AP Bio 1st Sem Review (Unit 1-5)

Experimental design

Controlled experiment that tests a hypothesis via using an independent variable, dependent variables, controlled variables, and a control group

Control variables

factor in an experiment that is kept constant to ensure that any changes in the dependent variable can be attributed to the manipulation of the independent variable

Control group

In a controlled experiment, a set of subjects that lacks the specific factor being tested

dependent variable

A variable whose value is measured during an experiment to see whether it is influenced by another variable

independent variable

A variable whose value is manipulated during an experiment to reveal possible effects on another variable

Comparing averages using SEM for Statistical significance

Errors bars = +/- 2 SEM from average > If overlap then no statistical difference/ if no overlap then statistical difference

Carbon bonding characteristics

Form 4 covalent bonds, creates molecule structure (long chains, multiple bonds, and ring structures), and biomolecules made from C-structures

Structures of carbon-based molecules

long chains, multiple bonds, and ring structures

SPONCH Molecules

Sulfur, phosphorous, oxygen, nitrogen, carbon,and hydrogen

Protein

CHONS

Lipids & Carbohydrates

CHO

Nucleic acids

CHONP

Electronegativity

The attraction of a given atom for the electrons of a covalent bond.

Hydrogen bonding

Dotted line where polar molecules are attracted to each other, forming these bonds between molecules (easily broken)

Polar Molecules & Why water is polar

This bond is between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive. Water is polar because of O’s electronegativity being partially negative, pulling e- from H+

Properties of water

Forms H-bonds, polar, cohesion (like molecules), adhesion (other molecules), solvent, and high specific heat & vaporizatio

Hydrogen bonding beteen water molecules

Polar molecules attracting to each other because of O’s electronegativity on H+, forming this bond as a dotted line

Dehydration synthesis

A chemical reaction in which two molecules covalently bond to each other with the removal of a water molecule.

Hydrolysis

A chemical process that lyses, or splits, molecules by the addition of water; an essential process in digestion.

Carbohydrates

Biological roles include energy storage and providing structure, ending with -ose. Monomers = monosacchardies (CH2O - 1:2:1)

Structure of polysaccharides

A polymer of many monosaccharides in a chain, formed by dehydration reactions.

Energy Polysaccharides animals vs plants

plants = starch (more separate), animals = glycogen (more branching for quick E release)

Structural Polysaccharides animals vs plants

plants = cellulose (plant cell walls), animals = chitin (arthropod exoskeleton & fungi cell walls)

Lipids

Biological role is to store energy, membrane structure, and hormones

Energy storage lipids

triglycerides (3 fatty acids of long hydrocarbon chains with carboxyl group connected to glycerol)

Membrane lipids

Phospholipids (glycerol, 2 fatty acids, and phosphate group) and cholesterol (steroid forming animal cell membrane components and synthesizes steroids - keeps membrane fluid)

Lipid structure vs carbohydrates

Not polymers, made of C, H, O (glycerol & long hydrocarbon fatty acids), and cone shaped vs monosaccharide polymers, made of C, H, and O (1:2:1), hydrophilic, and ring shaped

Lipid Properties

nonpolar & hydrophobic (minimal oxygen) - Except for phospholipids (amphipathic) 2 fatty acids & phosphate group

Protein

functional biological molecule consisting of one or more polypeptides folded into a specific three-dimensional structure.

Amino acid structure (central C, amino group, hydrogen, carboxyl, and r group)

R group

part of amino acids that is unique to each specific amino acid

Polar R group

having an O, N, or S at end of R-Group or any type of electronegative atom

Nonpolar R group

Only C and H or having N/S in the middle of the chain despite being electronegative for R groups

Basic R group

Amino group & having a + charge

Acidic R group

Having carboxyl or negative charge

Primary Structural level

AAs of polypeptide in word form that determine 3D shape, with #1 AA being amino end (H3N+), and last AA being Carboxyl end

Secondary Structure

Coiled/folded sections of polypeptide due to H-bonding (H-O) between amino and carboxyl groups (R-Group excluded). Alpha Helix = 1 structure, Beta pleated = 2 structure H - bonded

Tertiary Structure

Folding that results from interactions between R-Groups (ionic via acidic and basic, hydrophobic associating and avoiding water, disulfide bridges with covalent bonds between S atoms of Cysteines, and polar groups of H-bonds with each other (acidic, basic, H2O, and polar)

Quaternary Structure

2+ Polypeptides (2+ tertiary structures) attached to each other that are formed by R-group interactions in tertiary (not all proteins have this structure)

Backbone of Polypeptide

Carboxyl, central carbon, and amino/nitrogen (C-C-N) (Exclude R Group) - repeated coiling/folding of polypeptide backbone due to H-bonds at that location

R-group interactions stabilizing tertiary structure and quaternary structure.

tertiary - H-bonds, ionic bonds, hydrophobic interactions, and disulfide bridges, quaternary - same R group interactions from tertiary but now between 2 polypeptide (tertiary) structures

Denaturation

Disruption of protein shape and function due to environmental conditions (high salt, pH level difference, and high temp), affecting only 2-4 levels (weak bonds) but not 1, due to covalent peptide bonds

Nucleic acid

A polymer (polynucleotide) consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins, for all cellular activities. The two types are DNA and RNA.

Nucleic acid monomer structure

Nucleotides - sugar (deoxyribose - 2 OH/ribose - 3 OH) made from phosphate & nitrogenous base alternating phosphate and sugar

DNA and RNA differences

DNA has 2 OH w/ double helix & T, A, C, G and RNA has 3 OH w/ single helix & U, A, C, G

OH

hydroxyl

DNA bases

adenin, thymine, cytosine, and guanine (TACG)

RNA bases

Uracil, adenin, cytosine, and guanine (UACG)

Endergonic vs exergonic reactions

Absorb free energy, change in free energy (G) > 0, needed for building larg molecules vs Release energy, change in free energy (G) < 0, breaking down large molecules

Enzyme Catalytic Cycle

Enzymes not consumed in reaction, just catalyzes reaction repeatedly (enzyme + substrate > enzyme-substrate complex, enzyme + product)

How enzymes speed up reactions

Lowers activation energy barrier

Enzyme structure

Enzyme structure

Active site where substrate/reactant binds to in key in lock > products are output

Enzyme reaction Rate

(Change in substrate or change in products)/t = mmol/sec

Enzyme reaction saturation

Substrate concentration at which all enzymes have substrate molecules in their active site, in which increasing concentration above maximum reaction rate does not affect reaction rate

Enzyme inhibitors

bind to enzymes and decrease enzyme activity

Competitive inhibitors

bind to enzyme’s active site and prevents substrate binding but can be overcome with more substrate concentration

Temperature affecting Rxn Rate

Temperature increasing to optimal temperature results in increased motion and greater reaction rate but above optimal leads to reduction in reaction rate due to denaturing

pH affecting reaction rate

Enzyme’s optimal pH matching environment of enzyme’s pH lead sto higher reaction rate but above or below optimal pH leads to denaturing and decreased reaction rate

a. without inhibitor

b. with competitive inhibitor

c. with noncompetitive inhibitor

As substrate concentration increases rate increases (increases the frequency to enzyme and substrate colliding). X marks enzyme saturation. Increased substrate concentration above saturation does not increase the rate

Curve levels off over time as all substrate has been converted to products. Rate of reaction is = to the slope of the line

Plant cell features

Cellulose based cell walls (700x thicker than plasma membrane) & large central vacuole (retains water for turgor pressure, reproduction, growth, and development), and chloroplast

Ribosomes

Synthesizes protein from large and small subunit made from protein and ribosomal RNA

Nucleus

Double bilayer membrane/nuclear envelope with pores to store genetic material with nucleolus (rRNA synthesis & ribosomal subunits), in which proteins & RNA enter/exit via pores

Chloroplast

inner and outer membrane surrounding membrane bound thylakoids that do photosynthesis (absosrb light and synthesize sugar) from CO2 and H2O

Mitochondria

Double bilayer, inner folded for more surface area, for ATP synthesis (has circular DNA)

Endoplasmic reticulum

(builder) membranous network immediately surrounding nucleus (rough - makes membrane proteins and secretes proteins, smooth - makes lipids and detoxifies toxins)

Golgi Appratus

(modifier) series of flattened membrane bound sacs/cisternae to fold and chemically modify proteins then sorting proteins to cellular location

lysosomes

membrane bound organelle with hydroyltic enzymes to break down old/broken organelles and molecules

Animal cell features

no cell wall and has lysosomes (membrane bound organelle with hydroyltic enzymes to break down old/broken organelles and molecules)

Central vs Contractile Vacuole

Plants’ reproduction, turgor pressure, growth, and development vs ATP-based moving water from protists

Fluid mosaic model of membrane structure and behavior

Refers to membrane structure having various liquids in the form of unsaturated fatty acid tails/double bonded kinks & cholesterol preventing tight packing/making it fluid, and patterned/mosaic due to different molecules found in membrane (proteins & cholesterol)

role of cholesteriol = more fluid while fatty acid tail saturation = less fluidity

molecules associated with membrane (protein and carbohydrates)

Glycoprotein, peripheral protein, transmembrane/integral membrain proteins, and glycolipids

glycolipids

lipids with sugar attached

glycoproteins

proteins with sugar attached

Peripheral protein

A protein loosely bound to the surface of a membrane or to part of an integral protein and not embedded in the lipid bilayer.

Integral protein

Typically a transmembrane protein with hydrophobic regions that extend into and often completely span the hydrophobic interior of the membrane and with hydrophilic regions in contact with the aqueous solution on either side of the membrane (or lining the channel in the case of a channel protein)

Active vs passive transport

Solute transported against concentration gradient (low to high) in which ATP is used & pumps is the opposite of diffusion vs Follows concentration gradient of high to low & using no energy/ATP

Simple diffusion vs facilitated diffusion

Simple (no proteins) & facilitated diffusion (membrane protein used to diffuse solute across membrane) but still following concentration gradient

solute pumping concentration gradient as energy source/stored energy and role in cellular processes (cellular respiration etc..)

Movement of molecules is from high concentration to low concentration, pumping means to move from low to high which requires energy. In cellular processes, concentration gradient is potential energy, when particles mvoe down gradient (high to low), cells access stored potential energy

Endocytosis

Cellular uptake of biological molecules and particulate matter via formation of new vesicles from the plasma membrane

Exocytosis

The cellular secretion of biological molecules by the fusion of vesicles containing them with the plasma membrane.

Phagocytosis

endocytosis of large particles (bacterium)

Pinocytosis

endocytosis of small solutes near vesicle formation, triggered by ligand/molecule binding to a receptor

Bulk Transport

Transporting large solute/large quantity of small solutes via vesicles/phospholipid bilayer membrane in a sphere

Osmosis

Means that water diffuses across membrane by (from low solute to high solute)

Aquaporin

A channel protein in the plasma membrane of a plant, animal, or microorganism cell that specifically facilitates osmosis, the diffusion of free water across the membrane and down a concentration gradient (high to low water conc or low to high solute conc)

Water potential calculation

(ψ) = solute potential + pressure potential (in bars)

(ψ) Solute potential

0 = pure water, (ψ) decreases as solute concentration increases, positive not possible

(ψ) Pressure potential

pressure push water > pressure +, pressure pull water > pressure -, open container = 0

Net movement of water for water potential

area of higher ψ to lower due to water potential gradient moving from low solute concentration to high solute concentration (& flows to low water potential value)

NaCL - water potential

dissociates into 2 ions (Na and Cl) for water potnetial while sucrose = 1

Cell Surface Area/Plasma Membrane Area

membrane transport capability of cell due to metabolic needs (glucose)/waste (CO2) and efficiency > Bigger cell = more metabolic demands but bigger surface area = efficient transport

Endosymbiosis

Theory that mitochondria and chloroplasts were once prokaryotes that began living inside large prokaryotic cells

Evidence of endosymbiosis for mitochondria and chloroplasts

Multiple membranes (inner is from prokaryotic, outer is from host), DNA (circular chromosomes in both like prokaryotes), ribosomes (similar to prokaryotes, and divides like prokaryotes

Aerobic vs anaerobic respiration

A catabolic pathway that consumes oxygen (O2) and organic molecules, producing ATP. (effcieint catabolic pathway & pro/eukaryotic) vs o2 being low or nonexistent, producing ~2 ATP per glucose molecule (alcoholic fermentation for yeast/plants and lactic acid for animals)

Fermentation vs respiration

catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid. vs catabolic pathways of aerobic and anaerobic respiration, which break down organic molecules and use an electron transport chain for the production of ATP.

Stages & location n Cellular respiration - eukaryotic cell

1. Glycolysis (cytosol)

2. Intermediate step (mitochondrial matrix)

3. Krebs cycle (matrix)

4. Electron transport chain (ETC)/oxidative phosphorylation (inner mitochondrial membrane)