Biology 311C

Cell Structures

Eukaryotic Cells

Organelles

Genetic Material:
DNA

stores information

Ribosomes

Bound Ribosomes:
make proteins for membranes
or secretion

Free Ribosomes:
make enzymes & catalyze
sugar breakdown

Vacuoles

Food Vacuole:
cell engulfs food or other particles

Organelles
(membrane bound)

Nucleus

Chromatin:
DNA & protein of chromosomes

Nuclear Envelope:
double membrane

Nuclear Pores:
transport molecules
in & out nucleus

Nucleolus:
site of rRNA

Endoplasmic Reticulum (ER)

Smooth ER:
-lack ribosomes
-synthesize lipids, metabolize
carbohydrates

Rough ER:
-studded w/ ribosomes
-secrete glycoproteins, distributes
transport vesicles
-membrane factory

Golgi Apparatus

Cis Face:
receives cargo from ER

Trans Face:
releases cargo after making changes

Mitochondria:
-endosymbiont
-site of ATP reactions

Double Membrane:
-inner & outer
-inner folded into cristae
-inbetween: intermembrane space

Matrix
-space inside
-steps of cellular respiration
in mitochondrial matrix DNA
-free ribosomes

Peroxisome:
-endosymbiont
-single membrane
-packed w/ enzymes
-detoxify
-hydrogen peroxide to water

Lysosome
(animal cell only)

enzymes inside hydrolyze
biomolecules

Autophagy:
recycles cell's organelles

part of phagocytosis

Chloroplasts
(plant cell only)
-endosymbiont
-site of photosynthesis

Double Membrane
-inner & outer

Thylakoids:
-membranous sacs
-stack = granum

Stroma:
-internal fluid
-has DNA &
ribosomes

Central Vacuole
-plants only
-stores inorganic ions
-lots of water

Cytoskeleton

Microtubules

organelle movement

Centrosome
(animal cell only)

where microtubules
grow out of

Cilia & Flagella:
cell movement

Microfilament

muscle contractions

Amoeboid Movement:
crawling of a cell

cytoplasm movement

Intermediate
Filament

anchor organelles

cell shape
maintenance

nuclear lamina

Cell Wall
-plant cell only
-primary
-secondary
(multiple layers)

Extracellular Matrix
-outside cell
-various proteins

Integrins:
proteins in membrane
that connect ECM to
inside the cell

Cell Junctions

Plant Cell

Plasmodesmata:
-connect neighboring cells
-particles travel freely

Animal Cell

Tight Junctions:
-tightly packed membranes
-no fluid or substance can cross

Desmosomes:
-connection between cells
-some substance can pass through

Gap junctions:
-everything moves
between cells

Prokaryotic Cells
-includes bacteria & archaea domain

Endospores
(not all)

remain viable in
harsh conditions

-original cell copies chromosomes
-surrounds it multiple layers of cell wall

water is removed

metabolism halts

can be rehydrated and viable

Cell Wall:
shapes cell
protection

made of peptidoglycan
in bacteria

Plasma Membrane:
selectively permeable barrier

Organelles
(not membrane bound)

Gas Vacuole:
float in aquatic environments

Nucleoid:
location of DNA

Periplasmic Space:
hydrolytic enzymes

Inclusion Bodies:
storge of carbon, phosphate, etc.

Contractile Vacuole:
pump excess water out
of cell

Chemical Bonds

Polar Covalent

Pull between the atoms is unequal (electronegativity difference)

Dipole-Dipole

The force between + end of a molecule (polar) and a - end of a molecule (polar)

Hydrogen Bonds

Is a bond between a hydrogen atom and a very electronegative atom

Van der Waals

When two non polar atoms interact

Ionic Bonds

Bond that includes to oppositely charged ions, + -

Non-Polar Covalent

Bond when the electrons are shared equally, electronegativity is equal

Disulfide Bonds

Proteins and R Groups

Protein Structures

Primary

Amino acids interacting through peptide bonds

Secondary

Main chain groups interacting through Hydrogen bonds

Tertiary

R groups held together by disulfide bonds, hydrogen bonds, ionic bonds, and non-polar hydrophobic interactions

Types

Nonpolar Covalent

CH, ring, H

Polar Covalent

OH, NH, CO, SH

Acidic

Negative (-) Charge

Basic

Positive (+) Charge

Quaternary

Macromolecules

Lipids

-store energy

-cell protection

chemical messengers

CHO

Triglycerides

Phospolipids

Structure

contain four fused rings

Unsaturated

Saturated

Solid at room temperature

hydrocarbon chains of fatty acids are highly packed together and held by hydrophobic interactions

Liquid at room temperature

hydrocarbon chains of fatty acids are not tightly packed together (cis double bonding causes bending)

hydrophilic head, hydrophobic tail amphipathic= having hydrophobic and hydrophilic parts

Carbohydrates

CHO

-provide energy

-spare protein

Monosaccharides

Glucose

C6H12O6

-alpha=carboxyl group at carbon 1 is on top -beta=carboxyl group at carbon 1 is on bottom

Polysaccharides

glycogen (animals), starch (plants),

cellulose (plants), chitin (insects)

Disaccharides

formed when a dehydration reaction joins 2 monosaccharides creating a glycosidic linkage

Nucleic Acids

CHONP

storage of genetic code

nucleotide

DNA

double helix

A and T, C and G

phosphate group, nitrogenous base, pentose sugar (deoxyribose)

RNA

single strand

A and U, C and G

nitrogenous base, pentose sugar (ribose)

Cell Respiration and Fermentation

Glycolysis

Step 1: Hexokinase transfers
phosphate group
from ATP to glucose.
The charge on the
phosphate also traps
the sugar in the cell.

Step 2: G6P becomes Fructose 6 Phosphate

Step 3: Phosphofructokinase
transfers a phosphate
group from ATP to the
opposite end of the
sugar, investing a second
molecule of ATP. Fructose
1,6 bisphosphate is created.

Energy investment:
2 ATP

Energy Output:
4 ATP
2 NADH
2 Pyruvate + 2 H2O

Net Output:
2 ATP
2 NADH
2 Pyruvate + 2 H2O

Happens in the cytoplasm outside of the mitochondria

Pyruvate Oxidation

Pyruvate from Glycolysis is oxidized

Electrons from oxidation are transferred to NAD+ to form NADH

Acetyl Coenzyme A is formed.

Input:
2 Pyruvates, 2 NAD+, 2 CoA

Energy Output:
Acetyl CoA, 2 CO2, 2 NADH

Net Output:
Acetyl CoA, 2 CO2, 2 NADH

Oxygen is not present

Lactic Acid Fermentation

Pyruvate is reduced to form lactate

NAD+ is created and recycled through glycolysis

No CO2 is created

Happens in the cytoplasm

Energy Input: 2 pyruvate, 2 NADH

Energy Output (Net is same):
Lactate, 2 NAD+

Alcohol Fermentation

Happens in the cytoplasm

Energy Input: 2 pyruvate, 2 NADH

Energy Output (Net is same):
Ethanol, 2 NAD+

Pyruvate forms acetaldehyde and releases 2 CO2 in the process

Acetaldehyde is reduced to form ethanol

NADH electrons are reduced creating NAD+

NAD+ goes through glycolysis again

Happens in the matrix of the mitochondria

Oxygen Present

Citric Acid Cycle (Kreb's)

Acetyl CoA interacts with Oxaloacetate to form Citrate.

Citrate becomes isocitrate

Isocitrate oxidizes and NAD+ is reduced to form NADH

CO2 releases when isocitrate is oxidized

Cycle happens twice and NADH and FADH are created

Energy input:
2 Acetyl CoA molecules, 6 NADH, 2FAD

Energy Output:
6NADH, 2 ATP, 2 FADH2, 2 CO2

Net Output:
6NADH, 2 ATP, 2 FADH2, 2 CO2

Happens in the mitochondrial matrix

Fermentation

Oxidative Phosphorylation

Delivery of Electrons by NADH and FADH2

Electron Transport and Proton Pumping

Splitting of Oxygen to form Water

H+ Gradient goes through ATP synthase, creating ATP through oxidative phosphorylation

Energy Input:
10 NADH, 2
FADH2,
*oxygen is the final electron acceptor

Goes through electron transport chain

Energy Output:
26-28 ATP

Net Output:
26-28 ATP

Happens in the proteins in the inner membrane

Plasma Membranes

Phospholipid Bilayer

hydrophilic head
-on outside and inside of cell
hydrophobic tail
-face each other
-middle part of bilayer

Membrane Fluidity

specific phase transition temperature
-above, fluid
-below, rigid

unsaturated hydrocarbon
-tail kinks
-more fluidity
saturated hydrocarbon
-no tail kinks
-more viscous

cholesterol
-reduces movement at
moderate temps
-increases movement at
low temps
-ability to change amount
in membrane to environment

Membrane Proteins

N-terminus
-amino
c-terminus
-carboxyl

Protein Transport

Passive Transport
-no energy used
-with concentration gradient

Osmosis
-diffusion of free water

Aquaporin

Diffusion
-tendency for molecules to
evenly distribute across available
space

Ion Channels

Ungated
-always open

Gated
-open/close in response to stimuli

Stretch-gated
-when membrane
is mechanically deformed

Ligand-gated
-neurotransmitter binds

Voltage-gated
-response to changes in
membrane potential

Facilitated Diffusion
-passive transport aided by proteins
-spread evenly

Channel Protein
-corridor of channel

Carrier Protein
-undergo change in shape
-translocates solute

Active Transport
-uses energy
-against concentration gradient

Sodium-Potassium Pump

Electrogenic Pump
-transport protein that generates
voltage

Proton Pump

Cotransport
-coupled transport

H+/Surcose cotransporter
-active transport driven by
concentration gradient

Selective Permeability

Passes
-small, nonpolar molecules
-small, uncharged polar molecules

Doesn't pass
-large, uncharged polar molecules
-ions

Bulk Transport

Exocytosis
-release contents

Endocytosis
-take in contents

Phagocytosis
-take in food particle

Pinocytosis
-take in fluid

Receptor-Mediated Endocytosis
-solutes bind to receptor site
-form vesicle of bound molecules

Action Potential
-membrane charge flips

Resting State
-step 1
-Na+ and K+ channels
are closed

Depolarization
-step 2
-some Na+ channels
open

Rising Phase
-step 3
-most Na+ channels
open
-cell positive w/
respect to outside

Falling Phase
-step 4
-inactivation of Na+
channels
-K+ channels open
-cell negative again

Undershoot
-step 5
-Na+ closed
-some K+ open
-return to resting state

Metabolism

Catabolic Pathways

Pathways that release energy by breaking down complex molecules into simpler compounds.

Cellular Respiration

C6H12O6+6O2 ———-> 6CO2+6H2O+ Energy

Anabolic Pathways

Pathways that consume energy to build larger, complicated molecules from simpler ones.

Photosynthesis

6CO2+6H2O+Light—>C6H12O6+6O2

Potential Energy

Stored Energy

Example:
-Chemical

Kinetic Energy

The energy associated with the motion of molecules or objects

Examples:
-Thermal
-Light Energy

Thermodynamics

System- Matter within defined region of space

Closed system

Open system

Surroundings- Matter in the rest of the universe

First Law of Thermodynamics-
Energy can be transferred and transformed,
But it cannot be created or destroyed.

Second Law-Every energy transfer or transformation increases the entropy of the universe.

Free Energy

Free Energy Change -
The change in free energy (Delta G) during a chemical reaction is the difference between the free energy of the final state and the free energy of the initial state

Energy changes in chemical reactions

Exergonic

Endergonic

Gibbs Free Energy

Delta G>0
Cannot occur spontaneously. Endergonic Reaction

Delta G=0
A system is at equilibrium.
No change

Delta G<0
A reaction can occur spontaneously. Exergonic

Cell Signaling

-physical contact, local signaling, long distance signaling

membrane receptors (needs help from a second messenger)

G-protein linked receptor

1.) Signal molecule binds to GPRC, once bound, there is a slight alteration in the shape of GPCR which allows the G-protein to bind, this causes GDP to be replaced with GTP which now activates the G-protein

2.) This active G protein can activate a nearby enzyme

3.)nOnce the enzyme is activated, G protein removes the phosphate group from GTP and converts it back to GDP (G-protein has a phosphatase function), this inactivates G- protein

4.) The enzyme activated called Adenylyl cyclase converts ATP to cAMP

5.)cAMP (second messenger) activates other proteins until it leads to a cellular response

Tyrosine Kinase Receptor

1.) signal molecules binds to both receptors which then leads the receptors to bind forming a dimer

2.)Tyrosine is alone so ATP turns into ADP releasing a phosphate group

3.)There are 6 ATP so 6 phosphates and ADP from

4.)These phosphates bind to the 6 tyrosines which leads to cellular responses

Ion Channel Receptor

Ligand Gated Ion

1.) when the ligand attached itself to the receptor the channel opens and allows for specific ions to pass

2.) when the ligand is no longer attached to the receptor the channel remains closed and is inactive

Un-gated Ion Channel

the channel is always opened

signaling molecule (or signal or ligand) and receptor

Intracellular receptors (in cytoplasm and nucleus)

Steroid Hormone

1.) the steroid hormone aldosterone passed thought the plasma membrane (can only pass if it is non polar/ hydrophobic)

2.) aldosterone binds to receptor protein which activates it

3.) the hormone receptor complex enters the nucleus and binds to specific genes that starts the transcription of mRNA

4.) the mRNA is translated into a specific protein

Synaptic Signaling

1.) an action potential arrives, depolarizing the presynaptic membrane

2.) the depolarization open voltage- gated channels, triggering an influx of Ca^2+

3.) the elevated Ca^2+ concentration causes synaptic vesicles to fuse with presynaptic membrane, releasing neurotransmitter into the synaptic cleft

4.) the neurotransmitter binds to ligand-gated ion channels in teh postsynaptic membrane

Gene Expression

Transcription

Location

Prokaryotes:
cytoplasm

Eukaryotes:
nucleus

1. Start

First nucleotide
(+1)

DNA as template
(3'->5')

2. Initiation

RNA polymerases

Prokaryotes:
RNAP

Eukaryotes:
RNA polymerase II

Binds to promoter upstream
(before +1)

Doesn't need a primer

Makes a new strand
(5'->3')

3.Elongation

Transcription factors bind to DNA
(eukaryote only)

RNA polymerase binds
Unwinds DNA

RNA synthesis
(elongates transcript)

DNA reforms in double helix

4. Termination

Prokaryote
-RNA transcript released
-polymerase detaches from DNA

Eukaryotes
-sequence signal to cut
pre-mRNA (AAUAAA)
-release from DNA

RNA Processing
(in eukaryotes)

mRNA

5" End
-modified G nucleotide
-"5' Cap"

3' End
-poly A tail (1-200 A nucleotides)
-made by poly A polymerase

Help:
-exit from nucleus
-prevent degradation
-translation initation

RNA Splicing

Removal of introns

Joining of exons

Alternative Splicing

different combos of exons
are generated

introns help
removal of different ones

make different
proteins

Splicing by Spliceosomes

1. protein snRNA and other proteins
join to become a spliceosome

2. find intron and cut it, intron is recycled

3. join together exons

Translation and Gene Regulation

Translation

For Prokaryotes:
-Simply needs mRNA
-mRNA is already in the cytoplasm when it is created, and it stays in the cytoplasm for translation

mRNA contains code that will help with the formation of proteins
mRNA is made of nucleotides while proteins are made up of amino acids.

Codon chart utilized to show which set of three nucleotides (codons) is coded with which set of amino acids

mRNA in the cytoplasm attaches to free ribosomes:
Prokaryote: 70S ribosomes
Eukaryotes: 80S ribosomes

Aminoacyl-tRNA synthetase matches the correct tRNA with the correct amino acid.

tRNA anticodons bind to the corresponding mRNA codons. (Start codon is AUG)

tRNA first binds to the P site of the ribosome. Then another tRNA binds to the A site of the ribosome (in accordance to the codons on the mRNA) and the amino acid attached to the tRNA in the P site slides over to the tRNA on the A site. While this happens, the tRNA in the P site slides to the E (exit) site of the ribosome and the one in the A site slides to the P site. While this happens, a tRNA attaches itself to the A site. This process continues over and over until the stop codon on the mRNA is reached.

After a protein is created with all of the amino acid bonds, it has two different routes to be a part of the endomembrane system.

To organelles

Protein travels to mitochondria, chloroplast, peroxisomes, nucleus, or just stays in the cytoplasm

To Rough ER (bound ribosomes)

SRP (Signal-recognition particle) attaches to signal peptide

Travels to SRP receptor protein. SRP binds to a receptor protein in the ER membrane. SRP leaves and signal prptide is cleaved by an enzyme in the receptor protein complex.

Protein is released into the rough ER. Several carbohydrate groups are added by enzymes in the ER to the protein, creating a glycoprotein.

Protein travels through a vesicle to the cis Golgi then out of the golgi through the trans Golgi.

Protein then goes from the Golgi to either the plasma membrane, back to the ER, or it gets secreted outside of the cell.

For Eukaryotes:
-Needs mature mRNA
-Mature mRNA travels from nucleus to cytoplasm through nuclear pores.

Players in translation:
mRNA
tRNA
Ribosomes
Amino acids
Amino acyl tRNA synthetase
Peptidyl transferase
Initiation factors
Elongation factors
Release factor

Gene Regulation

In Eukaryocytes

Nucleosomes

Histones +proteins

8 histones in a histone core. Nucleosomes wrap around each histone twice and Linker DNA connects the nucleosomes

H1 Histone is the only one not a part of the nucleosome.

H2A H2B H3 and H4 make up the histone core (2 of each)

10-nm fiber
DNA winds around histones to form nucleosome “beads”
Nucleosomes are strung together like beads on a string by linker DNA

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

Metaphase chromosome
The looped domains coil further

Regulation can occur at the level of transcription

Transcription Factors

General:
factors bind to the promoter and regions near the promoter to bring about basal or background level of transcription.

Specific:
activators and repressors bind to distal control elements called enhancers and bring about increased level (activators) or low levels (repressors) of transcription.

Activators and repressors (proteins) are results of cell signaling and are created after transduction.

control elements

Proximal (close to promoter) control elements:
Sequences in DNA close to promoter
Bind general transcription factors

Distal (far from gene they control) control elements
Enhancers
Sequences in DNA upstream or downstream of gene
Maybe close to or far from the gene they control
Bind specific transcription factors (activators/repressors)

In Prokaryocytes

DNA Structure

Experiments

Where is the genetic material, DNA or proteins? - injected S. cells (pathogenic) and R.cells (nonpathogenic) into live mice. When the mice was injected with live S.cells, mixture of heat-Killed S cells and
living R cells the mice died. When injected with living R cells or heat -killed S cells the mice lived

A virus injects cells something to spread so what is being injected? -They infected bacteria with 35S (proteins) bacteriophages and another set of bacteria cells with bacteriophages with 32P (DNA). The bacteria and the bacteriophages were mixed in a tube, after some time they shook the tube to release the bacteriophages from bacterial surface. Then they centrifuged the bacterial cells and looked for the presence of radioactivity – in supernatant and in the pellet. The pellet was blue which meant that DNA was injected into the protein. DNA IS THE HEREDITY MATERIAL

Model of Replication- they showed that after switching bacteria from heavy to light nitrogen and allowing two rounds of replication, their DNA consisted of equal amounts of light and hybrid DNA. Demonstrated that DNA replicated semi-conservatively

The amount of Adenine equals the amount of Thymine. The amount of Guanine equals the amount of Cytosine

DNA is double-stranded, with complementary base pairing.

Replication

Eukaryotic- inside the nucleus prokaryotic- in cytoplasm

Initiation

At the origin of replication, an enzyme Helicase separates the two strands of DNA to form the replication bubble.

SSB or single stranded proteins keep the DNA single stranded. Another enzyme Topoisomerase helps relieve any strain caused by unwinding of the DNA.

Primase – makes RNA primers complementary to the DNA parent strand sequence

The sliding clamp binds to the 3' end, once this happens DNA polymerase lll will add nucleotides only to the 3’ end

Elongation

the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork. Only one primer is required, the strand is made in one direction 5’ to 3’

In forming the lagging strand, multiple RNA primers have to be laid down and then extended by DNA polymerase III to form short Okazaki fragments.

Another enzyme, DNA polymerase I removes the RNA and replaces it with DNA nucleotides.

Another enzyme called ligase seals any gaps by connecting nucleotides by phosphodiester linkages.

Termination

The 2 replication forks meet and are dismantled, the ends are joined by DNA ligase

2 daughter DNA molecules now have 1 parent strand and 1 new strand (semiconservative)

Protein Transport and Mutations

Destinations of Protein

Nucleus

Peroxisomes

Chloroplast

Mitochondria

Destinations in secretory

Back to the ER

Lysosomes

Membrane Protein

Secretion

Mutations

Mutations also known as mistakes

Can they be corrected? Yes

DNA Polymerase notices the mistakes , and corrects it.

Silent Mutations

Change in DNA= No Change in Amino Acid

Missense Mutations

Change in Change in DNA= Amino Acid Changed

Nonsense Mutations

Change in DNA= Stop Codon is made. Stopping the Sequence.

Frameshift mutations

Change in DNA= Reading Frame is changed