Cell Physiology

Introduction to the Cell

• All living organisms consist of one or more cells.
• The cell is the fundamental structural and organizational unit in organisms.
• All cells arise from pre-existing cells.

Prokaryotic Cells

• They lack a true nucleus or any membrane-bound organelles.
• Prokaryotic cells are smaller, ranging from approximately 1-5 µm.
• They are always unicellular organisms.
• Cell division occurs through binary fission.
• Asexual reproduction only
• Bacteria such as E. coli are examples.

Eukaryotic Cells

• Eukaryotic cells contain a nucleus and membrane-bound organelles.
• Larger in size, typically around 10-30 µm.
• Usually multicellular but can be unicellular
• Cell division happens through mitosis or meiosis.
• Reproduce either sexually or asexually.
• Plants and animals serve as examples.

Diversity of Cells

• Epithelial Cells
• They are protective barriers in tissues.
• They can absorb or secrete specific compounds.
• Muscle Cells
• They enable movement of the skeleton, heart, and internal organs like the stomach.
• Specialized structures and proteins allow these cells to generate motion.
• Nerve Cells
  • They transmit electrical signals.
  • They control muscle concentration.
  • Responsible for senses, including taste, touch, smell, sight, and hearing.
• Connective Tissue Cells
• They create extracellular material that holds tissue together.
• Can absorb or resist external forces such as tendons and vertebral discs.
• Bone Cells
• They form bones, providing strength and support.
• Include cells such as osteoclasts that degrade bone and osteoblasts that create new bone.
• Secretory Cells
  • They form glands and secrete substances like mucus, hormones, and enzymes.
• Adipose Cells
  • They are found throughout the body to store fat as triglycerides.
  • This fat can be released during fasting.
• Red Blood Cells
  • They are formed in bone marrow and are released to deliver oxygen throughout the body.
  • Lacking nuclei or mitochondria, they have limited lifespans that require continuous replacement.

Introduction to Organelles

• Peroxisomes
• These organelles break down molecules that produce hydrogen peroxide.
• Mitochondria
• These produce energy cells use.
• Nucleus
• Houses the cell's genetic material.
• Regulates access to genetic material
• Endosomes
• Sort and condense content entering the cell.
• Plasma Membrane
• Monitors cell entry and export to other organelles.
• Lysosomes
• Responsible for breaking down waste and debris.
• Endoplasmic Reticulum (ER) and Golgi Apparatus
  • Carries molecules, produces proteins and lipids, and processes and package proteins.
• Cytoskeleton
  • Generates motion and provides stabilization against deformation.

Molecular Building Blocks of the Cell

• Hydrophilic molecules attract other hydrophilic molecules and repel hydrophobic ones.
• Hydrophobic molecules attract other hydrophobic molecules and repel hydrophilic ones.
• Nonpolar carbon-based structures attract each other and repel water, a property used to form membranes and subcellular compartmentalization.

How Water Supports Cells

• Polarity facilitates the delivery of nutrients and removal of wastes.
• Polarity provides an environment for cell existence and movement of chemical messengers.
• High specific heat capacity of water allows thermoregulation by acting as a heat sink along the exchange of heat between liquid and air.
• Cell thermoregulation is important for warm blooded organisms
• Lipids serve as the building blocks for oils and fats.
• These hydrocarbon chains are highly hydrophobic and insoluble in water.
• They regulate cell membrane fluidity.
• Cholesterol serves as a biological precursor for compounds like steroid hormones, bile acids, and certain vitamins.
• Phospholipids are amphipathic (hydrophobic and hydrophilic) that form cell membranes.
• Containing a hydrophilic head and hydrophobic tail, they enable the formation of the phospholipid bilayer.
• Triglycerides form the main component of body fat in animals and are used to store energy.
• Carbohydrates
• Monosaccharides include single carbon, hydrogen, and oxygen carbohydrate molecules.
• Glucose, which is also referred to as sugar, is an example of a monosaccharide.
• Disaccharides are constructed of two monosaccharides linked by a glycosidic bond such as sucrose which contains linked glucose and fructose molecules.
• Oligosaccharides contain 3-10 monosaccharides linked together such as raffinose.
• Polysaccharides much larger chains that play importnat roles in the cell, like glycogen.

Amino Acids

• Amino acids are building blocks of peptides and proteins with a consistent structure of amino group, central alpha carbon with R-group, and a carboxylic acid group.
• Hydrophobic Amino Acids
  • Nonpolar amino acids that reside in the core of the protein or interact with other hydrophobic membrane molecules
  • Either aliphatic (straight or branching chains or non-aromatic rings) or aromatic (contains an aromatic ring with a double bond).
• Charged Hydrophilic Amino Acids
  • Have a positive or negative charge
  • They hydrophilic
  • Charge location helps interact with water
• Polar Amino Acids
  • Have polar and hydrophilic chains
  • Form hydrogen bonds that stabilize proteins
  • More common on the outside of proteins
• Aromatic Amino Acids
  • Have ring structures with double bonds.
  • Chemically distinct
  • Very large with deformation consequences if there is gain or loss.

Peptides and Proteins

• Amino acids form peptides when connected by peptide bonds.
• Proteins consist of long amino acid chains (typically more than 20).
• Polypeptides fold into a 3D structure for protein function.
• Proteins include enzymes, receptors, keratin, structural proteins, and hemoglobin.

DNA and RNA Structure

• The building blocks of DNA and RNA are nucleotides.
• A nucleotide consists of a five-carbon sugar, a phosphate group, and a nitrogenous base.
• The 5' end of sugar is where the phosphate group attaches in a single nucleotide.
• The 3' end is where the next nucleotide's phosphate group will bind
• RNA has an extra oxygen atom.
• Nitrogenous Bases
• Nitrogen-containing attached to the 1' carbon
• Purines: have two rings adenine and guanine.
• Pyrimidines: have one ring cytosine, thymine, uracil.

From Nucleotides to DNA

• Sugar-phosphate backbone of DNA is held together by phosphodiester bonds, added to the 3’ end.
• Complementary bases on each strand form hydrogen bonds that form cross-linkages, with purines pairing with pyrimidines.
• Strands run in opposite directions and therefore are antiparallel.
• The bases come into contact with as little water as possible given their hydrophobic composition.

Introduction to RNA

• Structurally similar to DNA.
• Plays a critical role in protein synthesis by relaying information from the nucleus (DNA) to the cytoplasm.
• Delivers information required for the synthesis of proteins.

How RNA Differs from DNA

• Uracil instead of thymine.
• RNA nucleotides contain ribose in place of deoxyribose.
• Single stranded and less stable than DNA.

RNA Functions and Types

• Messenger RNA (mRNA) carries protein synthesis instructions.
• Transfer RNA (tRNA) brings amino acids for protein synthesis during translation.
• Ribosomal RNA (rRNA) make up ribosomes for translating RNA into protein.

Central Dogma Part 1 - DNA Replication

• DNA carries genetic information inherited by offspring.
• Molecular biology central dogma explains that DNA contains instructions that build RNA and proteins Important for cell and body structure and function

Introduction to Genes

• DNA is divided into genes that contain synthesis instructions. Important to perform cell jobs
• Genes that encode proteins called coding DNA
• Genes are on chromosomes but are seperated with non-coding DNA Eukaryotes do not follow the DNA production
• Structure of a Gene Important to note that genes are not actually used to make proteins. Only small amounts are

Exons

• Genetic sections that contain the information that build the make up protein Introns sections that are not used and non-coding to build the protein Regulatory sequences Used control when gene is used to make a protein for a set job

Central Dogma of Molecular Biology

• Three processes are required for converting information from DNA to proteins
• Replication
• Replication is the coppied genetic information before DNA will be copied before a cell divides so daughter cells can have DNA
• DNA polyermase is a major ezymes used in process
• Transcription
• From informatio in DNA to RNA in tranport to nuceleaus for protien production
• RNA polyermase is major enyme for process
• Translation
• RNA will red so that a.a can preform jobs in cell
• Ribosomes are major enyzmes for porcess

Stages of DNA Replication

• Each cell will be have a DNA copy in full in cell
• The cell will divide and new cell will have genome copy
• Cell uses some conservation when copying DNA DNa is replicated and one parent dna is used with DAughter dna

Initiation of Replication

• Double standed DNA needs to be seperated to begin copying new DNA Protien binding Protien group that binds it ti replicated origin for DNA using DNA helicase
• DNA unwinding DNA unwinds for separtion.

DNA primers

• Enzyme primase adds a short number of RNA nucleotide that is called primer called RNA primer
• Elongation of Repication Adding RNA the enzyme starts copy DNA primer Direction DA na polymerase can add nuclited to only end and dna strans

Elongation of Leading vs Lagging Strand

• Dna polymerase can create in 5 / to 3/ directions so it can add as continuouis strand called leading and and otther will be in fragements ca;;ed lagging strand
• Leading strands
• Runs oteh way form parnter DNA
  • Create new strans that is going the same way as replicating for thus creating conitnous strands
• Lagging stands
• Bulit in in 5/ to 3 / directio
• dna polymase only bulids contisouly in 3/ to 5 directios
• Okazaik Frgamnets Final Dna molcues will go through RNA primay to create DNA molecule
• Enyme called ligate

Ligase

• Gap issue that enzyme calle dligase goes thoug DNA
• The enzyme joins the oka frgamets to the lagging strand

Termiantion DN Repicaiton

• Replication for will reach the end of dna molecuels.There will be a strand the is copied
• In order to do is their needs to ben an RNA primer a nd enyme polymserases to start DA repicatin This will ultmintly make a long single over hang

Overhang to shortening chromosome

• Very simlalr area is u replicateted The overhang de degrades very instable sinngle strand and the chromaomes begin to shrink
• telmerses and teolmerase

Telemerses nad telmerase

• Telmerase will prevent the chronsomes from shrining will add non-codinfd strand
• It's non functiona and can not effect cell after being degrded Tellmerase
• The enyem that adds telereare is called telmarase
• can bond to and exetnd pasrt DAN

RNA Template

Telamarse is Rna dependednt so it can maker dna from rna and temperalte

Overhang

• extra now with non fucntual Dna strand An RMA primer
• Dna and dna starts add likel usal

Chromosmes

• Telmears will repeat over in thos process so is can crate the logn DNA in chrsomorewoms
• Now noramla dn a can happent and

DNA helicase unwinds the DNA.

• RNA primase adds a primer.
• DNA polymerase begins synthesizing the leading and lagging strands.
• Primase continues to add new RNA primers to the lagging strand.
• DNA polymerase synthesizes DNA on lagging strand on new Okazaki fragments.
• An enzyme replaces the RNA primers with DNA.
• Ligase catalyzes phosphodiester bonds, forming the backbone of DNA
• T Central Dogma Part 2 — Transcription
• Transcription is the process by which information is rewritten, and refers to rewriting the DNA sequence of a gene into the analogous RNA sequence.
• Important Proteins in Transcription RNA Polymerase
• RNA Polymerase Is responsible for synthesizing most of the rRNA required for a functional ribosome
• RNA Polymerase II Synthesizes messenger RNA (mRNA)
• RNA Polymerase III Synthesizes transfer RNA (tRNA), as well as some other RNA molecules Transcription Factors
• A transcription factor is a group of proteins that binds to specific DNA sequences and controls the rate of transcription from DNA to RNA

Transcription Factors

• Bind regulatory regions of a gene and signal to transcriptional, transcription factors are able acticate and represse alterinf the process of RNA
• Stage 1: Initiation of Transcription*
• Begins whith transcription factors a specific DNA sequence is regulatory reion and controld wheter a gene ti tured an
• RNA Polymease is able to bond to dna whn attching to spefifc location.known start site and usly contains the nucletaides as TAta Box
• Stage 1: The Transcription Complex*
• Guides RNA polymserase in unwidning of DNA
• Stage 2: Elongation of Transcription*
• Process to extend the RNA molecule
• Region of DNA to protecd

Stage 3: Termination of Transcription

• Induces protein termination but process is still not known very understood Termination no ends and is separtly cleaves enzymes for coding RNA and polmymerase II diconnet To correcrt make RNA many molecules are make to enure it correclt

RNA is short so it can have dffernt parts made at different times so a way to keep make a big change Keep long enaough for ot produce This process is mad to presers makie fundtion to deliver to find lotacion termmed porst trancsirtiopla rna

RNA modification

• Methyl group to the to protect the RNA molecule from nuclues Gunasione tripohjate Adds a guanison trpotpatare to r na with unusial 5 to 5 linkgahe
• *rNA MODIACITON Polycatin AFTER METHYL IS ADDED AT TWO MORE DIFFUSETM AOTIN
• Polymeate to 209 addesoins Create RNA at ail

THE TAILS WILL ASTART TO MAKE PROTEINF

RNA SPlcing

Rna splace also happens after TAIL DO NOT CORRESPOND WIH PRODUcot NEEDREMOE SO trnltin occu

SPLICING and ALTERNATIVE Splciing

Some genes do rnkka tyo crate rna fron dna can causeexons to be skip and alteratice proeis

• TRANSPORT through nuclra pore colecp* Traancrption HAPPENS In nuclrues
• Neet end when donw and made
• Complex can hel transpot
• Recycles and helptracnript RNA wont go back and cell
• Exceptions TO dogma*
• RMA is used becuaes of some vurisus that cant ge dna and need specaised eneymzes

DNA Repliaiton Rveiw

• Locaitona nuclaues nad rna s trasctinve reivew locatin nuclures
• prodcuts make from on ea or two
• single diteions.tightly regulared eras

DNA RePliaiton and RN Trascript

The dna Is pRoorwdded RNA isnt RNA II IS MADE SEVRAl times w/O GOOD P RWOORQ

• SPeific too celtype

The Central Dogma Part 3 - Translation

Translation

• Translation involves taking the mRNA transcript of a gene and converting it into a functional protein.

From Nucleotides to Amino Acids

• Cells decode mRNA by reading their nucleotides in groups of three, called codons.

Amino Acids

Each codon corresponds to a specific amino acid.

Codons

• Consisted of three nucleotides long, it gives the cell enough possible combinations of nucleotides to account for the 20 amino acids in the genetic code.
• allows enough different combinations of the four nucleotides for multiple codons to encode the same amino acid.

Standrad Codon

one that code for only amino s acid

• stop codon*

• uga uaa

• stat codon AUg

• Codon Recundacy Lesse common to hae thea but coom to ahveer the most a.a.

• mRNA is delivered to the cytoplasm to make proteins

• Protein Factors are translation iatiation that bonds with the mRNA cap

• Elongation happens using EFs.

• The job of tRNA is to delviver correct amino acid

• A.A chains helr with eerey ot makde aa

Ribosme

• Compeisea with lgrae small subunits,

the small one is for bdigng 3 imp sites

initiao of r translatin

Ribossoma is assesmbled a a hel with correct

factorsthat bdond w 50 caps and atials that helo Complex atteahs RNA nad MET THEn it will craawl The dna bind Comples can be and that is it

Stage to of tranglation eolongation

• STEP CYCLE THAT IS conitus
• process requirt to for comsuito the RNA bindin Whreamino attach rinosmoes HAVE GTMP COPLEEMTARY Formed Conver GD
• • TRANCLCOTION**

MOCING mRNA

• The proteing chian ends hwhen ite is rreach on STOP (UAG UAA) UAG UNliike otgrer cant CONET

release factor

• Afeter realse targe is freed and canbe be for relsesd
• introuction ti mutaitn
• Eestimated siw errors* dna daner in mutation result
• Reiparing DNU During* Dna Dna Polymarase has reasingfuntion to check emsureo no mstks
• - Through our cell cylc* Repai protien
• *what hapesna
• dna and rna Chnaef

POINT

• Can make aminos acid chnage A Single nucite is that what you want
• Intertition add bse read frame delstion

MOTO MUTATIOn

LARGE MUTARION INSEITO can involve chrtomsoens

some cancer cause with protien acid charge Similar for structure MODLUE NUCules dna In order to protect the dna this has to be done to allow mRNA .dna has to reguated

• *COMPONets of rna dna se[prste chrstmin

Nucleu

• crreare rna can is assemble rnos
• Visuucal Rglayte

Evels of DNA PAcket DOUb neclies fibri heter

Nueosomes

• wrap twiec dna
• necleas

Fibri

Spirlay chrom Loops

• **loops furtherm comprimsnng DNA package Eurchimstin acitve
• *Memrbnaryy
• *Prosess protim
• *Eno
• *Edo

Nvcleua

LInk tto CISTer pores

RTR

Rbosime proteisn

ER

LIP procerss chol Vessicla Help MOC

• **GOLD aparatus

• *Tansp[rlt andmodicaitn bonds

• *Diks call cistern THE CIESRTAN roouh

• *W Ribosme

• Asemblese. here or fltot

• Lipid Synthesis steriids to it cholo

• CAIUL

• ***transpot

VESCILES shuttles Sma vecles bld t CARDO fuses and reach

• *ciss

• *meidal tran

• REcive froms er that ente

• Suger add send to

• • other oafntls the slysmes vesicle

• hold cel conte aeroses reaponisble In voles wasye

Perioxmies the

• Alos reaka down Neueralixwe can't dam

Endomembrane system overview

Acts aa high way protein translation

Trapsport Vesicle

• Endcosys tbring
• acst line posr otcfi deistntion involved protien

Targeted the cell

Unique sequence ARE TAGGE DO UTNI

• Detsined THE ceyiso secresded havnbe
• signak
• *the er transtac whtne
• Rbsmones duer faciltats to rpot
• a signal peptis
• *domaing.
• *transmes

protein enter

• Signal
• *modaitons PROTEINs
• Poteitn that
• bnd Biproty
• from react aminos
• aminos ca rotate but is rigid

tWOS distrnot proteisns

• LINE SEQ Alah Tight bond btewe the bancks

• plannse bonds by amine the

• THE COMPLTIE POORT*

• Molecuke

THE

DOMAIN

• It the funyton and structure

PROTEINS chnage

relativley

• NO COVI

• realtitie

• can incule

Proteisn trapprt from THE er

• Fold vesick
• m,amrbnes tranpsort
• gaterscargos can acuratey

Medat

• The outside
• *used you the coats can proietns is the acapt transports

The membraen

• *transporting
• *vesilce THE

can'd membrn

• *endosties import

Carth

• is that en

s

• *acros the cell Funtions
• *into THE cell Take IN

transpript

The low

• Proyt to the

• at that in

• A Conituns

• degated ph as

• *and protens SIGNAL TARGETS

• *endodites sOrt

• *vseicle RELYCIN B transpirt realyces

Plasma member lipits

• made up of phosphoil
• perams
• withen layers spiclai
• Phosolpias* independent Cluset ATTACH toe
• charge conmpnent

FADDY

• Tww hydrocsrbio
• Six type oh
• Major PHOOS PI CL pC*