Include the Plasma membrane and the Organelle Membrane

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Functions:

-Regulate what enters and leaves cells

-Maintain specific shapes

-Mediate interations between cells

Function:

-Compartmentalize functions

Fluidity of phospholipids

What does fluidity mean?

Saturation of phospholipids and fluidity?

Choloesterol and fluidity?

Fluidity means the shifting of phospholipid and some other proteins

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Fluid part- phospholipids and some proteins move

Fluidity is essential for function

Degree of unsaturation/saturation of phospholipds affects the fluidity

Also Cholesterol affects fluidity and temperature

High temps ==   fluidity

Low temps ==  fluidity

At low temps cholesterol hinders solidification (phospholipds can't pack)

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A. Enzymatic activity: Protein built into the membrane may be an enzyme with its active site exposed to substances in the adjacent solution. In some cases, several enzymes in a membrane are organized as a team that carries out sequential steps of metabolic pathway.

B. Cell-Cell recognition: Some glycoproteins serve as identification tags taht are specfically recognized by membrane proteins of other cells.

C. Attatchment to the cytoskeleton and extracellular matrix (ECM) Microfilaments or other elements of the cytoskeleton may be noncavalently bound to membrane proteins, a function that helps maintain cell shape and stabalizes the location of certain membrane proteins. Protains that can bind to ECM molecules coordiante extracellular and intracellular changes.

D. Cell joining: Membrane proteins of adjacent cells may hook together in various kinds of junctions such as gap junctions or tight junctions.

E. Signaling: A membrane protein (receptor) may have a binding site with a specific shape that fits the shape of a chemical messneger, such as a hormone. The external messenger (signaling a molecule) may cause a shape change in the protein that relays the message to the insode of the cell, usuually by binding to a cytoplasmic protein

F. Transport: A protein that spans the membrane may provide a hydrophillic channel across the membrane that is sleective for a particular solute. (Left) Other transport proteins shuffle a substance from one side to the other by changing shape. Some of these proteins hydrolyze ATP as an energy source to actively pump substances across the membrane. (Right).

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Biological membranes are selectively permeable

1. Simple Diffusion

2. Facilitated Diffusion

3. Osmosis

== Passive Transport

4. Active Transport

5. Vesicular (Bulk) Transport

Movement __down__ the concentration gradient

Passive transport

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Facilitated Diffusion

Channel Proteins and Carrier Proteins

Passive Transport

Movement __down___ the concentration gradient

No energy investment

Movement adied _____transport proteins__

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1. Channel Protein:Corridors-alloow specific molecule or ion to cross membrane

2. Carrier Protein: (ion/gated) open/close response to stimulus (alternates between two shapes) pg 135

Osmosis

Hypotonic and Hypertonic

Passive Transport

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Aquaporins are water channels

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(low to high)

Movement ____against__ the concentration gradient

Movement aided ___carrier proteins___

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addition of phosphate group to create energy

exchanges sodium for potassium across plasma membrane

pg 136

Comparison of Diffusion

-types of molecules

-membrane proteins required?

-energy required?

-movement down or against concentration gradient?

Movement of substance into and out of the cell by vesicles

Two main classes of vesicular transport:

Exocytosis : transport out of cell

Endocytosis: transport into cell (3 types)

Types of endocytosis

1. phagocytosis

2. pinocyctosis

3. receptor

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(cell-eating) large molecules, cells non-selective

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(cell-drinking) dissolved substances, non selective

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highly selective

receptor= membrane protein, specific shape

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Organization Complexity chart (Cells)

Bacteria, Archaea

-plasma membrane

-cytoplasm (fluid)

-cell wall

-chromsotome (nucleoid region)

-ribosomes (proteins made)

-plasmids (little pieces of DNA seperate from chromosome)

-flagellum (tail)

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membrane = nuclear envelope - 2 phospholip bi-layer

holes are nuclear pores (in nuclear envelope)

nucleolus-ribosomes made here

nuclear lamina-under nuclear envelope: long chains of proteins

Network composed of many proteins

-laminas

-lamina assocated proteins

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molecules move in/out of nucleus through pores

all proteins in nucleus that have to be imported into nucleus

they have a localization signal NLS

"cellular zip code"

Some molecules have to be exported

have nuclear export signal NES

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Form fits function

no ribosomes (looks smooth)

Functions:

lipid production

drug dexofication -OH added == H20 soluble (flushed to outside of cell == detoxify)

Stores CA++ (calcium ions)

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Contains ribosomes (makes it 'rough')

function: protein production (in ribosomes)

rough ER involved in protein synthesis

-packaged into transport vesicles == fuses w/golgi apparatus *makes way through cell)

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How does the protein "know" to go in the ER?

What happens to the protein in the ER?

-cellular "zip code" == signal peptide that tells protein to go into the ER

1. protein folds

Chaperones (proteins) stop improper action = help other proteins fold correctly

if improper folding persists = destruction of protein

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2. protein can be modified

possible attatchment: attatchment of chemical groups

ex: attatch oligosaccharide -> glycoprotein

possible modification: Cleavage (cutting, slicing, dicing) by enzymes

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How do proteins get from the ER to the golgi?

What happens inside of the golgi?

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Go to lysosome, plasma membrane, or outside of cell (secreated/exocytosis)

recycling center of cell

contains hydrolytic enzymes (hydrolysis) that break down marcomolecules

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How do materials get delivered to the lysosome?

how do monomers get out of the lysosome?

Material in cell (autophagy or self-eating inside cell already)

delivered into cell by endocytosis

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Tay-Sach's disease: high frequency in Ashkanzi Jewish community

Founder effect (small pop breaks off-> rare traits become more common)

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This deletion prevents normal transport of the protein from the ER to the cell membrane

"seen" as abornomal and degraded in ER

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microfilament (made up of actin subunits) O => pinch in two cell division

microtubule (made up of tublin subunit-diner/polypeptide)

intermediate filament (lung stretches of protein) =>are part nuclear lamina

All types of cytoskeleton involved in structural support of cell

chromosomal vesicle transport : add/take off pieces (varies size)

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motor protein: converts energy of ATP into motion

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breakdown of marcomolecules

-cellular marcromolecules (ex: fatty acids, toxins)

compartment => degrading enzyme -> breakdown product + H202 (hydrogen peroxide) (by product)

peroxisomal enzyme -> (catalase), breaks down into H2O + O2

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energy conversion

"powerhouse of the cell"

Mitochondria-site of cellular respiration

food energy -> ATP

Found in all eukaryotic cells

Choroplasts-sites of photosynthesis (plants and some algae)

solar energy -> chemical energy

Both have double membrane, DNA (small circular), ribosomes

Bacteria have same size (evidence for evolution from bacteria

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Nucleic Acids

Two types:

DNA (deoxyribonucleic acids)

RNA (ribonucleic acid) both work as polymers

monomers = nucleotides

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Origin of replication (ori)

short stretches of DNA having speicfic sequence of nucleotides (lots of A-T pairs)

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-repeated sequence

-do not contain genes

Telomerase-enzyme that can extend telomers

if cell can make telomerase-chromsomes don't shorten

Where is telomerase made?

cells of embryos

stem cells

Why isn't it present in all cells? Cancer

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nucelases-enzyme that can chop off nucleic acid

chops several not just incorrect -> DNA polymerase repairs chopped off part

DNA ligase fixes gap between the 3' - 5' (phospho-disaper backbone)

CH3 = methyl group-marks template strand (original methylated)

Defects in mismatch repair system -> accumulation -> some cancers

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Excison repair- UV light

A-T-T-C

A-T=T-C <- Thymine dimer, T bond buckles

Xeroderma pigmentosum-defect in fixing thymine dimers

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a genome is all genetic material contained in an organism

'human nuclear genome'

3.2. billion base pairs of DNA; 30,00 genes in genome

Every one of your body cells contains your entire genome

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segement of DNA trasncribed into RNA and then translated into a portein

Only small sub set of genes are transcribed in any given cell type at a specific time

specific nucleotide sequence where RNA polymerase attatches and begins transcription

TATA box is promoter for eukaryotes

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RNA folds with complementary bases

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enzyme that makes RNA; attatches and begins transcription

In eukaryotic cells, RNA polymerase cannot bind cirectly to DNA, proteins called 'transcription factors' have to bind first

RNA pol binds to promoter: DNA molecule has helix unwind where polymeraswe is

Can now add the complementary bases (RNA polymerase)

RNA pol doesn't need a primer/primase. No helicase is needed, just template

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RNA pol moves down gene-unwinds DNA, adds complementary bases

RNA transcription peels off

RNA synthesized 5' -> 3'

NO Helicase needed

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RNA pol goes till specific sequence of bases which indicate "end of genes"

RNA pol. goes away, RNA peels off completely

Eukaryotes modify RNA after transcription complete

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UTR = untranslated reigion

5' cap added : chemical structure, stabalizes RNA molecules so enzymes can't dissolve it

cap is used for binding to RNA at ribosome

3' Poly-A tail (Many A's); stability; longer tail= longer life = exit of RNA from nucleus

Proteins with nucleus export signal bind to Poly-A tail

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pre-mRNA => exons (expressed, left in), introns (intervening sequence, cut out)

Exonic splicing enhancer motifs (ESEs): 3-8 nucleotides near end of exons, "define" exon for splicesome (splicing complex)

splicesome = splicing machinery of cell; large RNA/protein complex that recognizes ESEs, cuts out intros, and connects exons

NES-containing proteins bind poly-A tail, create mature mRNA

moves nucleus to cytosol

=> mRNA is ready to be translated

1. Splicesome recognizes introns (loop out)

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Getting from nucleic acid language -> protein language mRNA

the "blue print"- a nucleic acid copy of a single gene tRNA: the "interpreter" reads nucleic acid, connects amino acids

ribosome: "the work bench"

translation: mRNA -> polypeptide

codon -triplet of bases: word that speicfies which amino put in polypeptide

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The genetic code (dictionary connecting codon to amino acid)

Not ambiguous (if you know a condon; you know which amino acid is in polypeptide)

Redundant- an amino acid can be specified by more than one codon

Universal

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connection between mRNA and protein (interpreter)

amino acid attatchment site (top of tRNA)

anti codon -will bind w/ complementary codon in mRNA (botton of tRNA)

Enzyme adds amino acid to correct tRNA in cytosol (attatchment site)

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"the work bench"

Large and small ribosomal subunits, composed of protein and rRNA are assembled in the nucleolus. They move out to the cytosol.

Enzymes involved in DNA replication, repair and transcription. Proteins that are part of ribosome have NLS and go into Nucleus through Nuclear pores

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 We can define 4 binding sites

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1. mRNA binds to small subunit of ribosome. 5' cap helps w/ position

2. Anticodons of initiation tRNA (tRNA met) binds to start codon

3. Large subunit binds

charged tRNA (meth)- tRNA attatched to amino acid

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1. anticodon of next charged tRNA binds to codon in A sac

2.tRNA-met bond broken; met forms peptide bind w/ next amino acid

3. Ribosome moves down mRNA: A site is vacant

4. uncharged tRNA in E site exits (repeat)

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-Stop codon enters A site

-Released factor binds in A site

-complex falls apart

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Endomembrane system

Proteins have ER "zipcode"

translation starts on cytosolic ribosome

zip code made first: signal recognition particle

cytosolic protein binds zipcode

Translation stops

whole complex dragged to ER

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Translation resumes

Protein imported into ER

any change in an organisms DNA

types:

Point mutation: mutation that changes only one small area of one nucleotide in a gene (2 types)

Nonsense: a codon for amino acid changed to a stop codon

Silent: alteration in codon that produces the same amino acid

Base Pair Insertion/Deletion: addition or loses of nucleotide pairs

mutation that changes only one small area or one nucleotide in a gene

• Base Pair substitutions: replacement of one base pair w/another

• Missense: One amino acid changed for another

effects can run from no effect to severe

Where in protein is amino acid changed?

What type of amino acid is encoded?

Sickle cell anemia

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a codon for amino acid changed to a stop codon

truncated (short) protein

ex: Cystic Fibrosis

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no effect on amino acid sequence

but not always 'silent'; change ESE, causing splicing mistakes

cause improper mRNA structure -> degredation

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addition or loses of nucleotide pairs

can lead to frame shift mutation but do not always lead to frame shift mutations

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No, only 2% genome are genes

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2n cell => 2 2n cells

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Centromere: region where sister chromatids attatch, site of kintechore formatoin

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Transcription and Translation occur throughout cell cycle

Interphase steps etc.

Centrosome= microtubule organizing center

Diploid cell 2n=4 -cell growth: G1 phase

DNA replication/synthesis- S phase

G2 phase: cell growth, centrosomes double, and appear

M phase: cytokensis/Mitosis

Interphase = G1, G2, and S

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Instead of non-kintechore microtubules, polar

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controlled at check points

proteins survey cell to ensure favorable conditons have been met

Signal to divide (external)- grwoth factor/hormone -> G1/ G2 check point

G1 check point:

-cell big enough?

-is DNA in godo shape (mutations?) => S if god -> G2

G2 checkpoint

-DNA replication complete? => M

Metaphase checkpoint:

are chromosomes attatched to kinetechore MTs?

If conditions are not correct, cell cycle stopped

If it can't be fixed and cells are allowed past, cancer develops

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Signal molecule, ex: growth factors

1. Reception: signal molecule binds to recptor: recptor is activated

binding of signal causes conformation change of attatchment of chemical group

2. Transduction- converting external signal to internal message

3. Response Activate cell cycle control proteins

-turn on cell cycle control genes -> activation of cell division

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1. Point mutation

source of point mutation

mistake in DNA replication

exposure to mutagene

virus inserting DNA into gene

2. Gene amplifications

-normal protein, but too much

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Causes breast cancer (over-expressed)

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Helps repair damaged DNA at G2

recognizes double-stranded breaks in chromosomes

recruits repair enzyme

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need accumulation of mutations to get cancer

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CDH1 cause two adjacent cells to stick together ; mutation: cells don't adhere -> metastasis

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overexpression -> reduces expression of adhesion protein

cells not held together

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(nonselective)

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Only function of meiosis is to produce haploid gametes

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In Meosis line up with homologous pairs (mitosis, no)

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sister chromatids not exact copies

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if monosomy (chromosome missing) in autosome (non-sex chromosome) always lethal

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1. Transmembrane Proteins

2. Peripheral membrane proteins

3. glycoproteins

Membrane proteins

integral proteins-pentrate hydrophobic cores, span membrane

Membrane proteins

appendages loosely bound to membrane

reduces membrane fluidity at mod. termperatures by reducing phospholipid movement

at low temperature hinders solidification (phospholipids can't pack together)

from golgi

used in vesicular transport : large molecules cross membrane in bulk

across concentration gradient (low to high) -uses all carrier proteins

Uses ATP (by adding a phosphate group to create energy)

Sodium potassium pump is a good example, where exchanges of sodium for potassium are made across the membrane

Used in facilitated diffusion and active transport

open/close response to stimulus (ion/gated)

one type of vesicular transport

secretion of molecules by fusion of vesicles with the plasma membrane

takes in particles by forming new veiscles from the plasma membrane

Three different types:

Phagocytosis

Pinocyctosis

and Receptor-mediated endocytosis

corridors allow specific molecule or iron to cross membrane

used in facilitated diffusino, and in osmosis (with aquaporins more specifically)