Kategóriák: Minden - eukaryotes - prokaryotes - gene - proteins

a Erika Garcia 3 éve

200

Cell Signaling

The process of translation initiates on free ribosomes within a cell, with notable differences between prokaryotic and eukaryotic systems. In prokaryotes, translation occurs in the cytoplasm and involves the 70S ribosome, comprising a 30S small subunit and a 50S large subunit.

Cell Signaling

Gene Expression

Regulation

regulation @ transcription initiation
enhancers: sequences on DNA in which are far away from the gene
uses transcription factors to bind onto promoters: activators & repressors

repressors: decreases level of transcription = less mRNA

activators: increases level of transcription = more mRNA

when activators are bound, it will cause the DNA to bend to bind to the mediator proteins to increase transcription

when different proteins are needed in different organs, one organ (ex. liver) may have an activator protein for one protein (ex. albumin) that the other organ (ex. eye) may not have; helps different organs have different functions from each other

DNA Replication

Steps of DNA Replication
7.) DNA Ligase links the Okazaki fragments together to create a single, new strand
6.) DNA polymerase I removes RNA primers and replaces them with DNA
5.) DNA polymerase III adds nucleotides to the 3' end of primers and continues elongation on both strands
4.) Primase adds the RNA primer to the template DNA so that polymerase can start replicating

Needs to continuously add primers to the lagging strand to make several Okazaki fragments

3.) Single Stranded Binding Protein (SSB) binds to the single stranded DNA and makes sure it stays apart
2.) Helicase binds and unwinds the two strands of the template DNA by breaking the hydrogen bonds
1.) Topoisomerase binds to the ORI and relieves strain due to DNA supercoiling
Leading & Lagging Strands
Lagging strand: discontinuous replication in the opposite direction of the replication fork movement

Okazaki fragments are eventually covalently combined by DNA Ligase

Replicates in multiple, small segments called Okazaki Fragments that each need and RNA primer

Leading strand: continuous replication in the same direction of the replication fork movement

Only 1 RNA primer is required for the replication of the leading strand

ORI & Replication Forks
Proteins bind to the ORI and separate the two strands of DNA, forming a replication fork (or bubble)

DNA replication proceeds bi-directionally

Replication forks: Y-Shaped regions at each end of the replication bubble where DNA is unwound

DNA replication begins at specific DNA sequences called the Origin of Replication (ORI)

Eukaryotes have multiple ORIs

Prokaryotes have 1 ORI

Components of DNA Replication
DNA Ligase

Covalently joins together Okazaki Fragments in lagging strands

DNA Polymerase I

Replaces RNA Primers with DNA

DNA Polymerase III

Builds new DNA strand using the old DNA strand as a template

Primase

Creates RNA Primers

Single Stranded Binding Protein (SSB)

Binds to and stabilizes single stranded DNA

Helicase

Unwinds DNA double helix at the replication fork

Topoisomerase

Relieves DNA supercoiling ahead of replication fork

Transport

5.) after the Golgi, the protein will go to its target organelle or leave the plasma membrane
target organelles: ER, plasma membrane, lysosomes
4.) after the rough ER, the polypeptide will be received by the cis side of the Golgi apparatus, modifications take place throughout the Golgi, then will be transported from the trans side of the Golgi
3.) polypeptides produced in free ribosomes go to bound ribosomes on the rough ER
2.) mRNA goes to free ribosomes in the cytoplasm to start translation
polypeptides have destinations from free ribosomes: mitochondria, nucleus, peroxisomes, chloroplast, cytoplasm
1.) transcription happens in the nucleus to produce mRNA; mRNA leaves via nuclear pores

DNA Structure

Chargaff's Rule
Erwin Chargaff made two important discoveries about DNA: 1.) DNA base composition varies between different species 2.) For each species, the percent of A&T bases are roughly equal, as were the percents of the G&C bases
Meselson-Stahl Experiment
The parental strands separate and act as templates to synthesize new DNA that is complementary to it
Semi-Conservative Model: Replicated DNA molecules have one old/parental strand and one newly built strand
In 1958, Meselson and Stahl demonstrated that E-coli replicates DNA via the Semi-Conservative model
The Hershey-Chase Experiment
Used a bacteriophage to show that DNA was injected into the bacteria and proteins were left outside of the coat
In 1952, scientists Hershey and Chase used bacteriophages to confirm that DNA is the genetic material, NOT proteins
The Griffith Experiment
Overall conclusion showed that some unknown factor was altering the bacteria. At the time, scientists did not know if this factor was DNA or proteins.
Showed that bacteria have the ability to transform genetic material (S strain, R Strain, and Heat-Killed S Strain) and injected it into mice to test

Live R Strain + Heat-Killed S Strain

Heat-Killed S Strain

Live R Strain

The mouse lived

Live S strain

The mouse died

In 1928, Fredrick Griffith's experiment identified that some unknown genetic factor controls the traits of organisms
Overall Structure
DNA consists of two strands (double helix) of nucleotide monomers repetitively linked together

Free hydroxyl group at the 3' ends

Free phosphate group at the 5' ends

Transcription

Eukaryotes (Nucleus)
Modification

A mature mRNA strand is formed.

The last process is called RNA splicing. A complex made out of RNA and proteins called spliceosomes splices certain sequences in DNA. Intron sequences are removed and exon sequences are joined together.

An enzyme called polyA polymerase adds a polyA tail (AAAAAA) to the 3' end of the pre-mRNA strand.

A guanine nucleotide modifies the 5' end of the pre-mRNA strand by adding a 5 CAP.

A sequence in the RNA called the polyadenylation signal sequence (AAUAAA) stops transcription. Proteins make a cleavage in pre-mRNA to release the strand.

RNA polymerase II reads the template strand (3' to 5') to make the RNA in the 5' to 3' direction. It adds nucleotides to the template strand to make RNA. It creates downstream.

RNA Polymerase II binds to the promoter with additional transcription factors to create the transcription initiation complex. It begins unwinding DNA at the transcription start point (+1) to begin RNA synthesis.

Proteins called transcription factors bind to the promoter before RNA Polymerase II.

Prokaryotes (Cytoplasm)

A sequence in RNA is the signal for the transcription process to stop. Once done, a mRNA strand is made.

RNA polymerase reads the template strand (3' to 5') to make the RNA in the 5' to 3' direction. It adds nucleotides to the template strand to make RNA. It creates downstream.

RNA polymerase unwinds DNA strand and start creating the RNA strand at the transcription start point. (+1)

RNA Polymerase binds to the promoter which is upstream.

Translation

Translation begins on free ribosomes (composed of rRNA and proteins) within a cell; ribosomes differ between prokaryotes and eukaryotes
Eukaryotes (80S); occurs in cytoplasm separate from transcription

60S consisting of 45 proteins

Separate from small ribosomal subunit unless mRNA is attached

40S consisting of 33 proteins

Occurs in the E site (exit site) of the ribosome; a stop codon is reached in the A site meaning translation no longer occurs. A release factor, also present in the A site, releases tRNA from mRNA and tRNA exits. A GTP driven process. Ribosomal subunits separate.

Occurs in the P site (peptidyl tRNA) of the ribosome; Formation of peptide bonds, formed by peptidyl transferase, between amino acids to form a polypeptide chain. Once a stop codon is reached, the carboxyl end of the polypeptide chain is detached from tRNA.

tRNA first binds to the 5' cap of mRNA and scans the mRNA until the start codon AUC is found. It then binds the UAG anticodon to begin the translation process; Met is the first amino acid attached to tRNA. GTP is required.

Prokaryotes (70S); occurs in cytoplasm w/ transcription

Large Ribosomal subunit

50S consisting of 31 proteins

Small Ribosomal subunit

30S consisting of 21 proteins

Termination

Occurs in the E site (exit site) of the ribosome; a stop codon is reached in the A site meaning translation no longer occurs. A release factor, also present in the A site, releases tRNA from mRNA and tRNA exits. A GTP driven process.

Elongation

Occurs in the P site (peptidyl tRNA binding site); Formation of peptide bonds btwn amino acids via peptidyl transferase; Adds more amino acids to the polypeptide chain until a stop codon is reached on the mRNA. Once a stop codon is reached, the carboxyl end of the polypeptide chain is released from tRNA.

Initiation

Occurs in A site (aminoacyl-tRNA) of the ribosome; UAG anticodon on tRNA binds to AUC codon on mRNA. The initiator tRNA also carrying the first amino acid, f-Met. This process requires GTP.

Cell Signaling

G Protein Coupled Receptor

Step 4) The enzyme is activated and is ready to start the next part of the cellular response
Step 3) The G protein leaves the receptor with the GTP molecule and diffuses across the membrane to bind to an enzyme.
Step 2) The receptor then changes it shape to bind its cytoplasmic side to the G protein. The G- Protein hold the GTP molecule.
Step 1) Signal molecule binds to the extracellular side of the receptor and activates it.

ATP

Oxidative Phosphorylation
Chemiosmosis

As H+ is heavily concentrated in the intermembrane space of the mitochondria, they will want to travel back inside down the concentration gradient with the help of ATP synthase (facilitated diffusion)

As the H+ travel down the gradient, the energy released (proton motive force) is used to add an inorganic phosphate to ADP to form ATP (aka osmosis)

Electron Transport Chain

Pumping of H+ protons into the intermembrane space from the matrix; H+ protons come from the NADH and FADH2 created in the Kreb's Cycle

Pumping of protons into the intermembrane space of mitochondria creates an H+ gradient across the mitochondria membrane

Kreb's Cycle
creates ATP through substrate-level phosphorylation as Succinyl CoA forms Succinate

Inorganic phosphate is used to convert GDP to GTP

Once G-protein is done activating an enzyme, GTPase removes the phosphate group from GTP, and a kinase gives that phosphate group to ADP to form ATP

Glycolysis
Energy Production Phase

A phosphate group is removed from 1,3-biphosphoglycerate and transferred to 2ADP becoming 2ATP; 1,3-biphosphoglycerate becomes 3-phosphoglycerate

In step 10, a phosphate group is removed from 2PEP and transferred to 2ADP becoming 2ATP; 2PEP becomes 2 pyruvate

Total of 4 ATP produced in glycolysis; net production of ATP is 2 ATP for the cycle

The ATP created is through a process called substrate-level phosphorylation: an enzyme reacts w/ a substrate that has a phosphate group, the reaction forms a byproduct and the transfer of the phosphate group to ADP to form ATP

Energy Investment Phase

ATP is invested in the first step of glycolysis converting glucose to glucose 6-phosphate

ATP is invested in the third step of glycolysis converting fructose 6-phosphate to fructose 1,6-biphosphate

Total of 2 ATP invested in glycolysis

Signal Transduction

Tyrosine Kinase
Step 4) Each tyrosine (6 tyrosines total in a dimer) then has a phosphate group attached to it (6 phosphate groups total) which can now activate other relay proteins to create cellular responses
Step 3) The unphosphorylated dimer then takes a phosphate group from ATP (b/c they are kinases) and attach it to the other polypeptide (aka autophosphorylation)
Step 2) The two monomers then dimerize (form a dimer) to be activated
Step 1) a signal molecule binds to each of the tyrosine kinase signal-binding sites
cAMP as a second messenger in a G protein signaling pathway
Step 5) cAMP, the second messenger, activates another kinase and continues on, leading to cellular responses

After starting this sequence of events, cAMP is converted to AMP by phosphodiesterase

cAMP jump starts the signal transduction cascade

Step 4) The activated adenylyl cyclase converts ATP to cAMP
Step 3) The activated G protein/GTP binds to the enzyme adenylyl cyclase GTP is then hydrolyzed, resulting in the activation of adenylyl cyclase
Step 2) The activated GPCR binds to the G protein, which is then bound by GTP, activating the G protein
Step 1) The signaling molecule (first messenger) binds to the G protein-coupled receptor (GPCR)
Phosphorylation Cascade
Step 4) Protein Phosphatases catalyze the removal of the phosphate groups from each of the activated protein kinases
Step 3) Active protein kinase 2 phosphorylates a protein that brings about the cell's response to the signal

Step 2 and Step 3 demonstrate a phosphorylation cascade

At each stage stage of activation, multiple molecules of the protein are activated, amplifying the effect of the signal molecule

Step 2) The activated relay molecule activates protein kinase 1. Active protein kinase 1 then activates protein kinase 2

Phosphate is taken from ATP (forming ADP)

Activated by an addition of a phosphate group by a previous kinase

Step 1) A signal molecule attaches to the receptor, resulting in the activation of the relay molecule

Cell Structure

- Membrane Proteins
- Integral Proteins

- For FACILITATED DIFFUSION, some transmembrane proteins contain a HYDROPHILIC INTERIOR to help transport ions, big/polar molecules in & out of cell

- Carrier Proteins: changes shape for the molecule to bind to & allows it to enter/leave the cell

- Channel Proteins: provides a road for specific molecules to pass through

- Contains nonpolar side chains (hydrophobic) that helps anchor itself to the phospholipid bilayer

- Bonds in Cell Proteins

- Quaternary Structure

- a dimer of two tertiary structured proteins

- Connected via HYDROGEN BONDS and VAN DER WAALS between the two subunits

- Tertiary Structure

- Bonds depends on the R groups involved

- acidic R group + basic R group = ionic bond

- polar R group + polar R group = polar bonds (hydrogen bonds)

- Only covalent bond present is DISULFIDE BONDS

- nonpolar R group + nonpolar R group = nonpolar (hydrophobic interactions)

- nonpolar R groups are "folded" into the protein away from water

- Secondary Structure

- Forms ALPHA helices and BETA pleated sheets

- Connected via HYDROGEN BONDS between MAIN CHAINS

- Primary Structure

- Connected via PEPTIDE BONDS

- Cell Membranes
- Intracellular/Extracellular sides

- Hydrophilic (polar) head face outside toward water around cells

- Hydrophobic (nonpolar) tails face inside away from water around cells

- Membrane Fluidity

- Cholesterol

- only found in animal cells

- dampens effects of temperature on cells making it where membranes aren't as susceptible to cold temperatures

- works as a buffer preventing cold temperatures from inhibiting fluidity and warmer temperatures from increasing fluidity too much

- Unsaturated

- fewer bound hydrogen atoms

- adjacent carbon atoms in the hydrocarbon tails bond together

- angle forms in tails because of the carbon atoms bonding together; tails no longer straight

- decreasing temperature does not compress the tails because of their shape so molecules are still able to squeeze through the membrane; high fluidity

- Saturated

- no double bonds between adjacent carbon atoms

- saturated with bound hydrogen atoms

- relatively straight hydrophobic hydrocarbon tails

- decreasing temperature "solidifies" membrane as the tails are compressed together; makes for low membrane fluidity

- Eukaryotic Cells
- Endomembrane System

- It is responsible for the protection of the cell and it selects what comes in and out of the cell.

- It consists of a phospholipid bilayer, which has phospholipids and proteins.

- Vacuoles (Membranous Sac)

- Central Vacuole

- It is a storage of inorganic ions in plant cells (Potassium and Chloride). Also plays a role in plant growth.

- Contractile Vacuoles

- Helps pump excess water out freshwater protists cell

- Food vacuole

- Formed by phagocytosis when a cell stores food.

- Lysosomes

- It uses enzymes to digest macromolecules by hydrolyzation. To digest food, a process called phagocytosis used.

- It is a membranous sac full of enzymes such as nucleases, proteases, lipases, etc.

M

- Modifies, stores and routes the products of the endoplasmic reticulum.

- Consist of flat membranous sacs called cisternae.

- Endoplasmic Reticulum

- Rough ER

- It helps fold proteins

- Has a rough surface due to the ribosomes all over it.

- Smooth ER

- It synthesizes lipids, metabolizes carbohydrates, detoxifies drugs and poisons, and stores calcium ions.

- Has a smooth outer surface, free of ribosomes.

N

- Regulates the traffic of proteins and RNA through its pores.

- Consists of a double membrane that has that has a continuous inner and outer membrane with pore structures in it.

- Ribosomes

- Help carry out protein synthesis by translating mRNA.

- It consist of ribosomal RNA and proteins.

- Cytoskeleton

- Gives support to the cell and maintain its shape.

- Consists of microtubules, microfilaments and intermediate filaments

- Peroxisomes

- Removes hydrogen atoms form certain molecules and adds them to oxygen, creating hydrogen peroxide.

- Consist of enzymes that make hydrogen peroxide.

- Nucleus

- Controls the activity of the cell and directs protein synthesis.

- Consists of DNA which is made of chromosomes. Chromosomes consist of chromatin.

- Mitochondria

- Uses oxygen to produce ATP for the entire cell

- Consist of a outer membrane and inner membrane that has cristae. Also has mitochondrial matrix which has ribosomes and DNA.

- Only in Animal Cells

- Animal Cell Junctions

- Gap Junctions

- Provides channels filled with cytoplasm from one cell to the adjacent cell so molecules can pass.

- Consist of membrane proteins

- Desmosomes

- Fastens cells together into strong sheets. For example, it attaches muscle cells to one another.

- Filaments made up of keratin proteins anchor desmosomes into cytoplasm.

- Tight Junction

- Prevents fluid from moving across a layer of cells.

- The plasma membrane of two cells use specific proteins to press tightly against each other.

- Centrosomes

- Organizes microtubules which helps organize the cytoskeleton.

- Consist of two centrioles which are consisted of microtubules.

- Extracellular Matrix (ECM)

- Regulates the cells behavior by attaching to integrins (which are membrane proteins) allowing it to send signals throughout the cell.

- The ECM consist of proteoglycans, polysaccharides, and glycoproteins such as collagen and fibronectin.

- Only in Plant Cells

- Plasmodesmata

- Channels that allows molecules to pass between adjacent plant cells.

- They are membraned lined channels filled with cytosol.

- Chloroplast

- Converts sunlight energy into stored energy in sugar.

- Consist of granum (stack of thylakoids) inside a membrane sack with ribosomes.

- The cell wall provides structure and support for a plant cell.

- The cell wall is has a primary cell wall, secondary cell wall, and middle lamela.

- Prokaryotic Cells
- Glycocalyx

- Protects the cell from outside threats

- The glycocalyx is mainly made up of polysaccharides and/or peptides

- Bacterial Chromosome

- The bacterial chromosome helps to store and transmit biological information to other cells. Its role also includes replicating, transcribing, and translating to form DNA, RNA, and protein.

- Bacterial chromosomes consist of DNA, RNA, and an assortment of proteins

- Fimbriae
- Plasma Membrane

- Encloses the cytoplasm. The primary function of the plasma membrane is to protect the cell from its surroundings. The plasma membrane also has selective permeability, which allows it to decide what can go through it

- The fimbriae is a type of appendage of prokaryotic cells. It allows for prokaryotes to stick to surfaces and to other prokaryotes (due to their hair-like protrusions)

- The plasma membrane is made up of the phospholipid bilayer, which contains phospholipids and proteins.

- Ribosome

- Ribosomes main job is to translate messenger RNA to protein (protein synthesis)

- Ribosomes in prokaryotes are mostly made up of ribosomal proteins and ribosomal RNA

- Nucleoid

- The nucleoid is the region where a cell's DNA is located. It also plays an essential role in controlling the activity of the cell

- The nucleoid seems to be composed of mainly DNA and some RNA as well

- Flagella

- The flagella is responsible for the cell's motility and movement

- The flagellum is made up of three structures; the basal body, the hook, and the filament. The flagellum also consists of protein flagellin

- Cell Wall

- Function:

- The cell wall provides structure to the cell and protects the plasma membrane by filtering what goes in and out

- Composed of:

- The main component that makes up the cell wall is peptidoglycan, which gives the cell its shape and surrounds the cytoplasmic membrane