Prokaryotes
have no nucleus/
membrane bound
organelles

Nucleoid

Capsules

Fimbrae

Pili

Endospore

Plasmid

Cell Wall

Slime Layers

Glycoacalyx

In common with
Eukaryotes

Ribosomes

Cytoplasm

Flagellum

Plasma Membrane

Biomolecules
cells are made of
4 kinds of biomolecules

Lipids
ex: cholesterol

Essential component in
PLASMA MEMBRANE

Made of phospholipds

Carbohdrates
ex: glucose

Nucleic Acids

DNA+RNA

Proteins:
ex: actin

Protein structures
Protein has 4 levels of structure

Primary

peptide bonds
Amino end bonds
to carboxyl end

Secondary

hydrogen bonds

alpha and beta sheets

Tertiary

ionic and covalent bonds; disulfide bonds

interaction of r groups

Quaternary

ionic and covalent bonds; disulfide

R-groups

polar

phospholipid

unsaturated

liquid at room temp

double bonds

ester linkage

fatty acid

cis

kinks

hydrogenation

trans

saturated

solid at room temp

no double bonds

cysteine

acidic

glutamic

basic

histidine

non polar

glycine

Eukaryotes

FOUND IN PLANTS

Cell Wall

Chloroplasts

Plasmodesmata

FOUND IN PLANTS,
ANIMALS, AND
FUNGI

Cytoskeleton

Cell Membrane

Nucleus

Nuclear Envelope

Nucleolus

Endoplasmic Reticulum

Smooth

Rough

Mitochondria

Peroxisomes

Vacuoles

In common with
Prokaryotes

Ribosomes

Cytoplasm

Flagellum

Plasma Membrane

FOUND IN ANIMALS

Lysosomes

Centrsome

Cilia

Cell Energy Processes

Plants

Chloroplast roughly 30-40 within each mesophyll

Light Reactions serves to convert solar energy to chemical energy, receiving products from Calvin Cycle

Thylakoid Membrane, is where this process occurs,

Cyclic Electron Flow- cycles electrons through PSI n n nm n, , m Non Cyclic Electron Flow- occurs in both PSI and PSII and electrons received from water^

Calvin Cycle serves to synthesize sugar made from products received from Light Reactions

Stroma, is where this process occurs and is found in the inner space of the chloroplast

Phase II: Reduction during this phase the products from phase I: Carbon fixation, 3 PGA, as well as 6 ATP and 6 NADPH →Out puts: 6 ADP, 6 NADP+ and 6 G3P, 1 is used to make Glucose, 5 move on to next step and are recycl^

Phase III: Regeneration uses 5 G3P, 3 ATP and coverts that to regenerate the RuBP acceptor creating 3 RuBp and 3 ADP and thus cycle repeats, phase I

Animals

Cellular Respiration and Fermentation

Glycolysis
(cytosol)

Process: Breakdown sugar, and has energy investment phase and energy payoff phase

Glucose + 2 ATP + 2 NAD+ = 2 Pyruvate,
2 NADH, 4 ATP
NET= 2 PYRUVATE, 2 NADH, 2 ATP

Step One: Hexokinase converts Glucose
to G6P
Step Three: Phosphofructokinase Fructose 6 Phosphate converted to Fructose 1, 6 Bisphosphate

ATP Production: Substrate Level Phosphorylation

AEROBIC

Pyruvate Oxidation
(cytosol to matrix)

Process: Pyruvates cannot enter the matrix as is, they must convert

2 Pyruvate + 2 CoA + 2 NAD+ = 2 Acetyl CoA &
2 NADH
NET= 2 ACETYL COA & 2 NADH

Important: The cycle is ran twice because pyruvate is not produced singularly

ATP Production: There is none

Citric Acid Cycle or Krebs
(mitochondrial matrix)

Process: Material is converted in order for the process to continue. There is a Redox reaction

2 Acetyl CoA + 2 FADH2 + 6 NAD+ = 2 FADH2,
6 NADH, 2 ATP
NET: 2 FADH2, 6 NADH, 2 ATP

Step One: Acetyl CoA + Oxaloacetate makes Citrate
Step Three: Isocitrate makes Alpha Ketoglutarate (redox reaction)

ATP Production: Substrate Level Phosphorylation

Oxidative Phosphorylation
(inner membrane to membrane space)

Process: Electrons are in the inner membrane. NAD+ is pumped through 1 and FADH is pumped through 2. They both go to Q, 3, Cyt C, and 4

The energy decreases as it goes on. Small amounts of energy are constantly released to stop lysing.

Protons rush beside it and their associated energy creates powers the creation of ATP

O2 + 10 NADH+ 2 FADH2 = H2O + 26-28 ATP
NET: H20 + 26-28 ATP

Key Step: ATP Synthase from ATP with an endergonic reaction. ADP + Pi

ATP Production: Chemiosmosis and Electron Transport Chain coupling

ANEROBIC (FERMENTATION)

lactate

ethanol

NADH-> NAD+

Cell Communication
cells can relay messages
to each other

Membrane Receptors
receptors are embedded
into the plasma membrane

G Protein

Reception

A signal molecule attaches to
the extracellular side
of a G protein coupled receptor,
causing GCPR to change shape

G protein phosphatase function:
removes a phosphate from GTP,
reverting it back to GDP

GDP: G protein is INACTIVE

Transduction

Adenylyl cyclase synthesizes
cyclic AMP from ATP
(2 phosphate groups are lost)

cAMP is the second messenger,
or a relay molecule

ATP is converted to ADP

Protein phosphatases
inactivate protein kinase 1

Phosphodiesterase
converts cAMP to AMP

Response

The last protein kinase in
the phosphorylation cascade
brings about response in cell

Response is AMPLIFIED
one signal molecule produces
more and more molecules
at each step of cascade

Response occurs in
cytoplasm or nucleus

Last kinase enters nucleus and
activates transcription factor,
transcripts gene into mRNA

mRNA directs protein synthesis

Tyrosine Kinase

Signal molecules bind to two
separate polypeptides, inactive
tyrosine kinase proteins

2 polypeptides DIMERIZE:
come together

AUTOPHOSPHORYLATION:
polypeptides function as kinases,
they each take phosphate groups
from ATP and add them to it's partner
(phosphate is added to tyrosines)

Intracellular Receptors
receptors are inside the cell

Signal molecule easily passes
through nonpolar (hydrophobic)
membrane

Signal binds to receptor (a protein) in
cytoplasm

Signal bound receptor enters the nucleus
and binds to specific genes

Receptor protein acts as a transcription factor
and transcripts gene into mRNA

mRNA is translated into a specific protein

DNA Replication

Eukaryotes

Located in the nucleus

Numerous amount of ORI

linear DNA

Replication is bidrectional and discontinuous

Origin of replication- two strands of DNA at ORI sequences and form a bubble

Visual

ORI

Leading stand

Forks out 5'

Lagging strand

Forks out 3'

Subtopic

Enzymes involved

Toperisomerase: helps relieve any strain caused by unwinding of the DNA

Helicase:untwists the double helix of DNA at the replication forks.

Single Stranded Binding Proteins: keeps DNA single stranded

Primase: joins RNA nucleotides to make the primer.

Prokaryotes

Located in the Cytoplasm

Only one replication bubble

Circular DNA

Replication is bidirectional

DNA Polymerase I and III

enzymes used

also involved

Translation

Occurs in the cytoplasm
Proteins are made from code in mRNA

Enzyme aminoacyl-tRNA synthetase cataylyzes
the bonding of an amino acid to a specific tRNA

Initiation

The small ribosomal subunit
binds to mRNA (first the 5' cap and then scans mRNA to find the start codon)

An initiator tRNA bound to the small ribosomal subunit with the correct anticodon base pairs with the mRNA. This tRNA carries the amino acid methionine, MET in eukaryotes and formylmethionine, FMET in prokaryotes

The large ribosome subunit, with E, P, and A sites then binds to the small, forming the translation initiation complex. Initiation factors are proteins needed for this process.

The initiator tRNA is now in the P site.

Elongation

The anticodon of an incoming
tRNA into the A site binds with the complimentary
mRNA codon.

A peptide bond forms with the help of the enzyme
peptidyl transferase between the new amino acid attached to the tRNA in the A site and the C end of the polypeptide in the P site. The polypeptide is removed from the tRNA in the P site and transferred to the tRNA in the A site.

The tRNA in the A site moves to the P site and the empty tRNA in the P site moves to the E site, where it exits. The mRNA is moving along allowing for the next codons to be exposed so that anticodons can bind in the A site.

mRNA is read from 5' to 3' and amino acids are joined together in the N to C direction (Amino end to carboxyl end).

Termination

When a stop codon is reached in the A site,
there is no tRNA to match this codon.

A release factor sits in the A site
and stops translation.

New Protein Pathway

Location is signaled based on the codons

Secretory Pathway

Polypeptide creation on a free ribosome

SRP stops synthesis for a while by binding to the peptide

SRP binds to an Endoplasmic Reticulum Receptor

SRP leaves which allows for synthesis to continue and some of the protein is inside of the ER

The signal is removed by an enzyme and the protein is left in the cell

Plants

Can go immediately to the mitochondria, nucleus, peroxisomes, and chloroplast

Order of Pathway

Nucleus- Creation

ER- leaves shipped through a vesicle

Golgi Bodies- package up proteins in order for them to be secreted.

RNA splicing

Introns

Removed using spliceosomes because they do not code for anything

pre-mRNA

Exons

Joined together once introns are removed

pyruvate forms acetaldehyde ^

Pyruvate is reduced

Recylcle of NAD+

Glycolosis

2 pyruvate= 2 lactate

Regeneration of NAD+

CAM (Crassulacean Acid Metabolism) stomata is open at night, product Malate

C4 photosynthesis uses enzyme PEP Carboxylase, product Malate

C3 Photosynthesis occurs in most plants, uses enzyme Rubisco, product G3P^

Forks out 3'

Lagging Strand

ORI

Leading Strand

Forks out 5'

Complementary DNA strand synthesized continuously 5' to 3' direction

DNA polymerase III, synthesis this strand

Sliding Clamp, changes DNA POL III from being distributive (falling off) to processive (staying on)

Discontinuously synthesized DNA strand that synthesized in a 5' to 3' direction

RNA primers, is what the strand is composed of

Okazaki gragments are what extend this RNA primer

DNA Polymerase I will remove RNA primers with new nucleotides (DNA)

Ligase enzyme: with phosphodiester bonds will make seam less bond