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)