Cell Signaling

- Prokaryotic Cells

- Cell Wall

- Composed of:

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

- Function:

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

- Flagella

- Composed of:

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

- Function:

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

- Nucleoid

- Composed of:

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

- Function:

- 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

- Ribosome

- Composed of:

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

- Function:

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

- Plasma Membrane

- Composed of:

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

- Function:

- 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)

- 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

- Fimbriae

- Function:

- Bacterial Chromosome

- Composed of:

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

- Function:

- 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.

- Glycocalyx

- Composed of:

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

- Function:

- Protects the cell from outside threats

- Eukaryotic Cells

- Only in Plant Cells

- Cell Wall

- 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.

- Chloroplast

- Converts sunlight energy into stored
energy in sugar.

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

- Plasmodesmata

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

- They are membraned lined channels filled
with cytosol.

- Only in Animal Cells

- 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.

- Centrosomes

- Organizes microtubules which helps
organize the cytoskeleton.

- Consist of two centrioles which are
consisted of microtubules.

- Animal Cell Junctions

- 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.

- 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.

- Gap Junctions

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

- Consist of membrane proteins

- 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.

- Nucleus

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

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

- Peroxisomes

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

- Consist of enzymes that make hydrogen
peroxide.

- Cytoskeleton

- Gives support to the cell and maintain its
shape.

- Consists of microtubules, microfilaments
and intermediate filaments

- Ribosomes

- Help carry out protein synthesis by
translating mRNA.

- It consist of ribosomal RNA and proteins.

- Endomembrane System

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.

- Endoplasmic Reticulum

- Smooth ER

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

- Has a smooth outer surface, free of
ribosomes.

- Rough ER

- It helps fold proteins

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

M

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

- Consist of flat membranous sacs called
cisternae.

- 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.

- Vacuoles (Membranous Sac)

- Food vacuole

- Formed by phagocytosis when a cell stores
food.

- Contractile Vacuoles

- Helps pump excess water out freshwater
protists cell

- Central Vacuole

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

- Plasma Membrane

- 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.

- Cell Membranes

- Membrane 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

- 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

- 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

- Intracellular/Extracellular sides

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

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

- Membrane Proteins

- Bonds in Cell Proteins

- Primary Structure

- Connected via PEPTIDE BONDS

- Secondary Structure

- Connected via HYDROGEN BONDS
between MAIN CHAINS

- Forms ALPHA helices and BETA
pleated sheets

- Tertiary Structure

- Bonds depends on the R groups involved

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

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

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

- Only covalent bond present is DISULFIDE
BONDS

- acidic R group + basic R group = ionic
bond

- Quaternary Structure

- a dimer of two tertiary structured proteins

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

- Integral Proteins

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

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

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

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

Phosphorylation Cascade

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

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

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

Phosphate is taken from ATP (forming ADP)

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 4) Protein Phosphatases catalyze the removal of
the phosphate groups from each of the activated
protein kinases

cAMP as a second messenger
in a G protein signaling pathway

Step 1) The signaling molecule (first messenger)
binds to the G protein-coupled receptor
(GPCR)

Step 2) The activated GPCR binds to the G protein,
which is then bound by GTP, activating the G protein

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 4) The activated adenylyl cyclase converts ATP
to cAMP

Step 5) cAMP, the second messenger, activates another
kinase and continues on, leading to cellular responses

cAMP jump starts the
signal transduction cascade

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

Tyrosine Kinase

Step 1) a signal molecule binds to each of the tyrosine kinase signal-binding sites

Step 2) The two monomers then dimerize (form a dimer) to be activated

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 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

Glycolysis

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

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

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

Oxidative Phosphorylation

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

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)

Step 1) Signal molecule binds to the extracellular side of the receptor and activates it.

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 3) The G protein leaves the receptor with the GTP molecule and diffuses across the membrane to bind to an enzyme.

Step 4) The enzyme is activated and is ready to start the next part of the cellular response

Translation begins on free ribosomes (composed of rRNA and proteins)
within a cell; ribosomes differ between
prokaryotes and eukaryotes

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

Small Ribosomal subunit

30S consisting of 21 proteins

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.

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.

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.

Large Ribosomal subunit

50S consisting of 31 proteins

Eukaryotes (80S);
occurs in cytoplasm separate from transcription

Small Ribosomal subunit

40S consisting of 33 proteins

Initiation

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.

Elongation

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.

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. Ribosomal subunits separate.

Large Ribosomal subunit

60S consisting of 45 proteins

Separate from small ribosomal
subunit unless mRNA is attached

Prokaryotes (Cytoplasm)

Initiation

RNA Polymerase binds to the promoter which is upstream.

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

Elongation

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.

Termination

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

Eukaryotes (Nucleus)

Initiation

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

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.

Elongation

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.

Termination

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

Modification

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

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

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.

A mature mRNA strand is formed.

Overall Structure

DNA consists of two strands (double helix) of nucleotide monomers repetitively linked together

Free phosphate group at the 5' ends

Free hydroxyl group at the 3' ends

The Griffith Experiment

In 1928, Fredrick Griffith's experiment identified that some unknown genetic factor controls the traits of organisms

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 S strain

The mouse died

Live R Strain

The mouse lived

Heat-Killed S Strain

The mouse lived

Live R Strain + Heat-Killed S Strain

The mouse died

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.

The Hershey-Chase Experiment

In 1952, scientists Hershey and Chase used bacteriophages to confirm that DNA is the genetic material, NOT proteins

Used a bacteriophage to show that DNA was injected into the bacteria and proteins were left outside of the coat

Meselson-Stahl Experiment

In 1958, Meselson and Stahl demonstrated that E-coli replicates DNA via the Semi-Conservative model

Semi-Conservative Model: Replicated DNA molecules have one old/parental strand and one newly built strand

The parental strands separate and act as templates to synthesize new DNA that is complementary to it

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

1.) transcription happens in the nucleus to produce mRNA; mRNA leaves via nuclear pores

2.) mRNA goes to free ribosomes in the cytoplasm to start translation

polypeptides have destinations from free ribosomes: mitochondria, nucleus, peroxisomes, chloroplast, cytoplasm

3.) polypeptides produced in free ribosomes go to bound ribosomes on the rough ER

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

5.) after the Golgi, the protein will go to its target organelle or leave the plasma membrane

target organelles: ER, plasma membrane, lysosomes

Components of DNA Replication

Topoisomerase

Relieves DNA supercoiling ahead of replication fork

Helicase

Unwinds DNA double helix at the replication fork

Single Stranded Binding Protein (SSB)

Binds to and stabilizes single
stranded DNA

Primase

Creates RNA Primers

DNA Polymerase III

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

DNA Polymerase I

Replaces RNA Primers with DNA

DNA Ligase

Covalently joins together Okazaki Fragments in lagging strands

ORI & Replication Forks

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

Prokaryotes have 1 ORI

Eukaryotes have multiple ORIs

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

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

DNA replication proceeds bi-directionally

Leading & Lagging Strands

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

Lagging strand: discontinuous replication in the opposite direction of the replication fork movement

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

Okazaki fragments are eventually covalently combined by DNA Ligase

Steps of DNA Replication

1.) Topoisomerase binds to the ORI and relieves strain due to DNA supercoiling

2.) Helicase binds and unwinds the two strands of the template DNA by breaking the hydrogen bonds

3.) Single Stranded Binding Protein (SSB) binds to the single stranded DNA and makes sure it stays apart

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

5.) DNA polymerase III adds nucleotides to the 3' end of primers and continues elongation on both strands

6.) DNA polymerase I removes RNA primers and replaces them with DNA

7.) DNA Ligase links the Okazaki fragments together to create a single, new strand

regulation @ transcription initiation

uses transcription factors to bind onto promoters: activators & repressors

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

repressors: decreases level of transcription = less mRNA

enhancers: sequences on DNA in which are far away from the gene