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Accelerated Biology Midterm

Updated: Mar 26, 2019


Author: Sophia Teng


Bio Midterms Study Guide

Scientific Process & Characteristics of Life

Scientific Process:

Hypotheses and Theories

  1. Make a claim

  2. Gather evidence for that claim

  3. Explain how the evidence is related to claim

Hypothesis: If, then, because format

Prediction based on observations about the natural world

Can never be proven, only supported or refuted

Theories (law) : a major explanation that has been affirmed through extensive testing, by different separate researchers

Controlled Experiments

  • controlled experiment: an experiment, one variable changed

  • control group: the group that is unchanged, serves as comparison

  • experimental group: group that is changed

  • constant variables: factors that are not changing in all groups

  • double-blind experiments: neither subjects or administer know which group is control

  • placebo effect: sense in brain amongst control group that they are feeling better even with no treatment

Data Collection and Variables

  • independent variable: manipulated/changed variable

  • dependent variable: variable that responds to changed of independent var, DATA

  • Line graph: change over time, both variables are quantitative

  • Bar graph: ind var is qualitative

  • Pie chart: percentage of a whole

Requirements in graph:

  • Label axes

  • Titles: both variables, avoid versus

  • Cation or annotation: brief summary of graph

  • Key or legend depending on data

  • Scale of axes

Statistical Analysis

Standard Deviation Standard Error

Standard error is generally better

Add or subtract standard error to find where true mean falls

Draw error bars, overlapping error bars mean no definitive difference.

Characteristics of Life

Characteristic

Explanation

Organized

  • have cells, basic unit of life

  • unicellular or multicellular

  • basic unit of structure and function in life

Acquire materials and energy

  • need materials to build new molecules

  • need energy for all chem reactions (metabolism)

Reproduce

  • able to pass genetic information to offspring (DNA/RNA)

  • asexual: one parent makes exact copy

  • sexual: 2 parents make diff. offspring

Respond to stimuli

  • changes in environment

  • protect organism from external harm

  • help w/ cell communication (internal)

Maintain homeostasis

  • maintaining relatively stable internal state

Grow and develop

  • will change throughout lifetime

  • grow in size, develop through changes in form

Adapt

  • population have certain characteristics that are favorable in environment, more common over time

Basic Chemistry Practice

Element

Atomic Number

Mass Number

Protons

Neutrons

Electrons

Li

3

6

3

3

3

S-2

16

32

16

16

18

Na+

11

22

11

11

10

Biochemistry

Properties of Water and pH

Structure of water molecule:

Polar covalent bonds

Oxygen more negative

Hydrogen more positive

hydrogen bonds between molecules, weak attractive force

Cohesion:

Molecules attracted to each other

Surface tension, water is strong and will resist

Adhesion:

Water attracted to different molecules; other charged surfaces

Work together in transpiration, drawing water upwards through plant tissue, capillary action

Density:

Less dense as solid than liquid

Ice floats

Important bcs water cannot freeze in winter, currents and fish

Universal Solvent:

Solution: mixture where one substance uniformly distributed throughout another

Solute- substance that is dissolved

Solvent- substance doing dissolving, usually a liquid

Water dissolves other polar and charged compounds

Hydrophilic and hydrophobic

Moves substances from one place to another

Helpful for waste removal, nutrient absorption

Heating

Takes long time, energy initially used to break hydrogen bonds

Cooling via Evaporation

Evaporation- transition from liquid to gas, cools earth bcs heat is removed

pH

Water dissociates to OH- (hydroxide base) and H+ hydrogen ions (acid)

Scale is logarithmic, each number increases by power of ten

Buffers are solutions that resist changes in pH

Have conjugate bases and acids in solution to counter

In blood, bicarbonate system, carbonic acid -> bicarbonate ion (base) and H+

Macromolecules

large molecules of repeating small units linked through covalent bonds

Monomer

Polymer

Dehydration synthesis forms polymers, is anabolic, and endergonic

Hydrolysis forms monomers, is catabolic, exergonic

Functional Groups: clusters of covalently bonded atoms, distinctive chem properties, responsible for characteristic reactions

Amino Group: -NH2 Hydroxyl Group: -OH Carboxyl group: -COOH Phosphate: -PO4

Carbohydrates

Functions:

  • quick energy gets broken down circulated through blood

  • energy storage: large carbs long chains of sugar energy in bonds

  • structure: long chains of structural support for some

  • Ratio of elements- 1C: 2H : 1O

Monosaccharides: single sugars; glucose fructose,

Disaccharides: two sugars, used for supply of sugars; sucrose lactose maltose

Polysaccharides: many sugars

  • structure, energy storage

  • Starch: energy storage for plants

  • Cellulose: structural component of plants, cell walls/ fibers

  • Humans cannot digest cellulose, but herbivores can. Fiber

  • Glycogen: energy storage for animals, branching structure in liver

  • Chitin: structure for arthropods and fungi

Lipids

Functions:

  • energy storage

  • cell membranes

  • insulation

  • cell signaling/hormones

Structure and elements: CHO, long straight chains or fused rings, very few oxygen, hydrocarbons

Hydrophobic

  • Saturated fats: single bonds, straight chain, packed right, solid room temp, try to limit

  • Unsaturated fats: double oxygen bonds in chain, appear bent, mono/polysaturated

  • Trans fats: not found in nature, unsaturated fats forced straight, not good for u

  • Triglycerides: most fats in body, extra long term energy. Glycerol bonded to 3 chains of fatty acids, sat or un sat

Fats have 2 times the energy of carbs

  • Phospholipids

  • Sterols: 4 rings of branching hydrocarbons, typically hormones, Cholesterol used to created testosterone and estrogen

Proteins

Functions: storage, structure, growth, transport, catalysts in enzymes,

Building blocks: 20 amino acids, only macromolecule w sulfur, R side chain determines characteristics

Bonds are called peptide bonds, between carboxyl and amino end groups, form polypeptides

Levels of protein structure:

  • Primary structure: between amino acids, polypeptide chains

  • Secondary structure: local folding of amino close together, alpha helix, beta sheet, hydrogen bonds between amino and carboxyl groups, nothing to do with R groups

  • Tertiary structure: long distance interactions, non-covalent, ionic bonds, disulfide bridges, hydrogen bonds (between R groups), hydrophobic interactions, ETC

  • Quaternary Structure: not all proteins, several different structure together, hemoglobin

Denature: changing of the secondary, tertiary, quaternary structure

Extreme temp, pH, salinity. Ex: albumin in egg whites

Nucleic Acids

2 types:

  • DNA- deoxyribonucleic acid, 2 double strand

  • RNA- ribonucleic acid, single strand

Components of nucleotide (a monomer):

  • Nitrogenous base (ex: adenine, thymine, etc)

  • 5 carbon sugar

  • phosphate group

Covalent phosphodiester bonds

Bases in DNA: Adenine, Thymine, Guanine, Cytosine

Bases in RNA: A, G, C, Uracil

Purines: A, G, 2 fused rings

Pyrimidines: T, C, U, 1 ring

Functions: genetic info in sequence of bases, energy transfer

ATP: Adenosine triphosphate, has adenine, ribose, 3 phosphate

Energy released when phosphate group broken off, energy in bond

Cells

Organelles

Organelle

Location

Function

nucleus

center of the cell

controls protein production and cell functions. contains DNA, nucleolus produces ribosomes

endoplasmic reticulum

around nucleus

prepare items for transport.

Rough ER: ribosomes, manufactures lipids/proteins

Smooth ER: produces lipids, breakdown toxins (liver)

transport vesicle

cytoplasm, around cells

buds off of membranes to transport materials around cell

golgi apparatus

in cytoplasm, near ER

labels, packages nutrients for the cells. Directs proteins and lipids. Like post office

lysosomes

around cytoplasm

waste disposal, breaks things down. pH 5 for enzymes. breaks things down, recycles and releases to cytoplasm

vacuole

in cytoplasm

Plants: central vacuole stores water, exerts turgor pressure, enzymes can break things down in plants

others: ions, sugars, pigments, storage

mitochondria

in cytoplasm

site of cell resp, converts glucose into ATP energy

chloroplasts

in cytoplasm

site of photosynthesis, converts CO2 water and light into sugars and O2

Endosymbiotic theory: mitochondria and chloroplasts have double membranes, own DNA and ribosomes, can divide by themselves. Used to be their own organisms, engulfed by larger cell, evolved together to form eukaryote 2.7-2.1 billion years ago.

cytoskeleton

right inside membrane

organizes interior, gives shape to walless cells, movement (interior or exterior)

  • microfilaments (smallest): cell crawling

  • intermediate filaments: multistrand, structure

  • microtubules (largest): movement/transport in cell

cilia

outside of cell

hairlike projections, increase SA, move liquid over cell, make cell more efficient in absorbing materials

flagellum

on outside

whiplike tail, wave motion to move cell

Making a protein:

  • Nucleus- holds DNA and instructions to make proteins

  • Ribosome- protein is made

  • (Vesicle)- transport materials

  • ER- rough ER finishes up proteins

  • Vesicle

  • Golgi apparatus- packages, labels, ships

  • cytoskeleton- structure, organizes, all, transport

Cell Membranes and Transport

Cell Membranes

  • 2 layers of phospholipids

  • amphipathic- both hydrophobic and hydrophilic component

  • referred to as fluid mosaic model because flexible, flows, changes its composition

  • influenced by

  • fatty acid components (sat or unsat)

  • cholesterol (carbon rings in membrane)

  • temperature (cold not as fluid)

  • has integral proteins (or transmembrane proteins)- span the whole width of membrane

  • Peripheral proteins- on either exterior or interior, not both

  • Glycoproteins and glycolipids

  • Outside cell, membrane is adhered to other cells or to the extracellular matrix

  • with the help of adhesion proteins

  • Selectively permeable- regulates what comes in and out of cell

  • only small and uncharged molecules directly through

  • O2, CO2, and sometimes water

  • based on solubility rules: “like dissolves like”

  • FUNCTIONS OF THE PLASMA MEMBRANE:

  • separate cell from environment

  • enclose in small space

  • take in needs, keep out unwanted

  • release waste

  • cell signaling

  • helps hold in place (some)

Passive Transport

  • Passive transport - movement of molecules does not need energy

  • Diffusion - movement of molecules from an area of high concentration to low concentration

  • molecules move down the concentration gradient

  • Will move until equilibrium is reached- having the same concentration

  • There is no NET movement of molecules; move both ways equal rates

  • factors that affect the speed of diffusion

  • Temperature: high temp, increased rate of diffusion (increased kinetic energy)

  • gradient concentration: how much initial particles, how many need to move (steepness of concentration gradient)

  • molecule size

  • Osmosis- diffusion of water

  • Isotonic- amount of solute and solution inside and outside is the same

  • hypertonic- more solute less water

  • hypotonic- less solute more water

  • Osmoregulation- balancing of water and solute outside cell

  • Facilitated diffusion- diffusion with assistance, uses proteins

  • solutes involved: glucose, large and uncharged

  • each protein is specific molecule it transports

  • Channel proteins- like a tunnel in the bilayer; always open

  • aquaporin

  • Carrier proteins- like a gate, change shaped based on solute

  • glut

Active transport

  • Active transport- forcing molecules low to high against concentration gradient

  • requires input of energy

  • uses carrier proteins

  • allows cells to maintain concentration of materials diff from ext environ; important for maintaining homeostasis

  • Sodium potassium pumps- transport sodium and potassium

  • 3 Na+ ions bind to pump (do not want too many sodium)

  • ATP supplies energy to protein so Na+ leaves

  • 2 K+ ions bind from outside and enter cell

  • Want more potassium for neurotransmission, sets up voltage and allows brain communication

  • Proton (H+) pumps- try to pump ions out, do not want bcs they make cell acidic

  • important for respiration and photosynthesis

  • Endocytosis- brings into the cell; bulk transport, lots of molecules, large molecules

  • Phagocytosis- cell eating, engulfing solid

  • Pinocytosis- cell drinking, engulfing liquid

  • Receptor-mediated endocytosis- will engulf specific molecules

  • Exocytosis- releasing out of cell, through transport vesicle

  • waste, proteins → insulin

Enzymes

  • Metabolism-all reactions that happen in your body

  • includes reactions that are catabolic (breaking down) and anabolic (building up)

  • First Law of Thermodynamics- energy is neither created nor destroyed, only changes forms

  • Potential energy- stored energy based on position/location

  • includes chemical energy (stored in bonds)

  • Kinetic energy- energy of movement

  • includes thermal, sound energy

  • Reactants- starting material

  • Products- materials formed

  • Enzymes- organic catalysts, speeds up reaction, mostly proteins, some RNA

  • Active site- place where substrate will bind

  • Enzyme substrate complex- interaction of enzyme and substrate

  • Induced fit model: when they interact, the substrate causes the enzyme to change shape

  • Enzymes lower activation energy- energy needed to start a reaction

  • Need to overcome barrier to react, even catabolic reactions

  • Characteristics of enzymes

  • specific for one substrate

  • remain unchanged by the reaction

  • are reused over and over

  • generally end in -ase

  • Conditions that affect enzymes

  • Temperature

  • pH

  • salinity

  • Enzyme concentration

  • Substrate concentration

  • Cofactors/ coenzymes

  • inhibitors

  • Cofactors (inorganic (metals)) and coenzymes (organic (vitamins))

  • Competitive inhibitors- another molecule that fils active sites, blocks substrate

  • Noncompetitive inhibitors- binds to allosteric site, changes shape of enzyme/active site

  • Metabolic pathway- chain of reactions, products one reaction are reactants for another

ATP

  • adenine base, a ribose sugar, 3 phosphate groups

  • ADP has 2 phosphate groups

  • Hydrolysis of ATP

  • H2O + ATP → ADP + P + energy

  • exergonic, catabolic

  • Phosphorylation

  • ADP + P → ATP + H2O

  • endergonic, anabolic

  • The ATP cycle

  • When ATP is hydrolyzed, free energy is available

  • Used for cellular processes, muscle contraction, protein synthesis, cell division, protein pumps, stored energy, cellular signaling, enzyme reactions, transport

  • ADP recycled back to ATP (phosphorylation)

  • by cell resp or photosynthesis

Molecular Energy Carriers

  • In metabolic pathways molecular energy carriers (small organic molecules that receive, store (deliver) transport energy) can be used to transfer products of one reaction to the next

  • Very important in cell resp and photosyn

  • To transfer energy, undergo oxidation and reduction “redox”

  • Oxidation- loss of electrons (from a molecule, atom, ion)

  • Reduction- gain of electrons (reduces the charge)

  • OIL RIG- Oxidation Is Loss, Reduction is Gain

  • Photosyn: NADP+ + 2e- + H+ → NADPH

  • resp: NAD+ + 2e- + H+ → NADH

  • they are being reduced, gaining electrons

  • stores energy

  • In the next reaction they will be oxidized

  • releases energy

Cellular Respiration

Overview

  • Producers (or autotrophs) - produce their own food through photosynthesis/chemosynthesis

  • Consumers (or heterotrophs) - must eat to obtain energy

  • Chemical equation for photosyn: 6CO2 + 6H2O → sunlight → C6H12O6 + 6O2

  • For respiration: C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP (energy)

  • 2 stages of Photosynthesis:

  • Light Reactions (light dependent reactions)- occur in presence of light

  • Calvin Cycle (light- independent reactions) - CO2 + ATP + NADPH → CH2O

  • does not require sunlight

  • 3 stages of Cellular Respiration (in presence of oxygen):

  • Glycolysis - break down glucose (in cytoplasm), some ATP

  • Krebs Cycle - in mito matrix, conversions for step 3 (ATP + CO2 )

  • Oxidative Phosphorylation (ETC) - across inner membrane of mito, add ATP, uses O2 produces H2O

  • Goal of respiration: energy in the form of ATP

  • Cellular resp in mitochondria

  • double membrane for separate space for each aspect to occur

  • Will abundant in cells that need energy, like muscles, nerve cells, brain, liver

Anaerobic Respiration (no oxygen)

  • Glycolysis- sugar splitting in cytoplasm

  • input = glucose (NAD+) (needs activation energy)

  • output = 2 pyruvate (pyruvic acid) 3 carbons each, 2NADH, 2ATP (net gain)

  • Glucose converted to 6 carbon intermediate

  • Needs phosphates from 2ATP

  • Split into 2 molecules G3P

  • G3P converted into pyruvate

  • Creates 4 ATP and 2 NADH

  • anaerobic respiration (fermentation) - without oxygen

  • after glycolysis in cytoplasm

  • input = 1 glucose

  • output = either 2 ethanol + 2CO2 or 2 lactic acid (fermentation), 2 NAD+ (2ATP and NADH (glycolysis))

  • Goal - to generate NAD+ to continue glycolysis

  • Alcoholic fermentation- occurs in cytoplasm

  • in bacteria

  • used to make beer, wine, cheese

  • pyruvate becomes acetaldehyde, ethanol

  • Lactic acid fermentation- occurs in muscle cells during exercise

  • creates lactic acid, can irritate nerve endings, burning sensation

  • no intermediate between pyruvate and lactic acid

Aerobic Respiration

  • Will follow glycolysis if oxygen present

  • Pyruvate oxidation- preparation for the next step of respiration

  • Input = pyruvate

  • output = 1CO2 1NADH, Acetyl coA

  • pyruvate enters mitochondria

  • CO2 and NADH are released

  • A coenzyme is added to create acetyl coenzyme A

  • Ends with 2 carbons, is oxidized (loss of electrons)

  • The citric acid (Krebs) cycle- creates materials for the last step of resp

  • Input = Acetyl coA

  • Output = 2CO2 3NADH, 1 FADH2 1ATP

  • occurs in matrix of mitochondria

  • starting material is half glucose; will turn cycle twice

  • Acetyl coA enters cycle and coenzyme leaves, remaining 2 carbon molecules bind to 4 carbon molecule oxaloacetate to create citric acid

  • molecule rearranged several times, releasing 2 molecules of CO2 to leave 4-carbon molecule (that becomes oxaloacetate)

  • rearrangements break covalent bonds drive formation of energy carriers ATP, NADH, FADH which go to final step

  • energy carriers are reduced

  • Oxidative Phosphorylation - final step of cellular respiration, includes electron transport chain and chemiosmosis

  • input = NADH, FADH2, O2

  • output = H2O, ~32 ATP per glucose

  • In cristae (folds) of the inner membrane

  • NADH and FADH2 donate their high-energy electrons to ETC

  • Energy released as electrons passed down chain of proteins

  • electrons accepted by oxygen (final electron acceptors) to make water

  • Protons pumped from matrix to intermembrane space; H+ is acidic, is attracted to electrons

  • forms a proton gradient, protons travel back through matrix through ATP synthase

  • adds a phosphate group to ADP, phosphorylation, generates ATP

Totals

Anaerobic Respiration

Stage

Net NADH produced

Net FADH2 produces

Net ATP produced

Glycolysis

2

0

2

Fermentation

0

0

0

Total

X

X

2

Aerobic Respiration

Stage

Net NADH produced

Net FADH2 produces

Net ATP produced

Glycolysis

2

0

2

Preparatory reaction and Krebs Cycle

4 (1from pyruvate oxidation and 3 from Krebs)

1

1

Oxidative Phosphorylation

0

0

~32

Total

X

X

~35

Anaerobic respiration evolved first:

  • Less oxygen

  • did not need as much ATP

  • materials dissolved in environment

Leaf structure

Structure

Function

Structure

Function

Cuticle

waxy, absorbs sunlight, protects from photodamage, prevents water from escaping

Epidermis (lower and upper)

protection (like skin0

Palisade mesophyll

absorbs light, sire of photosynthesis, many chloroplasts

Bundle sheath cells

contains xylem and phloem, regulated what enters and exits vein

xylem (part of vein)

carries water

Phloem (part of vein)

carries food, sugar

spongy mesophyll

allows for movement of gases

stomata

lets CO2 through, Calvin cycle

Guard Cell

open and close stomata, open when there is water

Stroma

cytoplasm like fluid in inner membrane of chloroplast

Thylakoid

chlorophyll, photosynthesis sire of light reactions

Membrane (inner and outer)

semipermeable, lets things in and out

Photosynthesis

Light and Pigments

  • Photons- what light is made of, streams of massless particles

  • Light has wave-like characteristics

  • Visible light is one part of electromagnetic spectrum

  • Fates of light:

  • Reflected- bounces back off object

  • Absorbed- taken in by object

  • Transmitted- passes through an object

  • Color of an object is determined by the wavelength it reflects

  • White object = reflects all light Black object = absorbs all light

  • Pigment- organic molecule that absorbs light

  • Chlorophyll- main light absorbing pigment in leaves

  • absorbs red and blue light, reflects green

  • provides energy for light reactions

  • Two types: a and b, absorb slightly different wavelengths

  • Accessory pigments- extra pigments to help plants increase light absorbed

  • Carotenoids- yellow orange pigments

  • protect plants from sunlight damage (photodamage)

  • Examples: lutein (in carrots good for eyes) B-carotene, xanthophyll

  • Leaves change color in the fall because chlorophyll breaks down, reveals hidden carotenoids

  • Chloroplasts- organelle of photosynthesis

  • Stomata pores in leaves for gas exchange

  • Stroma- fluid in chloroplasts, has materials needed

  • Thylakoids- separate location for light reactions

  • Thylakoid membrane and thylakoid space

Light Reactions (light dependent reactions)

  • Input = sunlight, water

  • Output = ATP, NADPH, O2

  • Occurs in thylakoid membrane

  • thylakoid membrane has clusters of pigments that capture energy called antenna complex

  • funnel light to reaction center- enzyme-chlorophyll complex where light reactions start

  • Antenna complex and reaction center make up photosystems (clump of pigments)

  • Steps

  • Sunlight splits water molecule called photolysis which generates electrons, oxygen gas, hydrogen ions

  • Excites electrons in photosystem II

  • electrons are passed along ETC, lose energy until they reach photosystem I

  • Light re-excites electrons

  • Passed and received by NADP+, reduction to NADPH

  • protons driven from stroma into thylakoid space (across thylakoid membrane)

  • creates concentration gradient

  • Pumped back out to stroma through ATP synthase

  • NADPH and ATP created will be used in next step

Calvin Cycle

  • Input = NADPH, ATP, CO2

  • Output - sugar, ADP, NADP+

  • Occurs in stroma

  • CO2 comes into cycle

  • Combines with 5-carbon molecule RuBP to form 6-carbon molecule

  • Catalyzed by enzyme rubisco, most abundant enzyme on planet

  • RuBP cut in half forming PGA, two 3 carbon molecules

  • Molecule is rearranged, using ATP and NADPH in the process

  • two molecules of G3P are formed, combine to make glucose

  • Regenerates RuBP

  • conversion of CO2 (inorganic) into PGA (organic) is carbon fixation

Plant Adaptations

  • C3 plants - most plants, 3- carbon molecule

  • Photorespiration

  • Rubisco should add CO2 to RuBP but can also add O2 when not as much CO2

  • 2-carbon molecule created, which will be lost as CO2 making photosynthesis less efficient when this occurs

  • Happen when low on CO2, dry → stomata closed

  • C4 plants - in hot sunny dry conditions (stomata are closed)

  • Carry out Calvin cycle in bundle sheath cells, converts CO2 into a 4-carbon molecule

  • molecule breaks up releasing CO2 directly into cells when needed

  • Ex: sugar cane, corn

  • CAM plants - live in very dry conditions

  • Open stomata only at night when air is not as dry

  • Take in a lot of CO2 convert it to a 4-C molecule that is stored in vacuoles

  • During day stomata close to conserve water and CO2 released from 4-C storage molecule

  • Cacti, pineapple

Type of photosynthesis

Where is carbon “captured”

When does carbon capture occur?

Where does the Calvin Cycle occur

In what type of environment does it occur?

C3

through stomata

Anytime, mostly day, when there is water

mesophyll

normal, moist

C4

stomata, bundle sheath

Anytime, mostly day

bundle sheath cells

hot and dry, sunny

CAM

through stomata, vacuole

at night when it is cooler

mesophyll

very dry conditions

Cellular Respiration Summary

cell resp - oxidation

Glycolysis: glucose - oxidized NAD+ - reduced to NADH

Fermentation: pyruvate - oxidized (in alcoholic fermentation NADH - oxidized to NAD+

Pyruvate oxidation: pyruvate - oxidized to become Acetyl coA NAD+ - reduced to NADH

Krebs cycle: acetyl coA - oxidized NAD+ - reduced NADH FAD+ - oxidized to FADH2

Oxidative Phosphorylation: O2 - reduced to H2O NADH - oxidized to NAD+ FADH - oxidized to FAD+ ADP - reduced to ATP

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