Biology 2 complete summary PDF

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Summary

Valence electrons & their influence on the type of bonding  ➔ Interactions  ◆ Exchanged (ionic)  ◆ Shared (covalent)  ➔ Goal: OCTET  ➔ Metal: usually lose electrons & turn positive   ➔ Non-metal: usually gain electrons & turn negative  ...

Description

• Valence electrons & their influence on the type of bonding ➔

Interactions ◆ Exchanged (ionic) ◆ Shared (covalent)

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Goal: OCTET Metal: usually lose electrons & turn positive Non-metal: usually gain electrons & turn negative Atomic # = # protons Isotopes: same # proton, diff # neutrons

• Bonds & interactions ➔

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Covalent bonds: ◆ strongest ◆ Gaseous or liquid at room temperature ◆ Between monomers of macromolecules Ionic bonds: ◆ Solid at room temperature Hydrogen bonds: ◆ Relatively weak interactions (much weaker than covalent) ◆ Made when one hydrogen atom participating in a covalent bond is attracted to another electronegative atom also participating in a covalent bond ● Possible between 2 org molecules w partial charges ○ In 2nd and 3rd structure of proteins ○ crucial for DNA and proteins ◆ Responsible for making H2O special solvent Van der Waals ◆ Weak: more susceptible to disturbance ◆ distance-dependent interaction between atoms or molecules: not result of chemical electronic bond ● Vanishes at longer distances ◆ These attractions do not affect chemical changes but are significant in influencing the physical properties of gases and liquids 

• The main functional groups and their properties.

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Methyl group used to turn on/off genes when added to DNA or proteins associated w DNA Polar groups: ◆ Carbonyl (found in sugars where they from ketones or aldehydes) ◆ Hydroxyl ● Turns molecule to alcohol ◆ Sulfhydryl ● Found in R groups of 2 amino acids ● Can stabilize tertiary structure of amino acid Non polar groups: ◆ Methyl Charged groups: ◆ Phosphate group

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● Important constituent of nucleotides (ATP, DNA RNA) and phospholipids ◆ Carboxyl (forms R-COO-) at pH of most biological systems (acidic) ◆ Amino (forms R-NH3+) at pH of most biological systems (basic) Aldehydes: double-bonded oxygen attached to a terminal carbon atom Ketones: double-bonded oxygen attached to an internal carbon atom

• Why carbon? ➔

Advantages of carbon ◆ 4 valence electrons promote complexity in compounds that can be formed ◆ Can form double and triple bonds (more variation in the molecular structure of organic compounds)

• Isomers ➔ ➔ ➔ ➔

Structural ◆ same molecular formula but connected differently Cis ◆ groups on the same side Trans ◆ Groups on diff sides Enantiomers ◆ mirror images of one another

 • The importance of water ➔ ➔

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All chemical rx in living organisms take place in an aqueous environment Why H2O special? ◆ molecular structure: v shaped and consequent distribution of electrons ◆ Covalent bond between O & H: electrons spend more time near oxygen: unequal sharing of electrons results in slightly negative pole and slightly positive pole (polar) ● Can bring about ionization of other substances bc of polarity ● Water is the universal solvent in biological systems: its polarity causes it to act as a solvent ◆ Temperature buffer ● Ice absorbs large amount of heat when it melts ● High latent heat of fusion: releases relatively large amounts of heat when going from liquid to solid ● One of the highest specific heats (can take up a lot of heat with relatively small shifts in temperature ● Prevents sharp changes in temperatures that would be destruction to structure of macromolecules ◆ High surface tension Average human body is 50-65% water (males on average have a higher percentage of body water than females because they have less body fat. More fat, less water.

• How hydrogen bonds affect water properties ➔

Water states ◆ When water freezes, water molecules form a crystalline structure maintained by hydrogen bonding. ● Ice is less dense than liquid water bc of orientation of H bonds (held in a relatively rigid geometric pattern by their hydrogen bonds, producing an open, porous structure) ◆

When water boiled, kinetic energy breaks hydrogen bonds: H2O molecules become gas ● High energy required bc of network of hydrogen bonds ●

As the water evaporates, energy is taken up by the process, cooling the environment ○

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Ex: Evaporation of sweat cools organisms down

In liquid water, hydrogen bonds are constantly formed and broken as the water molecules slide past each other

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Water’s high heat capacity

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Cohesion & surface tension

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a property caused by hydrogen bonding among water molecules (need lots of energy to break)

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Cohesion: attraction of molecules for other molecules of the same kind

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Water molecules have strong cohesive forces bc of their ability to form hydrogen bonds with one another

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Cohesive forces are responsible for surface tension

• Understand the pH scale and how a change in pH can affect the structure and function of macromolecules ➔ ➔

Puissance d'hydrogene ◆ Bc pH scale is logarithmic, each whole number drop on the scale represents a tenfold increase in acidity The optimum pH level varies depending on the molecule and where it functions

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↑ [electrically charged ions] interferes/influences the ability of molecules (specifically proteins) to chemically interact

• The four macromolecules of life: their basic structure, monomers, bonds, functions & solubility in water ➔

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Nucleic acids ◆ Monomers: nucleotides ◆ Polymers: DNA & RNA ◆ Structure: ● Nitrogenous base ○ Adenine, guanine, cytosine, thymine, uracil (RNA) ○ Purines: A & G ○ Pyrimidines: C & T ● Sugar containing five-carbon molecules ○ Deoxyribose (DNA) Ribose (RNA) ● Phosphate group ◆ Bonds: ● Bases of a pair bounded by hydrogen bonds ● Each sugar linked by phosphodiester linkage ◆ Function: genetic material ◆ Soluble in water: ✔ ◆ ATP build from nucleotide Proteins ◆ Monomers: amino acids ◆ Polymer: polypeptide ◆ Structure: ● Central carbon atom (alpha carbon) ● Amino group (NH2) (usually protonated + ) ● Carboxyl group (COOH) (usually deprotonated - ) ● Hydrogen atom ● R-group ◆ Bonds: C-N bond: peptide bond ● No hydrogen-bonding occurs in peptide bond ◆ Functions: ● Speed up the rate of reactions (enzymes) ● Structural proteins (ex collagen) ● Transport (ex hemoglobin) ◆ Soluble in water: ✔ Carbohydrates ◆ Monomer: monosaccharide ● Glucose, fructose, galactose ◆ Polymer: Disaccharides ● ○ Lactose, maltose, sucrose ● Polysaccharides ○ Starch, glycogen, chitin, cellulose ◆ Structure: ● Cx(H2O)y ● If has aldehyde group (carbonyl last in the chain): aldose sugar ○ Ex: glucose is aldose sugar ● If has ketone group (carbonyl internal): ketose sugar ○ Ex: fructose is ketose sugar ● Alpha form ○ Hydroxyl down ○ We can only digest alpha form ● Beta form ○ Hydroxyl up ●  ◆ Bonds: glycosidic bonds ◆ Functions: ● Energy ● Structural polysaccharides ○ Cellulose: in plant cell walls (rigid structure that encloses cell) ◆ In beta form ○ Chitin: in insects & crustaceans, cell wall of fungi ● Storage polysaccharides ○ Starch: energy storage for plants ○ Glycogen: energy storage for humans & other vertebrates (in liver & muscle cells)

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◆ Lipids ◆

When blood glucose ↓ glycogen broken down via hydrolysis to release glucose

Soluble in water: ✔ Fats & oils ● Structure: ○ Glycerol backbone ◆ small organic molecule with three hydroxyl (OH) groups ○ 3 fatty acid tails ◆ long hydrocarbon chain attached to a carboxyl group ◆ Saturated: ● only single bonds between carbons in hydrocarbon chain ● Saturated w hydrogen ◆ Monounsaturated: ● hydrocarbon chain has 1 double bond ◆ Polyunsaturated: ● Hydrocarbon chain has multiple double bonds ◆ Essential fatty acids ● Omega-3 : made from alpha-linolenic acid (ALA) ○ Found in fish, seeds ● Omega-6 : made from linoleic acid (LA) ● Found in nuts, grains, fats and oils from vegetables or fish ● Tryptophan, phenylalanine ◆ Important for energy storage and insulation ◆ After the liver stores all the glucose it can as glycogen, whatever remains is turned into triglycerides ◆ The triglycerides float through the bloodstream to be deposited into adipose tissue (squishy part of body) ◆  ● Fat molecules also called triacylglycerols or triglycerides ○ In human, it is stored in fat cells (adipocytes) which make up tissue called adipose tissue

 Phospholipids: ● 2 fatty acids and a phosphate group ● Part of membrane ◆ Steroids: ● 4 connecting carbon rings and a functional group that determines the steroid, generally create hormones ● Cholesterol is a steroid used to make testosterone and estrogen (also found in the membrane of the cell) ● Transported around the body by other lipids: if too much cholesterol in the bloodstream, then you have an excess of fats carrying it through your bloodstream (bad bc fats and cholesterol molecules can get stuck in your blood vessels, leading to blockages that cause heart attacks or strokes) ◆ fats are lipid soluble (water insoluble), hence their digestion and transport in the body needs water soluble molecules such as proteins (lipoproteins) ◆ Acid and alcohol yields an ester ◆ How might a plant cell compensate for the excessive membrane fluidity that occurs during prolonged exposures to elevated temperatures? ● Alter phospholipid composition to have longer fatty acids tails and fewer unsaturated fatty acids ○ Longer fatty acid, more saturated, fewer unsaturated fatty acids -> more solid ● When it’s warm: saturated fatty acid will interact together and prevent mvt ○ Cholesterol will prevent molecules from stacking, so more mvt ● When it’s cold: unsaturated or saturated acid act the same way (always rigid) ○ Cholesterol Lab 1: Intro to Homeostasis ➔ Homeostasis ◆ maintenance of dynamic equilibrium or relative internal balance by regulated change ➔ Normal pH of blood: 7.35-7.45 (below 6.8 or above 8 results in death) ◆

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Normal blood glucose levels: 80-100mg/100mL of blood OR 3.9-6.1mM Normal pH of human blood: 7.35-7.45 (outside this range=coma or death) ◆ Acidic conditions: metabolic or systemic acidosis ◆ Basic conditions: metabolic alkalosis

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Digestive system ◆ Allow nutrient absorption & availability ◆ Excrete waste ◆ Takes in nutrients, breaks them down, and eliminates unabsorbed matter (feces)

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Cardiovascular system

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Facilitate nutrient & waste transport

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Maintain constant body temperature Via the blood, distributes oxygen and nutrients to all body cells and delivers wastes and carbon dioxide to disposal organs Homeostatic regulation of pH

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● Uses buffering molecules & macromolecules that circulate in blood as defense in resisting blood pH changes Respiratory system ◆ Takes in oxygen and eliminates carbon dioxide ◆ Homeostatic regulation of pH ◆

● by increasing or decreasing respiratory rate CO2 is a product of ATP synthesis

◆ C O2 + H 2O ↔ H 2CO 3 ↔ H CO 3 −+ H +  ➔

Urinary system ◆ ◆ ◆ ◆

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Keep blood composition constant Excrete waste (eliminates nitrogenous waste produced through protein & amino acid breakdown and excess ions) Composed of kidneys, ureters, urinary bladder & urethra Produce erythropoietin (hormone) ● Involved in red blood cell maturation ● Synthesize glucose during periods of starvation Filters 150-180L/day of blood plasma (part of blood w no red nor white blood cells) ● Filtration allows kidneys to selectively process the resulting filtrate to remove waste products while retaining important molecules such as glucose Regulates body’s fluid, ion, pH homeostasis, blood pressure 1-1.8L of urine/day in a healthy person Control of blood glucose levels ● ●

All glucose present in the filtrate produced by the kidneys should be returned to blood Glycosuria ○ presence of glucose in urine ○ Temporary glycosuria ○

◆ When carbohydrate intake in diet exceeds normal levels Pathologic glycosuria ◆ Uncontrolled diabete mellitus ● Cells are unable to uptake glucose due to inadequate insulin production or

abnormalities in insulin receptors Kidneys attempt to maintain homeostasis by excreting glucose in the urine instead of reabsorbing it back into the blood Homeostatic regulation of blood pH ●

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Regulates concentrations of H+, HCO3- pH of urine fluctuates between 4.5-8 Diet high in protein decreases pH of urine Vegetarian & vegan diets increases pH of urine

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Metabolic or systemic acidosis & bacterial infections of the urinary tract can increase urine pH Urinary system maintains blood pH by excreting or reabsorbing back into the blood variable amounts of H+ & HCO3- ○ It can keep HCO3- to react w H+ and create more CO2 to push the equation to the left ○

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C O2 + H 2O ↔ H 2CO 3 ↔ H CO 3 −+ H + 

Skeletal, muscular systems ◆ Maintain constant body temperature Integumentary system (skin, hair, nails) ◆ Protects the body as a whole from the external environment ◆ Maintain constant body temperature Interstitial fluid (F  luid found in the spaces around cells) ◆ Nutrients and wastes pass between blood and cells via this fluid Coordination & communication among all the organ systems achieved by: ◆ Nervous system ● Messages conveyed along neurons to regulate other neurons, muscle cells & endocrine cells

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Endocrine system ●

Produces hormones ○ Regulate the activity of other cells & organs involved in homeostasis, growth, development & reproduction ○ Hormone released by endocrine cells into blood in cardio system ○ ○

Evoke responses from target cells that have precise receptors that recognize and bind that hormone 2 classes ◆ Steroid & other hydrophobic hormones ● Can pass through cell membrane

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● Bind to intracellular receptors in cytosol or nucleus ● Change in gene expression Polypeptide & amine hydrophilic hormones ● Cannot pass through cell membrane

Bind to cell surface receptors & trigger a signal transduction pathway (cascade of reactions) within the target cell ● Lead to intracellular responses Regulation of homoeostasis ●

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Uses negative feedback loops Uses antagonistic hormone pairs ◆ Chemicals synthesized & released by specific endocrine cells in response to a stimulus ◆ Function in a distinct pathway regulated by negative feedback

◆ Chemicals that share many of the same target cells but have opposing effects Control of blood glucose homeostasis ○ Insulin, glucagon, small intestine, liver, pancreas, fat & muscle are involved in blood glucose homeostasis ○

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Insulin ◆ Released by endocrine cells of pancreas called islet cells (specifically beta cells) ◆ Lowers blood glucose ◆ Promotes uptake of glucose in cells & storage as glycogen in the liver and muscle ◆ Stimulates conversion of excess glucose into fat for storage ◆ Slows down glycogen breakdown in the liver ◆ Inhibits of the conversion of molecules such as amino acids & glycerol to glucose Glucagon ◆ ◆ ◆ ◆

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Released by endocrine cells of pancreas called islet cells (specifically alpha cells) Increases blood glucose levels Increase glycogen hydrolysis Promotes conversion of amino acids & glycerol to glucose

Homeostatic control mechanisms involve: ◆ Receptor (sensor) ● detects stimulus ● Communicate w control center via an afferent (incoming) pathway ◆

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Control center or integrating center: ● determines appropriate response ● Communicates w effector via an efferent (outgoing) pathway Effector ●

Carries out response

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Stimulus produces change in variable Change detected by receptor

3. 4. 5. 6.

Receptor sends info along afferent pathway to control center Control center sends info along efferent pathway to effector Response of effector influence magnitude of stimulus Homeostasis returned

 Negative feedback mechanism ◆ Response reverse to the original stimulus Positive feedback mechanism

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Reinforces the stimulus, increases the stimulus

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Not homeostatic Ex: the release of oxytocin during childbirth, initial contractions stimulate the release of more oxytocin which increases contractions until delivery of the baby The chemical equation of aerobic cellular respiration:

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Key source of carbon skeletons for the biosynthesis of organic molecules: glucose Homeostatic regulation of pH 1000μL = 1mL

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Benedict’s reagent (blue) ◆ Tests for presence of certain carbs in a sln ◆ If carbs contain a free aldehyde or ketone, they will react w the reagent & sln will change colour ◆ If sln varies from green to brick red, glucose is present

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O 2 + Glucose ↔ AT P + H 2O + C O2 + H eat 

• The homeostatic mechanisms involved in glucose regulation ➔

Chemical equation for aerobic cellular respiration ◆ O2 + Glucose ⟶ ATP + H2O + CO2 + Heat

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Rise in blood glucose ◆ Insulin released by beta cells ● Promotes uptake of glucose into target cells by binding to specific plasma membrane protein receptors

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● Slows down glycogen breakdown in the liver ● Inhibition of the conversion of molecules (amino acids & glycerol) to glucose Drop in blood glucose ◆ Glucagon released by alpha cells

● Stimulates target cells in the liver to increase glycogen hydrolysis ● Promotes conversion of amino acids & glycerol to glucose Lab 2: Assessment of Blood Glucose Tolerance ➔ Concentration of glucose in blood depends on

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◆ How recently the person has eaten ◆ Whether carbohydrates were consumes ◆ If person has a disorder Glucose tolerance ◆ Ability of a person to clear glucose from the blood after a meal Hypoglycemia ◆ Blood glucose levels fall below the normal fasting level (lowest blood glucose level) ◆ In such a case, negative feedback mechanisms will attempt to reestablish homeostasis ● ● ●

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Breakdown of triglycerides in fat tissue to use as intermediate of cellular respiration However, certain organs, tissues & cells (ex: brain neurons) cannot use anything else than glucose as a reactant for cellular respiration That is why the brain is one of the first to feel the effects of hypoglycemia (hunger produces a feeling of

faintness/weakness, headache) ● Brain neurons are able to absorb glucose directly without the help of insulin (insulin-independent) Hyperglycemia ◆ High blood sugar ◆ If excess of glucose in blood, it can be converted to/stored as glycogen &/or fat Type 1 insulin-dependent (juvenile diabetes) ◆ Pancreatic beta islet cells unable to produce insulin ◆ Autoimmune disease ◆ 5-10% of diabetes cases ◆ Treatable by regular injections of genetically engineered human insulin Type 2 non-insulin-dependent (adult-onset diabetes) ◆ 90% of diabetics ◆ In the first stages of the disease, exercise & proper diet are often sufficient to manage the illness and reverse it Symptoms of untreated diabetes ◆ Glycosuria ● Excess of sugar in urine

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Polyuria ● Excessive loss of water in urine, high volume of urine Polydipsia ● Excessive...