Physiology Lecture Week 2

DNA (chains of nucleic acids made of nucleotides)

macromolecule made from nucleotides…connected through covalent bonds made through dehydration synthesis

nucleotides: base connected to 5-carbon sugar connected to phosphate

• nitrogenous base

• 5-carbon sugar

• phosphate

DNA backbone: phosphate…sugar…phosphate…sugar

• phosphodiester bonds…are strong covalent bonds

• base sticks off sugar

Purines vs. Pyrimidines

Purines: larger, 2-ring structure, A and G

Pyrimidines: smaller, 1-ring structure, C and T in DNA

backbone: strong covalent bonds between 2 DNA strands (hydrogen bonds)

strong to weak bonds

strongest: covalent

ionic

weakest: hydrogen

DNA Base Pairing

Adenine (A) pairs w/ Thymine (T) 2 hydrogen bonds

Guanine (G) pairs w/ Cytosine (C) 3 hydrogen bonds

the 2 DNA strands are antiparallel (run in opposite directions)

• 3 nucleotides translated to 3 nucleotides on RNA to 1 amino acid

• 3 billion base pairs in body…make 20-25 thousand proteins, every time cell replicates…must replicate 3 billion identical base pairs

Transcription (DNA to RNA) 1 nucleotide DNA transcribed to 1 nucleotide RNA

cell reads DNA sequence and makes RNA sequence

• makes all RNA’s:

  • mRNA (messenger RNA) carries genetic instructions from DNA to the ribosome

  • rRNA (ribosomal RNA) combines w/ proteins to form ribosomes

  • tRNA (transfer RNA) brings amino acids to ribosome during protein synthesis

• RNA polymerase function: polymerizes RNA

  • reads DNA, polymerizes sequence of RNA, makes single stranded RNA

  • goes in double-stranded DNA, pops hydrogen bonds apart, reads template strand, kicks out RNA, makes mRNA, rRNA, or tRNA

  • if damaged, we might not get functional mRNA

  • must know where to start and end reading DNA *promoter region

  • between start and end is the gene

• DNA polymerase function: polymerizes DNA

  • reads DNA, makes double stranded DNA

  • pops hydrogen bonds apart, reads strands to replicate DNA

*before any cell division…must replicate DNA

Transcription steps *can occur anywhere we have DNA (most in nucleus, some in mitochondria)

1) initiation: RNA polymerase binds to promoter region and initiates mRNA synthesis at start point on template strand

2) elongation: RNA polymerase generates an mRNA for the length of the template sequence

3) termination: mRNA synthesis ends when termination signal is reached

if hydrogen bonds can’t be broken…

• no RNA polymerase, no RNA, no protein

• no DNA polymerase, can’t replicate DNA

formaldehyde firms up body tissue (preserves)

mustard gas: covalently crosslinked 2 bases on opposite sides of DNA strands

nuclear pores

after RNA is produced in nucleus, it needs to reach cytoplasm

RNA leaves through nuclear pores in nuclear envelope

nuclear pores are complex and made of 30 different proteins

mRNA creates strand we read to make protein

Translation (RNA to protein) *3 nucleotides per amino acid

can occur anywhere we have ribosomes

ribosomes: rRNA + proteins

occurs:

• on surface of rough ER (put protein in rough ER or in membrane)

• floating in cytosol/cytoplasm

• 33 genes in mitochondria have own ribosomes

has to get out of cell: translated on RER

protein remains functional in cytosol: translated on ribosome in cytosol

*most proteins in mitochondria are coming from DNA that was transcribed in nucleus, translated on RER

get out through nucleopore:

• mRNA: creates strand we will read to make protein

• rRNA: is reading mRNA

• tRNA: brings amino acids in, allows making of covalent bonds

ribosomes reading mRNA, starts threading through pore inside RER

translation/transcription locations

need protein to go outside cell or in plasma membrane:

• transcribed in nucleus

• translated on RER

needed in plasma membrane:

• as it was translated, stay folded in membrane of rough ER

needed outside of cell:

• translated to center, pull membrane of RER off containing protein into vesicle and so forth

*Most of transcription on DNA…in nucleus

if mRNA will make protein in cytosol; throw onto ribosome in cytosol

• translated in cytosol & stays there performing function

• Example: tubulin (for microtubules), actin (for microfilaments), intermediate filaments (all cytoskeletal proteins, transcribed in nucleus & translated in ribosome in cytosol)

go to plasma membrane or outside cell: transcription, outside through nucleopore, onto ribosome (translated on surface)

• protein put in membrane of RER

• protein put in vesicle, into golgi to change, vesicle, fused w/ plasma membrane to go out of cell or into membrane

protein stays in cytosol: translation on free ribosome

protein goes outside cell or in plasma membrane: translation on rough ER

pathway

nucleus, RER, vesicle, golgi, vesicle…into plasma membrane OR outside cell

DNA … RNA; RNA … protein

transcribed; translated

post-translational modification

when protein isn’t done after translation, it needs to be modified further *mature protein here

• can make or modify other proteins, lipids, nucleic acids, or carbs

*if something goes wrong with DNA, RNA or protein…disease can result

• gene therapy: change/replace genetic info so cells produce functional protein

• RNA therapy: change protein without permanently changing DNA

• protein therapy: replace/supplement proteins if not functioning right

  • hormone replacement

  • antibody therapy

  • enzyme replacement

protein synthesis (essential for us to make and modify all macromolecules)

1) DNA transcribed to mRNA (in nucleus)

2) mRNA passes through nucleopore

• mRNA attaches to ribosomes (in cytosol) & is translated to protein

  • 3) in cytosol or

  • 4) on surface of RER

5) translation on RER results in protein inside RER or RER membrane

6/7) vesicle buds off RER containing protein & is shuttled to golgi for further modifications/packaging

8) vesicle buds off golgi & targeted to…

• 9) intracellular organelles

• 10) plasma membrane

  • membrane bound protein

  • secreted protein

Membrane Trafficking

movement of proteins and membrane components through cell using vesicles

• RNA move through double nuclear membrane

• to get outside of cell, had to go inside RER & remove part of membrane

Exocytosis

moving material OUT of the cell *after golgi

• proteins must be released by vesicle in specific places

V-snare (vesicular snare)… on vesicle

T-snare (target snare)…on target membrane

both snares bring membrane together, with right trigger signal, they fuse

• hydrophobic tails of phospholipids are connected to hydrophobic tails of phospholipids of vesicle

• outside and inside of vesicle is water

• vesicle fuses w/ plasma membrane, contents went outside cell & anything that was transmembrane in vesicle, is now transmembrane in plasma membrane

Calcium triggers exocytosis

increase in intracellular Ca2+ leads to vesicle fusion between vesicle and plasma membrane

• neurotransmitters

• hormones

• digestive enzymes

Ex: neuron

• Ca2+ rises in neuron, vesicle fuses w/ membrane, neurotransmitter released, signal reaches target cell

Endocytosis

moving material IN to cell

• plasma membrane folds inward & forms a vesicle

Pinocytosis “cell drinking”

• brings in extracellular fluid

• small vesicles

• takes in dissolved substances

Phagocytosis “cell eating”

• brings in large particles

• used by some immune cells

• particle is engulfed

• some white blood cells can engulf foreign material (neutrophils)

  • particle recognized, cell surrounds particle, particle enters vesicle, vesicle fuses with lysosome, contents broken down)

• too big to be engulfed…chronic inflammation…cancer

  • Ex: asbestos, microplastics

Transcytosis

• mix of pino and phago

• material enters 1 side of cell, travels through, exits other side

  • Ex: antibodies from mothers milk transported across infants intestinal cells

Receptor mediated endocytosis

• molecules bind to receptors on cell surface & trigger their uptake

Extracellular matrix (material located outside cells)

provides: structural support, strength, organization, mechanical properties

4 most common proteins:

• 1) collagen: most abundant in body, strong, 12 types

  • found in tendons, ligaments, bone, cartilage, skin, connective tissues

• 2) elastin

• 3) fibronectin

• 4) proteoglycans

collagen synthesis

1- formation of mRNA (transcription) in nucleus

2- pass out through nuclear pore

3- hydroxylation (OH group)

4- glycosylation (in RER)

5- through golgi

6- post translational modification occurs in RER

7- golgi

8- exocytosis

Procollagen: protein that can’t make covalent bonds on itself in cell

• transcription in nucleus

• translation on RER

• exocytosis (protease outside cell)

  • can stick together once out of cell

  • hydrogen or ionic bonds…covalent cross link into collagen using lysyl oxidase

lysyl oxidase

• comes in and creates covalent bond

• post translational modification

• tough collagen fiber for tendons, ligaments

• requires trace element: copper (found in meat, shellfish)

  • without copper…no covalent crosslink…flexible joints/soft spine

• vitamin C activates (found in citrus, peppers)

  • healthy gums, teeth, tissue

tough collagen…transcription, translation, post translational modification

high vitamin C, high copper…tough collagen, stronger skin/joints

carbohydrates

monosaccharides: 6 carbon

• glucose, fructose, galactose

disaccharides: 2 monosaccharides linked together via dehydration synthesis

• sucrose “table sugar”, maltose “malt sugar”, lactose “milk sugar”

OH groups make hydrophilic sugars

Proteoglycans

protein + long chains of sugars

• sugars have negative charge…water is attracted to charge…hold water…hydrated matrix

proteoglycans, glycosaminoglycans

cartilage “water-filled sponge”

contains many charges sugar molecules that help it retain water

• resists compression

• absorbs forces

• protects joints

articular cartilage has little/no direct blood supply…movement is key!

• compress, decompress, fluid moves, nutrients move

examples: tendons and ligaments, fibrocartilage, articular cartilage (hyaline) *avascular

ACL, sprained ankle, UCL takes long to heal

• cartilage has poor vascularity, relies on movement/diffusion, heals slow