNA)

Translation (information from the mRNA is used to make proteins)

nitrogenous based used are A, G , C, T

double stranded with complementary base pairing

ribonucleic acid (RNA)

Nitrogenous bases used are A, G ,C, U

polymers made of monomers called nucleotides

5 carbon sugar (pentose), a phosphate group, and a nitrogenous base

purines (A, G)

pyrimidines (C , T) also U in RNA

nucleotide (have a phosphate group)

make a phosphodiester bond

one end has a free phosphate group connected to a 5’ carbon of the sugar, while the other end has an OH group connected to the 3’ end of the end sugar. So we call one end of the nucleic acid 5’ end and the other end is the 3’ end.

nucleoside (do not have a phosphate group

Proteins

functions^

selective acceleration of chemical reactions

protection against disease

storage of amino acids

transport of substances

support

response of cell to chemical
stimuli

coordination of an organism’s
activities

movement

amino acids

central (alpha carbon)

main chain

carboxyl group

negative charge

hydrogen

amino group

positive charge

zwitterion in neutral pH within cell

side chain (R group)

hydrophilic

polar

charged

basic

acidic

hydrophobic

nonpolar

peptide bonds

polypeptides

primary

intramolecular polar covalent peptide bond through main chain

secondary

intermolecular hydrogen bond between main chain

alpha helices

beta pleated sheets

tertiary

intermolecular R group interactions cause polypeptide to fold

hydrophobic/van der waals

hydrogen bonds

form intramolecular disulfide bonds through oxidation (only covalent bond between R groups)

ionic bonds

quaternary

2 or more polypeptides come together to form a functional protein

intermolecular R group interactions

dimer

trimer

tetramer

hemoglobin

denaturation-protein unfolds back into primary structure (no longer biologically active)

only peptide bonds remain

renaturation-reverse conditions and test protein function

amino acid sequence determines protein structure

amino acid will go from surface of protein to buried inside

amino acid will go from buried within protein to the surface

Eukarya

Plantae

Plants, survive by capturing energy from the sun in photosynthesis

Fungi

Animalia

Protista

Bacteria

DNA

Frimbriae

Pili

Nucleoid

Glycocaly

Gas vacuole

Inclusion bodies

Endospore

Peptidoglycan in cell wall

Archaea

Extremophiles

Extreme halophiles

Live in highly saline enviroments

Extreme thermophiles

Thrive in very hot environments

Branching in membrane hydrocarbon tails of phospholipids.

Capsule

Main topic

Main topic

cycle repeated again to to form one molecule of glucose (6 carbons)

About half the sugar made consumed as fuel for cellular respiration. Sugar is transported to nonphotosynthetic cells as sucrose. Excess sugar is stored as starch in chloroplasts or in the cells of roots, tubers, seeds, and fruits

Endoplasmic Reticulum (ER)

Rough ER

Smooth ER

Metabolic Pathways

Nuclear Envelope

Nucleus

Nucleous

Chromatin

Catabolic Pathways

There is a release energy by breaking down complex molecules into simpler compounds

Anabolic Pathways

There is a consume of energy to build larger, complicated molecules from simpler ones

Subtopic

Polymerization

Energy

Kinetic Energy

Energy associated with motion of molecules or objects

Molecular Motion

Thermal Energy

Light Energy

Thermodynamic

System

matter within define region of space

Closed System

Open System

Surrounding

matter in the rest of the universe

Laws of Thermodynamic

First Law

Energy cannot be transferred and transformed, but it cannot be created or destroyed

Second Law

Every energy transfer or transformation increases the entropy of the universe

Gibb's Free Energy

H = G + TS

H = Total Energy (Enthalpy)

G = Gibbs

T = Temperature in Kelvin

S = Entropy

G = DH - TDS

Free-Energy Change (∆G)

∆G = G(final state) - G(initial state)

Exergonic

Energy released, spontaneous

∆G < 0

Energy from catabolism

ATP Cycle

Endergonic

Energy required, nonspontaneous

∆G > 0

Glutamic Acid conversion to Glutamine

∆G for ATP hydrolysis

Energy for Cellular Work

Equilibrium

No net change occurs

∆G = 0

Potential Energy

stores energy

due to position, location, or arrangment

Chemical energy

Molecular Structure

Food

Enzymes

Lowered Activation Energy

Catalytic Cycle

Substrate enter the active site; enzyme changes shape

Optimal Temperature

Optimal pH

Enzyme Inhibitors

Competitive Inhibitors

Mimics the shape of the substrate and competes with the enzyme for the active site. It then blocks the enzyme from sitting on the active site

Noncompetitive inhibitors

Binds to the enzyme away from the active site and alters the shape of the enzyme, so that when the substrate binds to the active site, it won't be as effective.

Allosteric Inhibitor

Inhibitor that enters the additional binding site of the Allosteric enzyme and stablizes the inactive form.

Cooperativity

Binding of one substrate molecule to the active site of one subunit locks all subunits in active conformation.

Feedback Inhibitation

Initial substrate binds to the active site of an enzyme and then the end product goes back and acts as the inhibitor to that same enzyme

Substrate are held in active site by weak interactions

The active site lowers EA and speeds up the reaction

Substrate are converted to products

Products are released

Active site is available for two new substrate

Gap junction

Diffusion of molecules between animal cells

Plasmodesmata

Diffusion of molecules between plant cells

Local signaling

When the releasing cell is in close proximity to the target cell and is able to send the signal molecules through a synapse or extra cellular fluid.

Lind distance signaling

When the signaling cell is far away from the target cell and must use other forms like the blood stream to send the signaling molecule.

Reception

Small and non polar molecules passes through the plasma membrane through a process called simple diffusion

Signal molecule bonds to an internal receptor in the cytoplasm

GPCR will receive a signal and bind/touch a G proteins to remove GDP to activate GTP after activated the G proteins will change its shape and detach from the GPCR and move to its next task

The GPCR will move along the membrane and attach self to an enzyme. Doing so the GPCR will alter the enzyme shape and function the enzyme will then be activated and complete the steps to cellular response.

In this process GTP will use energy to activate the receptor in which able to change back to GDP and will move back to original position. The process can then be repeated from the beginning.

Membrane receptors

Used by non polar signals since they can easily diffuse through the membrane. This receptor is found inside the cell.

G protein linked receptor

Tyrosine kinase receptor

These receptors are used when the molecule is hydrophilic and cannot cross the membrane due to the charge and polarity.

These receptors are made of two polypeptides, each polypeptide has the ability to function as a kinase. As a phosphate groups are added to tyrosines this is referred to as a tyrosine kinase receptor the activated receptor cannot interact with other proteins to bring about a response from the cell

Ion channel receptor

An ion channels receptor will remain close until a signaling molecule binds to it. Once that molecule binds the channel will open.

Once this channel is open specific ions are free to flow into the cell and are able to change the concentration of the cell affecting its function and activity

Once the signaling molecule removes itself from the ion channel, the ion channel closes and ions are no longer free to flow into the cell

Intracellular receptors

Signals that are polar or can not diffuse through the membrane must use this kind of receptors to enter the cell and fulfill its purpose

Transduction

The molecule and receptor bind enters the nucleus and binds to specific gene that controls water and sodium flow

The DNA is converted to RNA because of a gene was turned on

This process used different proteins that are activated throughout the process

Response

The protein a synthesize/proteins synthesis the mRNA is translated into a specific protein which changes the shape and function of the receiving cell

all of which are mostly made up of hydrocarbons containg non polar covelant bonds and are generally hydrophobic

made of glycerol

ester linkage made

fatty acids

saturated- commonly found in animal sources and solid at room temperature

no double covalent bonds

saturated with hydrogen atoms at every position^

unsaturated- commonly found in plant sources and liquid at room temperature

double covalent bonds are present

isomers

cis isomers having hydrogen atoms on the same side of the double bond

trans isomers having hydrogen on opposite sides of the double bond

three fatty acids

dehydration or condensation synthesis

breakdown using hydrolysis

a disaccharide is formed creating a covalent bond called a glyosidic bond/ linkage

storage polysaccharides

glycogen

connected through 1-4 glyosidic linkages and alpha glucose monomers

used in animals

startch

dextran

Structure Polysaccharides

cellulose^

made of beta glucose and connected by glyosidic linkages

help together by hydrogen bonds and form microfibrils

chitin

glycerol^

bilayer(hydrophobic tails, hydrophilic heads)

two fatty acids

phosphate group- polar contain both hydrophobic and hydrophilic parts^

four fused rings

beta isomer the OH group is on top of the structure

used in lplants

Amylose

amylopectin - contains branching

Animal Cell

Plasma Membrane

Ribosome

Flagella

Centrosome

Centrioles

Cytoskeleton

Microfilaments

Actin

Intermediate Filaments

Keratin

Microtubles

Tubulin Dimer

Microvilli

Peroxisome

Mitochondrion

ATP

Food Vacuole

Extracellular Matrix

Collagen Fibers

Fibronectin

Proteoglycan

Integrin

Cilia

Dyenin

Flagella

Lysosomes

Phagocytosis

Autophagy

Plant Cell

Cell Wall

Secondary Cell Wall

Primary Cell Wall

Middle Lamella

Chloroplast

Plasmodesmata

Vacuole

Central Vacuole

Contractile Vacuoles

Golgi Apparatus

Cell Junctions

Tight Junctions

Desmosomes

Gap Junctions

Cytoplasm

Cytosol

Cytoplasmic Streaming

Vesicle

shape determines function

CELLULAR RESPIRATION

mitochondria

pyruvate oxidation and the citric acid cycle STEP 2

glycolysis STEP 1

electrons are extracted from the glucose and added to an electron carrier NAD+ occurring in the cytoplasm outside the mitochondria

pyruvate formed in glycolysis enters the mitochondria and is oxidized. The product of oxidation enters the citric acid cycle generating more electron carriers, NADH, FADH2

NADH and FADH2 carries electrons down the electron transport chain and generates ATP through oxidative phosphorylation

occurs in the mitochondria the location of the ETC is in the inner mitochondrial membrane

there are 4 complexes in the ETC complexes 1, 3, AND 4 are H + pumps so they're job is to pump H+ against they're concentration gradient they get this energy because when electrons are transferred down energy is released

H+ in the intermembrane space go back down there concentration gradient through a membrane transport protein called ATP synthase the energy associated with the H+ gradient is used to add an inorganic phosphate to ADP to form ATP

1 glucose can form 30-32 molecules of ATP

oxidative phosphorylation STEP 3

catabolic process that uses food sources to form CO2 and water with the release on energy

used to make ATP

aerobic respiration

reduction

oxidation

redox reactions

C6H1206 +6O2 -----> 6CO2 +6H20 + ENERGY

C6H1206 is being oxidized (losing electrons)into 6CO2

These electrons are taken by an electron shuttle using NAD to form NADH+, H+

electrons can be directly transferred to Oxygen but this will cause an explosion due to the release of heat and light energy

an electron transport chain is used that was energy is released throughout each step

6O2 is being reduced (gaining electrons) to become 6CO2

substrate level phosphorylation

an enzyme reacts with a substrate that has a phosphate group

formation of a product and transfer of the phosphate group from the substrate to ADP to form ATP

enzyme hexokinase is used to add a phosphate from ATP to glucose to form gluccose 6P

then converted into fructose 6P

uses enzyme PFK ro convert Fructose 6phosphate to fructose 1,6 biphosphate

6 carbon sugar splits unto 2 molecules of 3 carbons forming DHAP and G3P

DHAP converts to G3P so at the end we have 2 molecules of G3P and 1 molecule of glucose

G3P id oxidized by transfer of electrons forming NADH a phosphate group is attatched to the oxidized substrate

phosphate group is transferred to ADP and G3P is oxidized to the carboxyl group of an organic acid

enzyme relocates the remaining phosphate group

enolase causes double bond to form in substrate by extracting a water molecule

the phosphate group is transferred from PEP to ADP forming pyruvate

once pyruvate us made if O2 is available it enters the mitochondria and is oxidized to form NADH and acetyl coenzyme A

Acetyl CoA adds its 2 carbon group to oxaloacetate producing citrate

isocitrate us oxidized and NAD+ is reduced

after CO2 is released the resulting 4 carbon molecule is oxidized then made reactive by addition of CaO

alcohol fermentation

pyruvate forms acetaldehyde which is reduced to form ethanol. CO2 is released and in the process of reduction electrons forms NADH are transferred to acetaldehyde recycling NAD+

Lactic acid fermentation

pyruvate is reduced to form lactate and recycling back NAD+ no CO2 is produces

leaves

mesophyll cells

choloroplasts

chlorophyll--light harvesting pigments

long hydrocarbon tail inserted in the thylakoid membrane

Porphyrin ring--light absorbing
“head” of molecule; magnesium
atom at center

^

CH3

CHO

When pigments absorb light, an electron is elevated from a ground state to an unstable, excited state

Electrons fall back down to the ground state, releasing photons that cause an afterglow, giving off light and heat

stomata-microscopic pores for CO2 to enter and O2 to exit

6 CO2 + 6 H2O + Light energy ---> C6H12O6 + 6 O2

6 CO2 + 18 ATP + 12 NADPH + 12 H2O --->
C6H12O6 + 18 ADP + 18 Pi + 12 NADP+ 6 O2 + 6 H2O + 12 H+

light reactions

convert solar energy into chemical energy

thylakoid membrane

Non-cyclic (linear) flow of e-

Photosystem I

photon of light absorbed by chlorophyll causes e- to be excited, as they go back to the ground state energy is released

main chlorophyll a molecules (P700) where e- are grabbed by a primary electron acceptor

electrons go to Ferridoxin (Fd) then on to NADP+ to form NADPH

Photosystem II

photon of light is absorbed by chlorophyll fouind in light harvesting complexes

causes e- to jump to excited state, and go back down to ground state, releasing energy

released energy absorbed by another molecule, and process repeats

main reaction center pair of chlorophyll a molecules (P680) where e- are grabbed by an electron acceptor molecule

splitting H2O (O2 is released)

electron transport chain

e- from primary acceptor go down plastoquinone (Pq), cytochrome complex,
Plastocyanin (Pc), ferredoxin (Fd)

chlorophyll molecules of photosystem I

formation of ATP by phosphorylation--energy from ETC used to pump H+ into thylakoid space against concentration gradient, and go back down concentration gradient through ATP synthase

cyclic flow of e-

excess NADPH present

only PSI used--as e- are transferred to Fd, instead of forming NADPH they are recruited to the cytochrome complex and plastocyanin molecules of the ETC

movement of electrons leads to formation of ATP by photophosphorylation

calvin cycle

produces sugar from C O2 with the help of the NADPH and ATP

stroma; outside thylakoid

addition of 3 CO2 from the atmosphere to RuBP using enzyme Rubisco

forms a 6 carbon unstable intermediate which splits to form 6 molecules of 3 phosphoglycerate

6 molecules of ATP and 6 molecules of NADPH used to form 6 molecules of G3P

5 molecules of G3P continue on to make more RuBP and 1 molecule of G3P leaves the cycle to form glucose and other sugars

other processes

C3 plants photorespiration--Rubisco favors to bind O2 instead of CO2, so if CO2 concentration is low, Rubisco will bind whatever O2 is present, releasing CO2; no ATP formed

alternative metods of carbon fixation

if stomata are partly closed, the little CO2 that can enter the leaf is fixed using PEP carboxylase (high affinity for CO2) in Mesophyll cells into a 4 carbon compound

CO2 released into a neighboring sheath cell wherein it is fixed using Rubisco and goes through the Calvin cycle to make sugars

plants open stomata at night and incorporate C O2 into organic acids

Stomata close during the day, and C O2 is released from organic acids and used in the Calvin cycle

DNA

Fredrick Griffith discovered that bacteria are capable of transferring genetic information through transformation

Hershey and Chase discovered that protein was not the genetic material, and that it was DNA

Chargaffs rule: The amount of Adenine equals the amount of Thymine. and the amount of Guanine equals the amount of Cytosine

the structure

nitrogenous base

base pairs are held together by hydrogen bonds

phosohodiester bond

sugar phosphate backbone

replication

the two strands of the double helix must be separated at the ORI (origin of replication) to be able to form a daughter strand. the ORI is a sequence of nucleotides in DNA

the enzume Helicase seperates the two strands to form the replication bubble, SSB (single stranded proteins) makes sure the DNA stays seperated while another enzyme called Topoisomerase helps relieve any strain

Primase makes RNA primers complementary to the DNA parent strand. This causes DNA polymerase lll to add nucleotides only to the 3' end

to connect these nucleotides that are in DNA together we have to use phosphodiester bonds using dehydration/ condensation reactions.

A protein called sliding clamp works with DNA polymerase lll and helps keep it on the parent strand so it does not fall off during replication

along the leading strand the DNA polymerase continuously moves forward towards the replication fork

to form the lagging strand multiple RNA primers are laid down and extended by DNA polymerase lll and making okazaki fragment. the primers are then removed by DNA polymerase l and replaced by DNA nucleotides. an enzyme called ligase seals any gaps by connecting nucleotides with phosphodiester linkages

double stranded with complementary base pairings

the double helix was predicted by the Messleson and Stahl experiment showing us that the helix is semi conservative meaning when the helix replicates each daughter molecule will have an old strand and a newly made strand

in this experiment they found an intermediate band as well as a high density band confirming the double helix was semiconservative

Watson and Crick stated that the specific base pairing suggested a possible copying mechanism for the genetic material where each strand wouls be a parent strand with the information to make another strand

linear flow of information from DNA to protein through the formation of mRNA

a process that forms mRNA from DNA

both transcription and translation occur in the cytoplasm in Prokaryotes, mRNA can be immediately translated

initiation

After RNA polymerase binds to the promoter, the DNA strands unwind, and the
polymerase initiates RNA synthesis
at the start point on the template strand.

elongation

RNA polymerase moves downstream, unwinding the DNA and elongating the RNA
transcript 5' to 3'. In the wake of
transcription, the DNA strands re-form a double helix.

termination

Eventually, the RNA transcript is released, and the polymerase detaches from the DNA.

Initiation

At initiation a small ribosomal subunit binds to am mRNA. The small ribosomal unit then scans the mRNA until it finds AUG, which is the start codon.

An initiator tRNA, that consists of an anticodon of UAC will base-pair with AUG. This initiator tRNA carries the amino acid MET, which is methionine.

An initiator tRNA is made up of a single strand of RNA with about 80 nucleotides. When in three dimension the tRNA is shaped in an upside down L and has the anti codon towards the bottom. On the top side of the upside down L it has a corresponding amino acid

The purpose of the tRNA is to bring the correct amino acid to the mRNA during translation.

A large subunit then joins and becomes a translation initiation complex. Translation factors are also used here to bring all the translation components together.

The initiator tRNA is located in the P site of the large ribosomal subunit, while the A site is open to receive the next tRNA with the corresponding amino acid.

Elongation

After the initiation process comes the elongation step. In the A site of the large ribosomal subunit a new incoming tRNA base-pairs with the mRNA. Many tRNAs will attempt to bind to the codon in the A site but only the appropriate anticodon will bind to the mRNA.

A peptide bond will then form between the amino acid in the P site and the A site. This bond occurs between the amino acid found in the A site and the carbonyl end of the polypeptide in the P site. This bond removes the polypeptide from the tRNA in the P site and adds it to the amino acid in the A site.

The last step in elongation is called Translocation. In this final step the tRNA shift down a site, meaning that the tRNA in the P is shifted to the E site and is released. The tRNA is shifted to the A site is moved the the E site and at the same time the mRNA iOS moved with its corresponding tRNAs. Meaning that the A site will be open for the next appropriate tRNA to bond.

The translocation step will repeat and repeat until it reaches the stop codon, which then leads to the termination process of translation.

Termination

Once the stop codon is reached a release factor will stand in the A site and this will dissociate the complex stopping translation

A stop codon is either UAG, UAA, or UGA. the dissociating of the complex stopping translation is a GTP driven processes as well.

Protein transport- all of protein synthesis begins on free ribosomes. The different sequence of amino acids tell proteins what their final location will be and their function.

During translation an SPR will bind to the peptide stand and will momentarily pause the synthesis. The SPR will then also bond itself to a receptor protein found in the membrane of ER.

This SRP will then leave the signal peptide which causes the polypeptide synthesis to resume its natural course. At the same time we have translocation of the protein in the ER membrane.

The protein is then cut by an enzyme found in the receptor. Once this happens the polypeptide is folded to its final conformation.

The protein the goes through further folding in the Golgi, it is shipped here from the ER through a vesicle.

After this the protein is then released into the cell so it cal reach its designated location. Whether it be another organelle like the nucleus or mitochondria, or secreted from the cell.

transcription occurs in the nucleus forming pre mRNA and translation in the cytoplasm

initiation

A eukaryotic promoter commonly includes a TATA box (a nucleotide sequence containing TATA) about 25 nucleotides upstream from
the transcriptional start point.

Several transcription factors, one recognizing the TATA box, must bind to the DNA before RNA polymerase II can bind in
the correct position and orientation.

Additional transcription factors bind to the DNA along with RNA polymerase II, forming the transcription initiation complex. RNA polymerase II then unwinds the DNA double helix, and RNA synthesis begins at the start point on the template strand.

elongation

RNA polymerase II moves downstream, unwinding the DNA and elongating the RNA
transcript 5' to 3'. In the wake of transcription, the DNA strands re-form a double helix.

termination

sequence AAUAAA is a signal for ribonuclease to make a cut in the newly formed pre mRNA and release it from DNA. At the 5’ end a modified G nucleotide CAP is added, and at the 3’ end a polyA tail is added by polyA polymerase. The 5’cap will be used for translation and the 3’polyA tail helps with stability of the mRNA.

Pre mRNA contains introns and exons. Introns are sequences that need to be removed before translation.

Before the pre mRNA exits the nucleus to be translated it has to remove introns and join together exons. Different genes contain different number of introns.

There is a complex of RNA and proteins called Spliceosome that binds the junctions of the introns and makes cuts to release the introns from the DNA. The exons are then joined together.

Presence of introns help alternate splicing. Different combinations of exons can be generated through removal of different introns to form different mRNAs and hence different proteins.

nucleotide in DNA where transcription starts (first nucleotide or +1) on template strand

Nucleotides in DNA to the right are labeled by positive numbers

To the left of the transcription start site nucleotides are numbered by negative numbers

Eukaryotic Cells

Nucleus

Chromosomes

Compacted Chromatid that are made of DNA (genes) and proteins

Chromatid

The fibrous double stranded DNA to which proteins are attached to, once it's compcted it formed Chromosomes

10nm Fiber

DNA winds around histones to form Nucleosomes "beads." They are then strung together like beads on a string by linker DNA

Nucleosomes

The packaged DNA (in the nucleous) that consist of DNA winding around a Histone protein

Histone

Small protein that DNA wraps around

Histone Core

H2A

H2B

H3

H4

H1

It's not part of the Nuclesome, but is involved in forming the next level of packaging

Linker DNA

The DNA connecting each nucleosome

30-nm Fiber

Interactions between Nucleosomes cause the thin tiber to coil or fold into this thicker fiber

300 nm-Fiber

The 30-nm fiber that forms looped domains that attach to proteins

Gene Expression

Gene makes RNA when needed

Differential Gene Expression

Almost all cells in an organism contains the same genes, because they are all the same BUT have differential expression (dependong on what they are and the difference purposes they want to express)

Regulation at Transcription Initiation

A Eukaryotic promoter (commonly includes a TATA box) about 25 Nucleotides upstream from the transcriptional start point

Several Transcription Factors (one that recognizes the TATA box) binds to the DNA before RNA Polymerase II can bind in the correction position

Additional Transcription Factors bind to the DNA along with RNA Polymerase II, forming the transcription initation complex. RNA Polymerase II then unwinds the DNA double helix, and RNA synthesis begins at the start point on the template strand

Transcription Factors

General

It binds to the promoter and regionsn ear the Promter to bring about basal or background level of Transcription

Specific

Binds to distal control elements caleld Enhancers and bring changes in the level of transcription

Activators

Increases levels of transcription

Repressors

Reduces levels of transcription

Control Elements in DNA

Proximal Control Elements

Sequences in DNA that is close to promoter and binds to general transcription facotrs

Distal Control Elements

Sequences in DNA that are upstream or downstram of DNA and binds to specific transcription factors (like Activators or Repressors)

Enhancers

Groupings of distral control elements which are far from the gene they control

Model for the Action of Enhancers and Transcription Activators

Activator proteins bind to distal control elements grouped as an enhancer in the DNA. This enhancer has three binding sites, each called a distal control Element

A DNA-bending protein brings the bound activators closer to the promoter, where General transcription facotrs, mediator proteins, and RNA Polymerase II are nearby.

The activator bind to certain mediator proteins and general transcription factors, helpingthem form an active transcription initation complex on the promoter

Cell Specific Transcription

Combinatorial Control of Gene Expression

In the Liver Cell, Activator proteins are present that bind to enhancer sequences that increases the expression of Albumin Gene. ON THE OTHER HAND, in the Lens cell, activator proteins are present that bind enhancer sequences of the Crystallin Gene and not the Albumin Gene. In this case (in the Lens), only Crystalline gene has high levels of expression while Albumin has basal or background expression.

Prokaryotic Cells

Cytoplasm

Operons

A cluster of functionally realted genes which are involved in the same pathway in the cell consisting of the coordinated control of a single on-off "switch."

Positive Regulation

The Operon gene expression if ON (expression is at a high level when the activator is bound to the operator)

Negative Regulation

When the Repressor protein is bound to the Operator sequence, then the gene expression if OFF

Lac Opern

It's found in E. Coli and is founded by Francois Job and Jacques Monod in 1962. It is an example of both Positive and Negative regulation.

Stuctural Genes

Lac Y

Lac Z

Lac A

Regulatory Gene

Lac I

Regulatory Region

Promoter

Operator

Operon OFF

Lactose absent, Repressor Active

When there is no Lactose, the Operon is OFF, because you need an enzyme. Due to this Transcription, Lac Z, Lac Y, and Lac A is blocked (thus causing the Operon to be OFF).

Lactose present, Glucose present (cAMP level is low): little lac mRNA is synthesized

If there is no Lactose, then Lac Repressor will be bound to the Operator preventing expression of Lac Operon genes.

The presence of Glucose blocks Adenylyl Cyclase preventing the production of CAMP (if there is no cAMP present then the CAP is inactive, so it can't help the RNAP bind to the promoter.

Operon ON

Lactose present, glucose (cAMP level is high), causing an abundant lac mRNA to be synthesized

When lactose is present, the Lac repressor protein binds Lactose, such that it can no longer bind to the operator sequence. RNAP can now bind promoter for transcription of lac operon genes.

The activator protein is present (because an activator protein is required for function) and it's called CAP (Catabolite activator protein). It is activated by cAMP. Adenylyl cyclase forms cAMP from ATP. cAMP binds CAP and CAP helps RNAP to bind promoter to facilitate transcription, so the operon is ON

Lactose present, Repressor inactive

When there is no Glucose and Lactose is present, then the Operon is ON, because an Inducible Operson (as expression of Lac Z, Lac Y, Lac A genes) is induced by the presence of Lactose

Metaphase Chromosome

The looped domains coil further