Skeletal System

1. Humans have endoskeletons, composed of bone and cartilage that grows with us
• does not limit space available for internal organs
• supports greater weight
• have a vertebral column (backbone) 
2. Cartilage
• type of dense connective tissue made of tough protein fibers
• function is to provide smooth surfaces for the movement of bones at a joint
• babies and children have more cartilage, and as they grow, the cartilage becomes bone tissue
3. Functions of bones
• gives shape and form to body
• structural support to body against the flow of gravity, and lower bones support trunk when standing
• protection of internal organs, especially soft ones
• fused bones of cranium make it less vulnerable to injury
• spinal cord and bones of rib cage help protect hear and lungs
• provides attachment surfaces for muscles and tendons, allowing body movement
• bones work together with muscles to produce body movement
• blood cell production takes place in certain bone marrow
• stores minerals, such as calcium, to support homeostasis
4. Structures of bones
• bones are organs
• compact bone
• dense outer layer of bones
• spongy bone
• lighter and less dense, and found toward center of bone
• periosteum
• tough, shiny, white layer that covers all surface of bones (except joints) 
• composed of layer of fibrous connective tissue and layer of bone forming cells
5. Compact bone (in detail) 
• accounts for 80% of total bone mass
• extremely hard, made of osteons (haversian systems) 
• act like strong pillars in bone to give bones strength and let it bear the weight of attached muscles
• made up of rings of calcium salts and collagen fibers called bone matrix
• calcium salts give bone strength, but shatter when stressed
• collagen fibers are tough and flexible
• together, they give the bones ability to bend and twist without breaking easily
• center of osteon is haversian canals
1. passageway for blood vessels and nerves
• within osteon, there are osteocytes
1. found in pockets called lacunae that are between layers of bone matrix
2. responsible for monitoring protein and mineral content of bone
• osteoblasts are responsible for growth of new bone
1. found near surface of bones
• osteoclasts remove calcium salts from bone matrix
6. Spongy bone (in detail) 
• occurs at ends of long bones
• less dense than compact bone
• "spongy" refers to appearance only, because spongy bone is quite strong
• forms porous network of bony branches (trabiculae), and gives bone strength and makes bone lighter
• allows room for blood vessels and bone marrow
• do not have osteons
• nutrients reach spongy bone by diffusion through tiny openings
• makes up bulk of interior of bones
7. Bone marrow
• connective tissue
• two types
• red bone marrow
1. produces red blood cells, platelets, and most white blood cells
2. newborns have red bone marrow only
3. as child ages, yellow bone marrow replaces red bone marrow
4. found mostly in flat bones of skull, ribs, vertebrae, and pelvic bone
• yellow bone marrow
1. produces white blood cells
2. color due to high number of fat cells
8. Periosteum
• hast tough, external fibrous layer
• internal layer with osteoblasts
• richly supplied with blood, lymph, and nociceptors
• provides nourishment to bone through rich blood supply
• connected to bone by strong collagen fibers (Sharpey's fibres) 
9. Bone shapes
• long bones
• longer than they are wide
• long shaft with two bulky ends
• mostly made of compact bone, but may have large amount of spongy bone at the ends
• classification refers to shape rather than size
• short bones
• roughly cube shaped
• have thin layer of compact bone surrounding spongy interior
• wrists and ankles
• sesamoid bones
• embedded in tendons
• act to hold tendon away from joint
• force of muscle is increased
• flat bones
• thin and generally curved
• two parallel layers of compact bones sandwiching spongy bone
• skull (cranium) bones, and sternum
• irregular bones
• bones that do not fit into above categories
• consists of thin layers of compact bone surrounding spongy interior
• pelvis and vertebrae
10. Cellular structure of bone
• osteoblasts
• bone-forming cells on inner and outer surfaces of bones
• make protein mixture that becomes bone matrix
• immature bone cells
• osteoblasts that get trapped in bone matrix become osteocytes, and direct the release of calcium from bones
• osteocytes
• originate from osteoblasts
• star-shaped
• occupy spaces called lacunae
• matrix maintenance and calcium homeostasis
• mature bone cells
• osteoclasts
• responsible for bone resorption
• remodeling of bone to reduce volume
• large cells with many nuclei
• located on bone surface
• secrete acids that dissolve calcium salts, releasing into blood stream
• causes calcium and phosphate concentration to increase
• constantly remove minerals from bone
11. Bone cells and calcium homeostasis
• bone resorption by osteoclasts releases stored calcium into bloodstream
• important in regulating calcium balance
12. Development of bones
• skeleton begins forming in early fetal development
• ossification begins after eight weeks
• at first, skeleton made of cartilage
• nutrients diffuse through matrix to chondrocytes
• bones of the body gradually harden in process called endochrondrial ossification
• cartilage still remains in your ear, joints, rib cage, the tip of your nose, and little discs between the vertebrae
13. Endochondral ossification
• process of replacing cartilage with bony tissue
• third month after birth, blood vessels transport osteoblasts and stem cells into interior to change cartilage into bone tissue
• osteoblasts form bone collar of compact bone around diaphysis of the bone
• osteoclasts remove material from center of bone to form central cavity
• cartilage at ends of long bones keep growing
• secondary ossification
• similar to ossification at center of bone
• however, spongy bone is kept instead of broken down to form cavity
• cartilage totally replace, except 2 areas
• region of cartilage over the surface of epiphysis
• another inside long bones at either end 
• called growth region
14. Intramembranous ossification
• happens in flat bones (cranial and clavicles) 
• in developing fetus
• future bones formed as connective tissue membranes
• osteoblasts migrate to membranes and secrete osteoid
• osteoid forms bony matrix

Cellular Respiration

1. Glycolysis
• does not require oxygen and does not take place in mitochondria
• takes place in cytoplasm (cytosol) 
• glucose: C6H12O6 --> two 3-carbon glucose molecules
• called glyceraldehyde 3-phosphate
• the breaking of glucose creates energy, which is transferred to ATP and NADH
• NADH holds small amounts of energy, later to be turned into ATP
• overall products: 2 pyruvate, 2 ATP, and 2 NADH
• 4 ATP were produced, but 2 were used on making glycolysis start. 
2. Fermentation
• anaerobic respiration: without oxygen
3. The Krebs Cycle
• in mitochondria, pyruvate is broken apart and combined with coenzyme (CoA) to form 2-carbon molecule, Acetyl CoA
• single atom of carbon is lost as carbon dioxide (byproduct) 
• energy released is stored in 2 NADH
• combines each Acetyl CoA with four-carbon carries molecule to make 6-carbon molecule of citric acid
• citric acid is carried through a series of chemical reactions, creating NADH, carbon dioxide, FADH2, and GTP (precursor for ATP) 
• overall: 2 ATP, 6 NADH, 2 FADH2
• glucose is completely broken down
4. Electron transport chain
• FADH and NADH give high-energy electrons to energy carrier molecules in membrane of mitochondria
• when passing from carrier to carrier, lost energy is used to pump hydrogen ions into intermembrane space
• hydrogen ions flow "down" the chain, and go out through ATP synthase channel, which transfers energy to ATP.
5. Post-electron transport chain
• low-energy electrons and hydrogen ions combine with water to form oxygen
• oxygen drives ATP-producing reactions by accepting "spent" hydrogens
• overall: 38 ATP from cellular respiration

Homeostasis

1. Homeostasis: stability, balance, or equilibrium within a cell or body. 
• organism's ability to keep constant internal environment
• adjustments must be made continuously to stay near a set point
2. Feedback regulation loops
• endocrine system plays important role
• hormones regulate activity of body cells
• response to stimulus changes internal conditions
• self-adjusting mechanism is feedback regulation
• negative feedback: response to stimulus reduces original stimulus
• positive feedback: response to stimulus increases original stimulus
3. Negative feedback loop
• most common feedback loop
• acts to reverse the direction of change
• Examples: carbon dioxide increase signals lungs to increase activity and exhale more carbon dioxide (breathing rate increases) 
• Body temperatures rises, receptors sense temperature change and send signals to the brain
1. Skin makes sweat and blood vessels near skin surface dilate
• positive feedback is less common in biological systems
• speed up direction of change
• Ex. Lactation. Baby suckles = more milk production
• since positive feedback speeds up direction of change, it leads to increasing hormone concentration, which is a state further away from homeostasis
4. Examples of homeostasis in animals
• regulation of amounts of water and minerals in body (osmoregulation) happens in the kidneys
• removal of metabolic waste (excretion). Done by kidneys and lungs. 
• regulation of body temperature, done mostly by skin
• regulation of blood glucose level. Mostly done by liver and insulin and glucagon secreted by pancreas
5. Endocrine system
• includes glands that secrete hormones into bloodstream
• hormones: created by cells that change other cells; messengers
• regulates metabolism and development through feedback mechanisms
• endocrine system release hormones that affect skin and hair color, appetite, and secondary sexy characteristics in humans
6. Urinary system
• rids body of protein and nucleic acid buildup in the blood
• directly involved in maintaining blood volume
• kidneys maintain correct salt and water content in body
7. Reproductive system
• does little for homeostasis of organism
• sex hormones have affect on other body systems
• no estrogen (from ovaries) = impaired bone development
8. Disruption of Homeostasis
• may lead to state of disease
• caused by two ways
• deficiency: cells not getting what they need
• toxicity: cells being poisoned by things they don't need
• when interrupted, body can become better or worse depending on external influences
9. Internal influences
• genetics
• some genes can be turned on or off depending on external factors
• some cannot be stopped from developing diseases and disorders
• medicine can help body return to homeostasis
• Example: Type 1 diabetes
• insulin replacement therapy brings body's handling of glucose back into balance
10. External influences
• nutrition: if diet lacks certain vitamins or minerals the cells will function poorly, and increases risk of developing disease
• physical activity: essential for proper functioning of cells and bodies
• adequate rest and regular physical activity is important
11. Mental health
• mental and physical health are inseparable
• negative stress can negatively affect mental health
• physical activity increases mental and physical wellbeing

Protein Synthesis in Detail

Transcription (in eukaryotes)

1. DNA --> RNA
• Binds RNA polymerase to promoter of a gene
2. Transcription elongation
• Adds RNA nucleotides
• DNA in front of RNA unwinds and RNA nucleotides are added to the 3' end of the RNA transcript
• Has a short DNA-RNA hybrid, 8 base pairs, where RNA is temporarily hydrogen-bonded to the DNA template strand
• mRNA can involve multiple RNA polymerases, so numerous mRNA's are produced from a single gene
• also involves proofreading mechanism that can replace RNA nucleotide
3. Termination of transcription (eukaryotes) 
• Adds string of A's to mRNA 3' end
• Proteins cut RNA transcript from polymerase
• Produces pre-mRNA step
4. Pre-mRNA processing
• Splicing
• exons: region of a gene that contains code for producing a protein
• introns: long regions of DNA that have no identified function
• splicing: introns are removed by spliceosome
• 5' cap addition
• modified guanine nucleotide added to the 5'-end of the mRNA
• crucial for recognition and proper attachment of mRNA to the ribosome
5. Polyadenylation
• addition of poly-A tail to 3' end of mRNA
• protects mRNA from degradation by exonucleases
6. Genetic code
• start and stop codons
• start: AUG
• stop: UAG, UGA, UAA
7. Reading frame
• starts reading in a frame of 3 nucleotides
• frameshift mutations: insertions or deletions of 3 nucleotide bases
• If reading frame is disrupted, mRNA may not be translated correctly
• results in premature stop codon = smaller protein with no function

Translation (RNA-protein)

1. Ribosomes
• has three binding sites (E, P, A) 
• initiation, elongation, and termination
2. Initiation (eukaryotes) 
• tRNA binds to AUG codon on mRNA
• translation can begin at all AUG codons
• only in-frame AUG will produce functional polypeptide
3. Elongation
• start tRNA sitting on AUG codon in P site next available codon at A site
• tRNA binds to codon and peptide bond joins between AUG and next amino acid
• entire ribosome complex moves along mRNA
• sends first tRNA to E site and tRNA into P site
4. Termination
• occurs when ribosome comes to one of stop codons

Cell Structures

1. Plasma Membrane (Cell Membrane) 
• Separates internal from external
• allows certain molecules in and out of the cell
1. selective permeability/semipermeability
• is a lipid bilayer
2. Phospholipids
• main type of lipid found in plasma membrane
• made of polar, phosphorus-containing head and two long fatty-acid non polar tails
• makes phospholipid bilayer
3. Membrane proteins
• 2 groups
• Integral membrane proteins
• Permanently embedded within plasma membrane
• channels/transports molecules across the membrane
• Transmembrane proteins span entire plasma membrane
1. found in all types of biological membranes
• Integral monotopic proteins-- permanently attached to membrane from one side. 
4. Cytoplasm
• gel-like material within cell is the cytoplasm
• organelles are suspended and held together by fatty membrane
• cytosol does not contain organelles (80-90% water) 
5. Cytoskeleton
• skeleton that crisscrosses the cytoplasm
• made of long, thin protein fibers
• helps maintain cell shape, holds organelles in place, and enables cell movement. 
• fibers
• Microtubules: hollow cylinders, thickest cytoskeleton structures
1. made of filaments, polymers of alpha and beta tublin
2. tublin forms pairs that twist around each other
3. holds organelles in place, allows them to move, and forms mitotic spindles during cell division
4. makes up parts of cilia and flagella
• Microfilaments
1. made of two thin actin chains that twist around one another
2. mostly concentrated beneath cell membrane
3. actin interacts with myosin to cause contraction in muscle cells
4. numerous in phagocytes
• Intermediate filaments
1. holds organelles and provide strength
2. found in hair, skin, and nail cells
6. Flagella
• long, thin structures that stick out from cell membrane
• helps cells move/swim towards food
• eukaryotic flagella bend and flex like a whip
7. Cilia
• much shorter than flagella
• covers the entire surface of some single-celled organisms
• also used for movement
8. Nucleus
• membrane-enclosed organelle
• contains DNA
• has genes/genetic information
• organized into chromosomes
• maintains integrity of genes and regulates gene expression
9. Nuclear Envelope
• double membrane that encloses genetic material
• made of two lipid bilayers, inside and outside
• outer membrane continuous with rough endoplasmic reticulum
• nuclear pores regulate exchange of materials between nucleus and cytoplasm
10. Nucleolus
• mainly involved in assembly of ribosomes
• exported to cytoplasm
11. Centrioles
• rod-like structures made of short microtubules
• important in cellular division
• arrange mitotic spindles that pull chromosome apart during meiosis
12. Mitochondria
• membrane enclosed organelle
• "power plants" because they make ATP (energy source) 
• mostly made in mitochondria
• has two phospholipid membranes
• smooth outer membrane separates it from cytosol
• inner membrane has many folds, called cristae
• fluid-filled inside (matrix) is where most ATP is made
• have their own DNA
• possibly descended from prokaryotes
• able to reproduce asexually
• endosymbiotic theory
1. once free-living prokaryotes that infected eukaryotic cells
2. protected inside eukaryotic host cell
3. supplied extra ATP to host
13. Endoplasmic Reticulum
• network of phospholipid membranes
• forms hollow tubes, flattened sheets, and round sacs
1. called cisternae
• two functions
1. transport: molecules cam move inside ER, like intracellular highway
2. synthesis: ribosomes make proteins. Lipids also produced in ER
• Rough Endoplasmic Reticulum
• studded with ribosomes, "rough appearance" 
• ribosomes makes proteins, transported by sacs (transport vesicles) 
• works with Golgi apparatus to move new proteins to correct place in cell
• membrane is continuous with outer layer of nuclear envelope
• Smooth Endoplasmic Reticulum
• lipid synthesis, calcium ion storage, and drug detoxification
• made up of tubules and vesicles that branch out to form networks
• interconnected network with rough endoplasmic reticulum
14. Ribosomes
• site of protein synthesis (assembly) 
• made of large and small subunits
• found alone or in groups in cytoplasm
• some attached to ER, and others attached to nuclear envelope
• ribosomes on rough ER usually produce proteins that are destined for cell membrane
15. Golgi Apparatus
• made up of 5-8 cup-shaped, membrane-covered discs called cisternae
• modifies, sorts and packages different substances for cell or non cell use
• close to nucleus of cell
• involved in transport of lipids around the cell
• pieces pinch off to form vesicles to transport molecules
• like a post office
• both in animal and plant cells
• plant cells have more Golgi stacks scattered throughout cytoplasm
• contains enzymes that synthesize cell wall polysaccharides
16. Vesicles
• small compartment that is separated from cytosol by one or more lipid bilayer
• mostly made in Golgi apparatus and ER, or from parts of the cell membrane
• space inside vesicle can be made to be chemically different from the cytosol
• basic tools of cells for organizing metabolism, transport, and storage of molecules
• chemical reaction chambers
• transport vesicles
• move molecules between locations inside the cell
• Lysosomes
• vesicles formed by Golgi apparatus
• contains powerful enzymes that could break down (digest) the cell
• breaks down harmful cell products, waste material, and cellular debris, then force them out of the cell
• digest invading organisms, like bacteria
• also breaks down cells ready to die (autolysis) 
• Peroxisomes
• uses oxygen to break down toxic substances in cell
• self-replicate-- grow bigger then divide
• common in liver and kidney cells
• named for hydrogen peroxide produced when breaking down organic compounds
1. broken down into water and oxygen molecules
17. Vacuoles
• have secretory, excretory, and storage functions
• many used as storage areas
• vesicles smaller than vacuoles

Special Structures in Plant Cells

1. Cell Wall
• rigid layer outside cell membrane and surrounds the cell
• contains cellulose, protein, and other polysaccharides
• provides structural support and protection
• pores in cell wall allow water and nutrients to move in and out
• prevents cell from bursting when water enters cell
• microtubules guide formation of plant cell wall
• cellulose lade down by enzymes forms primary cell wall
• some cells have secondary cell wall
• contains lignin
2. Central Vacuole
• most have one that occupies more than 30% of cell's volume
• can occupy as much as 90% volume
• surrounded by membrane (tonoplast) 
• used to maintain turgor pressure against cell wall
• proteins control flow of water in and out of vacuole
• contains large amount of cell sap
• mixture of water, enzymes, ions, salts, and others
• may also contain toxic byproducts
3. Plastids
• closely related to membrane-bound organelles
• responsible for photosynthesis, storage of starch, synthesis for cellular building blocks molecules
• contains own DNA and ribosomes
• may be descended from photosynthetic bacteria
• chloroplasts
• organelle of photosynthesis
• capture sunlight and use it with water and carbon dioxide to make sugar for plant
• chromoplasts
• make and store pigments that give colors
• leucoplasts
• do not contain pigments
• located in roots and non-photosynthetic tissues of plants 
• mostly do not have a major storage function
• make molecules; fatty acids, and amino acids