AP Bio

Warm up 1/22: What are disease-causing organisms?

• bacteria

• viruses

• protists

• fungi

Warm up 1/23: What is biochemistry?

• chemical compounds incorporated in living things (carbs, proteins, nucleic acids, lipids)

Unit 1

warm-up questions

1. what is the difference between an atom, element, and compound? An atom is basic the unit for all matter, element is one particular atomthat cannot be broken, compound is multiple elements chemically bonded together

2. what are the 3 main components of an atom? what are their chargers? protons: positive, nuetrons: no charge/nuetral, electrons (smallest) negative

3. what type of bonds are found in:

   1. H2O: covalent

   2. H2O-H2O: hydrogen

   3. HCl: covalent

   4. C6H12O6: covalent

   5. NaCl: ionic

cohesion- the attraction between 2 like molecules

adhesion- the attraction between unlike molecules

Matter:

• has mass and takes up space

• affected by gravity (9.8 Newtons)

• consists of elements and compounds

Energy:

• moves matter

• potential, kinetic

• ability to do work

• conversions

• sound, heat, light

Element

• “pure” substance

• can’t be broken down

• ex. Hydrogen (H), nitrogen (N)

Compound

• 2 or more different elements combined in a fixed ratio

• ex. H20, CO2

Elements of life

• 96%: C, H, N, O

• 4%: P, S, Ca, K, Cl, Mg, Na and other trace elements

• CHONPS are 6 essential (KNOW THESE)

Atomic structure

• atom= smallest unit of matter that retains properties of an element

• subatomic particles:

  Neutron 1AMU, in nucleus, neutral charge

  Proton 1AMU, in the nucleus, positive charge

  Electron negligible, in shell, negative charge

Isotopes

• # of neutrons varies, but the same # of protons

• radioactive isotopes used as tracers *used for medical diagnosis to find abnormal body processes (nuclear medicine)

• Carbon-14 radioactive isotope used for carbon dating

Chapter review

Warm up 1/24: What are the 6 essential elements of life?

• CHONPS (carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur)

• carbon- everywhere, the basis of all life, “king of elements” makes up most bonds between

• hydrogen-found in water, necessary for hydrogen bonding, important in DNA replication

• oxygen- breath, respiration, key component in forming ATP

• nitrogen- found in nucleic acids, make up macromolecules (proteins), important for amino acids (22)

• phosphorus- backbone for DNA and RNA and backbone in ATP

• sulfur- cell repair, metabolism, digestion (proteins act as enzymes), growth, amino acids

Valence electrons- important for chemical bonding (carbon most important element king of all elements, in valence electrons)

Chemical bonds

strongest bonds:

• covalent: sharing of e-

  • polar: covalent bond between atoms that differ in electronegativity ex: H2O

  • nonpolar: e- shared equally; ex: O2 or H2

• ionic: 2 ions (±) bond (givers/takers)

  • Na+Cl-, KCl, NaF, KF, NH4 (ammonium)

  • affected by environment (if saturated in water)

Weaker bonds:

• hydrogen: interaction involving a hydrogen atom between a pair of other atoms having a high affinity for electrons

  • amino acids= proteins

  • nitrogen bases= nucleic acids

Warmup 1/27: why is carbon known as the chemical basis for life? describe at least two compounds carbon is found in and why they are so important and effect life on earth.

• because it is found in every organic molecule because it has 4 valence electrons, glucose and carbon dioxide, CO2 is for photosynthesis, glucose gets broken down for energy

Weaker bonds: weakest

• Van der Waals Interactions: short attractions between atoms and molecules close together, consisting of cohesive ( 2 same molecules) and adhesive (2 different) forces

  • examples: gecko hairs + wall surface

    • proteins folding in our bodies (amino acids form into certain structures)

• a molecules structure (shape) affects a molecules function

• same # of atoms but different structure

  • exogenous: morphine, heroin, opiates, mimic endorphins which are endogenous

  • endorphins produced in pituitary gland and hypothalamus in the brain

  • increase dopamine in brain

  • both cause euphoria and relieve pain

how do we release endorphins

our endogenous pain and stress relievers

• acupuncture

• exercise

• meditation

• sex

• playing music

• laughter

• ultraviolet light

• eating

reactants → products

• what is this reaction?

• chemical equilibrium: point at which forward and and reverse reactions offset one another exactly

• 6CO2 + 6 H2O → C6H12O6 + 6 O2 (photosynthesis) takes place in chloroplast

• C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + ATP (cellular respiration equation)

• cellular restoration takes place in mitochondria and cytoplasm

Warm-up: compare endogenous/exogenous. How are endorphins released and what activities release endoprhins.

• exogenous is what you externally take into your body and endogenous is what taken in internally like endorphins

• endorphins are released by the pituitary and hypothalamus

• activities that make you happy exercise, uv light, eating, meditation, laughing

Water is a polar molecule

• unequal sharing of e- between O and H

• Hydrogen bond: slightly negative O attracted to slightly positive H of a nearby molecule

• H2O can form up to 4 hydrogen bonds allows for cohesion surface tension

Cohesive behavior

• cohesion= water cohesion is the property of water molecules that allows them to stick together through hydrogen bonds

• surface tension= measure of how difficult it is to break or stretch the surface of a liquid

• jesus lizard can walk on water due to surface tension which is from the cohesion between water molecules

Adhesion

• adhesions= bonding between unlike molecules

• adhesion of H2O to vessel walls (xylem (carries water) and phloem (carries nutrients) ) in plants counters the downward pull of gravity

• blood in blood vessels

Moderation of temperature

• thermal energy (heat)= total amount of kinetic energy in a system

• temperature= measure of the intensity of heat *highest specific heat capacity of any liquid -4.184 Joules plays a major role in the earth climate

Water= High specific heat

• changes temp less when absorbs and loses heat

• creates a stable marine/land environment

• humans ~ 65 - 70 % H2O →stable temp of 98.6 degrees Fahrenheit (37 C)

• we have gotten taller and fatter so “normal” temp has gone down

Notes 01/29/25

How are the following important to biology? (Life)

1. Cohesion- surface tension, and plants the water traveling up the plant against gravity.

2. Adhesion- unlike molecules, and blood in blood vessels

3. Moderation of temperature- water stores heat, and controls our weather and climate.

Evaporative cooling 

• Water has a high heat of vaporization. (high specific heat capacity)

• Keeps stable temp in lakes & ponds 

• Helps to cool plants and Transpiration = the release of water vapor out of the stomata of plant cells. (co2 in o2 out) 

• Human perspiration.  (homeostasis) (sweating, shivering, goosebumps for surface area)

Things we need to keep stable: pH levels: acids in our stomach, glucose in our blood: pancreas; produces insulin.

Exocytosis- active transport; using energy (moving insulin into blood using atp)

Expansion Upon Freezing

Insulation by ice- less dense, floating ice insulates liquid H20 below.

• Life exists under frozen surface (ponds, lakes, oceans)

• Ice density = 0.92_ g/ml

• Water density = 1.0 g/ml

Water = Solvent of Life

Solution = liquid, homogeneous mixture of 2+ substances

Solvent =  dissolve agent (liquid)

Solute = dissolved substance 

Water = versatile solvent 

Solvent of life “like dissolves like” (polar dissolves polar)

Hydrophilic   hydrophobic 

Affinity for H2O Repel H20

Polar, ions nonpolar

Cellulose, sugar, salt oil, water

Blood Cell membrane

Acids and Bases

• Acids = increases H+ concentration

Ex: (HCI)

• Base = reduces H+ concentration

Ex: (NaOH)

• Most biological fluids in living things have a pH range of 6 -8

(1-6)Acids- HCL (stomach acid) , Rain water  , urine (flushing out waste)

(7) Neutral - human blood, tears 

(8-14) Basic - Cleaners, antacids

Warm up 1/30: draw a pH chart label 3 acids/3 bases and describe how they are important to life

acid: rainwater plants use rain water, hydrochloric acid stomach acid helps break down food, lemon juice (vitamin C)

base: seawater hosts 80% of life, stomach small intestine uptakes nutrients through microvilli( absorb any nutrients we ingest) and brings them into blood stream, antacids rebalance pH act as buffers

Buffers: reduce concentrations of H+ and OH- in a solution (weak acids and bases)

• buffers keep blood at pH of 7.4

• blood drops to 6.8 (acidosis can lead to death) or up to 7.8 (alkalosis can lead to death)

carbonic acid (H2CO3) - bicarbonate (HCO3-) System: important buffers in blood plasma, controls blood from being in dangerous levels

renal- kidneys

3 lines of defence

• chemical buffers to protect blood pH, act immediately and release hydrogen ions

  • carbonic acid bicarbonate

  • phosphate buffer system

  • protein buffer systems- hemoglobin

• respiratory system controls the amount of carbon dioxide in blood

  • too much carbon dioxide makes blood acidic

  • depth and rate of breathing

  • when you get nervous carbon dioxide builds up in the system (paper bag)

  • low CO2 decreases depth and rate of breathing

• renal system

  • slower to respond but more powerful and longer-acting

  • too low- kidneys increase reabsorption of bicarbonate and excrete more hydrogen ions by pees

  • too high- kidneys increase excretion of bicarbonate and absorb more hydrogen ions

Ocean acidification: (carbonic acid)

• industrial revolution increase the concentration of carbon dioxide in the atmosphere

• the pH ocean waters has fallen by 0.1 pH (8.25 to 8.15) units which equals an increase of 30% in acidity

• CO2+ seawater → carbonic acid → lowers ocean pH

• CO2 dissolves and becomes carbonic acid

Importance of carbon

• organic chemistry: branch of chemistry that specializes in study of carbon compounds

• organic compounds: contain carbon (&H)

• major elements of life: CHONPS

• carbon can form large, complex, and diverse molecules, macromolecules/biomolecules

• carbon- basis for all life

• hydrogen- major component of water

• nitrogen - atmosphere, DNA, proteins

• phosphorus- DNA , proteins, nucleic acids

• sulfur- proteins

• oxygen- respiration, water

Diversity of Carbonit has 4 valence electrons

• most common bond partners= H, O, N

• bonds can be single (CH4), double (C2H4), or triple covalent bonds (CO)

• carbon can form large molecules

  • 4 classes of macromolecules and their monomers:

    • nucleic acid- nucleotide

    • carbohydrate- monosaccharide

    • lipid- glycerol, fatty acids

    • protein- amino acid

• multiple shapes: molecules can be straight chains, ring-shaped, or branched. *structure determines function*

• forms isomers

  • molecules have same molecular formula, but differ in atom arrangement

  • different structures → different properties/functions

• structural isomer- varies in covalent arrangements

• cis-trans isomer- differ in spatial arrangement

• enantiomers- mirror images of molecules

  *enantiomers (types of sterioisomers) have a pharmacological importance

  • mirror images of each other but could have a completely different function

• Ibruprofen- inflammation

• albuterol- asthma-

Warm up 1/31: Name the three ways to control our blood pH

• chemical buffer- carbonic and bicarbonate buffer systems

• respiratory- breathing rate

• renal- kidneys

know element definition

6 elements of life CHOPN

know polarity of water (polar)

what property of water is responsible to lower body temp through sweating

how are DNA molecules held together (hydrogen bonds)

what type of bond holds NaCl together? ionic

what are tiny amounts of elements in our body? trace elements

98.6 degrees body temp

know density of ice .92 and liquid water 1

how much are we made up of water 65-70%

how many bonds do carbon and water form? 4

name hydrophobic substances

know concepts of cohesion and adhesion and how they pertain to plants through xylem and stem and how water is carried

entaintiomers and how shapes of molecules can have diff effects

entaintiomers are stereoisomers

know what ibuprofen and albuterol do for us

acidosis vs alkalosis and how our body gets back to normal (buffers)

NSAID- non steroid antiinflammatory

4 macromolecules and monomers

name 5 ways to release endorphins

ph chart 5 acids 5 bases what range

what is ocean acidification mention chemical reactions how has pH changed since industrialization

carbon and how it’s important describe 2 compounds carbon is found in and why these compounds are important (C6H12O6, CO2)

important elements CHOPNS describe importance of each

endogenous and exogenous endorphins

Molecule structure determines its stgrucute

describe water properties

how do we control blood ph and normal blood ph

what are buffers and ex carbonic acid and bicarbonate system, kidneys, hemoglobin, respiration, phosphate buffer

describe water properties and how they benefit life