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Gene Regulation

por Alana Beard

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por siti syahirah abdullah azmil

DNA Structure, Replication, Expression and Regulation

por Ashley A Olvera

Floating topic

Extrons

DNA Ligase: Connects DNA together.

DNA Polymerase III: Needs a primer and only adds 5’ to 3’ to the daughter strand. Builds the DNA strand.

DNA Polymerase I: Needs a primer and only adds 5’ to 3’ to the daughter strand. Replaces RNA with DNA.

Single Stranded DNA Binding Protein (SSB): Keeps the parent strands separate.

Topoisomerase: Keeps the strands from tangling. Relieves tension in the parent strand from overwinding.

Transcription Factor: Controls gene expression.

Promoter Sequence: DNA sequence that defines where transcription begins.

RNA Polymerase II: Transcribes protein-coding genes to create mRNAs. (Eukaryotes)

RNA Polymerase: Transcribes DNA to RNA. (Prokaryotes)

Ribonucleotides: Forms the backbone of RNA molecules through phosphodiester bonds.

3 prime end

Poly-A Tail

5 prime end

GPPP Cap

Start Codon: AUG

Terminator Sequence

pre mRNA

mRNA

Release Factor: Ends translation by recognizing a stop codon in the mRNA.

Large Ribosome Subunit

A Site: First place tRNA attaches.

P Site: Holds the tRNA which is linked to the growing polypeptide chain

Peptide Bond

E Site: Releases tRNA.

Small Ribosome Subunit

Peptidyl Transferase: Catalyzes the formation of peptide bonds between amino acids

tRNA

Stop Codon: AG, UGA, or UAA.

Poly-A Polymerase: Adds a poly-A tail to the 3' end of RNA molecules.

Spliceosome: Removes introns from pre mRNA.

Introns

Protein Kinase A (PKA): Enzymes that catalyze the transfer of phosphate groups from ATP to proteins

Topic 1

Topic 2

Topic 3

Gene Regulation

Eukaryotic

Prokaryotic

Mutations

DNA Replication

Parental DNA

Origin of Replication

Helicase: Separates the parent strand into two individual strands.

Replication Bubble

Replication Fork

DNA Primase: Makes up the RNA primer.

DNA Primer

Lagging Strand (3' to 5')

Okazaki Fragments

Leading Strand (5' to 3')

DNA Translation

Signal Recognition Particle (SRP): Works with the SRP to ensure that proteins are correctly targeted to the ER membrane.

Free Ribosome

DNA Transcription

Template Strand (TAC): Used to build the RNA. 5' to 3' direction.

Cellular Respiration -A metabolic pathway that uses glucose to produce adenosine triphosphate (ATP )

Glycolysis -happens in the cytoplasm/ can happen without O2 1.One glucose molecules go in and gets turned into Glucose 6 Phosphate with the enzyme hexokinase (1 ATP need for this/ the ATP becomes ADP) 2. The glucose 6 phosphate magically becomes fructose 6 phosphate which gets turned into Fructose 1 6 Bisphosphate with the enzyme phospofructokinase ( 1 ATP Needed for this/ the ATP becomes ADP) 3. End result: 2 NADH, 2 Pyruvate, 4 ATP/ Net: 2 bc you used 2

Pyruvate Oxidation -Happens in the Matrix CoA gets attached to 1 Pyruvate and that makes 1 Acytyl CoA this process turned NAD+ to NADH

Citric Acid Cycle - Happens in the matrix also know as the kreb cycle -Oxaloacetate reacts with acetyl-CoA to produce citrate after a lot of stuff the citrate becomes isocitrate which then becomes ketogluterate and a NADH is produced the last steps of this cycle produce 1 ATP, 2 NADH and 1 FADH2 - Total Products for 1 cycle: 3 NADH (which are electron carriers), 1 ATP, 1 FADH2 ( which are also electron carriers)

Oxidative Phosphorylation

Energy Transfers and Transformations

Catabolic and Anabolic

Coupling

add together exergonic and endergonic, and delta G must equal a negative number for the reaction to happen

Anabolic

Photosynthesis

Consumes energy to build longer and more complicated molecules from simpler ones

Endergonic

Catabolic

Cellular Respiration

energy is released by a breakdown of a complex molecule into simpler components

Excergonic

Enzymes

Feedback Inhibition

the end product becomes an inhibitor and binds + changes the shape of the original enzyme's active site

end product molecule unbinds and the synthesis of the end product can continue.

Allosteric Regulation

Cooperativity

when one substrate molecule binds to the active site of a subunit and locks the other subunits into the active form.

Four subunits with an active site on each and a space inbetween the subunits to bind the regulatory molecules

activators and inhibitors

Inhibitors stabilize the enzyme but inhibit the function of the enzyme and does not allow the binding of other substrates

Activators stabilize the enzyme into a Stabilized Active Form

Functions

Noncompetitive Inhibition

function is only carried out to an extent or not at all

substrate may still be able to bind

particle binds to enzyme not at the active site and changes the shape.

Competitive Inhibition

function is not carried out

a mimic of the substrate binds to the active site

substrate binds to enzyme's site

effected by:

pH

ex: intestinal enzyme is at higher pHs than a stomach enzyme (more acidic)

Heat

heat loving enzymes ensure the reaction can happen at high temperatures

Lower activation energies

metabolic pathways

Gibb's Free Energy

Spontaneity

delta G is positive

Delta G is Negative

more stable + released free energy can be harnessed to do work

delta G = delta H - T delta S

The lower the free energy, the more stable and less work capacity

The higher the free energy,the less stable and greater work capacity

Cell Membranes

Endocytosis

Receptor Mediated Endocytosis

takes in specific molecules in bulk once specific substance is attached to receptor

Pinocytosis

cell drinking, pinches off into vesicle

Phagocytosis

Takes in food in food Vacuole

Neurons

Action Potential

Resting Phase

Depolarization

Rising Phase

Falling Phase

Hyperpolarization

K+ channels stay open, more negative inside cell

Na+ channels close, K+ channels open and K+ leaves

All Na+ channels open, all Na+ goes inside, inside of cell is positive, outside in negative

some Na+ channels open, becomes less negative inside

below threshold, no movement, K+ and Na+ channels closed

Membrane Potential

Inside neuron is slightly negative, outside is slightly positive

Semi-Permeable

Cholesterol

above and below phase temp

maintains fluidity (not too fluid, not to rigid)

hydrophilic head, hydrophobic tail

made with fatty acids

Unsaturated

makes membrane more fluid

above phase temp

Saturated

Membrane is more solid

below phase temp

Transport

Active Transport

Sodium Potassium Pump

charges, inside negative, outside cell is positive

2 K+ into the cell, and 3 Na+ out of the cell

moves substance from Low to High; goes against gradient

DO NOT require ATP

Passive Transport

diffusion of substance across cell membrane, concentration from High to Low, no transport protein needed.

Osmosis

Animal Cell

Normal

no net movement of water

Lysed

cell blows open

Shriveled

Plant Cell

Flaccid

plant cell is limp, still has water inside, no net movement of water

Turgid

Cell is full, has a little belly

Plasmolyzed

shriveled

Toncity

Hypotonic

out to higher solute concentration

solute is higher outside the cell than inside

Hypertonic

inside, to higher concentration

solute concentration is higher inside then outside

Isotonic

in and out of cell, no net movement

solute concentration is equal inside and outside

a solute cannot move across cell membrane, so water moves across membrane to balance concentration of solute on both sides

Facilitated Diffusion

Subtopic

transport protein

Cell Signaling

Second Messengers

Cyclic Adenosine Monophosphate (cAMP): Used for intracellular signal transduction.

Phosphodiasterase: An enzyme that breaks phosphodiester bonds such as in cAMP.

Stages

Reception: Signal molecule binds to the receptor.

Transduction: Triggers a process where a molecule changes the next molecule in the pathway.

Response: Activation of cellular response.

Signals: Molecules released by a cell which is received by another cell.

Long Distance: Reaches target cells located far away in the body using a system like the bloodstream.

Hormonal Signaling

Local Distance: Reaches neighboring target cells.

Paracrine Signaling: Signal that induces change to nearby cells.

Synaptic Signaling: Signal that allows neurons to communicate through the synapse to inhibit or activate the target cell>

Receptors: Target cells that receive the signal molecule.

Intracellular Receptors

Nucleus

Cytoplasm

Adenylyl Cyclase: An enzyme that converts ATP into cAMP.

G-protein

Guanosine Triphosphate (GTP): Active state

Guanosine Diphosphate (GDP): Inactive state

Membrane Receptors: Signal molecules are hydrophilic.

Ion Channel Receptor: Allows specific ions to flow through the membrane in response to a signal

G-protein Coupled Receptor (GPCR): Transmembrane protein.

Chemical Bonds

Properties of Water

Universal Solvent

High Heat of Vaporization

water needs a high temperature to change into its gas form

H-Bonds absorb heat and then break, turning liquid into gas

Denser as a Liquid than a Solid

ice floats, allowing life under ice layer

Expansion Upon Freezing

Ice

Insulator

crystal structure w/ stable hydrogen bonds

Cohesive Behavior

tendency for water to stick to itself, mainly caused by H-Bonds

forms H-bonds with each other, also get high surface tension

High Specific Heat

A high heat needed to raise one gram of water by one degree

H-Bonds absorb heat

Reform H-bonds and release heat

Intramolecular

Ionic

Covalent

Nonpolar

in water, get caged together

Polar

in water, form hydrogen bonds and dissolve

Intermolecular

Amphipathic

Phospholipid Bilayer

Hydrophilic Head

Hydrophobic Tail

Hydrogen Bonds

Hydrophobic

nonpolar molecules

Ion Dipole

polar and ion

positive attracted to negative charges

Dipole-Dipole

Attracted to opposite charges

Biomolecules

Carbohydates

Serve as fuel and building material molecules made of carbon, hydrogen, and oxygen that serve as an energy source and structural component in organisms

Glycogen -Unlike beta glucose, which has its -OH group attached above the ring, alpha glucose has its -OH group linked below the ring. Starch Dextran

Cellulose Chitin

Nucleic Acids Monomer: Nucleotide 2 type of nucleic aids: DNA and RNA The phosphodiester bond is a covalent linkage between the phosphate of one nucleotide and the hydroxyl (OH) group attached to the 3′ carbon of the deoxyribose sugar in an adjacent nucleotide, forming what is known as the “sugar-phosphate backbone” of DNA.

DNA Deoxyribonucleic Acid (Carbon 2 has one less O compared to RNA) Has a double helix: antiparallel The two strands are joined together by hydrogen bonds

Nucleotide 1. 5 carbon sugar (Pento) 2. Nitrogenous base DNA - T, A, C, G RNA - U, A, C, G Purines: A, G Ag (Silver is pur=e) Pyrimidines: U, C, T 3. Phospate Group

RNA -Ribonucleic Acid -Mostly exists in the single-stranded form, but there are special RNA viruses that are double-stranded. -Type of RNA: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)

Proteins Monomers: Amino Acids Polymer: Protein (Polypeptide) Chiral: 4 Distinct groups around the C central 4 R groups: polar, non polar, acidic, basic

Lipids

Triglyceride (TAG) Made up of 1 glycerol Head + 3 Fatty Acids Type of Bond between FA and glycerol head: Ester Linkages Non-polar molecule 1 TAG = 3 FA = 3 ester bonds 2 different types of FA

Unsaturated FA Liquid at room temp Has double bonds Hydrogenation is a process that can change the Unsaturated FA to Saturated by changing the double bonds to single bonds Example: Oil

Trans Unsaturated FA The hydrogens are on opposite sides Trans=opposite

Cis Unsaturated FA The hydrogens are on the same side cis= sisters or same side

Saturated FA No double bonds Solid at room temp Example: Butter

Phospholipids 1 glycerol + 2 FA + 1 phosphate group Is an amphipathic molecule (has a hydrophobic and hydrophilic part)

The Tails Made up of 2 FA's It is Hydrophobic which means it is water hating therefore it is non-polar

The Head Made up of Glycerol and phosphate Is Hydrophilic so it is water loving and polar

Sterols 4 fused rings AKA steroids

Cholesterol Found imbedded within the cell membrane Helps with membrane stability and fluidity High HDL and Low LDL = good to have Low HDL and High LDL = bad to have

Cell Structures

Prokaryotes

Archaea

Bacteria

Pili: Aids in DNA transfer between bacteria.

Fimbriae: helps bacteria stick to a surface.

Flagellum: Enables movement.

Capsule: Protective layer. Helps bacteria adhere to surfaces.

Cell Wall: Maintains cell shape.

Peptidoglycan: Structural support.

Nucleoid: Contains genetic material.

Eukaryotes

Plant

Microfilament: Maintains cell shape and movement. Made of actin protein.

Vacuole: Stores water, nutrients, and waste products within the cell.

Plasmodesmata: Connects adjacent plant cells.

Chloroplast: Provides energy through photosynthesis.

Cell Wall: Made of cellulose. Provides structure to plants.

Animal

Vacuole: Smaller in animal cells. Stores water, nutrients, and waste products within the cell.

Extracellular Matrix: Helps with cell communication, growth, and movement.

Vesicle: Transports materials within the cell.

Peroxisome: Break down fatty acids and amino acids.

Cytoskeleton: Maintains cell structure.

Intermediate Filament: Anchors nucleus and maintains cell shape. Made of proteins from the keratin family.

Microfilament: Maintains cell shape, movement, and aids in muscle contraction. Made of actin protein.

Microtubule: Maintains cell shape and cell/ organelle movement. Made of tubulin protein.

Cytoplasm: Protects genetic material and cellular structures.

Ribosome: Synthesizes proteins.

Golgi Apparatus: Process and package proteins and lipid molecules.

Lysosome: Break down and recycle cellular structures.

Rough Endoplasmic Reticulum: Has bound ribosomes for protein synthesis.

Smooth Endoplasmic Reticulum: Synthesizes lipids and breaks down toxins.

Cell Membrane: Regulates the transport of materials entering and exiting the cell.

Cell Junctions: Connections between cells.

Gap: Anything can pass through.

Desmosomes: Some stuff can get through.

Tight: Nothing can pass through.

Mitochondria: Powerhouse of the cell. Produces ATP.

Nucleus: Holds genetic information such as DNA and RNA.

Nuclear Envelope: Regulates transportation of molecules through nuclear pores.