Categorias: Todos - enzyme - transcription - dna - activation

por Tina Do 3 anos atrás

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eukaryotic cells

In cellular biology, complex processes govern gene expression and cellular responses. DNA serves as the template for the synthesis of mRNA through transcription, which occurs differently in prokaryotes and eukaryotes.

eukaryotic cells

ATP is present in a cell

Cellular respiration

Breaking down of glucose, and converting chemical energy from nutrients and oxygen molecules and turning it into ATP.

4 stages
Krebs cycle/ Citric acid cycle

Location: Mitochondrial matrix

Input: 2 Acetyl CoA

Output: 6 NADH, 2 FADH2, 2 ATP

Net products 6 NADH, 2 FADH2, 2 ATP

Pyruvate Oxidation

Location: Cytosol, then mitochondrial matrix

Input: 2 pyruvate, 2 CoA

Output: 2 Acetyl CoA, 2 NADH

Net products: 2 Acetyl CoA, 2 NADH

Doesn't produce ATP

Oxidative Phosphorylation

Location: Proteins in inner membrane

Input: Oxygen gas, 10 NADH, 2 FADH2

Output: Water, 30-32 ATP

Net products: Water, 30-32 ATP

Produces ATP through the coupling of Chemiosmosis with electron transport chain

Electron transport chain: Electron transport and pumping of protons (H+),which create an H+ gradient across the membrane.

Chemiosmosis: ATP synthesis powered by the flow of H+ back across the membrane

Hydrogen ions are pumped to intermembrane space

Glycolysis

Location: Cytosol

Input: 1 Glucose, 2 ATP

Output: 2 pyruvate, 2 NADH, 4 ATP

Net products: 2 Pyruvate, 2 NADH, 2 ATP

Produces ATP with substrate level phosphorylation

There are 6 tyrosine amino acids and they each need a phosphate group to activate so the kinase removes...

Substrate level phosphorylation: Production of ATP or GTP through the direct addition of a phosphate group to ADP or GDP

signal molecule - a hydrophilic molecule released by a cell to jump start a tyrosine kinase receptor

signal molecules goes to binding site

Signal binding site ( receptor) - the place where a signal molecule binds to the kinase receptors in the membrane
Inactive tyrosine kinase region - the tyrosine portion of the polypeptide that hasn't been phosphorylated.

Signal molecule binds to the kinase receptors

Dimer - when the two polypeptides that have a total of 6 tyrosine portions come together

Active tyrosine kinase region - its activated just because a dimer is formed. However it is not fully activated unless phosphate groups are attatched to the tyrosines.

Kinase - an enzyme that removes one phosphate group from ATP

ATP - Adenosine tri-phosphate. The main form of how a cell carries energy

kinase removes a phosphate group from ATP and forms...

ADP - Adenosine di-phosphate. ATP with a phosphate group removed

6 phosphate groups - the result of the kinases removing a phosphate group from each ATP

Tyrosine - an amino acid that needs a phosphate group attachment to activate

Fully activated tyrosine kinase region - when the tyrosine kinase is now able to induce a response from the cell

Now that the tyrosine kinase is fully activated inactive proteins come to it

Inactive relay proteins - proteins that relay a messages but aren't doing their job because they haven't been activated.

After interacting with the tyrosine kinases the inactive relay proteins receive a message so they become...

Active relay proteins - the relay proteins are now ready to relay a message after they've been activated.

After a long process of interacting with different relay proteins the cell can now induce a...

Cellular response - anything the signal molecule wants to the cell to do after the long events of protein interactions.

As soon as it starts, cAMP is converted to AMP

cAMP

Formed from ATP using Adenylyl Cyclase

cAMP binds to protein Kinase
Undergoes Domino Effect with other Kinase proteins

The last protein that activates brings the response form the cell.

and changes shape

G protein

GDP is replaced with GTP
G protein is now activated with GTP

binds to an enzyme

changes shape and activates

cellular response

Floating topic

Eukaryotic Cell Gene Regulation

Transcription Stage

bound activators come in contact with mediator proteins
mediator proteins interact with proteins at the promoter

protein-protein interaction help position the initiation complex on the promoter

the repressor/activator interacts with the RNA poly II to help reduce/increase transcription rates.

activator/repressor elements come the last activated molecule activated in transduction

Pre mRNA
control elements

critical for precise regulation of gene expression

distal control elements

enhancers

sequences upstream and downstream of gene

maybe close or far from the gene they control

bin specific transcription factors (activators/repressors)

proximal control elements

sequences closer to the promoter

bind general transcription factors

Transcription factors
Specific

like activators and repressors, they bind to distal control elements called enhancers

bring about increase levels of transcriptions (activators)

bring low levels of transcription (repressors)

enhancer sequences can be present close to the gene they control or on the other side.

General

bind to the promoters and regions near the promoter to bring about basal or background level of transcription

Activators / Repressors

Activation

Repressor
Repressor proteins binds to the distal region of a transcription factor

This will block the attachment of RNA polymerase to the promotor.

This shuts down transcription

Activators
Activator proteins binds to the distal region of a transcription factor

DNA bending proteins come and bring the activators closer to the promoter

The activators bind to mediator proteins and general transcription factors

an active transcription initiation complex is formed on the promoter

How they're created

A signal molecule comes into the cell
Binds to the receptor on the cell membrane

A chain reaction of secondary messengers occurs

The last signal molecule serves as a activator or a repressor in a transcription factor

DNA binding

limits transcription

increases transcription

high level gene expression

without repressor

operon ON

with repressor

without activator

operon OFF

with activator

operator- the "switch

Amylase

Hydrolyze glyosidic bonds (digestive)

Albumin

Transport hormones and maintain osmotic pressure in blood

Collagen

Fibrous protein that is a support structure for cells and makes up bones, ligaments, tendons, and cartilage

Insulin

Peptide hormone that regulates blood sugar levels

Protein Synthesis

Function

Examples
Used to maintain the various functions of the cell. Proteins have a variety of functions such as being enzymes for different reactions, acting as transport proteins in the cell membrane, acting as signaling molecules, acting as antibodies and more.

Destination

Protein destination depends on the sequence of amino acids
Protein for outside the cell

The Ribosome making the protein is bound to a signal recognition particle

The ribosome SRP complex is now bound to the rough endoplasmic reticulum.

The SRP leaves and the ribosome continues with protein synthesis.

The signal enzyme is cleaved by an enzyme in the rough ER which causes the ribosome to break apart leaving the protein alone.

The protein is then folded into its final shape

The protein is then moved into the Golgi apparatus

From the Golgi apparatus the protein is packaged and shipped to wherever it's needed in the body

Protein for inside the cell

The proteins are made useful in Eukaryotic cells with organelles such as mitochondria, Chloroplast, peroxisomes, and the nucleus

Pathway

After transcription the pre mrna is formed
The mrna is then formed

The trna with the correct anti codon matches with the codons in mrna in the ribosome

The ribosome uses its EPA site to guide the trna and its proteins until a release factor stops the process

The stacked up amino acids from trna forms a protein

Methionyl tRNA

Formyl methionyl tRNA

3 factors

12 factors

Four factors

Three release factors

One release factor

Longer half-life(few hours to a few days)

Short half-life(seconds to few minutes

A- tRNA

Each codon gets translated and corresponding amino acids are added, all linked by peptide binds

Termination
Stop codon

Ribosome

Polypeptide chain separates from tRNA

Chain gets released

Translation

Turning of mRNA to amino acid

Asynchronous with translation
Synchronous with transcription
mRNA

Initiation

Recognition of the start codon (5'AUG)

Binding of ribosome subunits

Elongation

P- site & A- site

P- peptide chain

Transcription

Eukaryotes

Nucleus
PreRNA & mRNA

Prokaryotes

mRna

DNA template

+1 Transcription start point

INITIATION

addition of transcription factors (proteins)

RNA polymerase

RNA polymerase II

RNA polymerizes bind to the promoter and make a new strand of mRNA in the 5' to 3' direction.

ELONGATION

the RNA polymerase moves downstream adding RNA nucleotides elongating the RNA transcript in the 5' to 3' direction.

TERMINATION

RNA transcript is released and the polymerase is released form the DNA

5'cap & 3'polyA sequences

Exons & Introns

introns help to alternate spacing

RNA Processing

introns are removed to bind exons

introns are released by RNA complex and Spliceosome protein.

hydrogen bonds- connect nitogenous bases

only in RNA

only in DNA

Uracil

Cytosine

Thymine

Guanine

Adenine

Cytoplasm

RNA

phosphodiester bonds- connects nucleotides

pentose sugar

nitrogenous base

nucleotides

DNA

EXTRACELLULAR COMPONENTS

Cell Wall

Plasmodesmata

ECM (Extracellular Matrix)

Tight junctions
Desmosomes
Gap junctions

Cytoskeleton

Membrane Proteins
Cholesterol
Phospholipids
Fibers
Microtubules

Organelle movement

Protein Kinesin

Vesicle

Grow in centromes and pair in centrioles

Help chromosome movement

Cilia & Flagella

Intermediate Filaments

Nuclear lamina

Keratin Family

Microfillaments

Plant Cells

Central Vacuole

Use to move nutrients

Provide Support

Muscle contraction

Myosin & Actin Protein interaction

ATP

Amoebiod movement

actively (needs energy)

bulk transport

pinocytosis
endocytosis
phagocytosis

electrogenic pumps

low to high concentration (against concentration gradient)

passively (no energy)

osmosis

diffusion of free water

facilitated diffusion

diffusion aided by protein channels

(simple) diffusion

membrane fluidity

Lysosomes - Hydrolyzes macromolecules

Chloroplast - Made up of thylakoids which converts sunlight energy to chemical energy

Centrosomes - Where cell microtubules are initiated. Contains centrioles.

Flagellum - Made up of microtubules and help the cell move (only in some animal cells)

Microvilli - projections that gives the cell more space

eukaryotic cells

Prokaryotic cells

Gene Regulation
operons- cluster of functionally related genes

two types of regulation

negative regulation

repressor- regulatory protein

methionine(MetJ)

positive regulation

activator- regulatory protein

CAP protein

Lack membrane bound structures
2 domains

Archaea

Bacteria

Structures

Cell wall: Maintains cell shape, protects the interior of the cell, and prevents bursting of the cell after taking up water.

Contains peptioglycan

Plasma membrane

Surrounds the cytoplasm , separating it from the environment outside.

Ribosomes

Protein sythesis

Nucleoid: Holds cells DNA.

Includes Proteins and enzymes that transcribe DNA & RNA that also aid in cell growth .

Cell structures and functions

Eukaryotic Animal cell structure

Eukaryotic Plant cell structure

Central Vacuole - A large organelle in plant cells. Functions as a storage, hydrolysis of big molecules, and breaks down waste products
Cell wall - Made up of proteins, cellulose, and polysaccharides. It protects the cell from damage and maintains the cell shape.
Plasmodesmata - Connects the cytoplasm of one cell to an adjacent cell by breaching the cell wall
Cell membrane - Made up of a phospholipid bilayer and controls what enters and exits the cell.
proteins
carbohydrates
extracellular matrix (ECM)
phospholipids

glycerol

hydrophilic fatty acid head

hydrophobic fatty acid tails

saturated

fluid and not tightly packed (good)

unsaturated

viscious and tightly packed (bad)

cholesterol

regulates movement of phospholipids

is selectively permeable
Membrane receptors

G protein coupled receptor

signal molecule

G protein coupled receptor (GPCR)

GPCR becomes activated

Tyrosine Kinase Receptor

molecule comes from another cell

Ribosomes - They bind to mRNA to synthesize proteins
Cytoskeleton - Made up of microfilaments, Intermediate filaments, and microtubules to reinforce the cell's shape.
Peroxisomes - a membrane bound organelle that produces hydrogen peroxide and then converts it to water
Golgi Apparatus - packages proteins and lipids to be transported out of the cell
Mitochondria - Makes ATP for the cells and cellular respiration occurs here
Endoplasmic reticulum - Made up of membrane sacs and tubes which synthesize, folds, and transport proteins
Smooth ER - Does not have ribosomes so it's appearance is smooth and it synthesizes lipids and phospholipids.
Rough ER - Filled with bound ribosomes that produces proteins for the cell
Nucleus - The control center of the cell
Chromatin - Mixed DNA and protein material
Nucleolus - Produces ribosomes in the nucleus
Nuclear Envelope - Membrane filled with pores around the nucleus. Controls what enters and exits the nucleus.