Chemical bonds, Cell Structures, and Functions

Cell Evolution

Macromolecules

Carbohydrates

Monosaccharides

Polymers - Disaccharides and Polysaccharides

Proteins

Amino Acids

Main Chain

Amino Group

Carboxyl Group

Side Chain (R Group)

Acidic

Negatively Charged R group

Basic

Positive Charged R Group

Polar

Ex: OH

Non-Polar

Ex: CH

Lipids

Glycerol/fatty acids

Saturated Fats

Ex: olive oil (liquid at Room temperature)

Unsaturated Fats

Ex: butter (solid at Room temperature)

Trans Fats

Ex: margarine (very processed)

Nucleic Acid

Nucleotides

Deoxyribose or Ribose (RNA) Sugar

Phosphate Group

Nitrogenous Base

Adenine-Thymine or Adenine-Uracil (RNA)

Cytosine-Guanine

Chemical Bonds

Covalent Bond

Non-polar covalent

e- shared equally

Hydrophobic

Sharing of e-

Polar Covalent

Hydrophilic

e- shared unequally

Hydrogen Bond

partial + attraction

Intermolecular interaction

Ionic Bond

to obtain a full octet by exchanging e-

Negative

Positive

Miller and Urey Experiment

Tried to prove Oparin’s hypothesis by replicating early earth atmospheric conditions Abiotic synthesis of organic molecules is possible meaning Oparin's bubble hypothesis is possible Amino Acids were formed

formation of protein and nucleic acid

Protocell

droplets with lipid bilayer membranes to keep internal chemicals separate for the packaging of proteins and nucleic acids.

Self Replicating RNA

jumpstarted biological evolution because it carries information and can make a copy of itself allowing for inheritanceRibozyme (it’s an dRNA with enzyme function)

Ribozyme

They are RNA with enzyme functions

PROKARYOTIC CELL

Components of a Prokaryotic Cell:Plasma membrane - allows things into and out of cellGas vacuole - to control buoyancy Ribosome - protein productionFlagella - transportation Endospore - protects chromosomes from harsh environment Inclusion body - storage for glycogenNucleoid - area of genetic material and has chromosomeCell wall - peptidoglycan; is modified sugar and amino acid; D enantiomerPeriplasmic space - oxidation of proteinsCapsule and slime layer - protects cells from environmentFimbriae and Pili - to reproduceNutrition :AutotrophPhotoautotroph: lightChemoautotroph: inorganic compounds HeterotrophPhotoheteroph: lightChemoheterotroph: organic compounds Metabolism of Oxygen :Obligate Aerobes: require oxygen for cell respirationObligate Anaerobes: the cell is poisoned by oxygen; fermentation anaerobic respirationFacultative Anaerobes: can do both aerobes and anaerobes functions depending on if oxygen is present or not

ENDOSYMBIOSIS SYSTEM

Host Cell

A cell with a nucleus and Endoplasmic Reticulum.

Prokaryotic Domains

Archaea

They are extremophiles, which are archaea that live in extreme environments. Archaea lipids are branched and have an ether bondthey have circular chromosomes some can live in temperatures over 100 degrees Celsiusthey have no peptidoglycan in their cell wallthey don't have a nuclear envelopethey don't have membrane-bound organelles

Methanogens

live in swamps and marchesthey produce methane as wastethey are strict anaerobes ( oxygen is toxic )

Extreme Halophile

live in highly saline environment

Extreme Thermophile

they live in very hot environments.

Bacteria

they have circular chromosomes they can't live in temperatures over 100 degrees Celsiusthey have peptidoglycan in their cell wallthey don't have a nuclear envelopethey don't have membrane-bound organelles

Metabolism of Oxygen

Obligate Aerobes

require oxygen for cell respiration

Obligate Anaerobes

the cell is poisoned by oxygen; fermentation anaerobic respiration

Facultative Anaerobes

can do both aerobes and anaerobes functions depending on if oxygen is present or not

cell wall

provides structure to cell and determines what enters or leaves cell

Movement

flagella

Endospores

protects chromosomes from harsh environment

Nutrition

Autotroph

Chemoautotroph

inorganic compounds

Photoautotroph

light

Heterotroph

Chemoheterotroph

organic compounds

Photoheteroph

light

Oparin’s bubble hypothesis: Simples organic molecules→ complex organic molecules

Earth had little oxygen, but water vapor and chemicals like carbon dioxide, hydrogen, methane, ammonia, and nitrogen oxides were released by volcanic activity. When the volcanoes erupt underwater, the gas bubbles make simple organic molecules that pop when they reach the surface of the water which allows the simple organic molecules to become complex organic molecules which then go back to the sea. Early atmosphere was reducing electrons and the volcanic eruption led to organic compounds becoming complex.Simples organic molecules→ Complex organic molecules

Mitochondrion Prokaryotic

Oxygen-using nonphotosynthetic prokaryoticthey are obligate aerobes prokaryotic

Mitochondria

double membranehas its own DNA and ribosomesis inherited maternallyperforms ATP synthesis and cellular respiration for energy

EUKARYOTIC CELL

peroxisomes

metabolized H2O2-> H2O

lysosomes

low pH; has enzymes

autophagy

phagocytosis

Golgi Apparatus

packaging proteins

Trans Face

releases vesible after altering it

Cis Face

revieves vesicles from ER

Vacuoles

Food vacuole

Contractile Vacuole

pumps water out of cell

Nucleus

nuclear membrane

nuclear envelope with lamina (α and β) and nuclear pores

Chromosome

Chromatin

DNA and histones

PROTEIN SYNTHESIS

RNA produced and leaves nucleous

RNA makes contact with ribosomes (free or bound on Rough ER)

proteins are produced

nucleolus

ribosomes produced; rRNA transcribed

Endoplasmic Reticulum

Smooth Er

synthesize lipids; metabolize carbs

Rough ER

bound ribosomes; distribute vesticles; secrete glycoprotein

Plasma membrane

permeable lipid bilayer and allows things into and out the cellhas protein and lipids in the bilayer; phospholipids

permeable lipid bilayer and allows things into and out the cell

ATP Synthesis and Cellular Repiration

Cyanobacterial Prokaryotic

Photosynthetic prokaryoticmakes their own food with light

Chloroplast

cell wall is made of cellulose performs photosynthesis for energy found in the plant domain

Photosynthesis light dependent and Calvin reaction

PLANT CELL

Cell Wall

made of Cellulose, gives cell structure, keep turgor pressure, control what enters and leaves the cell

Central Vacuole

cell sap with inorganic ions

stores water and regulates turgor pressure

Plasmodesmata Channels

controls flow of water out of cell

Cell Signaling

Sending Signals using Signals/Ligands and Receptors

Signal Transduction Pathway

Reception

ligand or signal is bonded to membrane receptor

Transduction

Long Distance Signaling

Receptors

Intercellular Receptor

Membrane Receptor

Phosphorylation Cascade

Amplification effect to be efficient and fast

Activiation of Cellular Response

Protein Kinase

enzyme catalyzes Pi from ATP to proteins

Phosphatase

Enzyme catalyzes removable Pi from protein with hydrolysis

Signals

G Protein Linked Receptors

GTP binds to GPCR

Phosphatase for GDP and Pi

Tyrosine Kinase Receptor

2 polypeptide dimers (protein kinase)

Tyrosine dimers

Ion Channel Receptor

Ligand Gated Ion Channel

Local Signaling

Physical Contact

Plant Cell: Plasmodesmata

Animal Cell: Gap Junction

Second Messenger: cAMP

AMP

Triggers Action Potential

depends on signal/ligand concentration (neurotransmitters)

Autophosphorylation

6 ATP-> 6 ADP + 6 Pi

Adenylyl Cyclase activated

ATP

Cellular Respiration

Glucose + Oxygen -> Carbon Dioxide + Water + Energy C6H1206 + 6O2 -> 6CO2 + 6H2O + ATP

1)Glycolysis

Occurs in cytosol SUBSTRATE LEVEL OXIDATION to produce ATP.

2)Energy Payoff Phase

4 ATP FORMED

2NAD+ -> 2NADH

1)Energy Investment Phases

2 ATP USED

Glucose -> Glucose 6 phosphate

ATP used

Fructose 6 phosphate

Fructose 1, 6 biphosphate

ATP used to convert Fructose 6 phosphate to Fructose 1, 6 biphosphate

G3P

Aldolase

DHAP (later forms G3P)

2)Pyruvate Oxidation

Occurs in mitochondria matrix.

Pyruvate + coA

Acetyl CoA

3)Kreb Cylce

Occurs in mitochondria matrixSUBSTRATE LEVEL OXIDATION for the production of ATP

Acetyl CoA

Citrate

Isocitrate

a-Ketoglurate

Succinyl CoA

Succinate

Fumurate

Malatate

Oxaloacetate

4)Oxidative Phosphorylation

Occurs in mitochondria OXIDATIVE PHOSPHORYLATION used for ATP production

Chemiosmosis

ATP Synthase

H Protons move down concentratin gradient to make 28-32 ATP

ETC

ETC = Electron Transport Chain Electrons move across integral proteins known as Complex I, III and IV.

Complex 1: NADH -> NAD

Oxidation occurs

Complex 2: FADH2 to FAD

Oxidation occurs

CoEnzyme Q10

Mobile carrier of electrons lying on Complex II

Complex 3

Cytochrome C

Complex 4

O2 is oxidized to make H20 with H protons

Cell Membranes and Selectively Permeable Membranes

Plasma Membrane

Phospholipid Bilayer

Hydrophilic Head

Hydrophobic tail

Fluidity Of Plasma Membrane

Fluid

Unsaturated hydrocarbon
tails with kinks

Viscous

Saturated hydrocarbon tails

Functions Of Membrane Proteins

Enzymatic Activity

Signal Transduction

Cell-Cell Recognition

Intercellular Joining

Attachment to the cytoskeleton and
extracellular matrix (ECM)

Transport

Selective Permeability Of Plasma
Membrane

Low Permeability

Ions (Cl-, K+, Na+)

High Permeability

Small Nonpolar Molecules (O2, CO2, N2)

Intermediate Permeability

Small, Uncharged Polar Molecules (H2O, Glycerol)

Large, Uncharged Polar Molecules (Glucose and Sucrose)

Transport Across Membranes

Passive Transport

Diffusion

Net passive movement of molecules or particles from regions of higher to regions of lower concentration.

Facilitated Diffusion

Osmosis

Isotonic Solution

Animal Cells - Normal

Plant Cells - Flaccid

Hypertonic Solution

Animal Cells - Shriveled

Plant Cells - Plasmolyzed

Tonicity

The ability of a surrounding solution to cause a cell to gain or lose water

Hypotonic Solution

Animal Cells - Lysed

Plant Cells - Turgid (Normal)

Aquaporins

Channel Proteins

Carrier Proteins

Ion Channels

Gated

Stretch-Gated

Sense-Stretch, Open when membrane is mechanically deformed

Ligand-Gated

Open and close when a neurotransmitter binds to channel

Voltage-Gated

Open and close in response to changes in membrane potential

Ungated

Always Open

Active Transport

Sodium-Potassium Pump

3 Na+ Out / 2 K+ In

Electrogenic Pumps

A transport protein that generates voltage across amembrane – membrane potential(-50 to -200 mV)Help store energy that can be used for cellular work

Proton Pump

Cotransport

Coupled Transport by aMembrane Protein-Occurs when active transport of a solute indirectly drivestransport of other substances

H+/Sucrose Cotransporter (Diffusion of H+ and Active Transport of Sucrose)

Bulk Transport

Phagocytosis

Pinocytosis

Receptor-Mediated Endocytosis

Action Potential In A Neuron

Step 1 - Resting Phase

The activation gates on the Na+ and K+ channelsare closed, and the membrane’s resting potential is maintained.

Step 2 - Depolarization

A stimulus opens theactivation gates on some Na+ channels. Na+influx through those channels depolarizes themembrane. If the depolarization reaches thethreshold, it triggers an action potential.

Step 3 - Rising Phase

Depolarization opens the activationgates on most Na+ channels, while theK+ channels’ activation gates remainclosed. Na+ influx makes the inside ofthe membrane positive with respectto the outside.

Step 4 - Falling Phase

The inactivation gates onmost Na+ channels close,blocking Na+ influx. Theactivation gates on mostK+ channels open,permitting K+ effluxwhich again makesthe inside of the cellnegative.

Step 5 - Undershoot

Both gates of the Na+ channelsare closed, but the activation gates on some K+channels are still open. As these gates close onmost K+ channels, and the inactivation gatesopen on Na+ channels, the membrane returns toits resting state.

Metabolism

Metabolic pathways

Starting molecule(A)

B(intermediate)

C(intermediate)

D(end product)

Adding an enzyme can catalyze a reaction.

Catabolic Pathway

Complex molecule

Simple molecule

Cellular Respriation

Glucose + 6 O2

6 Carbon Dioxide

6 H2O

Energy into the system

Anabolic Pathway

Simple molecules

Complex molecule

Photosynthesis

6CO2 + 6H20 + light energy

Simple to complex

Glucose

6 O2

Biosynthetic Pathways

Polymerzation

Forms of Energy

Kinetic energy

Motion

Thermal energy

Light energy

Potential energy

Stored energy

due to location or position

chemical energy in food

Electrons on outer shell have the highest PT

Thermodynamics

System

Surroundings

Universe

Open

Closed

Gibbs Free Energy

△G= △H-T△S

H = G + TS

H= enthlapy(potential of system)

T= Temperature (STP 273K)

S= entropy (measure of temp)

Exergonic

ΔG < 0

spontaneous reaction

energy released

Endergonic

ΔG > 0

non-spontaneous

energy input needed

ΔG = 0

1st Law

Energy can be transferred and transformed but no destroyed or created

2nd Law

Energy that is transferred and transformed increases the entropy of the universe

Free Energy Calculations

G(final)- G(inital)

Enzyme activity

Competitive Inhibition

Normal binding

Noncompetitive Inhibition

Allosteric Regulation

Cooperatiivity

one substrate stabilizes enzyme to help subunits lock on enzyme.

Feedback Inhibition

Initial Substrate

End product(inhibits pathway)

Can be inhibitor or activator

Binds at one protein site and affects function of other sites

Can stimulate or inhibit enzyme activity

Energy input needed to start

1, 3 Biphosphate glycerate

3 Phosphate glycerate

2 ATP is formed due to the extra phosphate group being transferred to ADP to form ATP

2 Phosphate glycerate

2 phosphoenol-pyruvate (PEP)

2 ATP is formed by the extra phosphate group on PEP being used with 2ADP to from 2 ATP

Floating topic

DNA Structure

Chargaff's Rule

Watson and Crick Experiments

Double Helix

antiparallel strans

Number of Adenine = Number of Thymine

Number of Cytosine = Number of Guanine

Hershey and Chase experiment

Bacteriophage

Phages or viruses that infect bacteria. They are made of DNA and proteins.

Lytic Cycle

The bacteriophages inject DNA to the bacteria so they make bacteriophages. The protein stay outside of the cell.

inject DNA into host

protein stays in cell

host grows bacteriophage parts and assembles in host cell

Cell bursts open

grown in 32 P

DNA is grown in Phosphorous because DNA has a phosphate group. DNA was found in the pellet.

grown in 35S

Sulfur for proteins because Proteins have sulfur. The protein was found in the supernatant fluid.

blended then centrifuged to see which was radioactive

DNA in 32P was radioactive not protein in 35S

DNA carried genes not protein

Hallmarks

Speed

E. Coli has 5 billion bases are copied at 2000 nucleotides per second.

Accuracy

Processivity

sliding clamp and polymerases

Messleson and Stahl Experiment

Proved Semi-conservative Model of Replication

Disproved Conservative and dispersive models.

Bacteria grown in N15

Bacteria moved to N14

centrifuged in CsCl

First Replication

Second Replication

Band in middle and top

DNA in less dense and dense area

Band in middle

Dense DNA in middle

Origin of Replication

Helicase

Separates 2 DNA strands to form a replication bubble. It unwinds the double helix at replication forks.

Single Stranded Proteins

Keeps DNA single stranded. It binds and stabilizes a single strand DNA.

Topoisomerase

It relieves overwinding by breaking, swiveling, rejoining DNA

Primase

Synthesize RNA primers on 5' end to 3' end for the Okazaki strand

DNA Polymerase 3

They add complementary bases to DNA and they add nucleotides on the 3' end (5'-> 3'). They need an RNA primer and need a sliding clamp.

sliding clamp

DNA Polymerase 1

removes RNA primer and replaces it with the DNA nucleotides

DNA ligase

It seals gaps in nucleotide with phoshodiester linkage. It joines 3' end of the DNA that replaces primer to rest of the leading strand and joins Okazaki fragments of lagging strand.

Eukaryotic Cell

long DNA molecule

Multiple Replication bubbles

speeds up replication

E. Coli Bacteria Cell

Circular DNA

1 ORI

Fredrick Griffith Experiment

In 1928, he wanted to create a vaccine for pneumonia

R strain and S strain

S strain has a smooth capsule and is pathogenic while R strain was nonpathogenic and had no capsule.

S strain injected rats died

R strain injected rates survived

Heat killed S strain with R strain injected rates died.

Something from the S had to be transferred into the R, making the bacteria lethal. Leading to the idea of transformation Bacteria can take up DNA from its environment

Bacteria Transformation

. Something from the S had to be transfered into the R, making the bacteria lethal . Leading to the idea of transformation . Bacteria can take up DNA from its environment

Bacteria taking DNA from environment

. Something from the S had to be transfered into the R, making the bacteria lethal . Leading to the idea of transformation . Bacteria can take up DNA from its environment

Lagging Strand Synthesis

Okazaki fragments

Floating topic

Transcription

Eukaryote Characteristics

Transcription occurs in the nucleus

TATA box

The TATA box is a DNA sequence (5'-TATAAA-3') within the core promoter region where general transcription factor proteins can bind.

5' Cap

G-P-P-P

RNA Processing

RNA Splicing

Removal of Introns

Exons are put together forming mRNA

Alternate Splicing

Used to make different proteins

Poly-A Tail

Formed by Poly-A Polymerase

Uses RNA Polymerase II

Forms Pre mRNA, snRNA, microRNA

Prokaryote Characteristics

Occurs in Cytoplasm

Transcription and Translation are coupled since they both occur in the cytoplasm

RNA Polymerase

Binds to promoter

Forms final mRNA

Shared Characteristics

- = upstream, + = downstream

Transcription template strand (3' - 5')

Transcription start site - Downstream (+1)

Unwinds the DNA and elongates the mRNA (5'-3') - Direction of transcription

RNA transcript is released and polymerase detaches from DNA

Central Dogma of Biology

DNA

mRNA

Protein

Translation

Prokaryotes

Occurs in cytoplasm

A small ribosomal unit attaches to Shine-Delgarno sequence

tRNA carrying amino acid formyl-Methionine (f-Met) attaches to start codon AUG

Large ribosomal unit attaches to mRNA consisting of A site (entry), P site (attaching) and E site (exit)

Another tRNA arrives at the A site carrying another amino acid and attaches to next codon following AUG

The second tRNA moves to P site and the amino acid of the first tRNA attaches while the first tRNA moves to E site

A new tRNA arrives at the A site with and moves to the P site attaching a new amino acid, forming a polypeptide chain

Elongation occurs until a stop codon (UAG, UAA or UGA) is reached

A release factor binds to the stop codon at the A site and acts a cleavage releasing the polypeptide from the last tRNA

The polypeptide released undergoes a modification process in which it is folded into a mature protein structure and translocated via mitochondria, ER lumen, plasma membrane, or lysosome.

The small and large ribosomal unit dismantles and awaits the next translation mRNA sequence

Eukaryotes

Occurs in cytoplasm consist of 5' cap (nucleotide Guanine) 3' poly A tail (100-250 Adenine nucleotides)

A small ribosomal unit attaches to 5'cap

tRNA carrying amino acid Methionine attaches to start codon AUG

Large ribosomal unit attaches to mRNA consisting of A site (entry), P site (attaching) and E site (exit)

Regulation of Gene Expression

Mutations

Nonsense

change in amino acid

3' TACTTCAAACCGATT 5'
5' ATGAAGTTTGGCTAA 3'

5' AUGAAGUUUGGCUAA 3'

Met- Lys- Phe- Gly- Stop

3' TACATCAAACCGATT 5'
5' ATGTAGTTTGGCTAA 3'

5' AUGUAGUUUGGcUAA 3'

Met- Stop

The change in DNA resulted in a stop codon so the rest of the mRNA is no translated

change in DNA

Frameshift

Insertion or deletion

inserts or deletes one or two nucleotides but never three

change in amino acid

change in DNA

3' TACTTCAAACCGATT 5'
5' ATGAAGTTTGGCTAA 3'

5' AUGAAGUUUGGCUAA 3'

Met- Lys- Phe- Gly- Stop

3' TACTTAGCAAACCGATT 5'
5' ATGAATCGTTTGGCTAA 3'

5' AUG AAU CGU UUG GCU AA 3'

Met- Asn- Arg- Leu- ... 3'

This translation is shifted due to the addition of the two nucleotides. The entire sequence is now read differently.

Missense

3' TACTTCAAACCGATT 5'
5' ATGAAGTTTGGCTAA 3'

5' AUGAAGUUUGGCUAA 3'

Met- Lys- Phe- Gly- Stop

Amino acid changed from Gly to Ser

3' TACTTCAAACCAATT 5'
5' ATGAAGTTTGGTTAA 3'

5' AUGAAGUUUGGAUAA 3'

Met- Lys- Phe- Ser - Stop

change in amino acid

change in DNA

Silent

change in DNA

no change in amino acid

3' TACTTCAAACCGATT 5'
5' ATGAAGTTTGGCTAA 3'

5' AUGAAGUUUGGCUAA 3'

Met- Lys- Phe- Gly- Stop

3' TACTTCAAACCAATT 5'
5' ATGAAGTTTGGTTAA 3'

Subtopic

Met- Lys- Phe- Gly- Stop

There's no change to the amino acid

The original G is replaced with A causing a mutation

Proofreading

exonucleolease function

nucleotide excision repair

1. Enzymes detects and
repairs damaged DNA

2. Nuclease enzyme cuts damaged DNA
at two points and removes it

3. Repair synthesis occurs and DNA poly fills missing nucleotides using undamaged template strand

4. DNA ligase seals the end of the new
DNA with the old DNA

Chemical bonds, Cell Structures, and Functions

Cell Evolution

Macromolecules

Chemical Bonds

Miller and Urey Experiment

formation of protein and nucleic acid

Protocell

Oparin’s bubble hypothesis: Simples organic molecules→ complex organic molecules

Mitochondrion Prokaryotic

Mitochondria

Cyanobacterial Prokaryotic

Chloroplast

PLANT CELL

Cell Wall

Central Vacuole

Plasmodesmata Channels

Cell Signaling

Sending Signals using Signals/Ligands and Receptors

Physical Contact

Second Messenger: cAMP

AMP

Triggers Action Potential

depends on signal/ligand concentration (neurotransmitters)

Autophosphorylation

6 ATP-> 6 ADP + 6 Pi

Adenylyl Cyclase activated

ATP

Cellular Respiration

1)Glycolysis

2)Pyruvate Oxidation

3)Kreb Cylce

4)Oxidative Phosphorylation

Cell Membranes and Selectively Permeable Membranes

Plasma Membrane

Transport Across Membranes

Action Potential In A Neuron

Step 1 - Resting Phase

Metabolism

Metabolic pathways

Forms of Energy

Thermodynamics

Enzyme activity

Energy input needed to start

1, 3 Biphosphate glycerate

3 Phosphate glycerate

Floating topic

DNA Structure

Chargaff's Rule

Hershey and Chase experiment

Hallmarks

Messleson and Stahl Experiment

Origin of Replication

Fredrick Griffith Experiment

Lagging Strand Synthesis

Okazaki fragments

Floating topic

Transcription

Eukaryote Characteristics

Prokaryote Characteristics

Shared Characteristics

Central Dogma of Biology

DNA

Translation

Prokaryotes

Eukaryotes

Regulation of Gene Expression

Mutations

Proofreading

RNA processing