Nuclear envelope- double membrane enclosing the nucleolus

Lined in nuclear Lamina-
A netlike array of protein filaments that lines the inner surface of the nuclear envelope and helps maintain the shape of the nucleolus

Cytoplasm- surrounds the organelles

Consists of double layer of phospholipids with various proteins attached to or embedded in it

Hydrophobic parts are found in the interior of membrane

Hydrophilic regions are in contact with aqueous solutions on either side

Carbohydrate side chains attached to proteins on the outside of the cell that are embedded into the plasma membrane

Amphipathic

contains both hydrophobic and hydrophilic components

Phosphate Group head
and Lipid tail, connected by Glycerol

Presence of Cholesterol

Membrane Fluidity

Above Temp: crystalline phase, fluid, unsaturated hydrocarbons tails

Below Temp: gel phase, rigid, saturated hydrocarbon tails

Peripheral Proteins
- proteins located on the outside
of the plasma membrane

Transmembrane (Integral) Proteins
- proteins that are located within the plasma
membrane
- composed of alpha helices, N-terminus outside and C-Terminus inside cell

Different Functions of Membrane Proteins

Selective Permeability

- regulates cell movement, cell traffic, and inter/extracellular interactions

HIGH: small, nonpolar

MEDIUM:-HIGH: small, uncharged polar

MEDIUM-LOW: large, uncharged polar

LOW: ions

Passive Transport

- Type of transport that doesn't require ATP
- High to Low
- Down Concentration Gradient

Diffusion

- the movement of particles down the concentration gradient

Facilitated Diffusion

- The diffusion of water and other polar molecules with the help of a protein that has a hydrophilic interior channel (aquaporin)

Osomosis

- the movement of water down the concentration gradient from high to low to help establish equilibrium, or water balance

Isotonic:
- solute concentration same inside and outside the cell
- no net water movement

ANIMALS: Normal
PLANTS: Flaccid

Hypotonic:
- the solute concentration less than inside the cell
- water moves inside the cell

ANIMALS: Lysed
PLANTS: Turgid (Normal)

Hypertonic:
- the solute concentration greater than inside the cell
- water moves outside the cell

Singled-Celled eukaryotes have contractile vacuoles that push out unnecessary water

Active Transport

- Type of transport that REQUIRES ATP
- Low to High
- Against Concentration Gradient

Pumps

Sodium Potassium Pumps

- Ions bind to the proteins stimulating phosphorylation by a kinase using ATP
- 3 Na+ transported outside, 2 K+ transported inside

Proton Pumps

Electrogenic Groups

- Transmembrane protein that generates voltage across the membrane establishing membrane potential
- Helps store energy for cellular work

CoTransport

- The transport of multiple substances simultaneously
- Driven by concentration gradient
- EX: sucrose moving into the cell as H+ diffuses out

Bulk Transport

- Vesicles and ATP are used to move fluids, solutes, and molecules in and out of the cell

EXocytosis:
- EXiting a cell:

ENdocytosis:
ENtering a cell

Phagocytosis:
Large food particles enter the cell

Pinocytosis:
Dissolved fluids enter the cell

Receptor-Mediated Endocytosis:
Receptors deployed by the cells bind to specific particles and bring them to the cell

- Carries out metabolic processes
- Membranes have active sites and chemical receptors that carry out sequential steps

- Possess certain receptors that are fit to receive messages from signaling molecules
- Molecules binds to cytoplasmic proteins which have ends that are outside and inside the cell.

- Glycoproteins serve as ID tags which are recognized by certain proteins and receptors of membrane cells
- Short-Lived Connection

- Membranes cells hook together in junctions
- Long-Lived Connection

Animal Cells

Gap Junctions:
Intercellular transport and cell signalling/communication

Proteins Present:
connexin proteins
such as kinases

Tight Junctions:
these junctions form continuous seals with the help of a protein that keeps solutes and fluids from moving across cells

Proteins Present:
occludin, claudin, and accessory proteins

Desmosomes:
similar to tight junctions but not as tight allowing selective fluids and solutes to pass through

Proteins Present:
2 cadherins, DSG2, DSC2, and 3 cytoplasmic plaque proteins

Plant Cells

Plasmodesmata:
- connects membranes and cytoplasm of adjacent cells- intercellular transport and cell signaling/communication

Connects to the cytoskeleton's
microfilaments non-covalently

The connection to the ECM helps
cell perform inter/extracellular changes

Endoplasmic reticulum-network of membranous sacs and tubes; active in membrane synthesis and other

Rough ER-
ribosomes are attached

secretes proteins

transport vesicles move the protiens

membrane factory for the cell

Smooth ER

synthesis of lipids, metabolism of carbohydrates, detoxification of drugs and poisons, and storage of calcium ions

steroids are produced

Golgi apparatus- organelle active in synthesis. modification, sorting, and secretion of cell products

products of the ER are modified and stored then sent to other destinations

consists of flat membranous sacs, called cisternae, stacked together

cis face, same side, is located near ER

trans face, opposite side is located gives rise to vesicles that pinch off and travel to other sides

vesicles around the Golgi engage in the transfer of material

Lysosomes-digestive organelle where macromolecules are hydrolyzed

carry out intracellular digestion in a variety of circumstances

Cytoskeleton- reenforces cell shape; functions in cell movement; components are made of proteins

cell motility-changes in cell location and more limited movement of cell parts

motor proteins-
interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell

Structures and functions of Cytoskeleton

Microtubules

maintenance of cell shape, cell motility, chromosome movements in cell division; organelle movements

involved in the separation of chromosomes during cell division

grow out of centrosomes

Hollow rods constructed from a globular protein called tubulin, each tubulin protein is a dimer

made up of alpha-tubulin and beta-tubulin

can be disassembled and used to build microtubes somewhere else

grow in length by adding tubulin dimers

Microfilaments

Maintenance of cell shape; changes in cell shape; muscle contraction; cytoplasmic streaming (plant cells); cell motility, cell division (animal cells)^

form structural networks when certain proteins bind along the side of such a filament and allow a new filament to extend as a branch

strutural role to bear tension

thin solid rods

also called actin filaments because that are built from actintwisted chain double chain of actin subunits

use a motor proteins called myosin to cause contraction of muscle cells

Intermediate filaments

maintenance of cell shape; anchorage of nucleus and certain other organelles; formation of nuclear lamina

more permanent fixtures of cells, often disassembled and reassembled in various parts of cell

Mitochondrion- cellular respiration occurs and ATP is generated

Produces ATP which is energy that the cell uses

outer membrane is smooth, but the inner membrane is convoluted, with folding called cristae; there are two compartments

intermembrane space- between the inner and outer membranes

mitochondrial matrix-
compartment of the mitochondrion containing enzymes and substrates for the citric acid cycle, as well as ribosomes and DNA

1. Glycolysis
(Steps 1 and 3)

- occurs in the cytoplasm
- Energy Investment and Energy Pay Off Phases
- ATP formed with Substrate-Level Phosphorylation (sLP)

INPUTS
- 1 Glucose
- 2 NAD+
- 2 ATP

OUTPUTS
- 2 Pyruvate
- 2 NADH
- 4 ATP

2. Pyruvate Oxidation

- occurs from the cytosol to the Mitochondrial Matrix

INPUTS
- 2 Pyruvate
- 2 CoA
- 2NAD+

OUTPUTS
- 2 Acetyl CoA
- 2 NADH

3. Citric Acid Cycle
(steps 1 and 3)

- occurs in the Mitochondrial Matrix
- ATP formed with SLP

INPUTS
- 2 Acetyl CoA
- 6 NAD+
- 2 FAD

OUTPUTS
- 2 ATP
- 6 NADH
- 2 FADH2

- NADH: I, Q, III, Cyt C, and IV
- FADH2: II, Q, III, Cyt C, and IV
- Oxygen is the final electron acceptor

As electrons move across the complexes, H+ is pumped out into the intermembrane space establishing a proton gradient.

The proton gradient coming back into the organelle through ATP Synthase produces ATP. Gradient spins motor that attaches the inorganic phosphate to ADP to create ATP.

INPUTS
- O2
- 10 NADH
- 2 FADH2

OUTPUTS
- H2O
- 26-28 ATP

Microvilli- increase the cells surface area

Peroxisome-
organelle with various specialized metabolic functions; produces hydrogen peroxide as a by-product and then converts it to water

Flagellum-
motility structure present in some animal cells, composed of a cluster of microtubules within an extension of the plasma membrane

Centrosomes-
region where the cell's microtubules are initiated; contains a pair of centrioles

p

use DNA to make proteins

carry out protein synthesis

consists of a small and large subunit

build proteins in two cytoplasmic locales

Free ribosomes-
suspended in the cytosol

Bound ribosomes-
attached to the outside of the endoplasmic reticulum or nuclear envelope

proteins destined for insertion into membranes; packing certain organelles suck as lysosomes or for export from the cell

Endomembrane system-
membranes of this system are related either through direct physical continuity of transfer by vesicles

Vesicles-
a membranous sac in the cytoplasm

Vacuoles-
large vesicles, that have many different function, selective in which solutes to transport

Specific to animal cells as plants have cell walls

COMPONENTS

Collagen fibers embedded in a web of proteoglycan complexes
Proteoglycan Complexes:- hundreds of proteoglycan molecules attached non-covalently to a single long polysaccharide molecule

Fibronectin attaches the ECM to the integrins in the Plasma Membrane
- Integrins:: membrane proteins with two subunits
- Binds to the ECM on the outside and microfilaments on the inside
- Helps transmit signals

carbon skeletons (can vary in..)

length

branching

double bond position

presence of rings

Isomers-compounds that have the same
# of atoms of the same elements but
different structures and properties.

Structural Isomers (differing placement of
same atoms/elements)

Geometric Isomers

cis isomer: on the same side

trans isomer: on opposite sides

Enantiomers (mirror images: differ due to the presence of an asymmetric carbon bonded to 4 different groups)

Polymers

Synthesis of Polymers: condensation/dehydration reactions

Breakdown of POlymers: hydrolysis

Functional Groups-chemical groups that affect
function by being directly involved in chemical interactions.

Hydroxyl, Carbonyl, Carboxyl, Amino, Sulfhydryl, Phosphate, and Methyl group.

Carbohydrates serve as fuel and building material

Aldoses (CO group at the end)

Glucose

Alpha glucose=starch
Beta glucose=cellulose

Galactose

Ketoses (CO group on the inside)

Fructose

Monosaccharides

Polysaccharides: formed when 100
or more monosaccharides are bonded
together through glycosidic linkages.

Storage Polysaccharide (energy)
- glycogen (animals)
- starch (plants)
- dextran (bacteria)

Structure Polysaccharide
- cellulose (Beta glucose) (plant cell walls)
- chitin (exoskeleton of insects, cell walls of fungi)

Disaccharide Synthesis: Glucose + Fructose = Sucrose
(Glycosidic bond/linkage formed from dehydration synthesis)

Fats

Triacylglycerol/triglyceride

1 glycerol & 3 fatty acids

C3H5O3 (glycerol)

Palmitic Acid (3 fatty acids)

Saturated
- animal sources
- solid at room temperature
- NO double bonds

Unsaturated
- plant sources
- liquid at room temperature
- double bonds

cis (hydrogen on the same side)
causes molecule to have a bend

trans (hydrogen on opposite sides
-called trans fat)

Phospholipids

make up the phospholipid bilayer (made out of hydrocarbons), which contain non polar covalent bonds= hydrophobic

Steroids

contain 4 fused rings

found in animals

common component in membranes

ex: cholesterol

Primary Structure
- sequence of amino acids/polypeptide (main chain)

Covalent Bonds

Peptide Bond- the basic bond that links amino acids in all protein structures ( through dehydration synthesis)

Di-sulphide bond- formed by the coupling of two thiol (–SH) groups/the only covalent bond between R-groups (intramolecular)

Secondary Structure
- main chain turns and folds
- alpha helices (twists)
- beta pleated sheets (folds)
- intermolecular (between 2 or more structures)

Hydrogen Bond- interaction involving a hydrogen atom located between a pair of other atoms having a high affinity for electrons

Peptide Bond- the basic bond that links amino acids in all protein structures

Di-sulfide bond- formed by the coupling of two thiol (–SH) groups.

Tertiary Structure
- polypeptide folds into a 3D shape
through interaction of R-groups

Hydrophobic bonds- the tendency of nonpolar groups or molecules to aggregate in water solution.

Hydrogen Bonds- interaction involving a hydrogen atom located between a pair of other atoms having a high affinity for electrons

Ionic Bonds- type of linkage formed from the electrostatic attraction between oppositely charged ions in a chemical compound.

Van der Walls forces - the relatively weak attractive forces that act on neutral atoms and molecules and that arise because of the electric polarization induced in each of the particles by the presence of other particles.

Di-sulphide bonds- formed by the coupling of two thiol (–SH) groups.

R groups

covalent bonds

A covalent bond is formed when two atoms exchange one or more pairs of electrons.

ionic bonds

When an element takes an electron from another to finish an octet level, an ionic bond is created. relates to electro negative as well.

Acidic and Basic

Although acidic and basic groups are hydrophilic, they are joined by ionic bonds.

Ion dipole bonds

Electron-electron interactions between two neutral molecules with dipoles cause ion dipole forces.

between r-groups in an acid and water

nonpolar groups

CH

hydrophobic interactions will occur

polar groups

OH, NH, SH, CO

hydrogen bonds will form

Quaternary Structure
- tertiary chains coming together (structure
maintained by interchain interactions)

Hydrophobic bonds- the tendency of nonpolar groups or molecules to aggregate in water solution.

Hydrogen bonds- interaction involving a hydrogen atom located between a pair of other atoms having a high affinity for electrons

Ionic bonds- type of linkage formed from the electrostatic attraction between oppositely charged ions in a chemical compound.

Van der Walls forces- the relatively weak attractive forces that act on neutral atoms and molecules and that arise because of the electric polarization induced in each of the particles by the presence of other particles.

Di-sulphide bonds- formed by the coupling of two thiol (–SH) groups.

DNA (deoxyribonucleic acid)

provides own information for replication

directs synthesis for mRNA and controls protein synthesis

gene expression

translation (info from mRNA makes proteins)

transcription (info from DNA is used to make RNA)

RNA (ribonucleic acid)

adenine, cytosine, uracil, and guanine

Organelles

Fimbriae- Bacteria can attach to particular receptor structures thanks to attachment structures.

Nucleiod- DNA situated here that is not membrane-enclosed

Cytoplasm- contains organic molecules and enzymes and is primarily composed of water.

Cell wall- rigid, external to the plasma membrane, provides security and shape

Glycocalyx- An outer layer is made up of a slime or capsule layer.

conserves fluids and guards the cell from being swallowed by other organisms. fights off phaagocytosis

Plasma Membrane- Selectively The cytoplasm is enclosed and controls the flow of substances during nutrition and waste transport as well as the location of metabolic processes.

Ribosomes-protein production and synthesization

Producers

Autotroph

Photoautotroph

Organism types:: Photo synthetic prokaryotes algae

Energy comes from a light carbon source CO2 HCO3

Chemoautotroph

Energy comes from in organic chemicals carbon source CO3 HCO3

Heterotroph

Photoautotroph

the sources are Light and organic compounds

Chemoautotroph

Organic Compounds

5 carbon sugar (pentose)

phosphate

a nucleoside DOES NOT have a phosphate group

nitrogenous base

purines (A and G)
2 carbon nitrogen ring bases

pyrimidines (C, T, and U in RNA)
1 carbon nitrogen ring bases

nucleotide polymers

joined by condensation/dehydration
reactions= phosphodiester bond/linkage

Functions

Caries out the transduction part of the signaling pathway

Most other intracellular receptors function in the same way

Details

1. Found in the cytoplasm or nucleus of target cell

2. Signaling molecule passes through target cell's plasma membrane

Steroid hormone interactions

1.The steroid hormone passes through the plasma membrane

2. Hormone binds to a receptor protein in the cytoplasm activating it

3. The hormone-receptor complex enters the nucleus and binds to specific genes

1.The hormone receptor complex turns on genes in a cells DNA function by being transcribed and processed into messenger RNA in the nucleus

2. Leaves the nucleus and is translated into specific proteins by ribosomes in the cytoplasm

3. Proteins called transcription factors control with genes are tuned on/ transcribed in mRNA

4. The bound proteins acts as a transcription factor , stimulating the transcription of the gene into mRNA

5. The mRNA is translated into a specific protein

1. First messenger binds to GPCR, activating it

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

3. Activated G protein/GTP binds to adenylyl cyclase. GTP is hydrolyzed, activating adenylyl cyclase

4. Activated adenylyl cyclase converts ATP to cAMP

5. cAMP (second messenger) activates another protein, leading to cellular responses

1. Signal molecule binds the each of the binding-sites

2. Polypeptides dimerize (join together), activating them (unphosphorylated dimer)

3. Autophosphorylation (phosphate group taken from ATP and added to the other polypeptide)

4. Fully activated receptor tyrosine-kinase (phosphorylated dimer)

5. Activated receptor now interacts with other relay proteins to bring out cellular response 1/2

gate allows specific ions (Na+ or Ca+) through a channel

very important in the nervous system

movement of ions in these channels may change voltage across membranes = triggers action potential

Action potential-
electrical signal that propagates along the membrane of a neuron or other excitable cells as a nongraded depolarization

COMPONENTS

PROCESS

:1. INITIATION:
- mRNA, tRNA, two ribosomal subunits come together
- GTP and initiation factors required to assemble this complex
- Small ribosome and tRNA bind to 5’cap, scans mRNA for AUG, and then large subunit assembles to form translation initiation complex

2. ELONGATION
- tRNA to A site with amino acid, moves to P site to for peptide bonds, then tRNA exits at E site
- peptide chain grows at the P site
- Each step GTP is used with GDP+P remaining
- Amino acids are added from N(amino) to C (carboxyl)
- peptidyl transferase creates the peptide bonds
- amino-acyl tRNA synthetase adds the appropriate amino acid after reading the mRNA codon

3. TERMINATION
- Stop codon read, release factors sits at A site, and then breaks apart the complex
- Driven by GTP

PROKARYOTES VS. EUKARYOTES

PROKARYOTES
- Occurs in the cytoplasm and uses mRNA and tRNA
- Ribosomal components: 70S, Large subunit: 50S (31 proteins) and Small subunit: 30S (21 proteins)
- All steps of translation the same, but elongation uses formal-MET, and lack of organelles means protein destinations are cytosol or plasma membrane

EUKARYOTES
- starts at free ribosomes (cytosol) but moves to
ER if initiated
- Ribosomal components: 80S, Large subunit: 60S (~ 45 proteins) and Small subunit: 40S (~ 33 proteins)
- these have more possibilities with more organelles and pathways than prokaryotes, and it just uses MET

Prokaryotes vs. Eukaryotes

Procces

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cytosol

Mitochondrion

Perixsome

Chloroplast

Nucleus

Endoplasmic Reticulam

Golgi Apparatus

cell exterior

plasma membrane

lysosomes

other parts of end-membrane system

In the cytosol, polypeptide synthesis starts on a free ribosome.

A signal peptide is bound by a signal recognition particle (SRP), the synthesis is momentarily stopped.

A receptor in the ER membrane is where SRP binds.

Polypeptide synthesis resumes when SRP leaves.

A receptor protein complex enzyme splits the signal peptide.

After leaving the ribosome, the finished polypeptide assumes its final configuration.

Becomes membrane protein

secreted outside the cell

Glycosylation

Glycoprotein (Carbohydrates and Protiens)

Secondary Protiens

Amylase is released by digestive enzymes.

Insulin is secreted by peptide hormones.

Casein is secreted by milk proteins.

Albumin is secreted by serum proteins

Proteins from extracellular matrix secrete collagen

additional locations