Digestive System

1. Digestion and absorption
2. Gastrointestinal tract (GI tract) 
• long tube that connects mouth with anus
• more than 9 meters long in adults
• upper and lower part
• upper includes mouth, esophagus, and stomach
• lower includes small and large intestines
• organs of gastrointestinal tract are covered by two layers of muscles that enable peristalsis
• peristalsis: rapid, involuntary, wave-like contraction of muscles
• pushes food through GI tract
• GI lined with mucous membranes
• mucous membranes moist tissues that secrete and absorb substances
• necessary for digestive system
3. Accessory organs of digestive system
• additional organs that play important roles in digestion
• food does not pass through them, but they make/store substances needed for digestion
• liver, gall bladder, and pancreas
4. Liver
• large organ next to stomach
• produces digestive substances that are carried by ducts, or tubes, to small intestine and gall bladder
• produces bile, which breaks down lipids
• maintains blood glucose levels
• gluconeogenesis: synthesis of glucose from certain amino acids, lactate or glycerol
• glycogenolysis: breakdown of glycogen into glucose
• glycogenesis: formation of glycogen from glucose
• liver is involved in getting rid of foreign substances and toxins, especially from gut
• toxins usually excreted in bile or urine
• breaking down toxins: drug metabolism
• usually done by using specialized enzymes produced in liver
• most blood being filtered comes from portal vein
• also carries blood to intestines
• liver can remove bacteria, fungi, viruses, and parasites from blood
• also does cholesterol synthesis and production of triglycerides
• cannot live without liver (of course) 
5. Pancreas
• exocrine gland: secretes pancreatic juice with digestive enzymes
• endocrine gland: produces several important hormones
• located below and behind the stomach
• endocrine cells grouped together in areas called islets of Langerhans
• produces insulin, glucagon, and somatostatin
• insulin and glucagon involved in controlling blood glucose levels
• insulin produced by beta cells and causes excess blood glucose to be taken up by liver and muscle cells
• stored as glycogen (polysaccharides) 
• glucagon produced by alpha cells and stimulates liver to break down glycogen into glucose, and released into the blood
6. Functions of digestive system
• 3 main functions
• digestion of food
• absorption of nutrients
• elimination of solid waste
• digestion: process of breaking down food into components body can absorb
• 2 types of digestion
• mechanical: physical breakdown of chunks of food into smaller pieces
• takes place mainly in the mouth and stomach
• chemical: breakdown of large, complex food molecules into smaller, simpler nutrient molecules that could be absorbed by blood
• mainly takes place in small intestine
• chemical digestion cannot take place without digestive enzymes
• digestive enzymes speed up reactions of chemical digestion
• secreted by glands in mucous membranes of mouth, stomach, small intestine, and pancreas
• digestive enzyme name typically ends with "-ase" (means enzyme) 
• after food is digested, nutrients are absorbed
7. Mouth
• the mouth begins digestion of starch
• enzyme: salivary amylase found in saliva
• mechanical digestion: tongue and teeth
• teeth shape reflects dietary habits
• humans are omnivores (both meat and plants) 
• incisors for cutting, canines for tearing, and molars for grinding
• saliva from salivary glands moistens food and makes it easier to chew
• muscular tongue mixes food with saliva and enzymes
• lump of chewed food (now called bolus) passes into pharynx
• pharynx connects mouth to rest of digestive tract
• connects mouth and nose to respiratory system
• when food is pushed back to back of the mouth by tongue, the pharynx is closed off from respiratory system
8. Esophagus
• bolus moves into esophagus
• narrow tube ~20 cm long
• begins at pharynx and ends at opening to stomach
• function: to pass food from mouth to stomach
• does not produce digestive enzymes and no digestive function
• sphincter: muscle at end of esophagus that controls entrance to stomach
• opens to let food in and closes again to prevent food from going back into esophagus
9. Stomach
• saclike organ located between end of esophagus and beginning of small intestine
• food digested both mechanically and chemically
• churning movement of stomach's muscular walls breaks down food mechanically
• also mixes food with fluids secreted by stomach
• hydrochloric acid (HCl) 
• gives stomach acidic environment
• helps destroy bacteria that entered stomach through food or drinks
• acidic environment needed for stomach's digestive enzymes to work
• digestive enzymes secreted in stomach helps break down proteins into peptides
• pepsin is main digestive enzyme in stomach
10. Small intestine
• narrow tube about 7 meters long
• site of most chemical digestion and most nutrient absorption
• small intestine much larger than large intestine
• called small because it is smaller in diameter
• pushes food along with peristalsis
• three parts: duodenum, jejunum, and ileum
11. Duodenum
• first part of small intestine
• 25 cm long
• most chemical digestion occurs there
• many enzymes active in duodenum
• only some produced by duodenum
• rest are produced by pancreas, and secreted in duodenum
• amylase: digests carbohydrates, made in pancreas
• trypsin: digests proteins, made in pancreas
• lipase, digests lipids, made in pancreas
• maltase: digests carbohydrates, made in small intestine
• peptidase: digests proteins, made in small intestine
• lipase: digests lipids, made in small intestine
• pancreas controlled by hormones
• gastrin (hormone) stimulates pancreas to secrete digestive enzymes
• bile reduces acidity of chyme (bolus that was churned around in stomach) entering from acidic stomach
• pancreas secretes biocarbonate, a basic substance that neutralizes acid
12. Jejunum 
• second part of small intestine
• 2.5 meters long
• most nutrients are absorbed into blood here
• mucous membrane of jejunum covered by villi
• villi have microvilli that increases surface area for absorption
• surface area adds up to the size of a tennis court
• greater absorption of nutrients
13. Ileum
• third part of small intestine
• 3.5 meters long
• few remaining nutrients are absorbed in ileum
• salts that form liver bile are absorbed
• also covered with villi and microvilli
• more absorption area
14. Large intestine
• connects small intestine with anus
• 1.5 meters long
• three parts: secum, colon, and rectum
• waste enters from small intestine (in liquid state) into the secum
• excess water is absorbed when waste passes through colon
• remaining solid waste called feces
• contains indigestible food substances, like fiber
• feces accumulates in rectum, and stored until eliminated from body
• sphincter controls anus and opens to let feces outside
15. Bacteria in large intestine
• large intestine provides home for intestinal bacteria and absorbs vitamin they produce
• most bacteria are helpful
• produce vitamins
• control growth of harmful bacteria
• break down toxin before they can poison the body
• break down indigestible food components
• produce substances that prevent colon cancer
16. Diseases of gastrointestinal tract
• inflammatory bowel disease
• inflammation of large intestine
• normal reaction of immune system
• causes swelling, redness, and pain
• 2 main forms
• Chrohn's disease
• abdominal pain, diarrhea, and weight loss
• caused by immune system reacting to body's own tissues
• no known cure, but treatment can control symptoms
• ulcerative colitis
• similar symptoms to Chrohn's disease
• unknown cause
• confined to colon and can be sometimes cured with surgery
• food allergies can affect GI tract
• disorders that occur when the immune system reacts to substances in food as if they were foreign invaders
• nuts, eggs, milk, fish, and shellfish
• symptoms: tingling in the mouth, vomiting, and diarrhea
• can also cause skin rashes and difficulty breathing
17. Diseases of stomach and esophagus
• layer of mucus normally protects lining of stomach from damage by stomach acid
• infection by Helicobacter plyori can weaken the mucus layer, causing gastritis or stomach ulcers
• gastritis is inflammation of lining of the stomach, and causes abdominal pain
• stomach ulcer is a sore in the lining of the stomach, and can cause severe abdominal pain and bleeding
• stomach acid can also damage lining of esophagus
• occurs when sphincter between stomach and esophagus do not close properly
• acid from stomach enters esophagus
• acid can cause esophagitis, or inflammation of the esophagus
• can be treated with medication and changes in diet
• if not treated, sometimes it will lead to cancer of esophagus
18. Diseases of the small intestine
• ulcers occur mostly in the duodenum because stomach acid enters duodenum during digestion
• symptoms and treatment of duodenal ulcers are similar to stomach ulcers
• salmonella and E. coli can cause infections in small intestine
• can enter body in contaminated foods or beverages
• symptoms: abdominal pain, cramping, vomiting, and diarrhea
• infections usually clear up without medical treatment
• celiac disease is immune reaction to gluten, found in grains
• tendency to have celiac disease is inherited
• symptoms: abdominal pain, diarrhea, and bloating
• gluten-free diet can prevent symptoms, but no cure for disease
19. Diseases of large intestine
• irritable bowel syndrome
• disorder in which large intestine is easily irritated
• common gastrointestinal disorders
• unknown cause, but may be due to excessive bacteria in intestine
• symptoms: abdominal pain, cramping, constipation, and diarrhea
• can be controlled with medication, stress management, and changes in diet
• no cure
• colitis
• inflammation of colon
• causes: bacterial infections to immune reactions against body's own tissues
• symptoms: pain and tenderness in abdomen
• treatment: medication, surgery, and changes in diet
• appendicitis
• inflammation of appendix
• most common in children and teens
• inflammation usually caused by bacterial infection
• symptoms: abdominal pain, loss of appetite, fever, and vomiting
• most often treated with surgery to remove infected appendix
• infected appendix can be fatal without treatment
20. Diseases of accessory organs
• cystic fibrosis
• affects the pancreas
• inherited disease where the body produces abnormally thick and sticky mucous
• mucus blocks the duct to duodenum, preventing pancreatic enzymes from reaching it
• proteins and lipids cannot be digested properly
• may take digestive enzymes by mouth to improve digestion
• no known cure
• hepatitis
• inflammation of liver
• caused by viral infection
• some viruses spread through contaminated foods or beverages, and others through sexual contact
• symptoms: fever, headache, vomiting, yellowing of skin and eyes, and abdominal pain
• disease may clear up without treatment if symptoms are mild
• however, if symptoms are severe, the disease may damage the liver so that it no longer produces bile
• medications are available to treat hepatitis
• some types can be prevented with vaccines
• gall stones
• crystals that form in the bile in the gall bladder
• caused by abnormal body chemistry or too much fat in diet
• may grow to size of golf ball
• may cause inflammation of gall bladder and severe abdominal pain
• only way to treat is to surgically remove gall stones or entire gall bladder

Integumentary System

1. External covering of the body, made up of skin, hair, and nails
2. Multiple roles in homeostasis
3. Structure and function of skin
• vital organ that covers entire outside of body
• protective barrier against pathogens and injuries from surroundings
• largest organ, covering entire outside of body
• 2 mm thick
• shields body against heat, light, injury, and infection
• other functions
• regulate body temperature
• gather sensory information from environment
• stores water, fat, and vitamin D
• acts as physical barrier to protect us from disease
• skin gets cut, scratched, and exposed to radiation every day
• naturally shed skin cells every day
• body replaces damaged or missing skin by replacing it
• two layers make up skin
• epidermis and dermis
• fatty layer, called subcutaneous tissue, or hyperdermis, lies under dermis
• not considered part of skin
• two types of skin on body
• thin and hairy
• thick and hairless
4. Epidermis
• outermost layer of skin
• forms waterproof, protective wrap over body's surface
• divided into several layers
• epithelial cells are formed in lowest layer
• epithelial cells move up through layers of epidermis
• changes shape and composition and become filled with tough, fibrous protein called keratin
• cells now called keratinocytes
• at surface, they form layer of flattened, dead cells
• about as thick as a sheet of paper, but has 25-30 layers of keratinocytes
• gets scraped off during everyday activities, and usually shed after a month
• melanin: brownish pigment that gives skin and hair their color
• melanocytes (cells that produce melanin) are at the bottom layer of epidermis (stratum basale) 
• difference in skin color is due to melanocyte's level of activity
• amount of melanin depends on genetics and amount of UV light exposure
• melanin absorbs UV rays from the sun
• when UV rays penetrates skin and damage DNA, damaged DNA triggers synthesis of more melanin
• skin also makes vitamin D from energy of UV light
• melanin is like a UV filter, so more melanin means more time a person has to spend in sunlight to produce same amount of vitamin D
• epidermis contains cells to process certain antigens from microbes that enter through the skin
• helps immune system recognize microbe as intruder, and mount an attack on it
• epidermis has no blood vessels, so lower portion of epidermis is nourished by diffusion from blood vessels of dermis
5. Structure and function of dermis
• layer of skin directly under epidermis and made of tough elastic connective tissue
• tightly connected to epidermis by membrane made of collagen fibers
• dermis contains hair follicles, sweat glands, sebaceous glands, and blood vessels
• holds many nerve endings that provide sense of touch, pressure, heat, and pain
• arrector pili (tiny muscles) contract and pull on hair follicles, causing hair to stand up
• happens when you are cold or afraid, causing goose bumps
• dermis has two layers
• papillary region (upper layer) 
• made of loose connective tissue
• contains touch receptors that communicate with central nervous system
• named for finger-like projections called papillae
• extend toward epidermis and secures the dermis to epidermis
• provides dermis with "bumpy" surface that causes distinctive friction ridges
• called friction ridges because they help hands or feet grasp things by increasing friction
• friction ridges occur in patterns that are unique to the individual
• fingerprints and footprints used as a means of identification
• reticular region (lower layer) 
• made of dense elastic fibers (collagen) 
• contains hair follicles and roots, nerves, and glands
• gets name from dense concentration of protein fibers that weave throughout it
• protein fibers give dermis properties of strength, extensibility, and elasticity
• tattoo ink is injected into the dermis
• stretch marks also in dermis
6. Glands and follicles
• opens out to the epidermis, but originate from dermis
• sebaceous gland (oil gland) secrets oily substance, called sebum
• sebum is made of lipids and debris of lipid-producing cells
• "waterproofs" hair and skin surface to prevent them from drying out
• also inhibits growth of microorganisms on skin
• sebum is cause of oily appearance of skin and hair
• odorless, but breakdown of sebum can cause odors
• if sebaceous gland becomes plugged and infected it develops into a pimple
• sweat glands open to epidermal surface through skin pores
• controlled by sympathetic nervous system
• evaporation of sweat on skin helps lower skin temperature
• skin also functions as excretory organ because it releases excess water, salts, and other wastes in sweat
• two kinds of sweat glands
• eccrine glands are "regular" sweat glands that releases sweat to cool body
• apocrine glands are located in the armpits and groin areas
• act as scent glands because they produce a solution that bacteria breaks down, causing "body odor" 
• mammary glands are enlarged and modified sweat glands and are a major characteristic of mammals
7. Subcutaneous tissue (hypodermis) 
• contains fat and loose connective tissue that holds larger blood vessels and nerves
• attaches the skin to underlying bone and muscle to supply skin with blood vessels and nerves
• layer is important in regulation of body temperature
• mostly made of adipose tissue (fat cells) 
• subcutaneous tissue contains 50% of body fat
• functions include insulation and storage of nutrients
• size of layer varies throughout  body and person to person
8. Functions of skin: skin and homeostasis
• used for protection, control of body temperature, sensory reception, water balance, synthesis of vitamins and hormones, and absorption of material
• main function to act as barrier against microbes and viruses
• also to prevent water and extracellular fluid loss
• acidic secretions also stop the grown of fungi on skin
• heat and cold receptors located in skin
• as body temperature rises, hypothalamus sends signal to sweat-producing glands, to release sweat
• evaporation of sweat reduces temperature on skin surface
• hypothalamus also causes dilation of blood vessels near skin, so more heat is released from skin surface
• as temperature decreases, sweat glands decrease production
• if temperature continues to fall, shivering starts, to warm up the body
• homeostatic functions of skin
• protection of body's internal tissues and organs
• protection against invasion by infectious organisms
• protection of the body from dehydration
• protection of the body against large changes in temperature
• excretion of wastes through sweat
• acts as a receptor for the senses of touch, pressure, pain, heat, and cold
• makes vitamin D though exposure to UV radiation
• stores water, fat, and vitamin D
9. Homeostatic imbalances of the skin
• infrared light: thermal energy, or heat rays that you feel
• UV light helps body produce vitamin D, but damages DNA in skin cells
10. UV radiation beneficial effects
• causes production of vitamin D in the skin
• tens of thousands of people die of premature death because of vitamin D deficiency
• UV radiation used in treatment of skin conditions, like psoriasis and vitiligo
11. Harmful effects of UV radiation
• excessive exposure causes some cancers
• many people do not take dangers posed by sunlight seriously enough
• because of tanning bed popularity
• many skin cancers are easily cured
• melanomas, a cancer, is a potentially fatal disease
• UV radiation excites DNA molecules in skin, causing bonds to form between thymine bases
• produces thymine dimer that changes DNA helix
• dimers can lead to mutations, and mutations can lead to cancerous growths
• skin cancer is a very common condition
• increased popularity of sun bathing results in increased exposure to UV radiation
• lighter-skinned people are more at risk of developing skin cancer than darker-skinned people are
• because of amount of melanin in their bodies
• lighter-skinned people have less, so they also have less protection against UV radiation
• darker-skinned people have more, so they have more protection against UV radiation and need more time outside under the sun to get the needed amount of vitamin D
• body tans when exposed to moderate level of radiation
• tanning helps block UV penetration and prevents damage to vulnerable skin tissues
• suntan lotion (sun block) partly blocks UV rays and is widely available
• sun protection factor (SPF) only blocks UVB rays, responsible for sunburns
• does not block UVA rays, which are responsible for cancer and wrinkles
• clothing also blocks UV rays
• protective clothing works well in protecting against UV rays
12. Acne
• most common form of acne is acne vulgaris
• "common acne" 
• teenagers get common acne; affects 85% of teenagers worldwide
• mostly disappears in early twenties
• some people have severe acne even after puberty and their early twenties
• excessive secretion of sebum leads to plugging of hair follicle with dead skin cells (corneocytes) 
• blockage caused by failure of normal process of shedding skin cells that line the pores 
• skin inflames, causing red bump (pimple) 
13. Nails
• nails made up of specialized epidermal cells
• contains tough protein called keratin and is actually modified hair
• nail grows from nail bed, which is thickened to form lunula
• no nerve endings in nail
• fingernails have two purposes
• protective plate and enhances sensation of function
• sensation is very important because fingernails act as counterforce to fingertip, providing more sensory input when we touch an object
• parts of nails
• free edge: part of nail that extends past the finger
• nail plate: the hard and translucent portion, composed of keratin
• lunula: crescent shaped whitish area of nail bed (when visible) 
• cuticle: fold of skin at end of the nail
• grows at rate of about 1 cm per 100 days
• fingernails: 4-6 months to regrow completely
• toenails: 12-18 months to regrow completely
• actual growth rate dependent on age, season, exercise level, and hereditary factors
• growth record shows history for recent health and physiological imbalances
• major illness will cause deep horizontal groove in nails
• indicators of illness in other areas
• discoloration
• thinning
• thickening
• brittleness
• splitting
• grooves
• spots
• lines
• receded lunula
• changes in shape of nail
14. Hair
• filamentous fiber only found on mammals
• made mostly of keratin
• hair emerges from epidermis, but grows from hair follicles deep in the dermis
• three kinds of hair
• lanugo is fine hair that covers nearly entire body of fetuses
• vellus hair is short, fine hairs that grows in most places on human body except for palms of hands and soles of feet
• terminal hair is fully developed hair that is generally longer, coarser, thicker, and darker than vellus hair
• vellus covers entire human body except lips, palms of hands, soles of feet, navel, and scar tissue
• density of hairs varies from one person to another
• function of hair
• insulate
• protect
• sense the immediate surroundings
• curly hair has biologically different structure than straight hair
• much drier than straight hair because oil does not travel down curly hair as quickly as it does on straight hair
• people with curly hair find this hair type to be dry, hard to manage, and often frizzy
• 3-6 months, body hair growth stops
• follicle shrinks and root of hair grows rigid
• another growth cycle starts after period of dormancy
• head hair grows for long duration and to a great length before being shed
• terminal hair genetically programmed to be straight, curly, or wavy, and tends to change over time
• hair color is result of pigmentation due to different forms of melanin
• more melanin: darker
• less melanin: lighter

DNA Replication

1. A cell's entire DNA is copied, or replicated
2. Occurs during the synthesis (S) phase during eukaryotic cell cycle
3. both strands of double helix can be template for reproduction of new strand
4. Helicase and Polymerase
• DNA helicase (enzyme) breaks hydrogen bonds holding two strands together and forms a replication fork
• results in two branching strands of DNA backbone with exposed bases
• exposed bases let DNA be read" by DNA polymerase (enzyme) 
• builds into complementary DNA strand
• 5'-->3'
• new strands are "built" in opposite directions
• leading strand: constructs in 5'-->3' direction
• made in continuous manner
• lagging strand: constructs in 3'-5' direction
• lagging strand synthesized in short segments called Okazaki fragments
• on lagging strand, primase (enzyme) builds short RNA primer
• DNA polymerase can then use free 3' OH group on RNA primer to make DNA in 5'-->3' direction
• RNA fragments are taken out, and replaced with DNA nucleotides
• DNA ligase (enzyme) attaches DNA nucleotides together, finishing the lagging strand
• there are many "points of origins" on a DNA strand
• DNA replication repeats until every point meets
• each resulting DNA molecule is identical to the original DNA molecule

Immune System Diseases

1. Immune system sometimes respond to harmless foreign substances as if they were pathogens
2. Sometimes mistakes self for pathogens and attacks own body cells
3. Certain diseases can also attack and damage immune system so it loses ability to defend body
4. Allergies
• immune system makes inflammatory response to harmless antigen
• antigen that causes allergic reaction is an allergen
• allergies vary from person to person
• tendency to develop allergies are inherited
5. Severity of allergies
• symptoms caused by release of histamines, chemicals that stimulate inflammation
• ranges from scarcely noticeable to fatal
• typical symptoms: itchy eyes, sneezing, and skin rashes
• uncomfortable but not life-threatening
• usually treated with antihistamines
• immunotherapy ("allergy shots") are recommended for more severe allergies
• injected with larger and larger amounts over the years
• desensitizes immune system
• reduces severity of allergy or eliminates it altogether
• most severe allergic reaction: anaphylaxis
• massive release of histamines
• causes collapse of circulatory system and constriction of breathing passages
• likely to b fatal if without emergency treatment
• injection of epinephrine treatment
• suppresses non-emergency body processes
1. including immune response
6. Immediate hypersensitivity reaction
• when exposure to antigen causes immediate allergy symptoms
• called immediate hypersensitivity reaction
• humoral immune response
• anaphylaxis may occur if allergy is severe
• affects mainly mucous membranes lining nose
• usually runny nose and nasal congestion
• pollen most common cause of allergic rhinitis
• also called hay fever, but pollen is most likely cause
7. Delayed hypersensitivity reaction
• antigen causes allergy symptoms hours or days after exposure
• cell-mediated immune response
• rashes may develop
8. Autoimmune diseases
• immune system fails to recognize body's own molecules and attack's own body cells
• ex: rheumatoid arthritis, type 1 diabetes mellitus, multiple sclerosis and systemic lupus erythematosis
• currently incurable
• treatment can help relieve symptoms and prevent long-time damage
• causes are unknown
• one way it may develop: molecular mimicry
• pathogens bearing similar antigens to person's own molecules
• immune system mounts attack, but also attack own cells
9. Acquired immunodeficiency
• immune function declines person who was born with normal immune system
• causes: 
• age: older people have a less effective immune system
• obesity
• alcoholism
• illegal drug abuse
• malnutrition in some third world countries
• medications can interfere with normal immune function
• immune suppressive drugs are deliberately given to people with autoimmune diseases and transplanted organs
• immune suppression can be a side effect
• chemotherapy
• cancer cells attack immune system cells
10. HIV transmission
• transmitted through direct contact of mucous membranes or bloodstream with body fluids that contain HIV
• body fluids: blood, semen, vaginal fluid, preseminal fluid, and breast milk
• transmission can occur through sexual contact or contaminated hypodermic needles
• in the past, transmitted through blood transfusions
• blood now screened for HIV, so it is no longer transmitted this way
11. HIV and the immune system
• HIV destroys helper T cells
• proteins on virus coat allows it to fuse with host's helper T cells
• injects own DNA into helper T cells and uses T cell's "machinery" to make copies of itself
• virus copies destroys cells in process of reproducing
• copies go to infect other helper T cells throughout body
• first several weeks, immune system will attempt to fight off virus
• at first, reduces number of virus copies in blood
• immune system unable to destroy virus
• virus continues to multiply in lymphatic system
• HIV avoids immune system by: 
• undergoing frequent mutations to keep changing antigens, so antigen-specific lymphocytes cannot develop to destroy virus
• virus uses host's membrane to cover up viral antigens to escape detection
• helper T cells continue to decline in the blood and copies of virus keep increasing
• helper T cells declining means immune response is weakened
• treatment can only slow down he increase of virus copies
• still no cure for HIV infection or AIDS, and no vaccine to prevent infection
• field of intense study by biomedical scientists
12. AIDS
• collection of symptoms and diseases
• result of years of damage to immune system by HIV
• AIDS diagnosed when helper T cells fall to very low levels
• opportunistic diseases also develop
• penumocytis pneumonia and Kaposi's cancer
• called opportunistic because the viruses take the "opportunity" to infect someone with damaged immune system
• often direct cause of death of someone with AIDS
• AIDs first identified in 1981

Immune Response

1. Third line of defense
• called immune response
• specific to particular pathogen
• allows immune system to "remember" pathogen after infection
• immune system can launch faster and stronger attack if affected again
• mainly involves lymphatic system
2. Lymphatic system (in detail) 
• three basic functions
• absorbs fatty acids after digestion of lipids in small intestine then transports fatty acids throughout bloodstream, and circulate throughout the body 
• removes excess fluid from body tissues and returns fluid to blood, filtered of pathogens
• produce lymphocytes, which are the type of white blood cells that are primarily involved in the immune response
3. Organs of lymphatic system
• red bone marrow
• produces leukocytes
• thymus
• gland located in upper chest behind breast bone
• stores and matures lymphocytes
• spleen
• gland in upper abdomen
• filters blood and destroys worn-out red blood cells
• destroys any pathogens filtered out of the blood
• tonsils
• glands on either side of the pharynx
• trap pathogens, which are destroyed by lymphocytes in tonsils
4. Lymphatic system (continued) 
• lymphatic vessels make up body-wide circulation system
• circulates lymph instead of blood
• lymphatic system does not need to pump to force lymph through vessels
• lymph circulates because of peristalsis of lymphatic vessels and rhythmic contraction of skeletal muscles
• valves prevents lymph from flowing bakwards
• lymph accumulates between cells, diffusing into lymphatic vessels, and moves through lymphatic system until it reaches the main lymphatic ducts in chest
• drains into bloodstream
• pathogens filtered at lymph nodes
• small, oval structures that act like filters
5. Lymphocytes
• key cells involved in immune response
• estimated two trillion lymphocytes in human body
• B lymphocytes (B cells) and T lymphocytes (T cells) 
• both produced in red bone marrow
• B cells mature in bone red marrow
• T cells mature in thymus
• both can recognize and respond to specific pathogens
6. Antigens
• B cells and T cells respond to antigens on pathogens, and not the pathogens themselves
• can "recognize" specific antigens because they have receptor molecules on surface
• fit between receptor molecule and specific antigen is like lock and key
• receptors on B and T cells recognize and bind to one type of antigen
7. Humoral immune response
• B cells responsible for humoral immune response
• takes place in blood and lymph and involves production of antibodies
• immunoglobins
8. B cell Activation
• Naïve B cells (unactivated B cells) are activated by an antigen
• B cell encounters matching antigen, and engulfs it
• displays fragments of antigen on surface
• helper T cells come to help bind B cells at antigen site and release cytokines
• help stimulate B cells to develop into plasma cells or memory cells
9. Plasma cells and antibody production
• plasma cells: activated B cells that secrete antibodies
• specialized to act like antibody factories
• antibodies produced by plasma cells circulate in blood and lymph
• each antibody binds to one antigen
• depends on plasma cell that produced it
• antigen-antibody complex
• flags a pathogen or foreign cell for destruction by phagocytosis
• liver removes antigen-antibody complexes from blood
• spleen removes it from lymph
10. Memory cells
• live much longer than plasma cells
• are activated B (or T) cells that retain memory of a specific pathogen after an infection
• helps launch rapid response against pathogen in the future
• remain in lymph
11. T cell activation
• B cells or macrophages engulf pathogens and display parts of the pathogen's antigen on surface
• antigen-presenting cell
• naïve T cells encounters matching antigen, and begins activation process
• different T cells play roles in immune response
12. Helper T cells
• do not kill pathogens or destroy infected cells
• necessary for immune response
• "managers" of immune response
• divide rapidly and secrete cytokines after activation
• cytokines from helper T cells help activate B cells and other T cells
• most helper T cells die out after pathogen has been cleared
• some remain in lymph as memory cells
• ready to produce large numbers of antigen-specific helper T cells if pathogen attacks again
13. Cytotoxic T cells
• destroys tumor cells, damaged cells, and infected cells once activated
• involved in rejection of transplanted organs
• divides rapidly to produce "army" of identical cells
• when they find antigen-carrying pathogens, it releases toxins that form pores in cell's membrane
• cell bursts, destroying the cell and virus inside of it
• most die off after viral infection is under control
• some also remain as memory cells
14. Regulatory T cells
• shut down cell-mediated immunity at the end of an immune response
15. Active immunity
• immunity that results rom pathogen stimulating immune response
• leaves you with memory cells for specific pathogen
• pathogen is unlikely to re-infect you and make you sick again
• some memory cells can last for a lifetime
• also can occur through immunization
• deliberate exposure of a person to pathogen to provoke immune response
• to prevent actual infections by pathogen
• pathogen typically injected
• weakened form is used to provoke immune response yet not actually infect
• immunized: measles, mumps, rubella, whooping cough, and chicken pox
16. Passive immunity
• humoral immunity that ends after a few days

Immune System: Nonspecific Defenses

1. Immune system protects body from "germs" and other harmful substances
2. First line of defense
• variety of barriers that keep most pathogens out of body
• pathogens: disease-causing agents, such as bacteria and viruses
• defenses in first line are the same regardless of type of pathogen
• mechanical barriers
• physically block pathogens from entering body
• skin is the most important defense against pathogens
• physical barrier between body and outside world
• skin is a tough, near-waterproof coating that is very difficult for pathogens to penetrate
• body openings (mouth, nose, etc) have different barrier
• mucous membranes line these openings
1. respiratory, gastrointestinal, and urinary tracts
• mucous membranes secrete mucus, a slimy substance that coats the membrane and traps pathogens
1. also have cilia, which sweep mucus and trapped pathogens toward body openings to be removed from the body
• pathogens removed from respiratory tract when you sneeze or cough
• tears wash away pathogens from eyes
• urine flushes pathogens out of urinary tract
• chemical barriers
• proteins that destroy pathogens at body's surface
• lysozymes kill pathogens by breaking open cell walls
• hydrochloric acid secreted by mucous membranes lining stomach kills pathogens that enter the stomach in food or water
• biological barrier
• living organisms that compete with pathogens
• bacteria cover skin, gastrointestinal, urinary, and genital tract areas
• bacteria are not harmful, and prevent harmful bacteria from becoming established in the body
• compete for food and space
• helpful bacteria may change pH to make conditions less suitable for harmful bacteria
3. Second line of defense
• inflammatory response
• red, warm, swollen, and painful injuries are signs of inflammatory response
• first responses of immune system to infection or injury
• triggered by cytokines and histamines
1. released when tissues are damaged
• cytokines: chemical signals used to communicate between cells
• histamines: chemicals that cause inflammation and allergies
• changes caused by cytokines and histamines help remove cause of damage and start the healing process
1. causes blood vessels to dilate, increasing blood flow to the area
4. White blood cells
• cytokines attracts white blood cells to the site of inflammation
• leukocytes are immune system cells that are specialized to fight infections
• primary cells of immune system and found all throughout the body
• leukocytes identify and remove pathogens, debris, and abnormal body cells
• some leukocytes are nonspecific
• monocytes, macrophages, neutrophils, eosinophis, and basophils
• part of second line of defense
• monocytes, macrophages, and neutrophils destroy pathogens in blood and tissues by phagocytosis
• process of engulfing and breaking down pathogens and unwanted substances
• pathogen broken down within macrophage

Respiratory System

1. Human respiratory system brings in oxygen and releases carbon dioxide
• oxygen drawn in through respiratory tract, then delivered to the blood
• above process called external respiration
• exchange of gases between blood and cells of body is called internal respiration
2. Cellular respiration vs. Respiration
• respiration is transport of oxygen from outside air to cells of body, and carbon dioxide in the opposite direction
• cellular respiration is the biochemical definition of respiration
• both very different from one another
• cellular respiration takes place in individual cells, while respiration involves transport of metabolites between organism and the external environment 
3. Structures of respiratory system
• nose and nasal cavity: filter, warm, and moisten the inhaled air
• nose hairs and mucus in the nose catch airborne particles and prvent them from reaching the lungs
• air passes through pharynx, a long tube shared by digestive system
• food and air pass through pharynx
• epiglottis closes over trachea when food is swallowed to prevent choking or inhaling food
• pharynx is important for vocalization in humans
• larynx (voicebox) is found just below the area where the pharynx splits into trachea and esophagus
• voice is generated in larynx
• air in lungs is needed for speech
• trachea (windpipe) divides into right and left bronchi in lungs
• bronchi branches out into smaller bronchioles (do not contain cartilage) 
• bronchioles lead to alveoli, where most gas exchange occurs
4. Respiration of oxygen (four stages) 
• ventilation from atmosphere into alveoli of lungs
• pulmonary gas exchange from alveoli into pulmonary capillaries
• gas transport from pulmonary capillaries through circulation to peripheral capillaries in organs
• peripheral gas exchange from tissue capillaries into cells and mitochondria
5. Ventilation (in detail) 
• air enters body through nose
• it is warmed, filtered, and passed through nasal cavity 
• passes larynx and move into trachea
• bronchi are lined with ciliated epithelium and mucus-producing cells
• breathing in is an active movement
• contraction of diaphragm uses ATP
• diaphragm: muscle found below the lungs
• contraction of diaphragm causes volume of chest cavity to increase, and air pressure inside lungs decrease
• pressure different causes air to rush into lungs
• relaxation of diaphragm causes lungs to recoil, and air is pushed out of the lungs
• exhaling is passive process powered by elastic recoil of the chest
6. Pulmonary gas exchange
• gas exchange occurs in alveoli by diffusion of gases between alveoli and blood passing in lung capillaries
• diffusion: high concentration to low concentration
• breathing results in loss of water from body
• oxygen transported across membrane of alveoli, and attracted to the hemoglobin within red blood cell
• oxygenated blood travels through aorta, to smaller arteries, arterioles, and into peripheral capillaries where gas exchange occurs
7. Peripheral gas exchange
• oxygen concentration in body cells is low, so oxygen diffuses from blood into body cells when it reaches peripheral capillaries
• carbon dioxide diffuses form cells to capillaries
• usually in the form of biocarbonate (HCO3) 
• biocarbonate is picked up by red blood cell, and turned into carbonic acid
• gas exchange between body and environment occurs in alveoli
8. Gas exchange and homeostasis
• equilibrium between carbon dioxide and carbonic acid is important for controlling acidity of body fluids
• if proper respiration is interrupted: 
• respiratory acidosis: arterial blood contains too much carbon dioxide, which drops the blood's pH
• respiratory acidosis results form increased respiration, causing blood pH to rise
9. Control of breathing by respiratory system
• can be controlled consciously and unconsciously
• conscioulsy: yoga, swimming, karate
• unconsciously: speech or vocal training
• muscular contraction and relaxation controls rate of expansion and constriction of lungs
• when carbon dioxide levels increase, causing blood pH to drop, the medulla (brain part that controls breathing) sends impulses to diaphragm and muscle between ribs
• causes them to contract and increase rate of breathing
• without breathing, oxygen levels fall, and can lead to permanent brain damage, followed by death
• healthy person cannot stop breathing voluntarily
• not inhaling leads to great air hunger
• not breathing leads to loss of consciousness, and autonomic nervous system takes over and resumes breathing
10. Inhalation
• started by diaphragm and supported by external intercostal muscles
• active process that needs ATP 
• normal respiration is 10-18 breaths per minute
• average adult will exchange 500 mL to 700 mL of air
• breath capacity is called lung volume, or tidal volume
11. Exhalation
• generally a passive process
• forced exhalation is carried out by abdominal and internal intercostal muscles
• lungs have natural elasticity, so they recoil from stretch of inhalation, and air flows out until pressures in chest and atmosphere reach equilibrium
12. Respiratory diseases and disorders
• term for diseases of the lung, bronchial tubes, trachea, and throat
• emphysema
• chronic lung disease
• loss of elasticity of lung tissue
• destruction of elastic structures that support alveoli and capillaries that feed alveoli, causing them to becoming hard and stiff 
• walls of alveoli break down and alveoli become larger
• amount of oxygen that can enter the blood per breath is reduced because large alveoli are not efficient
• symptoms: shortness of breath on exertion and and expanded chest
• damage to alveoli is irreversible
• caused mainly by smoking
1. leading cause of emphysema
• bronchitis
• inflammation of bronchi
• acute bronchitis caused by virus or bacteria, and may last several days or weeks
• characterized by cough and mucus production
• symptoms related to inflammation of airways and phlegm production
• chronic bronchitis usually part of syndrome called chronic obstructive pulmonary disease
• defined clinically as a persistent cough that produces mucus
1. at least three months in two consecutive years
• asthma
• chronic illness where airways narrow and becomes inflamed
• excessive amounts of mucus are made by the lungs
• happens in response to one or more triggers
1. exposure to allergen (mold, dust, or pet hair) 
• most common triggers in children are viral illnesses
1. causes symptoms such as wheezing, shortness of breath, chest tightness, and more breathing distress
• most patients feel well between asthma attacks
• may remain short of breath after exercise for longer periods of time than others
• symptoms of asthma can be controlled with combination of medicines and environmental changes
• pneumonia
• alveoli become inflamed and fill with fluid
• gas exchange cannot happen across alveoli membrane
• can result from variety of causes
1. infection with bacteria, viruses, fungi, or parasites
2. chemical and physical injury to the lungs
• symptoms include cough, chest pain, fever, and difficulty in breathing
• treatment depends on cause
• bacterial pneumonia is treated with antibiotics
• tuberculosis (TB) 
• common and deadly infectious disease
• caused by bacteria Mycobacterium tuberculosis
• most commonly attacks lungs
1. can also affect central nervous system, lymphatic system, circulatory system, genitourinary system, bones, joints, and skin
• 1/3 of world has been exposed to TB bacterium
• lung cancer
• epithelial (inner lining) tissue in lungs grow out of control
• leads to invasion of nearby tissue and growth of tumor beyond lungs
• most common cause of cancer-related death
• common symptoms: shortness of breath, coughing, and weight loss
• most common cause: exposure to tobacco smoke
1. radon gas, asbestos, and air pollution

Circulatory System

1. Main components: heart, blood vessels, and blood
2. Heart
• muscular organ that pumps blood through by repeated contractions
• cardiac means "related to the heart" 
• made up of mostly cardiac muscle tissue
• found in the left to middle of the chest
• largest part slightly to the left
• left ventricle is stronger
• left lung smaller because heart takes up space
3. Blood flow through the heart
• two different loops
• left side loop and right side loop
• right side
• collects deoxygenated blood from body and pimps it into lungs
• releases carbon dioxide and picks up oxygen
• left side
• carries oxygenated blood back from lungs
• through the heart, then through the rest of the body
4. Heart has four chambers
• two upper atria
• thin-walled blood collection chambers
• pump blood into ventricles
• two lower ventricles
• heart chambers that pump blood into the body
• right side of heart
• deoxygenated blood enters right atrium
• blood enters right ventricle and pumps blood through pulmonary arteries and into the lungs
• carbon dioxide is released and oxygen picked up
• pulmonary veins bring oxygenated blood back to heart and into left atrium
• blood moves to left ventricle, which pumps it into the body through the aorta
• lower ventricles are thicker and stronger than upper atria
• muscle wall surrounding left ventricle is stronger than muscle wall around right ventricle
1. left ventricle needs to exert enough force to pump blood throughout whole body
2. right ventricle only needs enough force to pump blood to the lungs
5. Valves
• maintains flow of blood by opening and closing in one direction only
• blood can only move forward through the heart, and prevented from flowing backwards by valves
• unidirectional flow
• atrioventricular (AV) valves make sure blood flows from atria to ventricles
• on right side of heart: tricuspid valve
• left side: mitral/bicuspid valve
• semilunar (SL) valves prevent blood flowing back from arteries into ventricles
• right side: pulmonary valve because it leads to pulmonary arteries
• left side: called aortic valve because it leads to aorta
6. Heartbeat
• meshwork of cardiac muscles
• interconnected by gap junctions
• allows electric stimulation to spread quickly
• self-exciting muscle
• contrast to skeletal muscle, which needs nervous stimulation to contract
• heart rate can be changed by nervous or hormonal signals
7. Control of heartbeat
• sinoatrial node (SA node) "cardiac pacemaker" 
• upper wall of right atrium
• responsible for wave of electrical stimulation by creating action potential
• causes cardiac cells to contract
• contraction reaches atrioventricular node (AV node) 
• lower right atrium
• conducts electrical impulse that comes from SAT node to ventricles
• impulse is delayed, so allows ventricles to fill with blood before ventricles contract
• heartbeat controlled by nerve messages from autonomic nervous system
• Bundle of His
• collection of heart muscle cells
• specialized for electrical conduction that transmits electrical impulses from AV node
• branches into Purkinje fibers
1. specialized cardiac muscles
2. conduct action potential
3. causes ventricles to contract in controlled way
8. Heartbeat: two parts
• systole: contraction of heart chambers, driving blood out of chambers
• distole: when heart relaxes after contraction
• all four chambers undergo systole and distole so blood would keep moving
• when chambers are referred to, usually talking about ventricles
9. Heart sounds
• lub-dub, lub-dub
• heart valve shutting down causes those heart sounds/heartbeat
• valve closes when pressure falls below aorta and pulmonary artery pressure
10. Blood vessels
• transport blood throughout body
• arteries: large, muscular vessels that carry blood away from the heart
• arteriole: small diameter blood vessel that branches from an artery and leads to capillaries
• veins: carry blood toward heart, especially low-oxygen blood from tissues
• venule: small vessel that allows deoxygenated blood to return from capillaries to veins
• capillaries: smallest of body's blood vessels, important for interchange of gases and other substances between blood and body cells
• structure: 
• endothelium: thin layer of cells that creates smooth inner lining
• endothelium tissue is specialized endothelium
• lines entire circulatory system, and has layer of smooth muscle, well developed in arteries
• connective tissue around smooth muscle (made mostly of collagen) 
1. contains nerves that supply smooth muscular layer
2. ones surrounding larger vessels contain capillaries to bring nutrients to tissue
• capillaries made up of single layer of endothelium and small amount of connective tissue
11. Arteries and arterioles (in more detail) 
• carries blood away from heart
• three major layers
• inner endothelium layer
• middle layer of smooth muscle
• outer layer of connective tissue (stretchy) 
• elastic quality allows them to carry pressurized blood from heart to body
• aorta is largest artery in body
• receives blood from left ventricle of heart through aortic valve
• branches into arteries and arterioles
• arterioles
• have thin muscular walls, one or two layers of smooth muscle
• primary site of vascular resistance
1. resistance to flow
2. blood must overcome this for it to be pumped through circulatory system
12. Veins and venuoles
• returns deoxygenated blood to heart
• most veins have one way flaps (valves) 
• prevents blood from flowing backwards and pooling in our limbs due to gravity
• venule structure
• inner endothelium, middle layer of muscle and elastic tissue, and outer layer of fibrous connective tissue
• middle layer is poorly developed, so venules have thinner walls than arterioles
13. Capillaries
• smallest blood vessels (5-10 μm in diameter) 
• connects arterioles and venules
• important for exchange of oxygen, carbon dioxide, and others
• made of only a single layer of endothelium cells
• molecules (water, oxygen, etc) can pass through by diffusion
• waste products can diffuse back into blood and be carried away
• blood cells need to pass through single file
14. Roles of blood vessels
• not involved in regulating transport of blood
• vasodilation
• blood vessels in body become wider due to relaxation of smooth muscle in vessel wall
• reduces blood pressure
• nitric dioxide is a vasodilator
• vasoconstriction
• constricting of blood vessels
• contracts smooth muscle in vessel wall
• controlled by some hormones and neurotransmitters
1. vasocontrictors
• permeability
• important for release of nutrients to the tissue
• allows certain molecules and ions to pass through by diffusion
• permeability increases during an immune response
1. allows white blood cells and other substances to get to the site of injury
• oxygen is most critical nutrient being transported
1. hemoglobin has 95-100% oxygen
15. Blood pressure
• refers to the force exerted by circulating blood on walls of blood vessels
• usually means arterial pressure, the pressure in large arteries
• results from force that is applied to blood by contracting heart
• systolic arterial pressure is peak pressure in arteries
• arterial pressure measured by sphygmomanometer
• height of column of mercury indicated pressure of circulating blood
• even though modern machines don't use mercury anymore, the measurement is still in mmHg
• range
• systolic: less that 120 mmHg
• diastolic: less than 80 mmHg
• usually written as systolic/diastolic mmHg
• people who have systolic pressure around 115 mmHg instead of 120 mmHg have less health problems
• hypertension is a condition when a person's blood pressure is chronically high
• 140/90 or higher
16. Arterioles and blood pressure
• arterioles have greatest influence on local blood flow and overall blood pressure
• pulmonary and systemic circulations
• double circulatory system of blood flow refers to pulmonary circulation and systemic circulation in mammals
• pulmonary circulation
• carries oxygen-poor (deoxygenated) blood away from heart to lungs, and returns oxygenated blood back to heart
• leaves right ventricle through pulmonary arteries (only arteries that carry deoxygenated blood) 
• in lungs, red blood cells release carbon dioxide and pick up oxygen during respiration
• oxygenated blood leaves through pulmonary veins, and return it to the left side of the heart, completely pulmonary cycle
• oxygenated blood distributed to rest of body through systemic circulation
• systemic circulation
• portion of cardiovascular system that carries oxygenated blood away from heart and returns deoxygenated blood back to heart
• oxygenated blood from lungs leaves left ventricle from aorta, and distributed to the organs and tissues
• deoxygenated blood then collected by venules and returns to the right heart, completing the cycle. 
• re-oxygenated through pulmonary circulation
• coronary circulation
• heart's own blood supply
• heart muscle tissue is so thick that it needs blood vessels to deliver oxygen and nutrients deep within it
• vessels that deliver oxygen rich blood are cardiac veins
• portal venous system
• capillary be drains into another capillary bed through veins
• uncommon because capillary beds usually drain to heart
• considered venous because blood vessels that join the two capillary beds are either veins or venules
17. Lymphatic system
• complex network of lymph nodes, lymph ducts, lymphatic tissues, lymph capillaries, and lymph vessels throughout the whole body
• conduit for fluid called lymph
• also called secondary circulatory system
• three functions
• removal of excess fluid from body tissue
• absorption of fats (fatty acids or lipids) and transport of fats to cardiovascular system
• production of certain white blood cells, which help in immune response
• lymph: blood plasma that leaks from capillaries of cardiovascular system
• fills space between individual cells of tissue
• becomes part of interstitial fluid
• plasma forced out of capillaries and forced back in because of hydrostatic pressure
• increases volume of interstitial fluid when outside of blood capillaries
• most interstitial fluid returned to capillaries by osmosis
• excess fluid collected by lymphatic system into lymph capillaries
• processed by lymph nodes before going back to circulatory system
• within lymphatic system, fluid called lymph and same composition as original interstitial fluid
• fatty acids transportation
• also known as fats or lipids
• transported through cardiovascular system differently than other nutrients
• absorbed by cells in villi in small intestine
• forms a complex with protein molecules
• lipo-proteins called chylomicrons
• transported via lymphatic system and eventually gets processed by liver
18. Lymph nodes
• filters or traps for foreign particles and contain white blood cells
• human lymph noes
• bean-shaped
• few millimeters to 1-2 cm
• white blood cells located in honeycomb of lymph nodes
• microorganisms and tissue debris are removed from lymph in lymph nodes
• swell and feel sore when the body is infected because of increased production of white blood cells
• spleen and tonsils are large lymphoid organs
• serve similar functions to lymph nodes
• spleen filters blood cells rather than bacteria or viruses 
19. Lymphatic circulation
• not closed and has no central pump
• lymph movement occurs slowly because of peristalsis, valves, and squeezing action of skeletal muscles
• move in one direction only
• valves in lymph vessels
• movement depends on movement of skeletal muscles to squeeze the lymph through, especially near joints
• lymph transported to larger lymphatic vessels that drain into circulatory system at right and left subclavian veins
20. Homeostasis Imbalance of Lymphatic System
• disease: elephantiasis
• infection of lymphatic vessels cause thickening of skin and enlargement of underlying tissues
• commonly caused by infection of parasitic roundworms
• lymphedema causes abnormal swelling mostly in arms and legs
• occurs if lymphatic system is damaged or underdeveloped
• lymphoma (lymphatic cancer): cancer of lymphatic system
• cells divide too rapidly and grow without order or control
• lymphoma can start almost anywhere
21. Homeostasis Imbalance of Cardiovascular System
• cardiovascular disease (CVD) usually refers to diseases related to atherosclerosis
• inflammatory response in walls of arteries that causes swelling and buildup of plague
• plague is made of cell debris, cholesterol, fatty acids, calcium, and fibrous connective tissue that build up around an area of inflammation
• plague grows and stiffens, which narrows the arteries and reduces the flow of blood
22. Atherosclerosis
• begins in later childhood
• usually found in most major arteries
• causes: high-fat diet, high cholesterol, smoking, obesity,  and diabetes
• becomes a threat to health when plague buildup interferes with blood circulation in heart or brain
• blockage in heart can lead to heart attack
• blockage in brain can lead to stroke
23. Coronary heart disease
• result of buildup of plague within walls of coronary arteries
• most individuals have no symptoms until a heart attack happens
• symptom includes chest pain (angina pectoralis) happens during times of stress or physical exertion
• pain means heart muscle fibers need more than they are getting
• heart attack (myocardial in farction) occurs when buildup and blockage of a coronary artery by plague blocks the blood supply to a part of the heart
• also caused by small piece of plague that breaks away when a larger piece of plague breaks apart
• small piece called embolus can get stuck in a coronary blood vessel, causing embolism
• cardiac muscle cells that are deprived of oxygen for more than five minutes will die, and cannot be replaced
• coronary heart disease is leading cause of death in adults in the U.S. 
24. Stroke
• loss of brain function due to stoppage of blood to the brain
• can be caused by blood clot (thrombosis), free-floating object (embolism) or bleeding (hemorrhage) 
• risk factors
• advanced age
• high blood pressure
• previous stroke
• high cholesterol
• cigarette smoking
• reduction of blood pressure is important for reducing the risk of a stroke
25. Preventing cardiovascular diseases
• non-controllable risk factors
• age: older people are more likely to develop cardiovascular disease
• gender: men under 64 are more likely to die of CHD than women, but gender difference declines with age
• genetics: family history of cardiovascular disease increases risk
• controllable risk factors
• tobacco smoking: give up smoking
• diabetes: causes metabolism changes, which are risk factors
• high cholesterol levels: "bad cholesterol" high levels are a significant risk factor
• obesity: fat around the torso increases risk significantly
• high blood pressure: hypertension can cause atherosclerosis
• lack of physical activity: aerobic activity helps keeps the heart healthy
• poor eating habits: nutrient poor food can lead to high cholesterol and weight gain
26. Congenital heart defect
• problem with structure of heart, present at birth
• most common type of major birth defect
• most defects obstruct blood flow in the heart or vessels, or cause blood to flow in an abnormal pattern through the heart
• treatment includes medicine, surgery, and other medicinal procedures
• some mild defects may be repaired by body over time

Muscular System

1. Muscle fibers
• specialized structures
• able to contract
• muscles are responsible for movement
• almost all movement in body is result of muscle contraction
2. Skeletal muscle tissue
• usually attached to skeleton
• used to move the body
• generally contract voluntarily (by somatic nervous system) 
• can contract involuntarily through reflexes
3. Smooth muscle tissue
• found within walls of organs and structures
• involuntary muscle: not under conscious control
4. Cardiac muscle
• specialized muscle
• found only within heart
5. Skeletal muscle (in detail) 
• responsible for body movement and body posture
• ~639 skeletal muscles in human body
• under conscious/voluntary control
• muscle cells that have many nuclei
• contains light and dark trips, called striations
• result of orientation of contractile proteins inside cells
• also called striated muscle
• adult males made of ~40-50% skeletal muscle tissue
6. Smooth muscle (in detail) 
• found in walls of hollow internal organs
• blood vessels, intestinal tract, urinary bladder, and uterus
• under control of automatic nervous system
• involuntary muscle (stated above) 
• do not have striations, so non-striated muscle
• spindle-shaped, with one nucleus in each cell
• generally arranged in sheets or bundles
• connected by gap junctions
1. little pores or gaps in cell membrane that link adjoining cells
2. allow quick passage of chemical messages between cells
• contracts slowly and rhythmically
7. Cardiac muscle (in detail) 
• found in walls of the heart
• involuntary muscle
8. characteristics of both smooth muscle and skeletal muscle cell
• one central nucleus, but striated muscle
• rectangular in shape
• contraction is strong and rhythmical
• highly resistant to fatigue
• has largest amount of mitochondria per cell of any other muscle
• more mitochondria = more energy = constant movement for a longer period of time
• similar to skeletal muscle in chemical composition
• however, structure is different
• muscle fibers typically branched like tree branch
• connect to other muscle fivers by inter-calculated discs (gap junction) 
9. Structure of muscle tissue
• skeletal muscle is made of skeletal muscle tissue, connective tissue, nerve tissue, and vascular tissue
• vary considerably in size, shape, and arrangement of fiber
• each skeletal muscle is single large, cylindrical muscle cell
• each nucleus in fiber originated from one single myoblust
• smooth and cardiac do not develop this way 
• individual skeletal muscle might be made of thousands of muscle fibers
• bundled together and wrapped in connective tissue called epimysium
• fascia surrounds and separates skeletal muscles
• parts of epimysium fold inward to create fascicles
• each fascicle contains bundle of muscle fibers
• skeleton muscle fibers are soft and fragile
• connective tissue gives support and protection
• helps them withstand forces of contraction
• also provides pathways for blood vessels and nerves
• blood vessel deliver nutrients and oxygen, and remove waste products
10. Muscles and bones
• muscles can only actively contract
• extend passively
• ability of muscles to move parts of the body in different directions
• requires that they be attached to bones in pairs that work against each other (antagonistic pairs)
• muscles are attached to one end of a bon, skip a joint, and attached to a point on other side of joint
• connective tissue forms tendon
• thick, ropelike structure
• the origin (attachment point) does not move when muscle contracts
• tendons and muscles work together and exert pulling force on joints
• flexor: muscle that causes angel of joint to become smaller
• extensor: muscle that causes a joint to straighten out
• joints in body act like levers that reduce amount of effort to make large movements
11. Muscle contraction
• occurs when muscle fiber generates tension through actin and myosin
• muscle fiber contains cellular proteins and myofibrils
• myofibrilis is a long, cylindrical organelle
• made up of actin and myosin
1. actin is thin and threadlike
2. myosin is thicker
• actin and myosin organized into sarcomeres
• actin filament anchored to Z lines
• one Z line to another is a sarcomere
• all sarcomeres contract at the same time when a muscle fiber contracts
12. Neuromuscular junction
• voluntary muscles 
• brain sends nerve signals in form of action potential
• reflexes
• signal to contract can originate in spinal cord through reflex arc
13. Sliding filament theory
• how muscles contract
• presence of calcium ion allows interaction of actin and myosin
• troponin and tropomyosin act as barriers between actin and myosin, preventing contract
• Ca2+ binds to actin filament, and toponin-tripomyosin complex changes.
• allows actin and myosin to come into contact
• action potential arrives at axon terminal of motor neuron
• arrival of action potential activates voltage-dependent calcium channels at axon terminal
• calcium rushes into neuron
• Ca2+ causes vesicles to fuse with plasma membrane, releasing acetylcholine into synaptic cleft
• activation of acetylcholine receptors on muscle fivers open sodium/potassium channel, triggering action potential in muscle fiber
• spreads through muscle fiber network and depolarizes inner portion of muscle fiber
• activates specialized storage sites throughout muscle (sarcoplasmic reticulum) to release Ca2+
• sarcoplasmic reticulum is a special type of smooth endoplasmic reticulum
• Ca2+ ions bind to actin filaments of myofibrils and activate actin for attachment by myosin head filaments
• activated myosin binds strongly to actin filament
• upon binding, myosin rotates at myosin-actin interface, and bends a region in the myosin head
• shortening of muscle fiber occurs when bending part of myosin pulls actin and myosin filaments across each other. 
• binding of ATP with myosin lets myosin head detach from actin
• ATP breaks down into ADP + Pi, and the breaking of bonds gives energy to myosin bead, which allows it to bind to actin again
• repeats as long as ATP and Ca2+ are available
14. Motor units: groups of individual muscle fibers that are called motor units
• each muscle fiber contracts either all the way or not at all
15. Cardiac muscle contractions
• good blood supply = provides nutrients and oxygen
• highly resistant to fatigue
• heart is unable to pump well when there is a lack of blood to heart muscle tissue, which leads to heart attack
• cardiac muscle can initiate contraction by itself
• heart can still beat properly even after connections to central nervous system are severed
• a single cardiac muscle cell can contract rhythmically
• after heart attack or cardiac arrest, fibrillations can result
• life-threatening
• can be stopped by defibrillation
16. Smooth muscle contractions
• must often ben stretched
• elasticity
• do not depend on motor neurons to be stimulated
• however, automatic nervous system is connected
• also can be affected by hormones
• oxytocin causes contraction of uterus during childbirth
• muscle contraction caused by sliding of myosin and actin filaments
• calcium initiates contractions in a different way in smooth muscle

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