Chemical bonds, Cell Structures, and Functions

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Regulation of Gene Expression

RNA processing

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

Mutations

Silent

no change in amino acid

The original G is replaced with A causing a mutation

Subtopic

There's no change to the amino acid

Missense

3' TACTTCAAACCAATT 5' 5' ATGAAGTTTGGTTAA 3'

5' AUGAAGUUUGGAUAA 3'

Met- Lys- Phe- Ser - Stop

Amino acid changed from Gly to Ser

Frameshift

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.

Insertion or deletion

inserts or deletes one or two nucleotides but never three

Nonsense

change in DNA

3' TACTTCAAACCGATT 5' 5' ATGAAGTTTGGCTAA 3'

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

5' AUGAAGUUUGGCUAA 3'

Met- Lys- Phe- Gly- Stop

change in amino acid

Translation

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

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

Central Dogma of Biology

DNA

mRNA

Protein

Transcription

Shared Characteristics

RNA transcript is released and polymerase detaches from DNA

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

Transcription start site - Downstream (+1)

Transcription template strand (3' - 5')

- = upstream, + = downstream

Prokaryote Characteristics

RNA Polymerase

Binds to promoter

Forms final mRNA

Occurs in Cytoplasm

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

Eukaryote Characteristics

Uses RNA Polymerase II

Forms Pre mRNA, snRNA, microRNA

Poly-A Tail

Formed by Poly-A Polymerase

RNA Processing

RNA Splicing

Alternate Splicing

Used to make different proteins

Removal of Introns

Exons are put together forming mRNA

5' Cap

G-P-P-P

TATA box

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

Transcription occurs in the nucleus

Lagging Strand Synthesis

Okazaki fragments

DNA Structure

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.

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

R strain injected rates survived

S strain injected rats died

Origin of Replication

E. Coli Bacteria Cell

Circular DNA

1 ORI

Eukaryotic Cell

long DNA molecule

Multiple Replication bubbles

speeds up 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.

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.

sliding clamp

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

Band in middle

Dense DNA in middle

Second Replication

Band in middle and top

DNA in less dense and dense area

Hallmarks

Speed

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

Accuracy

Processivity

sliding clamp and polymerases

Hershey and Chase experiment

Bacteriophage

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

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

grown in 32 P

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

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

Chargaff's Rule

Number of Adenine = Number of Thymine

Number of Cytosine = Number of Guanine

Watson and Crick Experiments

Double Helix

antiparallel strans

Floating topic

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

2 Pyruvates

Energy input needed to start

Metabolism

Enzyme activity

Allosteric Regulation

Can be inhibitor or activator

Can stimulate or inhibit enzyme activity

Binds at one protein site and affects function of other sites

Feedback Inhibition

Initial Substrate

A

B

C

D

End product(inhibits pathway)

Cooperatiivity

one substrate stabilizes enzyme to help subunits lock on enzyme.

Noncompetitive Inhibition

Normal binding

Competitive Inhibition

Thermodynamics

Free Energy Calculations

G(final)- G(inital)

2nd Law

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

1st Law

Energy can be transferred and transformed but no destroyed or created

System

Gibbs Free Energy

ΔG = 0

Endergonic

energy input needed

non-spontaneous

ΔG > 0

Exergonic

energy released

spontaneous reaction

ΔG < 0

△G= △H-T△S

S= entropy (measure of temp)

T= Temperature (STP 273K)

H= enthlapy(potential of system)

H = G + TS

Closed

Open

Surroundings

Universe

Forms of Energy

Potential energy

Electrons on outer shell have the highest PT

chemical energy in food

due to location or position

Stored energy

Kinetic energy

Light energy

Thermal energy

Motion

Metabolic pathways

Anabolic Pathway

Simple molecules

Polymerzation

Biosynthetic Pathways

Photosynthesis

6CO2 + 6H20 + light energy

Simple to complex

6 O2

Glucose

Catabolic Pathway

Complex molecule

Simple molecule

Cellular Respriation

Glucose + 6 O2

Energy into the system

6 H2O

6 Carbon Dioxide

Starting molecule(A)

Adding an enzyme can catalyze a reaction.

B(intermediate)

C(intermediate)

D(end product)

Action Potential In A Neuron

Step 1 - Resting Phase

The activation gates on the Na+ and K+ channels

are closed, and the membrane’s resting potential is maintained.

Step 2 - Depolarization

A stimulus opens the

activation gates on some Na+ channels. Na+

influx through those channels depolarizes the

membrane. If the depolarization reaches the

threshold, it triggers an action potential.

Step 3 - Rising Phase

Depolarization opens the activation

gates on most Na+ channels, while the

K+ channels’ activation gates remain

closed. Na+ influx makes the inside of

the membrane positive with respect

to the outside.

Step 4 - Falling Phase

The inactivation gates on

most Na+ channels close,

blocking Na+ influx. The

activation gates on most

K+ channels open,

permitting K+ efflux

which again makes

the inside of the cell

negative.

Step 5 - Undershoot

Both gates of the Na+ channels

are closed, but the activation gates on some K+

channels are still open. As these gates close on

most K+ channels, and the inactivation gates

open on Na+ channels, the membrane returns to

its resting state.

Cell Membranes and Selectively Permeable Membranes

Transport Across Membranes

Active Transport

Bulk Transport

Receptor-Mediated Endocytosis

Pinocytosis

Phagocytosis

Cotransport

Coupled Transport by a

Membrane Protein

-Occurs when active transport of a solute indirectly drives

transport of other substances

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

Electrogenic Pumps

A transport protein that generates voltage across a

membrane – membrane potential

(-50 to -200 mV)

Help store energy that can be used for cellular work

Proton Pump

Sodium-Potassium Pump

3 Na+ Out / 2 K+ In

Passive Transport

Ion Channels

Ungated

Always Open

Gated

Voltage-Gated

Open and close in response to changes in membrane potential

Ligand-Gated

Open and close when a neurotransmitter binds to channel

Stretch-Gated

Sense-Stretch, Open when membrane is mechanically deformed

Facilitated Diffusion

Carrier Proteins

Channel Proteins

Osmosis

Aquaporins

Hypotonic Solution

Plant Cells - Turgid (Normal)

Animal Cells - Lysed

Tonicity

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

Hypertonic Solution

Plant Cells - Plasmolyzed

Animal Cells - Shriveled

Isotonic Solution

Plant Cells - Flaccid

Animal Cells - Normal

Diffusion

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

Plasma Membrane

Selective Permeability Of Plasma Membrane

Intermediate Permeability

Large, Uncharged Polar Molecules (Glucose and Sucrose)

Small, Uncharged Polar Molecules (H2O, Glycerol)

High Permeability

Small Nonpolar Molecules (O2, CO2, N2)

Low Permeability

Ions (Cl-, K+, Na+)

Functions Of Membrane Proteins

Transport

Attachment to the cytoskeleton and extracellular matrix (ECM)

Intercellular Joining

Cell-Cell Recognition

Signal Transduction

Enzymatic Activity

Fluidity Of Plasma Membrane

Viscous

Saturated hydrocarbon tails

Fluid

Unsaturated hydrocarbon tails with kinks

Phospholipid Bilayer

Hydrophobic tail

Hydrophilic Head

Cellular Respiration

Glucose + Oxygen -> Carbon Dioxide + Water + Energy

C6H1206 + 6O2 -> 6CO2 + 6H2O + ATP

4)Oxidative Phosphorylation

Occurs in mitochondria

OXIDATIVE PHOSPHORYLATION used for ATP production

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

Chemiosmosis

ATP Synthase

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

3)Kreb Cylce

Occurs in mitochondria matrix

SUBSTRATE LEVEL OXIDATION for the production of ATP

Acetyl CoA

Citrate

Isocitrate

a-Ketoglurate

Succinyl CoA

Succinate

Fumurate

Malatate

Oxaloacetate

2)Pyruvate Oxidation

Occurs in mitochondria matrix.

Pyruvate + coA

Acetyl CoA

1)Glycolysis

Occurs in cytosol

SUBSTRATE LEVEL OXIDATION to produce ATP.

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

DHAP (later forms G3P)

Aldolase

G3P

2)Energy Payoff Phase

4 ATP FORMED

2NAD+ -> 2NADH

Adenylyl Cyclase activated

ATP

Autophosphorylation

6 ATP-> 6 ADP + 6 Pi

Triggers Action Potential

depends on signal/ligand concentration (neurotransmitters)

Second Messenger: cAMP

AMP

Cell Signaling

Physical Contact

Animal Cell: Gap Junction

Plant Cell: Plasmodesmata

Sending Signals using Signals/Ligands and Receptors

Local Signaling

Long Distance Signaling

Receptors

Membrane Receptor

Ion Channel Receptor

Ligand Gated Ion Channel

Tyrosine Kinase Receptor

2 polypeptide dimers (protein kinase)

Tyrosine dimers

G Protein Linked Receptors

Phosphatase for GDP and Pi

GTP binds to GPCR

Signals

Phosphorylation Cascade

Phosphatase

Enzyme catalyzes removable Pi from protein with hydrolysis

Protein Kinase

enzyme catalyzes Pi from ATP to proteins

Activiation of Cellular Response

Amplification effect to be efficient and fast

Intercellular Receptor

Nonpolar signal

Signal Transduction Pathway

Reception

Transduction

ligand or signal is bonded to membrane receptor

PLANT CELL

Plasmodesmata Channels

controls flow of water out of cell

Central Vacuole

cell sap with inorganic ions

stores water and regulates turgor pressure

Cell Wall

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

Cyanobacterial Prokaryotic

Photosynthetic prokaryotic

• makes 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

Mitochondrion Prokaryotic

Oxygen-using nonphotosynthetic prokaryotic

• they are obligate aerobes prokaryotic

Mitochondria

• double membrane
• has its own DNA and ribosomes
• is inherited maternally
• performs ATP synthesis and cellular respiration for energy

ATP Synthesis and Cellular Repiration

EUKARYOTIC CELL

Plasma membrane

permeable lipid bilayer and allows things into and out the cell

has protein and lipids in the bilayer; phospholipids

permeable lipid bilayer and allows things into and out the cell

Endoplasmic Reticulum

Rough ER

bound ribosomes; distribute vesticles; secrete glycoprotein

Smooth Er

synthesize lipids; metabolize carbs

Nucleus

nuclear membrane

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

nucleolus

ribosomes produced; rRNA transcribed

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

Vacuoles

Contractile Vacuole

pumps water out of cell

Food vacuole

Golgi Apparatus

packaging proteins

Cis Face

revieves vesicles from ER

Trans Face

releases vesible after altering it

lysosomes

low pH; has enzymes

phagocytosis

autophagy

peroxisomes

metabolized H2O2-> H2O

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

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 inheritance
• Ribozyme (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 cell
• Gas vacuole - to control buoyancy
• Ribosome - protein production
• Flagella - transportation 
• Endospore - protects chromosomes from harsh environment 
• Inclusion body - storage for glycogen
• Nucleoid - area of genetic material and has chromosome
• Cell wall - peptidoglycan; is modified sugar and amino acid; D enantiomer
• Periplasmic space - oxidation of proteins
• Capsule and slime layer - protects cells from environment
• Fimbriae and Pili - to reproduce
• Nutrition :
• Autotroph
• Photoautotroph: light
• Chemoautotroph: inorganic compounds 
• Heterotroph
• Photoheteroph: light
• Chemoheterotroph: organic compounds 
• 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

Nutrition

Heterotroph

Photoheteroph

Chemoheterotroph

organic compounds

Autotroph

Photoautotroph

light

Chemoautotroph

inorganic compounds

Endospores

protects chromosomes from harsh environment

Movement

flagella

cell wall

provides structure to cell and determines what enters or leaves cell

Metabolism of Oxygen

Facultative Anaerobes

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

Obligate Anaerobes

• the cell is poisoned by oxygen; fermentation anaerobic respiration

Obligate Aerobes

require oxygen for cell respiration

Prokaryotic Domains

Bacteria

• they have circular chromosomes
• they can't live in temperatures over 100 degrees Celsius
• they have peptidoglycan in their cell wall
• they don't have a nuclear envelope
• they don't have membrane-bound organelles

Archaea

They are extremophiles, which are archaea that live in extreme environments.

• Archaea lipids are branched and have an ether bond
• they have circular chromosomes
• some can live in temperatures over 100 degrees Celsius
• they have no peptidoglycan in their cell wall
• they don't have a nuclear envelope
• they don't have membrane-bound organelles

Extreme Thermophile

• they live in very hot environments.

Extreme Halophile

live in highly saline environment

Methanogens

• live in swamps and marches
• they produce methane as waste
• they are strict anaerobes ( oxygen is toxic )

ENDOSYMBIOSIS SYSTEM

Host Cell

A cell with a nucleus and Endoplasmic Reticulum.

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

Chemical bonds, Cell Structures, and Functions

Chemical Bonds

Ionic Bond

to obtain a full octet by exchanging e-

Positive

Negative

Hydrogen Bond

partial + attraction

Intermolecular interaction

Covalent Bond

Polar Covalent

e- shared unequally

Hydrophilic

Sharing of e-

Non-polar covalent

Hydrophobic

e- shared equally

Macromolecules

Nucleic Acid

Nucleotides

Nitrogenous Base

Cytosine-Guanine

Adenine-Thymine or Adenine-Uracil (RNA)

Phosphate Group

Deoxyribose or Ribose (RNA) Sugar

Lipids

Glycerol/fatty acids

Trans Fats

Ex: margarine (very processed)

Unsaturated Fats

Ex: butter (solid at Room temperature)

Saturated Fats

Ex: olive oil (liquid at Room temperature)

Proteins

Amino Acids

Side Chain (R Group)

Non-Polar

Ex: CH

Polar

Ex: OH

Basic

Positive Charged R Group

Acidic

Negatively Charged R group

Main Chain

Carboxyl Group

Amino Group

Carbohydrates

Monosaccharides

Polymers - Disaccharides and Polysaccharides

Cell Evolution