Nuclear envelope- double membrane enclosing the nucleolus

Cytoplasm- surrounds the organelles

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

Amphipathic

Different Functions of Membrane Proteins

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

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

Selective Permeability

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

Passive Transport

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

Active Transport

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

Pumps

Electrogenic Groups

CoTransport

Bulk Transport

- 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

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

Smooth ER

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

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^

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

Structures and functions of Cytoskeleton

Microtubules

Microfilaments

Intermediate filaments

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

Ribosomes

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

Specific to animal cells as plants have cell walls

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

Prokaryotes
-Occurs in cytoplasm, allows coupling between translation and transcription, means as the mRNA made can immediately be translated
-Only RNA polymerase

Eukaryotes
-occurs in nucleus, pre-mRNA is formed
-different RNA polymerases are used to make different RNAs, focus on RNA polymerase II
- initiation uses transcription factors that bind to promoter before RNA polymerase II can bind and uses the transcription initiation complex
-At termination 5' end a CAP is added, and at 3' end a polyA tail is added with the help of polyA polymerase

Procces

Initiation
1. RNA polymerase bind to DNA on the upstream at start site called promoter and then uses a DNA strand as a template strand
2. DNA strand unwinds, polymerase begins to transcribe at start site
3. RNA polymerase make new strand from 5' to 3' but read it from 3' to 5'

Elongation
1. Polymerase moves down stream, unwinding DNA as it transcribes
2. Polymerase add nucleotides to the 3' end of growing RNA molecule
3. New RNA molecule peels away from DNA template and the DNA double helix re-forms

Termination Eukaryotes
1. RNA polymerase II transcribe a signal sequence of AAUAAA to cut RNA transcript free from polymerase
2. pre-mRNA is released then undergoes processing

Termination Prokaryotes
1. The polymerase detaches from DNA and releases then transcript with the help of a transcribed terminator

Transcription Factors
-Eukaryotes use these in initiation the transcription factor bind to promoter before polymerase II
- forms transcription initiation complex

Eukaryotes RNA modifications

RNA Processing
1. ends or pre-mRNA are modified; the 5' end receives a cap and the '3 end receives a poly-A tail
- helps with export of mature mRNA from nucleus, help protect from degradation and help ribosomes attach to 5' end in cytoplasm

RNA Splicing
1. Introns are cut out of molecule and exons are joined together with the help of a complex called spliceosome

Structure made up of...
Nucleotides (connected together through condensation/dehydration reactions & held together by hydrogen bonds)

Composed of...
Phosphate Group
Sugar (deoxyribose)
Nitrogenous Base

Start of Replication...
separate 2 strands of DNA at ORI (origin of replication) sequences and form a bubble
- Helicase separates strands
-SSB (single stranded proteins) keep DNA apart
-Topoisomerase relieves strain on DNA

-Primase synthesizes RNA Primers
- DNA polymerase 3 adds nucleotides to 3'
(needs the help of another protein-sliding clamp-keeps DNA on parent strand)

Synthesis of leading strand
-DNA POlymerase 3 synthesizes
moving toward replication fork (5' to 3')

Synthesis of lagging strand
-multiple RNA primers are laid out, DNA pol 3 extend, okazaki fragments are formed
-Dna Polymerase 1 removes RNA and replaces it with DNA nucleotides
-ligase seals gaps

cytosol^

mitochondriion

Perixsome

chloroplast

nucleus

Endoplasmic Reticulam

Golgi Apparatus

cell extersior

plasma membrane

lusosomes

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 protien

selected outside the cell

Glycosylation

Glycoprotein (Carbohydrates and Proteins)

Secondary Proteins

Amylase is released by digestive enzymes

Insulin is secreted by peptide hormones

Casein is secreted by milk proteins

Albumin is secreted by serum protiens

Proteins from extracellular matrix secrete college

additional locations