biology final exam review part 1 mrs. depasse. chapter 1 – life on earth – evolution is the...
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Biology Final Exam Review Part 1
Mrs. Depasse
Chapter 1 – Life on Earth
– Evolution is the process by which modern organisms descended, with modifications, from preexisting forms of life
– Changes in DNA within populations occur over the course of generations, which results in evolution
Definitions
• Mutations occur when changes in genes are mistakenly copied. They can also result from damage to DNA.
• Natural selection is the process by which organisms with certain inherited traits survive and reproduce better than others in a particular environment
Levels of biological organization
Fig. 1-10
Table 1-1
Eukaryotic cell
– Eukaryotic (“true nucleus” in Greek)• They are larger than prokaryotic cells• They contain a variety of organelles, including a
nucleus• This cell type is found only among members of the
domain Eukarya• They are extremely complex
Prokaryotic cell
– Prokaryotic (“before nucleus” in Greek)• They are only 1–2 micrometers in diameter• They lack organelles enclosed by membranes • They lack a nucleus• This cell type is found in the domains Bacteria and
Archaea• They are smaller and much simpler than the eukaryotic
cell
Scientific theory
• A scientific theory is a general and reliable explanation of important natural phenomena that has been developed through extensive and reproducible observations and experiments
Chapter 2- Atoms, Molecules
• An atom is the smallest unit of an element, and retains all the chemical properties of that element
• Atoms are composed of subatomic particles• In the central atomic nucleus, there are positively
charged protons and uncharged neutrons• In orbit around the nucleus are negatively charged
particles called electrons
Table 2-2
Electrons role in bonds
• Life depends on electrons capturing and releasing energy
• Each electron shell holds a specific number of electrons
• There are three types of chemical bonds, which are the attractive forces holding atoms together in molecules: ionic bond, covalent bond, and hydrogen bond
Table 2-3
Ions
–Atoms that have lost electrons become positively charged ions (e.g., sodium: Na)
–Atoms that have gained electrons become negatively charged ions (e.g., chlorine: Cl)
Water Molecules
• Water molecules attract one another– Cohesion is the tendency of the molecules of a
substance to stick together– Cohesion of water molecules along a surface
produces surface tension– Water is an excellent solvent– Water-soluble molecules are hydrophilic
Water Molecules
• Water-insoluble molecules that repel and drive together uncharged and nonpolar molecules such as fats and oils are hydrophobic
• The energy required to heat 1 gram of a substance by 1°C is called its specific heat
pH scale and buffers
– The degree of acidity of a solution is measured using the pH scale
• pH 0–6 is acidic (H OH)• pH 7 is neutral (H OH)• pH 8–14 is basic (OH H)
• A buffer is a type of molecule that helps a solution maintain constant pH
Chapter 3 Biological Molecules
• Organic refers to molecules containing a carbon skeleton bonded to hydrogen atoms
• Inorganic refers to carbon dioxide and all molecules without carbon
• The unique bonding properties of carbon are key to the complexity of organic molecules– Functional groups in organic molecules determine
the characteristics and chemical reactivity of the molecules
Biological Polymers
• Biological polymers are formed by removing water and split apart by adding water
– Monomers are joined together through dehydration synthesis, at the site where an H and an OH are removed, resulting in the loss of a water molecule (H2O)
Hydrolysis
–Polymers are broken apart through hydrolysis (“water cutting”)• Water is broken into H and OH and is
used to break the bond between monomers
Biological Molecules
– All biological molecules fall into one of four categories
• Carbohydrates• Lipids• Proteins• Nucleotides/nucleic acids
Table 3-2
Polysaccharides
• Polysaccharides are chains of monosaccharides– Storage polysaccharides include
• Starch, an energy-storage molecule in plants, formed in roots and seeds
• Glycogen, an energy-storage molecule in animals, found in the liver and muscles
– Both starch and glycogen are polymers of glucose molecules
Lipids
• Fats that are solid at room temperature are saturated (the carbon chain has as many hydrogen atoms as possible, and mostly or all C–C bonds); for example, beef fat
– Fats that are liquid at room temperature are unsaturated (with fewer hydrogen atoms, and many CC bonds); for example, corn oil
• Unsaturated trans fats have been linked to heart disease
Proteins– Proteins are molecules composed of chains of
amino acids– Proteins have a variety of functions
• Enzymes are proteins that promote specific chemical reactions
– Proteins are polymers of amino acids joined by peptide bonds– All amino acids have a similar structure
• All contain amino and carboxyl groups• All have a variable “R” group
Chapter 4 – Cell Structure
• All cells share common features – Include plasma membrane– Include cytoplasm– Use DNA as hereditary blueprint– Use RNA to copy the blueprint and guide
construction of cell parts– The plasma membrane encloses the cell and
allows interactions between the cell and its environment
Cell Structure
– All cells contain cytoplasm• The cytoplasm consists of all the fluid and structures
that lie inside the plasma membrane but outside of the nucleus
Figure 4-3 A generalized animal cellmicrofilaments
cytosol
cytoplasm
polyribosome
lysosome
Golgiapparatus
free ribosome
vesicles releasingsubstances fromthe cell
plasmamembrane
mitochondrion
smoothendoplasmicreticulum
centriole
ribosomeson roughER
intermediatefilaments(cytoskeleton)
vesicle
roughendoplasmicreticulum
basal body
flagellum(propelssperm cell)
nucleus
microtubules(cytoskeleton)
nuclear envelope
nuclear pore
chromatin (DNA)nucleolus
Figure 4-4 A generalized plant cell
nucleus
nuclear envelopenuclear porechromatinnucleolus
mitochondrion
smoothendoplasmicreticulum
chloroplast
centralvacuole
intermediatefilaments(cytoskeleton)
vesicle
microtubules(cytoskeleton)
plasmodesmata
cytoplasm
ribosomes
Golgi apparatus
free ribosome
cell walls of adjoiningplant cells
plastid
roughendoplasmicreticulum
cell wallcytosol
plasmamembrane
DNA and RNA
– All cells use DNA as a hereditary blueprint and RNA to copy the blueprint and guide construction of cell parts
• All cells use DNA (deoxyribonucleic acid) as a hereditary blueprint
• All cells use RNA (ribonucleic acid) to copy the blueprint and to guide construction of proteins
Type of cells
• There are two basic types of cells: prokaryotic and eukaryotic
• Prokaryotic (“before the nucleus”) cells form the bodies of bacteria and archaea, the simplest forms of life
• Eukaryotic (“true nucleus”) cells form the bodies of animals, plants, fungi, and protists
• The cytoplasm of eukaryotic cells includes a variety of organelles, such as the nucleus and mitochondria
Table 4-1
Role of DNA
• The nucleus, containing DNA, is the control center of the eukaryotic cell – Because proteins are synthesized in the
cytoplasm, copies of the protein blueprints on DNA must leave the nucleus through the nuclear membrane
– To do this, genetic information in DNA is copied into messenger RNA (mRNA), which travels through the nuclear pores to the cytoplasm, where it directs protein synthesis
The Endomembrane System
• The eukaryotic cytoplasm contains membranes that form the endomembrane system– The endomembrane system segregates molecules
from the surrounding cytosol to ensure the orderly occurrences of biochemical processes
– The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, and vacuoles
Figure 4-13 A protein is manufactured and exported
Antibody protein is synthesized on ribosomes and is transported into channels of the rough ER
The protein is packaged into vesicles and travels to the Golgi apparatus
Vesicles fuse with the Golgi apparatus, and carbohydrates are added as the protein passes through the compartments
Completed glycoprotein antibodies are packaged into vesicles on the opposite side of the Golgi apparatus
Vesicles merge with the plasma membrane and release antibodies into the interstitial fluid
Golgi apparatus
forming vesicle
vesicles
(interstitial fluid)
(cytosol)
Prokaryotic Cells
• Prokaryotic cells are small and possess specialized surface features
• Prokaryotic cells have fewer specialized structures within their cytoplasm
• Most prokaryotic cells (bacteria) are less than 5 µm long, with a simple internal structure compared to eukaryotic cells
Chapter 5 - Cell membrane & function
• All the membranes of a cell have a similar basic structure – Proteins suspended in a double layer of
phospholipids• Phospholipids are responsible for the isolating
function of membranes• Proteins are responsible for selectively exchanging
substances and communicating with the environment, controlling biochemical reactions, and forming attachments
Plasma membrane functions
• Functions of the plasma membrane– It isolates the cell’s contents from the external
environment– It regulates the exchange of essential substances– It allows communication between cells – It creates attachments within and between cells– It regulates biochemical reactions
Fluid Mosaic Model
• Membranes are “fluid mosaics” in which proteins move within layers of lipids– The “fluid mosaic” model of a membrane was
proposed in 1972 by S.J. Singer and G.L. Nicolson• This model indicates that each membrane consists of a
mosaic, or “patchwork,” of different proteins that constantly shift and flow within a viscous fluid formed by a double layer of phospholipids
• A fluid is any substance whose molecules can flow past one another and includes gases, liquids, and cell membranes
Phospholipid bilayer
• The fluid phospholipid bilayer helps to isolate the cell’s contents– Phospholipids are the basis of membrane
structure and consist of two very different parts• A polar, hydrophilic head• Two nonpolar, hydrophobic tails
– The outer surfaces of animal plasma membranes are bathed in watery interstitial fluid, a weakly salty liquid resembling blood without its cells or proteins
Phospholipid bilayer
– Cholesterol stabilizes membranes, affecting fluidity and reducing permeability
– Proteins are embedded within, or attached to, the phospholipid bilayer
– Many proteins have attached carbohydrates (glycoproteins) on their outer membrane surface
Membrane Proteins
– Membrane proteins may be grouped into five major categories
• Enzymes• Recognition proteins• Receptor proteins• Connection proteins• Transport proteins
Movement of substances
• A solute is a substance that can be dissolved (dispersed as atoms, ions, or molecules) in a solvent
• A solvent is a fluid capable of dissolving a solute– Water is called the “universal solvent”
– The concentration of a substance defines the amount of solute in a given amount of solvent
– A gradient is a physical difference in temperature, pressure, charge, or concentration of a particular substance in a fluid between two adjoining regions of space
Diffusion
• Diffusion is the movement of solutes from regions of higher concentration to regions of lower concentration
– Summary of principles of diffusion• The greater the concentration gradient, the faster the rate
of diffusion• The higher the temperature, the faster the rate of diffusion• If no other processes intervene, diffusion will continue until
the concentrations become equal throughout the solution; that is, until the concentration gradient is eliminated
Permeable
• Plasma membranes are selectively permeable because they allow only certain ions or molecules to permeate
– There are two types of movement across the plasma membrane
• Passive transport is the diffusion of substances across cell membranes down concentration gradients
• Energy-requiring transport is transport that requires the use of cellular energy
Table 5-1
Osmosis• Osmosis is the diffusion of water across
selectively permeable membranes– Selective permeability is in response to gradients
of concentration, pressure, or temperature– Water diffuses from a region of high water
concentration to one of low water concentration across a membrane
– Dissolved substances reduce the concentration of free water molecules (and hence the purity of the water) in a solution
Cell connections
• Four major types of cell-connecting structures– Desmosomes– Tight junctions– Gap junctions– Plasmodesmata
• Restricted to plant cells
Chapter 6 – Energy flow
• Energy is the capacity to do work• Work is a transfer of energy to an object,
which causes the object to move• Chemical energy is the energy that is
contained in molecules and released by chemical reactions– Molecules that provide chemical energy include
sugar, glycogen, and fat
Types of Energy
• There are two fundamental types of energy– Potential energy is stored energy
• For example, the chemical energy in bonds
– Kinetic energy is the energy of movement• For example, light, heat, electricity, and the movement
of objects• The laws of thermodynamics describe the basic
properties of energy– Energy can neither be created nor destroyed (the first law
of thermodynamics), but can change form
Chemical reaction• A chemical reaction is a process that forms or
breaks the chemical bonds that hold atoms together– Chemical reactions convert one set of chemical
substances, the reactants, into another set, the products
– All chemical reactions either release energy or require a net input of energy
• Exergonic reactions release energy• Endergonic reactions require an input of energy
Coupled reactions
• Coupled reactions link exergonic with endergonic reactions– In a coupled reaction, an exergonic reaction provides the
energy needed to drive an endergonic reaction– Sunlight energy stored in glucose by plants is transferred
to other organisms by the exergonic breakdown of the sugar and its use in endergonic processes such as protein synthesis
– The two reactions may occur in different parts of the cell, so energy-carrier molecules carry the energy from one to the other
Enzymes as catalysts
• Catalysts are molecules that speed up the rate of a chemical reaction without themselves being used up or permanently altered
– All catalysts have three important properties1. They speed up reactions by lowering the activation
energy required for the reaction to begin2. They speed up only exergonic reactions3. They are not consumed or changed by the reactions
they promote
Enzyme structure
• Each enzyme has a pocket called an active site into which one or more reactant molecules, called substrates, can enter
– There are three steps of enzyme catalysis1. Both the shape and the charge of the active site allow
substrates to enter the enzyme only in specific orientations2. Upon binding, the substrates and active site change shape to
promote a reaction3. When the reaction between the substrates is finished, the
product(s) no longer properly fit(s) into the active site and diffuse(s) away
Metabolic Pathways
• Cells regulate metabolic pathways by controlling enzyme synthesis and activity – Enzyme activity may be controlled by competitive
or noncompetitive inhibition• In competitive inhibition, a substance that is not the
enzyme’s normal substrate binds to the active site of the enzyme, competing with the substrate for the active site
• In noncompetitive inhibition, a molecule binds to a site on the enzyme distinct from the active site
Figure 6-14 Allosteric regulation of an enzyme by feedback inhibition
As levels of isoleucine rise,isoleucine binds to the regulatorysite on enzyme 1, inhibiting it
intermediates
enzyme 1 enzyme 2 enzyme 3 enzyme 4 enzyme 5
enzyme 1
isoleucine
isoleucine(end product)
threonine(initial
reactant)
Enzyme Activity
– The activity of an enzyme is influenced by the environment
• The three-dimensional structure of an enzyme is sensitive to pH, salts, temperature, and the presence of coenzymes
• Enzyme structure is distorted (denatured) and function is destroyed when pH, salt concentration, or temperature is too high or low.
Chapter 7 - Photosynthesis
• Photosynthesis is the process by which solar energy is trapped and stored as chemical energy in the bonds of a sugar
• Photosynthesis in plants takes place in chlorophyll-containing organelles called chloroplasts, most of which are contained within leaf cells
Chloroplasts
– Chloroplasts are organelles with a double membrane enclosing a fluid called the stroma
– Embedded in the stroma are disk-shaped membranous sacs called thylakoids
– The light-dependent reactions of photosynthesis occur in and adjacent to the membranes of the thylakoids
Figure 7-3 An overview of the relationship between the light reactions and the Calvin cycle
energy fromsunlight
chloroplast
thylakoid
lightreactions
Calvincycle
sugar
C6H12O6O2
CO2H2O 66
(stroma)
ATP
NADPH
ADP
NADP
Overview of Photosynthesis
• During the light reactions, chlorophyll and other molecules embedded in the chloroplast thylakoid membranes capture sunlight energy and convert some of it into chemical energy stored in the energy-carrier molecules ATP and NADPH
• In the reactions of the Calvin cycle, enzymes in the stroma use CO2 from the air and chemical energy from the energy-carrier molecules to synthesize a three-carbon sugar that will be used to make glucose
Figure 7-6 Energy transfer and the light reactions of photosynthesisH2O CO2
ATP
ADP
NADPH
NADP
lightreactions
Calvincycle
sugar
high
O2 C6H12O6
primaryelectronacceptor
lightenergy
e
e
ener
gy le
vel o
f ele
ctro
ns
pigmentmolecules
electrontransportchain II
e
e
reaction centerchlorophyll a molecules
ATP
Photosystem II
H
O2
2H2O
low
e
ee
NADP H
NADPH
electrontransportchain I
Photosystem I
½
Figure 7-7 Events of the light reactions occur in and near the thylakoid membranethylakoid
chloroplast
lightenergy H is pumped into
the thylakoid spaceH
electron transport chain II
e
e
e
e
e
H
H H
H
H
photosystem II
2
H2O O2
A high H concentration iscreated in the thylakoid space(thylakoid space)
(stroma)
electrontransportchain I NADP
NADPH
ATPsynthase
ADP
e
photosystem I
H
H
HH
thylakoidmembrane
The flow of H downits concentration gradientpowers ATP synthesis
HPi
ATP
sugar
Calvincycle
C6H12O6
CO2
½
The Calvin Cycle
– The Calvin cycle occurs in three steps1. Carbon fixation2. The synthesis of G3P3. The regeneration of ribulose bisphosphate (RuBP)
Figure 7-9 The Calvin cycle fixes carbon from CO2 and produces the simple sugar G3P
H2O CO2
ATP
NADPH
ADP
NADP
Calvincyclelight
reactions
sugar
O2 C6H12O6
CO2
3 Carbon fixation combines three CO2
with three RuBP usingthe enzyme rubisco
3 6
RuBP PGA
Calvincycle
6
6
6
6
6
G3P
ATP
ADP
NADPH
NADP
G3P
ADP
ATP3
3
5
G3P
G3P G3P glucose
1
1 1 1
Using the energyfrom ATP, the fiveremaining moleculesof G3P are convertedto three moleculesof RuBP
Energy from ATPand NADPH is usedto convert the sixmolecules of PGA tosix molecules of G3P
One molecule ofG3P leaves the cycle
Two molecules of G3P combineto form glucose and other molecules
Alternate pathways for carbon fixation
– When plant stomata are closed in hot environments to prevent water loss, oxygen builds up in the plant cells and RuBP combines with it, rather than CO2, in a wasteful process called photorespiration
– This process prevents the Calvin cycle from synthesizing sugar, and plants may die under these circumstances
Chapter 8 Cell Respiration
• Cells break down glucose in two stages: glycolysis, which liberates a small quantity of ATP, followed by cellular respiration, which produces far more ATP
• Photosynthesis is the ultimate source of cellular energy– Photosynthesis
• 6 CO2 6 H2O light energy C6H12O6 6 O2
– Complete glucose breakdown• C6H12O6 6 O2 6 CO2 6 H2O ATP energy heat
energy
How cells obtain energy
• Glucose is a key energy-storage molecule– All cells metabolize glucose for energy– Plants convert glucose to sucrose or starch for
storage– In humans, energy is stored as long chains of
glucose, called glycogen, or as fat– These storage molecules are converted to glucose
to produce ATP for energy harvesting
Figure 8-2 A summary of glucose breakdown
(cytosol)
glycolysis
2 CO2
cellularrespiration
ATP
ATP
1 glucose
2 pyruvate
2 lactate
fermentation
2 ethanolIf no O2 is available If O2 is available
CO26 H2O6
O2
mitochondrion
6
Summary of Glycolysis
– During the energy investment stage, phosphate groups and energy from each of the two ATP are added to glucose to produce fructose bisphosphate
– Fructose bisphosphate is broken down into two G3P molecules
– During the energy harvesting stage, the two G3P molecules are converted into two pyruvate molecules, resulting in four ATP and two NADH molecules
– A net of two ATP molecules and two NADH (high-energy electron carriers) are formed
Overview of Cell Respiration• Cellular respiration breaks down the two pyruvate molecules into
six carbon dioxide molecules and six water molecules – The chemical energy from the two pyruvate molecules aids in
the production of 32 ATP– Cellular respiration occurs in mitochondria (powerhouses of the
cell), organelles specialized for the aerobic breakdown of pyruvate
• Mitochondrion has two membranes– The inner membrane encloses a central compartment
containing the fluid matrix– The outer membrane forms the outer surface of the
organelle, and an intermembrane space lies between the two membranes
Figure 8-5 Reactions in the mitochondrial matrix
Formation ofacetyl CoA
coenzyme Acoenzyme A
pyruvateacetyl CoA
NADHNAD
Krebscycle
NADH
NAD
3
3
FADH2
FAD
ADP
ATP
CO2
The electron transport chain– During glycolysis and the mitochondrial matrix reactions, the
cell captures many high-energy electrons in carrier molecules: 10 NADH and 2 FADH2 for every glucose molecule that was broken down
– These carriers each release two electrons into an electron transport chain (ETC), many copies of which are embedded in the inner mitochondrial membrane
– Without oxygen, electrons would be unable to move through the ETC, and H would not be pumped across the inner membrane
– ATP generation continues only when there is a steady supply of oxygen
Figure 8-6 The electron transport chain
(innermembrane)
(matrix)
ATPsynthase
NADH
NAD
P
FADH2
FAD
ADP ATP
ETC
(intermembrane space)
Chemiosmosis
• During the third stage of cellular respiration, chemiosmosis generates ATP– Chemiosmosis is the process by which energy is
first used to generate a gradient of H, and then captured in the bonds of ATP as H flows down its gradient
– As the ETC pumps H across the inner membrane, it produces a high concentration of H in the intermembrane space and a low concentration in the matrix
Figure 8-7 The energy sources and ATP harvest from glycolysis and cellular respiration
1 glucose
Krebscycle
CO2
(matrix)
NADH
FADH2
ATP
(cytosol)
22 glycolysis
2 pyruvate
NADH2
ATP2
ATP32
2
2 acetyl CoA
NADH6
CO24
mitochondrion
O2H2O
electron transport chain
Total: 36 ATP
CoA
2
Figure 8-8 Glycolysis followed by lactic acid fermentation
2 pyruvate(glycolysis)
NADHNAD 22
ADP ATP
NADH NAD22
22
2 lactate1 glucose(fermentation)