Cell

Has Plasmodesmata

Has a central vacuole

Has a nucleus

Contains both smooth and rough ER

Has a Golgi apparatus

Has a Mitochondria

Contains Peroxisomes

Contains Ribosomes

Has a nucleus (nuclear envelope, nucleolus, and chromatin)

Contains Lysosomes

Has a Golgi Apparatus

Has a Plasma membrane

controls what goes in and out of cell

passive transport

osmosis

water molecules move with gradient

diffusion

facilitated diffusion

uses specialized proteins to move ions and molecules across membrane

simple diffusion

small molecules move from high to low concentrations

active transport

ion channel

form pores in cell membranes, allowing ions to pass through

protein pumps

Na+ and K+ pump

3 Na+ out

2 K+ in

establishes proton gradient

Contains both smooth and rough ER

In animal

Glycolysis

Starting organic molecule (Glucose)
(C6H12O6)

Redox reaction happens, oxidation of gluclose
(C6H12O6 + 6O2 -> 6 CO2 + 6 H2O + Energy)

Glucose is oxidized

interacts with Hexokinase

Glucose 6 Phosphate

Interact with Phosphoglucoisomerase

Fructo 6 phosphate

Interact with Phospho-fructokinase

Fructo 1,6-biphosphate

Interact with aldolase

Glyceraldehyde
3-phosphate (G3P)

Dihydroxyacetone
phosphate (DHAP)

1 ATP used

1 ATP used

Oxygen is reduced

Forms water

NAD+ (already in cells)

Oxidative Phosphorylation

Electron Transport Chain

This happens to all the electron carriers in the cells

FADH2

NADH

Chemiosis

This happens with all the protons that were
pumped against their concentration gradient

Goes through ATP Synthase

The energy released is used to add a Phosphate to ADP

ATP

Oxidative Phosphorylation is Chemiosis coupled with ETC

In plant

Photosynthesis

Light Reaction

If no excess NADPH

Starts in PS2

Photons go through stroma

Excites electron

Energy gets transfer through chain of stroma with
each excitement of electrons

Energy reaches special pair of chlorophyll

Electron is grabbed by electron acceptor

Transfer down electron transport chain to
PS1 chlorophyll, going through cytochrome complex on the way

Same reaction happens as in PS2

Electron goes down second electron transport chain

Goes through NADP+ reductase

NADPH

Enter calvin cycle

1 ATP

Using ATP, H+ is pumped through the thylakoid
spoce against their concentration gradient

Goes through ATP synthase

ATP

Enter calvin cycle

H+ goes to the stroma, down their concentration gradient

If excess NADPH

Start in PS1

Cyclic flow of electrons is
used to make more ATP, not NADPH

ATP

Photosystems

Photosystem 1

Accept light of wavelength 680nm

P680

Photosystem 2

Accept light of wavelength 700nm

P700

Electrons

Electrons are gained from the break down
of H2O

Calvin Cycle

Phase 1: Carbon Fixation

3 CO2

Interacts with Rubisco

6 3-Phosphoglycerate

6 ATP is released

6 1,3-Bisphoglycerate

Phase 2: Reduction

6 Glyceraldehyde-3-phosphate
(G3P)

1 Glyceraldehyde-3-phosphate
(G3P) leaves the chain to become sugar

Phase 3: Regeneration ofthe CO2 acceptor (RuBP)

3 ATP is used

Ribulose bisphosphate(RuBP)

6 NADP+

6 P

Photorespiration

in hot and dry conditions the stomata are partly closed due to which CO2 concentration is low in cells. Rubisco favors to bind O2 instead of CO2, so if CO2 concentration is low, Rubisco will bind whatever O2 is present, releasing CO2

CAM Plants

Takes in CO2 at night

Photosynthesis during the day

C4 Plants

Use PEP carboxylase
instead of rubisco cause it
favors CO2 over oxygen

Can either be

Anaerobic: can't handle oxygen

Aerobic: can handle oxygen

Facultative Aerobic: can do both

Has Flagella for movement (the tail)

Has ribosome

used for protein syntehsis

made of RNA and protein

Read tRNA and translates it into amino acid chains

amino acid

monomer of protein

comprised of:

R group

carboxyl group

amino group

H

Has slime layer or capsule

Has fimbria or pili for DNA exchange

Has nucleioud

Has plasmid

No Nucleus

Is branched into:

Has no circular DNA

No membrane bound organelles

Has Peptidoglycan in cell wall

Has Circular DNA

Has branching cell wall

No membrane bound organelles

Can survive in extreme conditions

Halophiles can tolerate extreme saline environment

Thermophiles can tolerate high heat

Methanogen can tolerate high acidity

Has ether bond for its Phospholipid

Catabolic Pathways

Cellular Respiration

Occurs with the net release of energy

Thermodynamics

System

Open system: Energy is free to come in or out in its surroundings

Closed system: Only energy can come in and out of its surroundings, but not matter

Surroundings

Laws of thermodynamics

1st law: Energy cannot be created or destroyed

Chemical Reactions

2nd law: Every transfer of energy increases entropy in the universe

Entropy

Measure of disorder

Gibbs' free energy

G= H-TS or H=G+TS

Spontaneous Process

Energy isn't needed

Change in free energy is negative

Catabolic

Exergonic

Energy released

Spontaneous process

In equilibrium

Change in free energy is 0

No net changes occurs

Non-spontaneous Process

Energy is needed

Change in free energy is positive

Endergonic

Non-spontaneous process

Free-Energy Change

When more free energy is present then it is less stable

More work capacity

Change in free energy during a chemical reaction

Change in energy can be calculated by doing G final state-G initial state

When there less free energy present then it is more stable

Less work capacity

Gravitational Motion

Objects moving spontaneously from higher places to lower places

Diffusion

the movement of molecules or ions from an area of higher concentration to an area of lower concentration

Chemical Reaction

Enzymes can speed up chemical reactions in cells

Hydrolysis

Energy coupler in cells

Inorganic Phosphate + ADP + H20 = ATP with 7.3kcal of energy

Chemical reactions are powered by ATP

Can cause higher free energy

Can cause lower free energy

Transport work

ATP phosphorylates transport proteins when ATP is added to tranport proteins

Causes higher free energy

Unstable

Coupling

Exergonic + Endergonic

coupling allows cells to carry out complex and energy-demanding tasks by taking advantage of the free energy released by exergonic reactions (ex: ATP hydrolysis).

Binding

Enzyme

Can be used to speed up chemical reactions

Enzymes achieve this by lowering the activation energy

Temperature can affect enzyme activity

Optimal temperatures

Temperature at which cell works just right

Too high (temperature) will cause for cell to denature

To low (temperature) will cause the cell to have a slow reaction

pH can affect enzyme activity

pH affects enzyme activity by influencing the enzyme's shape and ability to bind to substrates. If the pH is too far from the enzyme’s optimal range, it can lead to reduced activity aka denaturation

Catalytic cycle of an enzyme

Substrates enter and change site

Substrates are not help very strong, there is weak interaction

Active site lowers energy and speeds up reactions

Substrates are converted to products

Products are released and active site is free for new substrates to enter again

Enzyme-catalyzed reactions

Rate of reaction increases as substrate concentration increases

Enzyme-substrate binding

Substrate enters site and changes shape of protein

Anabolic Pathways

Polymerization

Photosynthesis

Biosynthetic Pathways

DNA's structure consists of: Phosphate group, nitrogenous bases, and a sugar backbone

Nitrogenous bases can be: Adenine, Cytosine, Guanine and Thymine

Nitrogenous bases are held together by hydrogen bonds

Chargaff's rule: Amount of Adenine = amount of Thymine, amount of Cytosine = amount of Guanine

Can be found going from 5' to 3'

DNA Replication

Semi-Conservative

Parental molecules separate

They both become templates for a new and complementary strand

Conservative

Parental molecules reassociate

They both act as templates for the new strands, which restores the parental helix

Dispersive

Both strands of daughter molecules contain old and new DNA

Experiments involving DNA

Hershey and Chase (1953)

Utilized bacteriophage injected with radioactive protein and radioactive phosphorus

After letting the bacteriophage infect, they centrifuged the infected cells.

Radioactive protein was found on the outside and not inside the pellet, where all the concentration is at. Radioactive protein was not entering the cells.

Radioactive phosphorus was found in the pellet, with the DNA.

They led to the conclusion that DNA is the genetic material

Griffith (1928)

Injected rats with 4 different types of cells

S-cells: Pathogenic

R-cells: Non-pathogenic

S-cells (heat killed): Non-pathogenic

Mixture of heat killed S-cells and R-cells: Pathogenic

Found that even though cells are heat killed, they can still transfer their DNA.

Meselson and Stahl (1957)

Found that DNA was semi-conservative

Used density gradient centrifugation to track the replication of DNA, grew E. coli in heavy nitrogen and incorporated it into DNA, then centrigued with light nitrogen to receive their results.

Comprised of glycerol and 3 fatty acids

Formed by dehydration or condensation sysnthesis

an ester linkage connects each fatty acid to an OH in glycerol

Carboxylic acid group at the end of each chain

Have geometric isomers

Major function is energy storage

Saturated fatty acids

Commonly found in animal

solid at room temperature

no double covalent bonds

saturated with hydrogen atoms at every position

common example: butter

hydrocarbon chains are tightly packed together by hydrophobic interactions

Unsaturated Fatty acids

come from plant sources

are liquid at room temperature

one or more double covalent bonds are found within the carbon chain

do not have hydrogen atoms at every position

Isomers of unsaturated fatty acids

trans fat

hydrogens on the opposite side of the carbon chain

cis fat

the presence of double bonds in cis far causes the molecules to have a kink/slight bemd

hydrogens on the same side of the carbon chain

common example: oil

Phospholipids

amphipathic

contains both hydrophilic and hydrophobic parts

hydrophilic polar head groups

hydrophobic parts gather together in H2O

glycerol is linked to 2 fatty acids

at 3rd OH another group is attached containing a phosphate group

polar

form closed bilayers in waater

Steroids

contain 4 fused rings

ex: cholesterol

found in animals

common component of membranes

precursor to other steroids

HDL vs LDL

High density lipoprotein 'good cholesterol'

low density pipoprotein ' bad cholesterol

sat and trans fat can increase LDL

Histone core protein

In order to start replication we need:

Double Stranded DNA

ORI (Origin of Replication)

This creates a replication bubble/fork

RNA Primer

Helicase

Topoisomerase

SSB

DNA Polymerase

DNA Polymerase I

DNA Polymerase II

DNA Polymerase III

Leading Strand

RNA Primer made and DNA Polymerase III makes the leading strand

Leading strand is elongated from 5' to 3' direction

Lagging Strand

DNA Polymerase I helps remove RNA Primers and replaces them with nucleotides

DNA ligase helps from having the strand fall apart

Summary

Gets reduced

Electrons

Complex Q is reduced

FAD+

NAD+

Energy released

Used to pump H+ against their concentration
gradient in complex 1,3,4

Interacts with Oxygen

Forms water

atp required

Fold together into a condensed chromatin

Fold into an X shaped chromosome

Altogether, this creates a strand of DNA

These 2 convert back and forth
before interacting with Isomerase

Isomerase

Converts all to Glyceraldehyde
3-phosphate (G3P)

G3P is oxidized

2 NADH formed

Energy is released

G3P interact with Triose Phosphate Dehydrogenase, adding a Phosphate to G3P

Forms 2 1,3-Biphosphoglycerate

Interacts with Phosphoglycerokinase

1,3-Biphosphoglycerate gets oxidized with
Phosphoglycerokinase

2 3-Biphosphoglycerate

Interacts with Phospho-
glyceromutase

2 2-Phospho-
glycerate

Enolase, form Double bonds in the substrate through hydrolosis

2 Phosphoenol-
pyruvate (PEP)

Interacts with Pyruvate
kinase and 2 ADP

2 Pyruvate

If there is oxygen

Pyruvate Oxidation

Starting Molecule (Pyruvate)

Goes through oxidation

Acetyl CoA

Enters citric acid cycle

Citric Acid Cycle

Starting Molecule: Acetyl CoA

Interacts with Oxaloacetate

Citrate

Attaches to an H20

Isocitrate

Gets Oxidized

CO2

NADH

alpha-ketoglutorate

Gets oxidized

CO2 release

NADH

Interacts with CoA-SH

Succinyl CoA

Interacts with succinyl CoA synthetase

ATP

Succinate

Gets oxidized

FADH2

Fumarate

Gets Hydrated

Malate

Gets Oxidized

Oxaloacetate

NADH

CoA-SH

NADH

CO2

If there isn't oxygen

Fermentation

Pyruvate gets reduced

Lactate/Alcohol

The Cori Cycle

NAD+

2 ATPs

2 Phosphates groups added to 2 ADP

2 ATP

Enzymes that take part in DNA replication

no atp required

Proteins gets transported to golgi appartus through vesicle

Gap junctions within the animal cell

Plasmodesmata within the plant cell

These contacts allow molecules to pass from one cell to the other, allowing the recipient to respond

Endocrine signaling

If the cell releasing the signal is far from the cell that has the receptor to receive the signaling

ex: Hormonal signaling

Reception

Signaling molecule binds to receptor

Transduction

signal relayed in molecules in a signal transduction pathway

Phosphorylation cascade

an example of signal transduction pathway that uses kinases and phosphatases

1) a relay molecule activates protein kinase 1

2) active protein kinase 1 activates protein kinase 2

3) active protein kinase 2 phosphorylates a protein that brings about the cells response to the signal

4) protein phosphatases catalyze the removal of the phosphate groups from the proteins, making the proteins inactive again

Response

Activation of cellular response

Paracrine signaling

Synaptic signaling

Signaling molecule/signal/ligand

Molecule released by a cell which is received by another cell (target cell)

Receptor

Present in a target cell that receives the signal molecule

Two types of receptors

Membrane receptors

Signal molecule is hydrophilic

receptors in membrane

Ex: G protein linked reeceptor (GPCR)

Transmembrane protein - part is inside, part is outside of the cell

ex: Ion channel receptor

1) channel remains closed until a ligand receptor binds to it

2) ligand binds to receptor, channel opens, specific ions can flow through the channel and rapidly change the concentration of that particular ion inside the cell, may directly affect the cell

3) ligand dissociates from receptor, channel closes and ions no longer enter the cell

Intracellular receptors - In cytoplasm and nucleus

Second messengers

relay molecules that carry the message from the first messenger (signal) inside the cell

cAMP is a second messenger in a G protein signlaing pathway

1) 1st messenger binds to GPCR, activating it

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

3) Activated G protein.GTP binds to adenyl cyclase. GTP is hydrolized, activating adenyl cyclase

4) Activated adenyl cyclase converts ATP to cAMP

5) cAMP, a second messenger, activates another protein, leading to cellular response

Kinsases

enzymes that catalyze the transfer of phosphate groups from ATP to proteins

additional/removal of phosphate groups to and from proteins is one way cells regulate protein functions -> can change the shape of a protein, and thus it's function

can take a phosphate from ATP and add something to it to activate it

Phosphatases

enzymes that catalyze the removal of phosphate groups from proteins by hydrolysis

Protein can be stopped at any of these steps

Transcription

Prokaryote

Lac I

Promoter

Operator

Lac Z

Lac Y

Lac A

Gets binded by

Repressor

Reverts to baseline level or below gene expression

In presence of lactose

Repressor binds to lactose instead of Operator

Activator

Activates enhanced level gene expression

In presence of Glucose

Glucose blocks adenyl cyclase

No cAMP is produced

CAP is not activated

No Activator is made

RNA Polymerase binds here to activates gene expression

Constitutive production of repressor

Eukaryote

Distal Control Element (enhancer)

Gets binded by

Activator

Activates enhanced level gene expression

Repressor

Reverts to baseline level or below gene expression

Proximal control element (promoter)

Gets binded by

RNA Polymerase 2 to activate gene expression

General transcription factors

DNA Packaging

Formation of Nucleosome

DNA

Histone Proteins

H1

Linkage protein

H2A

H2B

H3

H4

Gene production can be stop here

Chromatin modification

Nuclesomes

H1

RNA Processing

pre-mRNA

5'

gets attached to a G group, called a 5' cap

3'

using Poly A polymerase

Attaches a poly A tail to the sequence AAUAA in the 3'

After 3' and 5' end has been modified, mRNA gets modified by spliceosome

Introns are removed

Exons stay

alternative splicing

some exons are removed

exons are rearranged

Transportation out of the cytoplasm

Gene production can be stopped at this point

Translation

mRNA

Gets attached free smaller subunit ribosome

it slides down and find the start codon (AUG)

tRNA with Met attaches to it

bigger subunit of ribosome sits on top

Translation starts

tRNA enters through A side

its Amino acid gets attached to the amino acid of the first tRNA using peptidyl transferase

exits through the E site

this continues until a stop codon is reached

Translation stops

SRP protein is snipped off

protein is snipped off from tRNA

if signal sequence is reached

Signal Receptor Protein gets attached to it

translation stops

the entire complex enters ER membrane

translation starts

Protein processing

protein enters golgi apparatus through cis side

in Golgi, protein is modified with the addition of tags such as phosphate groups

protein is then exited through trans site, in which it has several destinations

Lysosome to be broken down

protein is regulated

Gets secreted

Go to membrane protein

Go back to the ER

Summary