outputs
inputs
Outputs
Inputs
types
type
oxidized into
to
Formed from adding two carbon to oxaloacetate
oxidized to
begins with
outputs
inputs
output
input
Component
Third process
alternate second process without oxygen
how ATP is made
Second process
First process
tension ahead relieved by
sealed together by
contains
follows
done in a
synthesizes new DNA for
kept processive on the DNA by
template for
determined by direction of
placed continuously
RNA primers synthesized by
stabilized by
creates
unwinded and separated by
allows DNA replication to be
forms
involves
begins at
is generally
when
when
begins with
includes
includes
includes
includes
in
tyoe
tyoe
occurs in
involved with
then
then
then
begins with
such as
can go to
can go to
occurs because of
then
first
then
then
first
next
first (prokaryotes)
first (eukaryotes)
starts on
final step
second step
first step
occurs in the
is
then
first
component
component
next
lastly
then
then
recongnition
lastly
then
then
first
then
bind
recongnition
contained
contains 25 upstream of start point
contained
step 3
step 2
step 1
includes
process
process of autophosphorylation
G Protein-coupled Receptor in action
present in
example
example
stages
contains
example
example
example
example
ATP is added causing ADP to be come out
final product
product
a portion of the carbon
a small portion of carbon
product enters new cell
next
next
the difference from CAM cycle
step 1
the difference from C4-Cycle
next
next
next
next
next
byprouduct
next
next
next
next
next
step 1
next
next
next
next
final
next
if needed
next
2nd part for energy consumption
next
next
next
step 1
allows for light energy consumption
an alternate form of photosynthesis
an alternate form of photosynthesis
The "synthesis" of photosynthesis
The "photo" of photosynthesis
such as
then
then
then
then
starts with
such as
converted to
synthesized by
involves
involves
involves
used for
Contains
Contains
Contains
Type
Type
examples
2 cysteines
acidic/basic
nonpolar
polar
can be
can be
structure
structure
structure
structure
can be
can be
can be
can be
composed of
composed of
polymer
monomer
composed of
composed of
example
example
contains
isomer
isomer
contains
contains
contains
contains
can be
can be
used for
composed of
composed of
can be
can be
made of
made of
made of
can be
can be
made of
made of
made of
used for
can be
can be
contains
contains
contains
contains
includes
includes
broken apart by
formed by
redox reactions
determined by direction of
Proteins with signal sequences that indicate movement to the ER and Golgi appartus undergo modifications and may be embedded in the cell membrane. An example is the glycoproteins seen in cell membranes.
plants undergo photosynthesis in order to gain energy from the sun
created by
completed protein moves onto
This is an example of a use for a gated channel protein
The excision of introns from RNA and fusing together of exons (RNA splicing) is unique to eukaryotic cells. This process does not occur in prokaryotic cells.
The carbohydrate glucose is one of the final products of photosynthesis.
this is the eukaryotic version of cellular translation
inputs of
Signal transduction pathways activate proteins that can trigger the transcription of a specific gene to form necessary proteins.
works at
receptor molecules can be found within the plasma membrane
The promoter that initiates DNA replication is made of nucleic acids linked together by phosphodiester bonds
Reduced as
starting phase for creating proteins
Biomolecules (fats, carbohydrates, and proteins) are used as the reactants in cellular respiration.
The product of cellular respiration-- ATP-- is used in translation by aminoacyl tRNA synthetase to catalyze the binding of an amino acid to a tRNA molecule.

Eukaryotic Cells

Organelles-cell organs

Nucleus-brain of cell

Chromosomes-holder of genetic information

Chromatin-what makes up Chromosomes

DNA-genetic information

Nuclear Membrane-encloses nucleus contains Chromosomes

Nucleolus-a structure surrounding the nucleus during interphase

Ribosomes-made up of RNA, it is responsible for protein synthesis

Proteins-make up Ribosomes

Endoplasmic Reticulum-responsible for things like protein synthesis, protein folding, lipid and steroid synthesis.

Rough ER-ribosomes attach

Smooth ER-ribosomes cannot attach

ribosomes leaving in vesicles from ER to cause protein synthesis and combination with products like carbohydrates and lipids

Golgi Apparatus-intracellular transport and secretion

Vacuole-cavity containing fluid(plants only)

Lysosome-waste management

lipids proteins and one enzyme make up Lysosomes

Mitochondria-powerhouse of the cell

Cellular Respiration-chemical reactions that cause glucose to breakdown into ATP causing cell energy production

ATP-energy in the cell

Chloroplast-photosynthesis(plants only)

Chlorophyll-cellular solar panels

Flagella or Flagellum-cell movment(rare)

Cell Membrane

Active Transport-the action of moving cellular material through the cytoplasm with means of cellular energy

Protein Transport

Channel Protein-water and small ions pass through

Carrier Protein-a protein which has a substance it transports across the cell

Gated Channel Protein-a gate must open for a molecule to pass through

Cytoplasm-jelly like substance filling cell

Vacuoles-space in Cytoplasm

Cytosol-a component of the cytoplasm where organelles and particles are suspended

carbohydrates-found in Golgi Apparatus and Cytoplasm

lipids-found in Golgi Apparatus and Cytoplasm

Cytoskeleton-gives shape to cell(animal)

Microfilaments-the equivalent to muscle contractions

protein

Microtubules-made up of a-tubulin and b-tubulin. also takes part in cell growth and intracellular movement

Diffusion-movement from a high concentration to a power concentration. both solute and solvent molecules move freely

Osmosis-movement from a high concentration to a power concentration. only solvent molecules move freely

Centriole(only active during cell division in animal cells)

Cell wall-gives shape to cell(plants only)

plant and animal cell with an enclosed cell membrane and cell nucleaus

Floating topic

Biomolecules
Molecules created by
living organisms.

Carbohydrates

Simple (Sugars)

Monosaccharides

Pentoses: 5-carbon

Ribose

Deoxyribose

Hexoses: 6-carbon

Glucose

Alpha: OH is below the
ring

Beta: OH is above the ring

Galactose

Fructose

Disaccharides

Sucrose

Lactose

Maltose

Complex

Storage polysaccharides

Glycogen

Alpha glucose & 1-4 and 1-6
glycosidic linkages (lots of branching)

Starch

Amylose

Alpha glucose & 1-4 glycosidic
linkages (no branching)

Amylase

Alpha glucose & 1-4 and 1-6
glycosidic linkages (some branching)

Dextran

Structure polysaccharides

Cellulose

Beta glucose & 1-4 glycosidic
linkages (no branching)

Chitin

Nucleic Acids

DNA

deoxyribose sugar

phosphate

nitrogenous base

Purines

Adenine (A) & Guanine (G)

Pyrimidines

Cytosine (C) & Thymine (T)

RNA

ribose sugar

phosphate

nitrogenous
base

Purines

Adenine (A) & Guanine (G)

Pyrimidines

Cytosine (C) & Uracil (U)

Gene expression

Lipids

Triglycerides

Glycerol

3 Fatty acids

Saturated

No double bonds & H atoms
at every position

Solid at room temp

Unsaturated

One or more
double bonds &
H atoms are notat every position

Liquid at room temp

Cis: H on same side
of double-bonded carbons.
Has a kink

Trans: H on different sides
of double-bonded carbons

Energy storage

Steroids

4 fused rings

Cholesterol

HDL: Carries excess to
liver for excretion (good)

LDL: Carries excess to
blood vessels (bad)

Testosterone

Phospholipids

Hydrophobic tail:
Glycerol &
2 Fatty acids

Hydrophilic head:
Phosphate group

Form bilayer in water

Proteins

Amino acids

Main chain: Amino &
carboxyl groups

Side chain:
R group

Polar: Has OH, SH,
or NH groups

Nonpolar: Has H, CH,
or carbon ring

Acidic: Complete
negative charge

Basic: Complete
positive charge

Polypeptide

Primary: Amino acids
connected through peptide
bonds

Secondary: Main chains form
hydrogen bonds

Alpha helix

Beta-pleated sheet

Tertiary: R groups interact
to from 3D shape

Hydrogen bonds

Hydrophobic
interactions

Ionic bonds

Disulfide bond

Quaternary: 2 or more
polypeptides form a
functional protein through
R group interactions

Monomer: 1 PP

Dimer: 2 PPs

Trimer: 3 PPs

Tetramer: 4 PPs

dehydration reaction

hydrolysis

Floating topic

Cell membranes

Function

transport

smaller molecules

facilitated diffusion

passive transport facilitated by proteins

channel proteins are needed

active transport

protein pumps

low->high concentration

ex:sodium-potassium pump

osmosis/diffusion

Isotonic

Hypotonic solution

turgid(normal in a plant cell)

Hypertonic solution

plasmolyzed (plant loses water)

larger molecules

endocytosis

pinocytosis

phagocytosis

receptor-mediated

exocytosis

barrier, support, protection

separates organism from the environment

Structures

are

selectively permeable

made of

phospholipid bilayer

hydrophobic tail (fatty acid chain) and hydrophilic head (polar) which help control membrane fluidity

proteins

Ion channels

Un-gated (always open)

Gated (stretch-gated, ligand-gated, voltage-gated)

sodium potassium-pump, potassium channel, sodium channel

Transmembrane proteins have an extracellular and cytoplasmic side

transport, enzymatic activity, cell-cell recognition, signal transduction, intercellular joining, and attachment to the cytoskeleton and extracellular matrix (ECM)

Floating topic

Floating topic

Floating topic

Floating topic

Prokaryotes

r

Prokaryotes - A type of organism that is single celled, lacks a nucleus, and contains no membrane bound organelles.

Nutrition Modes

Autotrophs

Photoautorophs

Light

r

Organisms that utilize light to synthesize organic molecules are known as photoautotrophs, such as cyanobacteria.

Chemoautoroph

Inorganic chemicals

r

This mode, as an autotroph, means a prokaryote gets its energy from inorganic chemicals.

Heterotrophs

Photoheterotroph

r

The prefix photo refers to light, which this mode utilizes for energy. This trait is unique to certain aquatic and salt thriving prokaryotes. Since its a heterotroph it utilizes carbon from organic compounds.

Chemoheterotroph

r

Chemoheterotrophs utilize carbon from organic compounds, and are characteristics of many prokaryotes.

Types

Bacteria

Archaea

r

A category of prokaryotic micro-organisms

Types

Extreme halophiles

r

These kinds of archaea are able to thrive in extremely saline environments, referred to as extreme as very little amounts of organisms can survive in similar conditions.

Extreme thermophiles

r

This kind of prokaryote can thrive in high temperatures that few other organisms can survive in. They are commonly found in many extreme temperature environments such as hot springs and hydrothermal vents.

Methanogens

r

Another prokaryote in the archaea domain are methanogens. These can be found in hydrothermal vents, the guts of animals, and wetlands. They are anaerobic, meaning oxygen is poisonous to them, and remove excess hydrogen.

Common Structures

Plasma membrane

r

The plasma membrane is a selectively permeable barrier for the cell. It provides boundaries between the inside of the cell and its environment, facilitates the transport of nutrients and waste, and is where metabolic processes occur.

Specific structures

r

The plasma membrane is made up of an amphipathic phospholipid bilayer, with hydrophilic heads bordering the outside and inside of the cell, and the hydrophobic tails making up the interior of the membrane. This arrangement is held together by weak Van der Waal forces that allow lipids to move within the membrane and provides fluidity.The membrane also consists of proteins located on the surface (surface proteins), within the membrane (integral proteins), and with chains of polypeptides (glycoproteins).

Transport of molecules

r

The membrane being selectively permeable means only certain molecules can pass through without assistance.Molecules that can transport across the membraneSmall non polar Small uncharged Molecules that cannotLarge uncharged polar moleculesIons

Factors of fluidity

r

The weak Van der Waal forces present in the membrane allow for the movement of lipids. The fluidity of the membrane however is determined by a few factors.

Temperature

r

At a specific lower temperature, the membrane's phospholipids change from their more liquid, crystalline phase, to a more gel-like phase.

Types of fatty acids present

r

The ratio of unsaturated fatty acids to saturated fatty acids also affects the fluidity of the membrane. Saturated fatty acids lack the structural kink that is present in unsaturated fats, allowing the phospholipids to pack together more tightly, and resulting in a more rigid structure.

Cholesterol

r

Cholesterol embedded within the plasma membrane allows for the regulation of the movement in phospholipids by reducing movement at moderate temperatures and preventing the overpacking of saturated fatty acids at low temperatures by acting as a buffer.

Fimbriae and pili

r

Fimbriae are short abundant structures used by bacteria to stick to other bacteria, while longer pili assist in transferring DNA between cells.

Cell wall

r

Present in all prokaryotes, the cell wall maintains the cell's shape, and provides protection and support. This structure is made of modified sugars with short polypeptides called peptidoglycan.

Peptidoglycan

r

This substance that makes up the cell wall is unique to bacteria, and can be used to target them specifically.

Cytoplasm

r

The cytoplasm consists of gel-like cytosol, water based solution with ions and small molecules, and makes up the internal part of the cell inside the plasma membrane.

Ribsomes

r

Ribosomes are present in both prokaryotes and eukaryotes, and are essential for protein synthesis.

Flagella

r

The flagella is important for the cell's motility, and contains a hook a basal body. It can exist either around the surface of the cell, or be concentrated in one area.

Capsules and slime layers

r

This structure surrounds the cell wall of bacteria as a sticky later of polysaccharide or protein, and helps the cell for adhesion and protection.

Gas vacuoles

r

Gas vacuoles assist in buoyancy for flotation in aquatic environments.

Endospore

r

Endospores are essential for bacteria living under extreme conditions. It protects the DNA of the cell by making a dormant and resistant cell that can survive various circumstances.As the rest of the cell disintegrates, the DNA is protected by the multiple layers of cell wall material surrounding it, forming the endospore.

Nucleoid

r

Prokaryotic cells don't have a membrane bound organelle for their DNA, rather they have a recognized region where DNA is located known as the nucleoid.

Materials Present

Bacterial Genome

RNA

r

Controls the synthesis of proteins and provides essential messenger functions for DNA.Its structure varies from DNA in that it has ribose sugars instead of deoxyribose, is single-stranded, and has uracil instead of thymine

Proteins

Metabolism

Obligate aerobes

r

Organisms that require oxygen for cell respiration

Obligate anaerobes

r

Organisms that cannot tolerate environments with oxygen present as it would lead to cell death and instead utilize fermentation anaerobic respiration.

Facultative anaerobes

r

This kind of organism utilizes aerobic respiration when oxygen is present, but can also use fermentation when oxygen is not.

Concept Map 1

Signal Transduction

Amplification of signals and
coordination/regulation of
cellular response

Reception

Ligand (signaling molecule) binds
to membrane receptor (e.g., GPCR)

GCPR adds GTP to
G protein, which then activates
membrane enzyme

Common relay molecule:
Cyclic AMP

ATP using the enzyme
Adenylyl cyclase

AMP after it activates
the next step. Converted by
phosphodiesterase (PDE).

Transduction

Phosphorylation cascade

Activation of relay molecule
(small, water-soluble molecule/ion),
triggered by reception of ligand

Activation of a protein kinase 1

Activation of protein kinase 2
as protein kinase 1 transfers a
phosphate group to it

Activation of an inactive protein as
protein kinase 2 transfers a phosphate
group to it

Activated protein triggers cellular response

Response

Cellular response is activated
after the transduction pathway
is completed.

Expression of a gene

Photosynthesis

Light Reaction

Photosystem II(P680)

light and water enter the complex

electrons from water are attached to the chlorophyll as protons and O2 are excecated out. light then causes the electrons to jump to an excited state

as the electrons jump to an excited state they are accepted by the primary acceptor

the electrons then go out a electron transport chain causing ATP to be released. the chain consist of plastoquinone (Pq), Cytochrome Complex,
and Plastocyanin (Pc)

Photosystem I(P700)

as the electrons for the ETC enter the chlorophyll and more light exciting them they enter the primary acceptor

this causes another ETC consisting of ferredoxin (Fd) to NADP+ reductase.

NADP(+
)+ 2 H+ binds with NADP+ causing NADPH+H+ to be formed

Cyclic Electron Flow-only used when the cell needs more ATP

Cytochrome Complex to the Plastocyanin creating ATP

plastocyanin then brings its energy to the chlorophyll

electrons get excited to the primary acceptor

electrons are then taken by Ferredoxin back to the Cytochrome Complex

Photophosphorylation: ATP from ETC
is used to pump H+ into thylakoid space.
H+ diffuses down its concentration gradient
through ATP synthase, forming more ATP.

Calvin Cycle

CO2 is introduced due to Rubisco

Phase 1 Carbon Fixation

as CO2 binds with rubisco it creates a short lived intermediate

after the short lived intermediate 3-Phosphoglycerate is made

with the introduction of 6 ATP and excretion of ADP 1,3-Bisphoglycerate is made.

with the introduction of 6 NADPH and the excretion of NADP+P we enter a new phase

NADP+P

Phase 2 Reduction

Glyceraldehyde-3-phosphate
(G3P) is created by phase 1 and is the main sugar used by plants

Phase 3 Regeneration of the CO2 acceptor

3 ATP are introduced cause 3 ADP to leave

this creates Ribulose bisphosphate (RuBP)

CAM Cycle

Temporal separation of steps

C4-Cycle

CO2 enters the mesophyll cell through PEP carboxylase

Oxaloacetate(4C) is formed

malate(4C) is formed

Bundle Sheath cell

CO2

calvin cycle

sugar

vascular tissue

Pyruvate (3C)

PEP (3C)

Spatial separation of steps

Cell Signaling

Physical Contact

Gap Junction (animal cells

Plasmodesmata (plant cells)

Releasing a signal

Local signaling

Paracrine signaling

Synaptic signaling

Long distance signaling

Hormonal Signaling

Receptors

Membrane receptors

includes

G protein linked receptor

signal molecule binds to the GPCR

slight alteration in the shape of GCPR allows for the G protein to bind to it

GDP is replaced with GTP on the G protein

G protein with GTP bound to it is active and it can now activate a nearby enzyme

all of the above steps occur in reception

Tyrosine kinase receptor

Polypeptide on dimerization functions as a kinase

it takes a phosphate group from ATP and adds it to another polypeptide

Ion channel receptor

when a signal molecule binds to the receptor, the gate allows a specific ion like sodium or calcium through the channel in the receptor

movement of ions through these channels may change the voltage across membranes

this would trigger action potential

Intracellular receptors:in cytoplasm & nuclues

steroid hormone aldosterone

target cell that receives the signal molecule

reception

transduction

response

Concept Map 2

Floating topic

Transcription

Initiation

Promoter

TATA box-using for recognition of transcription factors

Transcription Factors-used to RNA polymerase ii can bind in the correct position

RNA Polymerase ii-add RNA nucleotides

RNA polymerase ii and Additional transcription factors bind in order to make a transcription initiation complex.

start point-point of transcription

Elongation

RNA polymerase ii bind to the template strand of DNA 3'-5'

RNA polymerase ii unwinds DNA and then adds RNA nucleotides

the RNA being created resembles the non-template strand of DNA 5'-3'

pre-mRNA strand is now created 5'-3'

Termination

the pre-mRNA is noticed by ribonuclease an amino acid which cuts the pre-mRNA from the DNA

a 5'cap is added to the pre-mRNA

a 3' poly-A tail is added
by polyA polymerase

the pre-mRNA is now ready
to undergo processing

RNA Processing

intron-filler material

exon-material containing suitable nucleotides for protein function

introns are cut out by spliceosome

exons are brought together through spliceosome

mature mRNA is created
and ready for translation
into proteins

Translation

The reading of mRNA codons by tRNA
and its anticodons (attached by aminoacyl tRNA synthatase) to form amino acid chains

direction

similar process

Small ribosomal subunit binds
to the G cap and walks along
the mRNA until it reaches AUG,
the start codon. Initiator tRNA
with anticodon UAC and amino acid
methionine base-pairs with
AUG.

Large ribosomal subunit completes
initiation complex. GTP provides energy
for assembly. The initiator tRNA is in
the P site. The A site is available for
the next tRNA.

Small ribosomal subunit binds an mRNA
and recognizes a specific nucleotide
sequence just upstream of the start codon AUG. Initiator tRNA with anticodon UAC and amino acid formyl methionine base-pairs with AUG.

Elongation

mRNA codon is recognized
by anticodon of incoming
tRNA.

Peptide transferase catalyzes
the formation of a peptide bond
between the amino group of the
new amino acid in the A site and
the carboxyl end of the polypeptide
in the P site.

Ribosome translocates the tRNA
in the A site to the P site. The
empty tRNA in the P site is moved
to the E site, where it is released.
mRNA moves with bound tRNA,
bringing the next codon to the A site.

Termination

The stop codon reaches
the A site. There is no
tRNA that corresponds with
it.

Instead, a release factor sits
in the A site, disassociating the
complex, stopping translation.
Disassociation is driven by GTP.

free ribosomes

Protein Transport

Signal sequences, which
dictate proteins' final
location in the cell

Organelles

Peroxisomes, mitochondria,
chloroplasts (in plants), nucleus

Endomembrane
system

Signal-recognition particle
carries ribosome to endoplasmic
reticulum.

SRP leaves, protein synthesis
continues until finished. Then,
signal peptide is cleaved and the
polypeptide leaves the ribosome
and enters the ER.

Protein travels in a vesicle to the
Golgi apparatus where it is modified.
Modifications include glycosylation,
the addition of carbohydrates to proteins
to make glycoproteins.

Protein can be carried in vesicles to
lysosomes or the plasma membrane
to become a membrane protein
or be secreted.

Gene Regulation

DNA Packing

Histones

First level of packaging involves attaching proteins (histones) to DNA

Made of H2A, H2B, H3, H4 at the core

10 nm fiber

DNA winds around histones to form nucleosome “beads”

30 nm fiber

Interactions between nucleosomes cause the thin fiber to coil or fold into this thicker fiber

300 nm fiber

The 30-nm fiber forms looped domains that attach to proteins

Transcription

signal protein

General

Bring about low levels of transcription (background/basal)


Specific

changes level of transcription

Activators:increases level

Inhibitor: reduces level

In Eukaryotic cells

1) A eukaryotic promoter
commonly includes a TATA
box (a nucleotide sequence
containing TATA) about 25
nucleotides upstream from
the transcriptional start point

2)Several transcription
factors, one recognizing
the TATA box, must bind
to the DNA before RNA
polymerase II can bind in
the correct position and
orientation.

3)Several transcription
factors, one recognizing
the TATA box, must bind
to the DNA before RNA
polymerase II can bind in
the correct position and
orientation.

Prokaryotes

Lac operon

Active

Lactose present, cAMP is present

Lactose present, CAP is active

Lactose present no glucose

Inactive

glucose is present

Concept Map 3

DNA Replication

Fast and accurate

Origin of replication: Sequence of nucleotides that indicates
the beginning of DNA replication

Replication bubble

Bidirectional forks- located at each
end of the replication bubble

Double stranded DNA- with a complimentary, antiparallel structure

Helicase- enzyme

Single-stranded DNA

Single-stranded Binding
Protein (SSBs)- enzyme

Primase-enzyme

Leading strand

Parental DNA

DNA polymerase III

sliding clamp

Daughter strand

5' to 3' direction

Chargaff's rule- states purines and pyrimidine must be paired with one another, specifically the same proportion of
adenine to thymine and guanine to cytosine

Lagging strand

Okazaki fragments

DNA ligase- fills in the gaps left by
removed RNA primase with nucleotides
complimentary to the parent strand

Replication forks- located at each end
of the replication bubble

Topoisomerase- enzyme

Cellular Respiration

Glycolysis

Energy Investment Phase

ATP

Glucose

ADP

Energy Payoff Phase

NADH

Protons

Phosphate

Electrons

NAD+

Protons

Pyruvate

Water/H2O

Pyruvate Oxidation

Pyruvate

c

Citric acid cycle begins

Citrate

Isocitrate

a-ketoglutarate

Succinyl CoA

Succinate

Fulmarate

Malate

Oxaloacetate

Substrate level phosphorylation

Anerobic respiration

Alcohol Fermentation

ADP

NAD+

ATP

NADH

Lactic Acid

ADP

NAD+

ATP

NADH

Oxidative Phosphorylation

Electron Transport Chain

Inner mitochondrial membrane

Chemiosmosis ATP Synthesis

concentration gradient

transport protein - ATP Synthesis

NADH

Gene regulation occurs in the nucleus of the cell because this is where transcription occurs

The cell membrane is composed of many lipids, some with glycerol (a three carbon molecule) acting as the backbone

Another function that was not added until later is cell signaling, with examples like the kinase receptors

Floating topic