AP Biology Midterm

Unit 8

8.1 Responses to an Environment

• An organisms behavioral and/or physiological response is related to environmental changes

  • a stimulus is an external, internal, or combination of signals that causes a resonse from an organism

• An organisms behavioral response can affect their overall fitness

  • Organisms exchange information with one another in response to internal and external signals

  • communication between organisms can change behavior

    • known as signaling behavior

• Signaling behavior produces changes in the behaviors of other organisms

  • can result in differential reproductive success

• Animals communicate through various mechanisms

  • Audible

  • tactical

  • visual

  • electrical

  • communication mechanisms have multiple uses

    • establish dominance

    • find food

    • ensure reproductive success

• Response and communication impact natural selection and evolution

  • Natural selection favors innate and learned behaviors that increase survival and reproductive success

    • innate behaviors are genetically controlled and can occur without prior experience or training

    • Learned behaviors are a product of experience

  • Cooperative disorders increases teamwork between organisms of the same species

    • increases the fitness of the individual

    • increases survival of the population

Key takeaways

1. Organisms respond to changes in their environment to maintain homeostasis, which increases survivability

2. Organisms exchange information about changes in the environment through various mechanisms

3. Organisms have a variety of signaling behaviors that can help increase the survival chance of other members in the population, resulting in differential reproductive success

   1. organisms of the same population/environment use signaling mechanisms to alert others of changes in the environment —> increases chances of reproduction

4. Animals use visual, audible, tactical, electrical, and chemical signals to indicate dominance, find food, establish territory, and ensure reproductive success

5. Cooperative behavior tends to increase the survival of the individual and increase the fitness of the population

8.2 Energy flow through ecosystems

Organisms use different strategies to regulate body temperature and metabolism

• Endotherms use thermal energy generated by metabolism to maintain homeostatic body temperature

  • Changes in heart rate, fat storage, muscle contraction (shivering)

• Echotherms lack efficient internal mechanisms to maintain internal body temperatures

  • rely on behaviors to regulate temperatures (moving in or out of the sun)

Organisms use energy to grow and reproduce

• there is a relationship between metabolic rate per unit of mass and the size of an organism

  • metabolic rate is the amount of energy expended by an animal over a specific amount of time

    • a net gain in energy can result in energy storage or growth

  • A net loss of energy can result in loss of mass and possibly death

  • generally, the smaller the organism the higher the metabolic rate

• Different organisms use various reproductive strategies in response to energy availability

  • some species produce alot of offspring at one time

    • less energy efficient

    • often occurs in unstable environments where the resources are not readily available and the environment experiences frequent change

  • Some species produce few offspring at one time

    • more energy efficient

    • common in stable ecological environments

Changes in energy availability affect populations and ecosystems

• changes in energy availability can result in changes in population size

• Changes in energy availability can result in disruptions to an ecosystem

  • a change in energy resources such as sunlight can affect the number and size of trophic levels

  • a change in the number of producers can affect the number and size of other trophic levels

    • a trophic level is a position an organism maintains in a food chain

Changes in availability can result in changes in population size

• A food chain shows the direction of nutrient transfer from one organism to another

  • each organism occupies a different tropic level and reflects how many energy transfers came before it

  • primary producer —> primary consumer —> secondary consumer —> tertiary consumer —> quaternary consumer (apex) —> decomposer

• Food webs consist of many interconnected food chains

• The transfer of energy between trophic levels is inefficient

  • typically around 10% efficient

  • This energy inefficiency limits the length of food chains and the size of populations

    • typically, population size decreases up trophic levels

The activities of autotrophs and heterotrophs enable the flow of energy within an ecosystem

• Autotrophs are organisms that capture energy from physical or chemical sources in the environment

  • photosynthetic organisms capture energy from sunlight

  • Chemosynthetic organisms capture energy from small inorganic molecules present in their environment with or without organisms

• Heterotrophs capture energy present in carbon compounds produced by other organisms

  • Metabolize carbohydrates, lipids, and proteins, as sources of energy by hydrolysis

Key Takeaways

1. Endotherms and ectotherms utilize different mechanisms to regulate body temperature and metabolism

2. Different organisms use various reproductive strategies in response to energy availability

3. There is a relationship between the metabolic rate per unit of body mass and the size of multicellular organisms generally the smaller the organism —> the higher the the metabolic rate

4. A net gain in energy results in energy storage and growth, whereas a net loss in energy results in loss of mass and potentially death

5. Changes in energy availability can result in changes to population size and disruption to an environment

6. Heterotrophs capture energy present in carbon compounds produced by other organisms

7. Autotrophs such as photosynthetic and chemosynthetic organisms capture energy from physical or chemical organisms in an environment

8.3 Population ecology

A population is comprised of individual organisms of the same species

• a population is comprised of indvidual organisms of the same species in a particular area

  • individuals interact with one another in complex ways

  • individuals in a population usually interbreed with one another of the same species rather than mating with other populations

Many adaptations are related to obtaining and using energy in a particular environment

• the size of populations largely depends on available resources

  • when food is less available, the population size decreases

    • less food energy is available to support individuals

    • reproduction rates decrease

    • offspring survivability decreases

  • when food is readily available, the population size increases

    • reproduction rates increase

    • More food for offspring

    • Survival rates increase

• Different species have adaptations for when energy is not readily available

  • storage of fat during winter months

  • losing leaves or growing leaves when the day length changes

  • migrating in response to changes in food availability

Population growth dynamics depend on a number of factors

• several factors can effect population growth

  • age at reproductive maturity

  • number of offspring produced

  • frequency of reproduction

Reproduction with no constraints results in the exponential growth of a population

• Exponential growth refers to sharp increase in the growth of a population

  • occurs under ideal conditions, when resources are abundant

  • more individuals are reproducing

  • How long it takes to produce offspring is the same

• Exponential growth is represented by a J shaped curve

Key Takeaways

1. Populations comprise individual organisms of the same species thst interact with one another and with the envornment in complex ways

2. Population growth dynamics depend on several factors, including time, birth rate, death rate, and population size

3. Reproduction without constraints results in the exponential growth of a population

8.4 Effect of Density of Populations

• Resource availability in an environment impacts population density

  • Population density refers to how close individuals within a population live near one another

    • Higher reproductive rate

    • space is limited

• When doos is limited, the density of a population may decrease

  • Lower reproductive rate

  • individuals can spread out in the limited space

• Limits to population growth are due to density dependent and density independent

  • Density dependent factors are abiotic or biotic factors whose effect on population size relies on a population’s density

    • Competition for resources

    • territoriality

    • disease

    • predation

• Density independent factors are abiotic or biotic factors that affect population size regardless of population density

  • Natural disasters

    • floods

    • forest fires

    • volvanic eruptions

  • pollution

• A population can produce a density of individuals that exceeds the systems resource availability

  • a logistic growth model describes population growth that intially starts slowly, immediately followed by exponential growth, and ends with a relatively stable maximum growth

  • illustrated in an S shaped curve

  • Maximum number of individuals an environment can sustain is referred as the carrying capacity

• Both density dependent and density independent limiting factors cause a population to reach carrying capacity

• Under certain conditions, a population can temporarily exceed the carrying capacity

  • limiting factors will always bring population size back down

  • fluctuations in population size can naturally occur at or near carrying capacity

• Population dynamics can be represented using mathematical models

Key Takeaways

1. A population can produce a density of individuals that exceeds the system resource availability

2. When density dependent and density independent factors are imposed, a logistic growth model generally ensues

8.5 Community Ecology

• The structure of a community is described according to species composition and diversity

  • a community refers to a group of different species living together in the same location and interacting with one another

  • Communities are described based on species diversities and species composition

    • species diversity refers to the variety species and the quantity of individuals included in each species within a given community

  • Species composition refers to the identity of each species in the community

• The structure of community is measured in terms of species composition and diversity

  • species diversity can be measured using an equation called the simpsons diversity index

    • used to measure the biodiversity of a habitat

    • the higher the index value, the more diverse the community

    • based on random samples in the environment

• Interactions among populations determine how they access energy and matter

  • communities change over time depending on interactions between populations

    • competition is an interaction that can affect how populations access energy and matter

  • can result in a change in community structure

  • competition for food an habitats

  • Can be positive, negative, or neutral

• Positive interactions

  • mutualism : both species benefit

  • Commensalism : one species benfits but the other is not harmed or helped

• Negative interactions

  • parasitism : one species uses another for a food source

  • predator prey : one species uses another for a food source

• Neutral interactions have no impact on the species involved

• Interactions among populations determine how they access energy and matter

  • bracket or shelf fungi are tree parasites

    • they produce fruiting bodies that grow on the bark of the tree

    • the absorb nutrients from the outer bark of the tree

    • can cause weakening of the external structure of the tree

      • redued canopy and reduced foliage desnity

      • frees out resources

  • Can infect interior parts of the tree

    • provides new availabile niches and habitats

• They provide microhabitats for insects and other organisms

  • Insects can live in the holes the fungi make in the tree bark

• They provide a food source for insects and other organisms

  • some insects use the fungi as a food source

• Relationships among interacting populations can be modeled

Key Takeaways

1. The structure of a community is measured and described in terms of species composition and species diversity

2. Communities change over time depdening on interactions between populations

3. Interactions among populations determine how they acces energy and matter within a community

4. Relationships among interacting populations can be characterized by positive and negative effects and can be modeled

5. Competition, predation, and symbioses, including parasitism, and commensalism, can drive population dynamics

8.6 Biodiversity

• Ecosystem diversity is related to its resilience to changes in the environment

  • natural and aritifical ecosystems with fewer component parts and with little diversity among the parts are often less resilient to changes in the environment

  • the diversity of a species within an ecosystem may influence the organization of the ecosystem

  • The long term structure of an ecosystem cab be stabilized with more diversity

  • less vulnerable to drastic structural changes when environment changes or when organisms are added and or removed

• Changes in diversity can cause short term and long term structural changes in the community

• Abiotic and biotic factors contribute to maintaining the diversity of an ecosystem

  • the diversity of species within an ecosystem may influence the organization of the system

  • abiotic factors help maintain system diversity

    • climate

    • water and nutrient availability

    • light availability

  • Biotic factors help maintain ecosystem diversity

    • producers help maintain ecosystem diversity

      • many populations depend on producers for food and habitats

      • reduce erosion

  • Dominant predators keep prey populations under control

    • Have diversified diets

    • dont put too much pressure on any one population

• The effects of keystone species are disproportionate relative to their abundance

  • keystone species are species the community structure depends on

  • smaller populations compared to other populations in the community

  • When they are removed from the ecosystem, the ecosystem often collapses

    • they often control the size of multiple other populations

    • Overpopulation depletes resources

Key Takeaways

1. Natural and artificial ecosystems with fewer component parts and with little diversity among the parts are often less resilient to changes in the environment

2. The longer term structure of an ecosystem can be stabilized with more diversity. Changes in diversity can cause short term and long term structural changes in a community

3. Keystone species, producers, and esstial abiotic and biotic factors contribute to maintaining the diversity of an ecosystem

4. The effects of keystone species on the ecosystem are disproportionate relative to their abundance in the ecosystem, and when thet are removed from the ecosystem, the ecosystem collapses

8.7 Disruptions to Ecosystems

• Evolution is characterized by change in the genetic makeup of a population over time

  • an adaptation is a genetic variation that is favored by selection

    • is manifested as a trait that provides an advantage to an organism in a particular environment

    • can arise through mutations

      • mutations are random and are not directed by specific environmental pressures

    • Will increase in frequency if environment continues to select for this trait

      • increases biodiversity

      • populations evolve

      • specitation can occur

• Invasive species affect ecosystem dynamics

  • the availability of resources can result in uncontrolled population growth and ecological changes

  • an invasive species is one that is not native to a specific area and harms the community it is introduced to

  • the introduction of an invasice species can be intentional or unintentional

  • invasive species exploit new niches

    • nich is free of predators or competitors

    • outcompete other organisms for resources

    • population increases unchecked

• The distribution of local and global ecosystems changes over time

  • habitat change can occur because of human activity

  • human impact accelerates change at local and global levels

    • urbanization

    • deforestation

    • erosion

    • extinction

    • pollution

    • climate change

  • The introduction of new diseases can devastate native species

    • human migration and overpopulation can accelerate spread of disease

• Geological and meterological activites lead to changes in ecosystems

  • geological and meteorological events affect habitat change and ecosystem distribution

    • large habitat disruptions

    • chemical disruptions

  • Can accelerate evolution

    • reproductive isolation

    • change in selective advantage

    • new niches

  • Can Cause extinction

  • Biogeographical studeis illustrate these changes

    • analyze species disitribution

    • can be used to characterize biomes

Key Takeaways

1. An adaptation is a genetic variation that is favored by selection and is manifested as a trait that provides an advantage to an organism in a particular environment

2. The intentional or unintentional introduction of an invasive species can allow the species to exploit a new niche free of predators or competitors or to outcompete other organisms for resources

3. The introduction of new diseases can devastate native species. Habitat change can occur because of human activity

4. Geological and meteorological events affect habitate change and ecosystem distribution

Unit 1

1.1 Structure of Water and Hydrogen Bonding

• The subcomponents of biological molecules determine the properties of that molecule

  • Water is composed of 2 main elements, oxygen and hydrogen, in a 1:2 ratio respectively

  • Covalent bon is the term used to describe the bond type in which atoms share electrons

  • oxygen is more elctronegative compared to hydrogen, resulting in an unequal sharing of electrons between oxygen and hydrogen

  • Covalent bonding can result in plarity when there are differences in atomic electronegativities, a water molecule has polarity

• A hydrogen bond is a weak bond interaction between the negative and positive regions of two separate molecules

• Water can form hydrogen bonds with other water molecules or with other charged molecules

• When two of the same molecules form hydrogen bonds with eachother this is called cohesion

• When two different molecules form hydrogen bonds with eachother this is called adhesion

• Living systems deoend upon properties of water

  • the hydrogen bonds between water molecules can result in surface tension

  • cohesion, adhesion, and surface tension allow for water to demonstate additional chemical behaviors known as emergent properties

Key Takeaways

1. Water contains 1 oxygen atom covalently bonded to 2 hydrogen atoms

2. Oxygen has a higher electronegativity compared to hydrogen resulting in a water molecule having polarity

3. Polarity allows molecules to form hydrogen bonds when oopositely charged regions of two molecules interact

4. The term cohesion refers to molecules of the same type forming hydrogen bonds with one another and adhesion refers to different types of molecules forming hydrogen bonds with one another

5. Living systems depend upon waters properties, like surface tension

1.2 Elements of life

• Living systems require a constant input of energy

  • the law of conservation of energy states that energy cannot be created or destroyed only transformed

  • Living systems follow the laws of energy

  • Living systems need a constant input of energy to grow, reproduce, and maintain organization

  • Living systems mainly use the energy stored in chemical bonds

• Living systems require an exchange of matter

  • atoms and molecules from the environment are necessary to build new molecules

  • carbon is used to build bilogical molecules such as carbohydrates, proteins, nucleic acids, and lipids

  • nitrogen is sued to build proteins and nucleic acids

  • Phosphorus is used to build nucleic acids and certain lipids

• Carbon is used to build macromolecules

  • caron can bond to other carbon atoms creating carbon skeletons to which other atoms attatch

  • carbon skeletons allow for the creation of very large and complex molecules

  • carbon containing molecules can be used to store energy

  • carbon contsining molecules can be used to form basic cell structures

Key Takeaways

1. living systems need a constant input of energy to grow, reproduce, and maintain organization

2. atoms and molecules from the environment are necessary to build new molecules

3. Carbon is used to build all macromolecules, store energy, and form cells

4. Nitrogen is used to build proteins and nucleic acids

5. Phosphorus is used to build nucleic acids and certain lipids

1.3 Introduction to biological macromolecules

• Monomers have important properties

  • monomers are chemical subunits used to create polymers

  • polymer is a macromolecule made of many monomers

  • a covalent bond is formed between two interacting monomers

  • monomers have specific chemical properties that allow them to interact with one another

  • polymers are specific to the monomers they consist of

    • monosaccharide is the monomer of carbohydrates

    • amino acids are monomers of proteins

    • nucleotides are monomers of nucleic acids

    • fatty acids are monomers of lipids

• Dehydration synthesis reactions form covalent bonds

  • dehydration synthesis reactions are used to create macromolecules

  • the subcomponents of a water molecule are removed from interacting monomers and a covalent bond forms between them

  • The H and OH join together to form a molecule of water, water is a byproduct of this reaction

• Hydrolysis reactions cleave covalent bonds

  • polymers are hydrolyzed into monomers during a hydrolysis reaction

  • covalent bonds between the monomers are cleaved during a hydrolysis reaction

  • A water molecules is hydrolyzed into subcomponents and each subcomponent is added to a different monomer

• Dehydration synthesis creates carbohydrates

  • carbohydrate monomers have hydroxides and hydrogen atoms attatched

  • one monomer will lose an entire hydroxide while the other monomer will only lose a hydrogen from a hydroxide

  • A covalent bond will form where the hydroxide and hydrogen atom were removed

  • The hydroxide (OH) and hydrogen (H) join forming a water molecules (H2O)

• A dehydration synthesis creates proteins

  • protein monomers are called amino acids

  • each amino acid has an amino group (NH2) terminus and a carboxyl group (COOH) terminus

  • a hydroxide (OH) is lost from the carboxyl group of one amino acid and a hyrdrogen atom is lost from the amino group of another amino acid

  • a covalent bond will form between the monomers in the location where the hydroxide and hydrogen atom were removed

  • The hydroxide and hydrogen atom will join forming a water molecule

• Proteins can undergo hydrolysis reactions

  • covalent bonds between amino acids can be cleaved

  • a water molecle is hydrolyzed and each subcomponent of water will be bonded to different amino acids

  • the result is separate amino acid molecules

Key Takeaways

1. all monomers contain carbon and are used to build biological macromolecules

2. covalent bonds are used to connect monomers together

3. dehyrdation synthesis reactions are used to create biological macromolecules and water is an additional product

4. Hydrolysis reactions use water to break down biological macromolecules

1.4 Properties of biological molecules

• Function is related to structure

  • living system are organized in a hierarchy of structural levels

  • at every level of organization, function is related to structure

  • A change in structure generally results in a change in function

  • in living systems the proterites of biological molecyles are determined by the structure and function of the molecules

• The structure of Nucleic acids determine functions

  • nucleic acids are polymers comprised of monomers called nucleotides

  • Nucleotides have a basic structure that contains 3 main subcomponents : a five carbon sugar, a phosphate group, and a nitrogen base

  • All nucleic acids store biologcial information in the sequence of nucleotide monomers

• There are differences in nucleic acid structure

  • DNA and RNA are examples of nucleic acids

  • DNA and RNA nucleotides differ in the type of sugar contained (deoxyribose and ribose)

  • DNA and RNA nucleotides can differ in the nitrogen base contained (adenine, guaning, thymine, cytosine, uracil)

  • Although both DNA and RNA store biological information, the structural differences between them result in specific functional differences

• Proteins have different structures and functions

  • amino acids are the monomers that make up proteins

  • Amino acids have directionality with an amino terminus and a carboxyl terminus

  • a polypeptide, the primary structure of a protein, consists of a specific order of amino acids and determines the overall shape the protein can achieve

• The chemical properties of R groups varies

  • amino acids differ in the R group, the atoms attatched to the central carbon

  • The r group can be hydrophobic, hyrdrophyllic, or ionic

  • A protein can have different amino acids in the polypeptide allowing the protein to have regional differences in structure and function

• Carbohydrates and lipids vary in structure and function

  • complex carbohydrates can have monomers whose structures determine the properties and functions of the carbohydrate

  • Lipids are nonpolar macromolecules that do not have true monomers but are comprised of subunits such as fatty acids and gylcerol

  • Lipids have fatty acid components that determine structure and function based on saturation

  • Specialized lipids, called phospholipids, contain hydrophilic and hydrophobic regions that determine their interactions with other molecules

• Membranes contain lipids and proteins

  • phospholipids and proteins are two main molecules that make up biological membranes

  • Phospholipids and some membrane proteins have hydrophilic and hyrdrophobic regions

  • The hydrophilic regions of phospholipids and proteins can interact with eachother and the water environments

  • The hydrophobic regions of phospholipids and membrane proteins can interact with eachother but cannot interact with water environments

Key Takeaways

1. Nucleotides can vary in the sugar and base components resulting in nucleic acids with different structure and function

2. The amino terminus and carboxyl terminus give amino acids directionality and determine how amino acids assemble into protein polymers

3. R group properties determine how amino acids interact within the polypeptide and determine the structure and function of the protein

4. Differences in the components of carbohydrate monomers determine how the monomers assemple into complex carbohydrates and determine function

5. Lipids are nonpolar macromolecules and difference in saturation determine the structure and function of lipids

6. Phospholipids contain polar regions that interact with other polar molecules and nonpolar regions

1.5 Structure and Function of Biological Macromolecules

• Directionality of the subcomponents influences structure of nucleic acid polymers

  • the linear structure of all nucleic acids is characterized by a 3’ hydroxyl and 5’ phosphate of the sugar in the nucleotide

  • DNA is a nucleic acid polymer containing two strands, each strand in an antiparallel 5’-3’ direction

  • Adenine - Thymine base pairs are held together by 2 hydrogen bonds and guanine - cytosine base pairs are held together by 3 hydrogen bonds

  • hydrogen bonds between base pairs in a DNA molecule stabilize the molecules structure

  • The linear sequence of nucleotides encodes biological information

  • Any change to the sequence of the nucleotides may lead to a change in the encoded information

• Directionality influences the synthesis of nucleic acids

  • During the synthesis of nucleic acid polymers, nucleotides can only be added to the 3’ end

  • Covalent bonds are used to connect free nucleotides to the strand

Key Takeaway

1. The linear sequences of all nucleic acids is defined by the 3’ hydroxyl and 5’ phosphate of the sugar in the nucleotide

2. DNA is structured as an antiparallel double helic with two strands running in opposite 5’-3’ directions. This allows for the two strands of DNA to be held together by hydrogen bonds between the base pairs. A-T held together by 2 hydrogen bonds, G-C held together by 3 hydrogen bonds

3. During DNA and RNA synthesis, nucleotides can only be covalently added to the 3’ end of a growing nucleotide strand

4. Changes in the linear structure of the nucleotide bases may lead to differences in the encoded biological information or the structural stability of the molecule

• Directionality of the subcomponents influences structure of proteins

  • proteins comprise linear chains of amino acids that have directionality with an amino terminus and carboxyl terminus

  • Covalent bonds are connected by the formation of covalent bonds at the carboxyl terminus of the growing peptide chain

• PRIMARY STRUCTURE is determined by the sequence of amino acids held together by covalent bonds, called peptide bonds

• SECONDARY STRUCTURE arises through local folding of the amino acid chain into elements such as alpha helices and beta pleated sheets

• TERTIARY STRUCTURE is the overall 3d shape of the protein and often minimizes free energy ; various types of bonds and interactions stabilize the proteins at this level

• QUATERNARY STRUCTURE arises from the interactions between multiple polypeptide chains

• Four elements of protein structure

  • primary

  • secondary

    • alpha helices

    • beta pleated sheets

  • Tertiary

    • 3d functional form for most proteins

  • Quaternary

Key Takeaways

1. amino acids have directionality with an amino terminus and carboxyl terminus on the other. Amino acids are added to the carboxyl terminus of a growing peptide chain by the formation of covalent bonds

2. There are 4 elements of protein structure : primary, secondary (alpha helices, beta pleated sheets), tertiary, quaternary. Levels of structure beyond primary linear sequence of amino acids arise through local folding and other chemical interactions among amino acids. The resulting 3d shape gives rise to the proteins specific functions.

3. A change in amino acid subunit at the primary level of structure may lead to a change in the structure and function of the protein.

• Directionality of the subcomponents influences structure and function of carbohydrates

  • carbohydrates comprise linear chains of sugar monomers connected by covalent bonds

  • small direction change in the components of a molecules can result in functional differences

  • carbohydrate polymers may linear or branched

  • starch and glycogen both function in energy storage (starch in plants glycogen in humans and other vertebrates)

  • Cellulose functions as support and provides strength in plant cell walls

Key Takeaways

1. carbohydrate comprise linear chains of sugar monomers connected by covalent bonds. Sugar monomers may vary in the direction of some their components, such as the bond orientation of OH groups linked to carbon chain

2. Depending on the type of sugar monomer used in its formation, a carbohydrate polymer may have a linear or branched structure and can differ in function

1.6 Nucleic Acids

• Similarities between DNA and RNA

  • both are assembled from a nucleotide subunits which are comprised of a

    • 5 carbon sugar

    • phosphate group

    • nitrogenous base

  • Each nucleotide monomer is connected by covalent bonds forming the sugar phosphate backbone

  • Each linear strand of nucleotides has a 5’ and and a 3’ end

  • The nitrogenous bases are perpendicular to the sugar phosphate backbone

• Differences between DNA and RNA

  • DNA contains deoxyribose and RNA contains ribose

  • DNA contains thymine and RNA contains uracil

  • RNA is usually couble stranded ; RNA is usually single stranded

  • The two DNA strands in double stranded DNA are antiparallel

Key Takeaways

1. Both DNA and RNA are formed from nucleotide subunits connected by covalent bonds to form linear molecule with 5’ and 3’ ends. Each nucleotide is comprised of a sugar, phosphate group, and nitrogenous base

2. Differences include the type of sugar, one of the nitrogenous bases (RNA has uracil whereas DNA contains thymine), and number of strands. DNA has two nucleotide strands that are antiparallel

Unit 2

2.1 Cell Structure : Subcellular Components

• Subcellular components universal to all cells

  • all living cells contain a genome and ribosomes, reflecting the common ancestry of all known life

  • Ribosomes synthesize protein according to mRNA sequences and the instructions that are encoded in that mRNA sequence originate from the genome of the cell

• structure and function : ribosomes

  • ribosomes consist of two subunits that are not membrane enclosed

  • Ribosomes are made of ribosomal RNA and proteins

  • Ribosomes synthesize protein according to mRNA sequences

• Structure and function : endoplasmic reticulum

  • the endoplasmic reticulum is a network of membrane tubes within the cytoplasm of eukaryotic cells

  • Two forms of ER

    • Rough ER

      • has ribosomes attatched to its membrane

      • compartmentalizes the cell

        • rough ER is associated with packaging the newly synthesized proteins made by attatched ribosomes for possible export from the cell

    • Smooth ER

      • does not have ribosomes attatched

      • functions include detoxification and lipid synthesis

  • Structural differences between rough ER and smooth ER leads to functional differences

• Structure and function : golgi complex

  • series of flattened membrane bound sacs found in eukaryotic cells

  • involved in correct folding and chemical modification of newly synthesized proteins and packaging for protein trafficking

• Structure and function : mitochondria

  • has a double membrane

  • outer membrane is smooth and inner membrane is highly convuluted, forming folds called cristae

  • Functions in production of ATP energy that eukaryotic cells can use for work

• Structure and function : lysosomes

  • membrane enclosed sacs found in some eukaryotic cells that contain hydrolytic enzymes

  • hydrolytic enzymes can be used to digest a variety of materials such as damaged cell parts or macromolecules

• Structure and function : vacuoles

  • membrane bound sacs found in eukaryotic cells

  • plays a variety of roles ranging from storage of water and other macromolecules to the release of water from a cell

• Structure and function : chloroplasts

  • found in eukaryotic cells such, as photosynthetic agae and plants

  • double outer membrane

  • specialized for capturing energy from the sun and producing sugar for the organism

Key takeaways

1. ribosomes are not enclosed by a membrane and are subcellular components found in all forms of life, reflecting the common ancestry of all known life. Ribosomes function to synthesize proteins for cells.

2. Eukaryotic cells have additional membrane enclosed organelles that perform specialized functions for the cell. These include the rough er, smooth er, golgi complex, mitochondria, lysosomes, vacuoles, and chloroplasts

2.2 Cell structure and function

• Structure and function : chlorplasts

  • specialized for photosynthesis and capturing energy from the sun to produce sugar

  • Within chloroplasts are distinct compartments

    • thylakoids :

      • highly folded membrane compartments that are organized in stacks called grana

      • Membranes contain chlorophyll pigments that comprise the photosystems and electron transport proteins can be found between the photosystems, embedded in the thylakoid membrane

      • Light dependent reactions occur here

      • Folding of these internal membranes increases the efficiency of these reactions

    • Stroma

      • fluid between the inner chloroplast membrane and outside thylakoids

      • the carbon fixation reactions occur here

• Structure and function : mitochondria

  • double memrbane provides compartments for different metabolic reactions

  • Mitochondria capture energy from macromolecules

  • The krebs cycle reactions occur in the matrix of the mitochondria

  • Electron transport and ATP synthesis occur in the inner mitochondrial membrane

  • Folding of the inner membrane incereases the surface area, which allows for more ATP to be made

• Structure and function : vacuoles

  • vacuoles play a variety of roles, including storage and release of water, macromolecules, and cellular waste products

  • in plants, vacuoles aid in retention of water for turgor pressure

  • turgor pressure is an internal cellular force, usually caused by water pushing up against the plasma membrane and cell wall

• Structure and function : lysosomes

  • contain hydrolytic enzymes and can contribute to cell function in the following ways :

    • intracellular digestion

    • recycling of organic materials

    • programmed cell death (apoptosis)

• Structure and function : endoplasmic reticulum

  • the ER performs the following functions for the cell

    • provides mechanical support

    • plays a role in intracellular transport

    • rough er carries out protein synthesis on ribosomes that are bound to its membrane

Key takeaways

1. Subcellular components and organelles interact to support cell function. The ER, mitochondria, lysosomes, and vacuoles, each have specialized functions that occur within their membrane enclosed structures which increases the efficiency of the cell to perform chemical reactions and store materials

2. Chloroplasts and mitochondria are structural features of eukaryotic cells that allow organisms to capture, store, and use energy. The folding og the inner membrane in both these structure increases the surface area which allows for more ATP to be synthesized.

2.3 Cell Size

• Cells are typically small

  • moving materials in and out of cells gets more difficult the larger a cell is

• Effects of surface area to volume ratios on the exchange of materials

  • smaller cells typically have a higher surface area to volume ratio and more efficient exchange of materials with the environment

  • As cells increase in volume, the relative surface area decreases making it difficult for larger cells to meet the demand for internal resources and remove waste sufficiently

  • these limitations can restrict cell size and shape

Key Takeaways

1. Smaller cells typically have a higher surface area to volume ratio and more efficient exchange of materials with the environment

2. Surface area to volume ratio affects the ability of a biological system to obtain necessary resources, eliminate waste products, acquire and dissipate thermal energy, and otherwise exchange chemicals and energy with the environment

3. Using the formulas given on the AP formula sheet, surface area and volume calculations can be done for a variety of cell shapes. Using calculated surface area and volume, a ratio can be determined

2.4 Plasma Membrane

• Cells have membranes that allow them to establish an internal environment

  • cell membranes provide a boundary between the interior of the cell and the outside environment

  • Cell membranes control the transport of materials in and out of the cell

• Phospholipids have both hydrophyllic and hydrophobic regions

  • phospholipids are amphipathic

    • hydrophyllic phosphate head is polar

    • Hydrophobuc fatty acid tail is nonpolar

  • Phospholipids spontaneously form a bi layer in aqueous environment

    • tails are located inside the bilayer

    • Heads are exposed to the aqueous outside and aqueous inside environments

• Embedded proteins can be hydrophyllic or hydrophobic

  • peripheral proteins

    • loosely bound to the surface of the membrane

    • hydrophyllic with charged and polar side groups

  • Integral proteins

    • span the membrane

    • Hydrophilic with charged and polar side groups

    • Hydrophobic with nonpolar side groups penetrate hydrophobic interior of bilayer

• Embedded proteins play various role sin maintaining the internal environment of the cell

  • membrane protein functions

    • transport

    • cell cell recognition

    • enzymatic activity

    • signal transduction

    • intercellular joining

    • attatchment for extracellular matrix or cytoskeleton

• The framework of the cell membranes is described as the fluid mosaic model

  • structured as a mosaic of protein molecules in a fluid bilayer of phospholipids

  • The structure is not static and is held together primarily by hydrophobic interactions which are weaker than covalent bonds

  • Most lipids and some proteins can shift and flow along the surface of the membrane or across the bilayer

• Fluid mosaic model includes steroids

  • chlosterol, a type of steroid, is randomly distributed and wedged between phospholipids in the cell membrane of eukaryotic cells

  • cholesterol regulates bilayer fluidity under different environmental conditions

• Fluid mosaic model components include carbohydrates

  • diversity and location of the carbohydrates and lipids enable them to function as markers

    • glycoproteins : one or more carbohydrate attached to a membrane protein

    • Glycolipids : lipid with one or more carbohydrate attatched

Key Takeaways

1. Phospholipids spantaneously form a bi layer in an aqueous environment with hydrophilic phosphate regions oriented toward the aqueous external or internal envronment and the hydrophobic fatty acid regions face each other within the interior of the membrane

2. Embedded proteins can be hydrophilic, with charge and polar side groups, and or hydrophobic with nonpolar side groups

3. Embedded proteins have a variety of functions including transport, cell to cell regognition, enzym activity, signal transduction, intercellular joining, and attatchement to cytoskeleton and extracellular matrix

4. The fluid mosaic model consists of structural framework of phospholipid molecules that are embedded with proteins, steroidsm glycoproteins, and glycolipids that can flow around the surface of the cell within the membrane

2.5 Membrane permeability

• The structures of the cell membrane

  • phospholipids are amphipathic

    • hydrophilic phpshate head is polar

    • hydrophobic fatty acid tail is nonpolar

  • Phospholipids spontaneously form a bi later in an aqueous environment

  • Fluid mosaic model : a moving phospholipid bilayer composed of varying types of molecules

  • Selective permeability is a direct consequence of membrane structure

• The cell membrane is selectively permeable

  • small nonpolar molecules pass freely

    • N2

    • O2

    • CO2

  • Hydrophilic substances such as large polar molecles and ions can not freely move across the membrane

  • Hydrophilic substances move through transport proteins

    • channel proteins : a hydrophilic tunnel spanning the membrane the allow specific target molecules to pass through

    • Carrier proteins : spans the membrane and change shape to move a target molecules from one side of the membrane to the other

  • Small polar molecules can pass directly through the membrane in minimal amounts

• The cell wall is a structural boundary and permeable barrier

  • as a structural boundary

    • protects and maintains the shape of the cell

    • prevents against cellular rupture when internal water pressure is high

    • Helps plants stand up against the force of gravity

  • As a permeable barrier

    • plasmodesmata : small holes between plant cells that allows the transfer of nutrients, waste, and ions

  • Animal cells do not have cell walls

• Cell walls are composed of complex carbohydrates

  • cell wall : composed of complex carbohydrates

    • plants : cellulose

      • Polysaccharide

    • Fungi : chitin

      • polysaccharide

    • Prokaryotes : peptidoglycan

      • polymer consisting of sugar and amino acids

Key Takeaways

1. The structure of cell membranes results in selective permeability

2. Cell membranes separate the internal envornment of the cell from the external environment

3. Selective permeability is a direct consequence of membrane strucutre, as described by the fluid mosaic model

4. Small nonpolar molecules freely pass across the membrane

5. Hydrophilic substances move across the membrane through embedded channel and transport proteins

6. Polar uncharged molecules pass through the membrane in small amounts

7. Cell walls provide a structural boundary, as well as a permabilirt barrier for some substances to the internal environments

8. Cell walls of plants, prokaryotes, and fungi are composed of complex carbohydrates

2.6 Membrane transport

• Selectively permeable membranes allow for the formation of concentration gradients

  • concentration gradient is when a solute is more concentrated in one area than another

  • A membrane separates two different concentrations of molecules

• Passive transport is the net movement of molecules from a high to low concentration

  • net movement of molecules from high concentration to low concentration without metabolic energy such as ATP

  • Plays a primary role in the import of materials and the exports of wastes

• Diffusion : movement of molecules from high concentration to low concentration s

  • small nonpolar molecules pass freely

• Facilitated diffusion : movement of molecules from high concentration to low contration through transport proteins

  • allows for hydrophilic molecules and ions to pass through membranes

• Active transport requires energy

  • active transport requires the direct input of energy to move molecules from regions of low concentrations to regions of high concentrations

• Endocytosis requires energy to move large molecules into the cell

  • in endyocytosis, the cell uses energy to take in macromolecules and particulate matter by forming new vesicles derived from the plasma membrane

    • phagocytosis : cell takes in large particle

    • pinocytosis : cell takes in extracellular fluid containing dissolved substances

    • receptor mediated endocytosis : receptor proteins on the cell membrane are used to capture specific target molecules

• Exocytosis requires energy to move large molecules out of the cell

  • in exocytosis : internal vesicles use energy to fuse with the plasma membrane and secrete large macromolecules out of the cell

    • proteins such as signaling proteins

    • hormones

    • waste

Key Takeaways

1. Passive transport is the net movement of molecules from high concentration to low concentration without the direct input of metabolic energy

2. Active transport requires the direct input of energy to move molecules from regions of low concentration to regions of high concentration

3. the selective permeability of membranes allows for the formation of centration gradients of solutes across the membrane

4. in exocytosis, internal vesicles use energy to fuse with the plasma membrane and secrete large macromolecules out of the cell

5. in endocytosis, the cell uses energy to take in macromolecules and particulate matter by forming new vesicles derived from the plasma membrane

2.7 Facilitated diffusion

• Membrane proteins are necessary for facilitated diffusion

  • facilitated diffusion : movement of molecules from high concentration to low concentration through transport proteins

    • large and small polar molecules

    • largeg quantities of water can pass through aquaporins

    • charged ions require channel proteins

• Active transport establishes and maintains concentration gradients

  • active transport moves molecules and ions against their concentration gradient from low to high concentration

    • carrier proteins called pumps require metabolic energy

    • establishes and maintains concentration gradients

• Membrane proteins are necessary for active transport

  • cotransport : secondary active transport that uses the energy from an electrochemical gradient to transport two different ions across the membrane through a protein

    • symport : two different ions are transported in the same direction

    • Antiport : two different ions are transported in opposite directions

• Membranes may become polarized by movement of ions

  • the cell membrane allows for the formation of gradients

    • electrochemical gradients

      • type of concentration gradient

      • membrane potential : electrical potential difference across a membrane

    • membranes may become polarized by movement of ions across a membrane

• The NA+ K+ ATPase contributes to membrane potential

  • NA+ K+ ATP ase contributed to the maintenance of the membrane potential

    • 3 NA+ pumped

    • 2 K+ pumped

Key takeaways

1. membrane proteins are required for facilitated diffusion of charged and large polar molecules through a membrane

2. large quantities of water pass through aquaporins

3. Membranes become plarized by the movement of ions across the membrane

4. Membrane proteins are necessary for active transport

5. Metabolic energy is required for active transport of molecules and ions across the membrane and to establish and maintain concentration gradients

6. The NA+ K+ ATPase contributes to the maintenance of the membrane potential

2.8 Tonicity and Osmoregulation

• Water moves by osmosis

  • osmosis is the diffusion of free water across a selectively permeable membrane

    • large quantities of water move via aquaporins

  • Osmolarity is the total solute concentration in a solution

    • water has high solvency abilities

    • solute is the substance being dissolved

    • solvent is a substance that dissolves a solute

    • Solution is a uniformed mixture of one ore more solutes dissolved in a solvent

• Tonicity effects a cells physiology

  • tonicity is the measurement of the relative concentrations of solute between two solutions

  • Internal cellular environments can be hypotonic, hypertonic, or isotonic to external environments

    • hypotonic

      • more solute less solvent

    • Hypertonic

      • less solute more solvent

    • isotonic

      • equal concentrations of solute and solvent

  • Water moves by osmosis to the area with a higher solute concentration

    • water concentrations and solute concentrations are inverselt related

    • water would diffuse out of a hypotonic environment to a hypertonic environment

    • solutes diffuse along their own concentration gradients, from the hypertonic environment into the hypotonic environment

  • When a cell is in an isotonic environment, a dynamic equilibrium exists with equal amounts of water moving in and out of the cell at equal rates

    • no net movement of water takes place

• Osmoregulator mechanisms contribute to survival

  • in plant cells, osmoregulation maintains water balance and allows control of interal solute composition / water potential

  • Environmental hypertonicity

    • less cellular solute and more cellular water

    • plasmolysis

  • Isotonic solution

    • equal solute and water

    • flaccid

  • Environmental hypotonicity

    • more cellular solute and less cellular water

    • turgid

  • The cell wall helps maintain homeostasis for the plant in environmental hypotonicity

    • osmotic pressure is high outside of the plant cell due to environmental hypotonicity

    • water flows into the plant vacuoles via osmosis causing the vacuoles to expand and press against the cell wall

    • The cell wall expands until it begins to exert pressure back on the cell, this pressure is called tugor pressure

    • turgidity is the optimum state for plant cells

  • In animal cells, osmoregulation maintains water balance and allows control of internal solute composition / water potential

    • environmental hypertonicity

      • less cellular solute and more cellular water

      • shriveled

    • isotonic solution

      • equal solute and water

      • normal

    • environment hypotonicity

      • more cellular solute and less cellular water

      • lysed

Key Takeaways

1. external environments can be hypotonic, hypertonic, or isotonic to the interal envornment of cells

2. Water moves by osmosis from areas of low osmolarity/solute concentraation to area of high solute concentration

3. Growth and homeostasis are maintained by the constant movement of molecules across membranes

4. Osmoregulation maintains water balance and allows organisms to control their internal solute composition

• The components of an effective graph

  • title

    • experiment details and what is being measured

  • Labeled axes with units

• Line graph

  • reveals trends or progress over time for multiple groups or treatments

  • track chanegs over time concentrations

• XY graph

  • scatterplot

  • to determine relationships between two different things

  • compare two variables that may or may not have a linear relationship

• Histogram

  • show how values in a data set are distributed across evenly spaced or equal intervals

  • explore the relationship between two or more variables

• Bar graph

  • compare multiple groups or treatments to each other

• Box and whisker plots

  • show the variability in a sample

  • ideal for comparing distributions in relation to the mean

Key takeaways

1. the components of a graph include a title, correctly labeled axis with units, unifromed intervals, identifiable lines or bars, and trend lines

2. The graph type used is based on the type of data collected

3. Graphs can be used to show trends over time, comparisons, distributions, correlations variability in samples, and relationships between variables

• Water moves by osmosis

  • water potential measures the tendency of water to move by osomsis

    • calculated from pressure potential and solute potential

    • 

• Water moves from an area of high water potential to an area of low water potential

• The more negative the water potential, the more likely water will move to the area

• Osmoregulation allows organisms to control their internal solute composition and water potential

  • increasing the amount of solute in water will cause

    • increase solute potential

    • decreased water potential

• Increasing water potential

  • an increase in pressure potential

• Decreasing pressure potential will cause

  • decrease in water potential

• Water potential is equal to solute potential

  

Key Takeaways

1. Water moves by osmosis from areas of high water potential to areas of low water potential

2. Water moves by osmosis from areas of low solute potential to areas of high solute potential

3. Osmoregulation maintains water balance and allows organisms to control their internal solute composition/water potential

2.9 Mechanisms of Transport

• Passive transport is the net movement of molecules down their concentration gradient

  • diffsuion : movement of molecules from high concentration to low concentraiton

    • small nonpolar molecules pass freely across a cell membrane

    • small amounts of very small polar molecules can diffuse across a cell membrane

  • facilitated diffusion : movement of molecules from high concentration to low concentration through transport proteins

    • large and polar molecules

    • charged ions require channel proteins

• Osmosis is the diffusion of water across a selectively permeable membrane

  • large quantities of water move via aquaporins

  • Differences in relative solute concentrations can facilitate osomosis

• Active transport is the movement of molecules against their concentration gradient

  • active transport moves molecules and or ions against their concentration graident, from low concentration to high concentration

    • protein pumps are carrier proteins used in active transport

    • requires metabolic activity

    • establishes and maintains concentration gradients

• Movement of large molecules into and out of cells requires energy

  • in endocytosis, the ccell uses energy to take in macromolecules and particulate matter by forming new vesicles derived from the plasma membrane

    • the types of endocytosis are phagocytosis, pinocytosis, and receptormediated endocytosis

  • In exocytosis, internal vesicles use energy to fuse ewith the plasma membrane and secrete large macromolecules out of the cell

Key Takeaways

1. Passive transport is the net movement of molecules from high concentration to low concentration without direct inpiut of energy

2. Water is transported in small amounts across the membrane by simple diffusion and in large amounts via facilitated diffusion through aquaporins embedded in the membrane

3. Active transport requires the direct input of energy to move molecules from regions of low concentration to regions of high concentration

4. Large molecules and large amounts of molecules are moved into the cell by endocytosis and out of the cell by exocytosis

2.10 Compartmentalization

• Compartmentalization in Eukaryotic cells

  • cells have a plasma membrane that allow them to establish and maintain internal environments that are different from their external environments

  • Eukaryotic cells have additional internal membranes and membrane bound organelles that compartmentalize the cell

  • Cellular compartments allow for various metabolic processes and specific enzymatic reactions to occur simultaneously, increasing the efficiency of the cell

• Cellular compartments : lysosomes

  • membrane minimizes competing interactions

  • The hydrolytic enzymes of the lysosome function at an acidic environment

  • By having this compartmentalization, th inside of the lysosome can maintain a more acific pH and allow for efficient hydrolysis to occur

• cellular compartments : mitochondria

  • membrane folding maximizes surface area for metabolic reactions to occur

  • electron transport and ATP synthesis occur in the inner mitochondrial membrane

  • folding of the inner membrane increases the surface area, which allows for more ATP to be made

• Cellular compartments : chloroplasts

  • membrane folding maximizes surface area for metabolic reactions to occur

  • the thylakoids are highly folded membrane compartments that increase the efficienty of the light dependent reactions

Key takeaways

1. eukaryotic cells contain various membrane bound organelles.These structures compartmentalize intracellular processes and enzymatic reactions increasing the efficiency of cellular function

2. Internal membranes facilitate cellular processes by minimizing competing interactions and by increasing surface areas where reactions can occur

3. Loss of these intraceullular compartments or changes to unique internal surfaces and environments within membrane bound organelles may hinder proper cell function

2.11 Origins of cell compartmentalization

• Comparison of compartmentalization in prokaryotic and eukaryotic cells

  • both cell types have plasma membrane that separates their internal environment from their surrounding environment

  • Prokaryotic cells have an internal region, nucleoid region, that contains its genetic material

  • Eukaryotic cells have additional internal membranes and membrane bound organelles that compartmentalize the cell

    • genetic material is contained within a membrane bound nucleus

• The evolution of membrane bound organelles

  • the nucleus and other internal membranes are theorized to have formed from the infoldings of the plasma membrane

  • Mitochondria evolved from previously free living prokaryotic cells via endosymbiosis

    • a free living aerobic prokaryote was engulfed by an anaerobic cell through endocytosis

    • the engulfed cell became beneficial to the cell

Key takeaways

1. Both prokaryotic and eukaryotic ccells have external plasma membranes. However, whereas prokaryotes only have internal regions where specialized structures and function can occur, eularyotic cells have additional internal membrane bound organelles that compartmentalize the cells

2. According to the theory of embosymbiosis, a previously free living prokaryotes was engulfed by another cell through endocytosis

3. Evidence supporting the evolution of mitochondria and chlorplasts via endosymbiosis includes the presence of double membranes, circular dna, and ribosomes in both these organelles

   Unit 3

3.1 Enzyme Structure

• what are enzymes

  • enzymes are macromolecules

  • biological catalysts that speed up biochemical reactions

  • most enzymes are proteins

    • have a tertiary shape that must be maintained

  • what is an active site?

    • interacts with the substrate (a molecule that interacts with the active site of an enzyme)

    • enzymes have an active site specific to the substrate (unique shape and size + can have charges + must have specific properties that are compatible with the substrate)

  • enzyme names often indicate the chemical reactions involved

    • often end in -ase (sucrase: digests sucrose)

  • Enzymes are reusable

    • they are not chemically changed by the reaction

    • cells usually maintain a specific enzyme concentration

• Enzymes can facilitate synthesis or digestion reactions

• Enzymes speed up reactions by lowering activation energy requirements

• The structural characteristics of an enzyme make the reactions very enzyme-specific

• the shape and charge of the substrate must be compatible with the active site of the enzyme for a reaction to occur

enzymes are not consumed by a reaction; they are reused

3.2 Enzyme Catalysis

• each enzyme only facilitates one specific reaction (enzymes are really specific)

• what is activation energy?

  • the initial starting energy

  • some reactions result in a net absorption of energy and others result in a net release of energy

    • typically reactions resulting in a net release of energy require less activation energy compared to reactions that absorb energy

  • What do enzymes do? : they lower activation energy, which accelerates the reactions

• A controlled experiment is a scientific investigation

  • there are 2 groups

  • control : they’re intentionally not changed

    • generates data under conditions with no manipulation

    • generates data under normal conditions

    • considered baseline data

      • negative control : not exposed to manipulation or any treatment

      • positive control : exposed to a treatment that has a known effect

        • not exposed to experimental effect

  • experimental group

    • generates data under abnormal/unknown conditions

    • generates data under manipulated conditions

    • often compared with the control group to determine impacts of manipulation

3.3 Environmental Impacts on Enzyme Function

• Enzymes may have unique conformational shapes : different tertiary structures

  • changes in these shapes is denaturation

• denaturation can occur to :

  • changes in temperature

  • changes in environmental pH

• denaturation is typically irreversible (catalytic ability of the enzyme is lost or significantly decreased)

  • in some cases, its reversible

• Enzymes have optimum temperatures

  • range in which their mediated reactions occur the most efficiently

  • reaction rates change when the optimum temperatures arent maintained

• When there is an environmental increase in temperature

  • the reaction rate typically increases: increased speed of molecular movement

  • temperature increases outside of the optimum temperatures, result in denaturation

• When there is an environmental decrease in temperature

  • the reaction rate is generally slowed

  • decrease the frequency of enzyme-substrate collisions

  • does not interrupt enzyme structure ; no denaturation

• pH changes can affect enzyme activity

  • pH measures the amount of hydrogen ions in a solution

  • Optimum pH

    • same thing as optimum temperature : range in which enzyme mediated reactions occur the fastest

    • changing the pH out of the range will slow or stop enzyme activity

    • enzyme denaturation can occur

• When the substrate concentration increases

  • initially, the reaction rate increases

  • more substrates means more of a chance to collide with the enzyme

  • substrate saturation will eventually occur, there will be no further increase in the rate —> the reaction rate will remain constant if the saturation levels remain the same

• changes in enzyme concentration can also change reaction rates

  • less enzymes = slower reaction rate

    • less opportunity for substrates to collide with an active site

  • more enzymes = higher reaction rate

    • more opportunity for substrates to collide with an active site

• Competetive inhibitor : molecules can bind reversibly or irreversibly to the active site of an ezyme

  • competes with normal substrate for the enzymes active site

  • if inhibitor reactions exceed substrate : the reactions are slowed

  • if inhibitor binding is irreversible, enzyme activity will be prevented and vis versa.

• Enzymes can have regions other than the active sites called the allosteric sites

  • noncompetitive inhibitors : do not bind to the active site

  • causes conformational shape change

  • binding prevents enzyme function because the active site is no longer available → reaction rate decreases

3.4 Cellular Energy

• All living systems require a constant input of energy

  • sunlight is the main source of energy

  • autotrophs capture sunlight and turn it into useable energy by all sources

  • during some energy transformations, energy is typically lost (as heat)

• Every energy transfer increases the disorder of the universe

  • living cells are not at equilibrium: there is constant flow in and out of the cell

• Cells maintain energy by energy coupling

  • energy releasing processes drive energy-storing processes

• Within cells, the product of one reaction can serve as the reactant for another

3.5 Photosynthesis

• Structure of Chloroplast

  • surrounded by double membrane

  • central fluid filled space : stroma

  • system of interconnected membranous sacs : thylakoids

  • stacks of thylakoids : grana

  • fluid filled compartment in thylakoids : lumen

• Two stages of photosynthesis

  • Light reactions (light dependent reactions)

    • convert solar energy to the chemical energy of ATP and NADPH

    • happens in thylakoid

    • noncyclic electron flow

      • linear flow of electrons

      • move in one direction from water to NADPH

      • create a concentration gradient of H+ that drives the production of ATP through ATP sythase

    • Cyclic electron flow

      • only produces ATP (no NADPH no OXYGEN)

      • makes more ATP

  • calvin cycle (light independent reactions)

    • uses energy from the light reactions to incorporate CO2 from the atmosphere into sugar

    • happens in stroma

    • Carbon fixation : carbon dioxide is attatched to RuBP

      • carbon is unstable and immediately splits in to 2 3-PGA

    • Reduction : ATP provides energy / NADPH provides power to reduce intermediates

      • 6 G3P are produced —> 1 leaves the cycle leaves the cycle to be made in glucose

    • Regeneration : rest of the G3P rearrange to regenerate the starting RuBP molecules

3.6 Cellular Respiration

OILRIG : oxidation and reduction are coupling reactions

Photosynthesis and cellular respiration are coupling reactions.

oxidation: losing electrons

reduction : gaining electrons

Cellular respiration

the process by which cells convert glucose and oxygen into energy, carbon dioxide, and water. This process can be divided into three main stages: Glycolysis, the Krebs cycle, and the Electron Transport Chain.

Cellular respiration is the catabolism of organic molecules within cells to generate energy, ATP.

equation : C6H12O6 + 6O2 —> 6CO2 + 6H2O + energy (ATP)

1) Glycolysis

happens in the cytoplasm

Glucose cannot fit into the mitochondrial matrix naturally, so it must be broken down.

• Six-carbon glucose is converted into two 3-carbon molecules of pyruvate.

• Step 1 -3 : 2 ATP are input and broken down into ADP (endergonic reactions —> require energy) ; the bonds between the 2nd and 3rd phosphates are high energy bonds, so the energy released from these bonds in the early steps of glycolysis powers the rest of the reaction

• Step 4 : the six-carbon sugar is split into two 3-carbon sugars

• step 5 -10 : the three carbon sugars are further processed through exergonic reactions, producing 4 ATP molecules and 2 NADH molecules

the net gain for glycolysis of one glucose molecule is two molecules of ATP and 2 NADH

NADH and NAD+ are intermediary molecules that transport electrons

2) Pyruvate Oxidation

Pyruvate oxidation occurs in the mitochondrial matrix.

Pyruvate oxidation links glycolysis and the citric acid cycle by oxidizing (taking away electrons) from pyruvate to form acetyl coA

Step 1 : pyruvate undergoes decarboxylation —> the two 3-carbon sugars lose 2 CO2

• —> NAD+ is released

  —> NAD+ is reduced (gains electrons) to form NADH

  —> One molecule of NADH is produced per pyruvate, resulting in 2 NADH molecules

  —> NADH is reduced to capture the high-energy electrons that are found in NAD+

  2 Acetyl CoA is produced: the main purpose is for its acetyl group to be donated to the four-carbon compound oxaloacetate to form the six-carbon molecule citrate

3) Krebs Cycle (Citric Acid Cycle)

Acetyl CoA is the starting point for the citric acid cycle; the pathway of 8 reactions oxidizes the two-carbon acetyl group to two molecules of CO2

• Step 1: Acetyl CoA

• Step 2 : oxidized: it loses 2 electrons, which are given to the 4 carbon molecule oxaloacetate to form citrate

• Step 2-3: NAD+ is reduced to form NADH, loses a CO2 (this happens 2 times so 2 carbons are lost —> forms a four-carbon molecule)

• Step 8: NAD+ is reduced again to regenerate oxaloacetate

the citric acid cycle harvests energy from the oxidation of acetyl CoA

4) Electron transport chain

a series of redox carrier proteins embedded in the inner membrane of the mitochondrion

the electron transport chain takes NADH and oxidizes it to NAD+, so the electrons and hydrogens pass through the carrier proteins to the outer mitochondrial matrix, thus setting up a concentration gradient

the H+ ions move through the final carrier protein, ATP synthase which uses the H+ gradient to synthesize ATP by chemiosmosis

chemiosmosis is when the ATP synthase receives the H+ ions, a spinning enzyme begins to rotate which causes ADP to gain phosphate and become ATP

the H+ ions are passed back to the inner mitochondrial matrix, where they are attracted to oxygen —> the oxygen is reduced to H2O to keep the concentration gradient higher on the outside so H+ keeps going through the ATP synthase

FOR EVERY GLUCOSE MOLECULE 34-38 ATP ARE CREATED UNDER AEROBIC CONDITIONS

Fermentation

under anaerobic conditions, the electron transport chain cannot operate and NADH produced by glycolysis would not be reoxidized, causing glycolysis to stop because there would be no NAD+ for step 6 of glycolysis —> to solve this problem organisms use fermentation to reoxidize the NADH

Fermentation pathways occur in the cytoplasm

only 2 ATP per glucose is made in fermentation (restricted to the amount of glucose made in glycolysis because fermentation doesn’t go further than the cytoplasm and glycolysis)

Lactic acid fermentation

• glycolysis occurs

• pyruvate serves as the electron acceptor and the product is lactate

• NADH oxidized back to NAD+

• reversible

Alcoholic fermentation

• glycolysis occurs

• pyruvate is converted to ethanol 

• NADH oxidized back to NAD+ & CO2 is a byproduct

• reversible

3.7 Fitness

• cells can vary

  • molecular shape

  • molecular types (carbohydrates, lipids)

  • variation increases fitness

• Individual fitness

  • refers to an individual organisms ability to survive and reproduce

  • individual fitness connects to species fitness

  • the more variation a species has, the more likely the species is to thrive and survive

Unit 4

4.1: Cellular Communication

How do cells communicate with one another

• Cells can signal to themselves (autocrine)

• direct contact with other cells (juxtacrine)

  • cells of multicellular organisms maintian physical contact with other cells

• cells can also send chemical signals into adjacent cells (paracrine)

  • cell membrane and cell wall modifications aid in this (ex. plant cells have plasmodesma + in animal cells, there are gap junctions)

• Cells communicate over short and long distances

  • the cell recieving the signal is referred to as the target cell

  • short distance

    • cell sends out local regulator (local = close)

    • target cell is within short distance of the signal (local signalling)

    • often used to communicate with cells of the same type

      • same communication

      • close proximity

  • long distance (endocrine)

    • target cell is not in the same area as the signal

    • signal travels a long distance

    • often used to signal cells of other type

Key takeaways

1. cells use local regulators to communicate across short distances

2. cells can release chemical signals with the ability to travel over long distances to target cells of other types

3. structural modifications of the cell membrane and cell wall allows cells to send signals directly into adjacent cells

4.2: Introduction to Signal Transduction

• signal transduction pathways link signal reception with cellular responses

• 3 steps of cell communication

  • reception

    • detection of a signal molecule coming from outside the cell

  • transduction

    • how the signal is converted to a form that can bring about a cell response

  • response

    • specific cellular response to the signal molecule

• many signal transduction pathways include protein modification and phosphorylation cascades

  • regulation protein synthesis by turning genes on or off in the nucleus

  • regulate activity of proteins in the cytoplasm

  • cascades of molecular interactions relay signals from receptors to target molecules

• Phosphorylation cascade : enhance and amplify signal

• Signalling begins with the recognition of a chemical messenger, a ligand, by a receptor protein in a target cell

  • the ligand binding domain of a receptor recognizes a specific chemical messenger in a specific one to one relationship

• Signalling cascades relay signals from receptors to cell targets, often amplifying the incoming signals, resulting in the appropriate responses by the cell

  • after the ligand binds, the intracellular domain of a receptor protein changes shape, initiating transduction of the signal

  • secondary messangers are molecules that relay and amplify the intracellular signal

  • binding of ligand to ligand gated channels can cause the channel to open or close

• Large, polar molecules typically bind to extracellular receptors while small, nonpolar molecules bind to intracellular receptors

Key takeaways :

1. A singal transduction pathway is the binding of singalling molecules to receptors located on the cell surface or inside the cell that trigger events inside the cell, to invole a response

2. Cells use signal transduction pathways to link signal reception with cellular response

3. a singal transduction pathway begins when a receptor / ligand binds to external receptors or an intracellular receptor

4. The role of protein modification in signal transduction pathways is to cause a conformational shape change due to ligand binding. This change elicits an intracellular response, which causes a secondary messenger to be activated.

5. A phosphorylation cascade is a signalling pathway where one enzyme phosphorylates another, causing amplification of the reaction, leading to the phosphorylation of thousands of proteins

4.3 : Signal Transduction

• Signal transduction pathways typically occur in 4 steps

  • signaling

  • reception

  • transduction

  • response

  • signaling and reception are typically one step

• signal transduction pathways influence how the cell responds to its environment

  • the environment is not static, and organisms need to regulate pathways to respond to changes in the environment

  • the ability to respond to stimulus is a characteristic of life and necessary for survival

• Signal transduction may result in changes in gene expression and cell function

  • singalling pathways can target gene expression and alter the amount or type of a particular protein produced in a cell

    • changes in protein production can result in phenotype changes

  • apoptosis can be a result of signal transduction

G Protein coupled receptors

• look for the signal “moving over”

• ligand binds to receptor and receptors shape changes

• the receptor binds to the G protein

• GDP is replaced with GTP to activate the G protein

• the G protein binds to an enzyme to activate it —> leads to transduction and cellular response

  

Steroid Signalling

• Happens inside the cell

  

Tyrosine Kinase receptor

• “two to one”

• dimer is formed

• the bottoms of the dimer are usally connected with phosphate groups

  

Key Takeaways

1. The environment is not static and organisms need to respond to changes in the environment. The ability to respond to stimuli is characterstic of life and necessary for survival

2. Signal transduction pathways are used to influence cellular responses when the environment changes. Transduction pathways can regulate gene expression in response to changes in the environment or lead to apoptosis.

4.4: Changes in signal transduction pathways

• Changes in signal transduction pathways can alter cell response

  • mutations in any domain of the receptor protein or in any component of the signaling pathway may affect the downstream components by altering subsequent transduction of the singal

  • change in protein structure can result in change of function

  • one disruption in the pathway can affect the downstream reactions

• Chemicals that interfere with any component of the signalling pathway may activate or inhibit the pathway

Key Takeaways

1. A mutation that alters the ligand / receptor specificity can lead to incompatibility which can alter the signal transduction pathway. The receptor will not undergo proper conformational shape change, resulting in an inactive internal pathway.

2. Chemicals can activate a singal transduction pathway, which can lead to amplification of the pathway

3. Chemicals can inhibit a singal transduction pathway, which can lead to the pathway not occurring

4.5: Feedback

• Organisms use feedback mechanisms to maintain their internal environments and respond to environmental changes

  • the internal and external cell environments are constantly changing

  • homeostasis is the maintenance of a stable internal environment

  • feedback mechanisms are processes used to maintain homeostasis by increasing or decreasing a cellular response to an event

• Negative feedback mechanisms maintain homeostasis for a particular cell condition

  • Negative feedback mechanisms maintain homeostasis for a particular condition by regulating physiological processes

  • if a system is disrupted, negative feedback mechanisms return the systems back to its target set point

  • ex.

    • Human increases physical activity causes increased dissolved Co2 in the blood

    • The Co2 reacts with water in the blood to form a weak acid which lowers the pH of the blood

    • The medulla of the brain registers the drop in pH and signals to the diaphragm and heart to increase respiration

    • Co2 is cleared from bloodstream

• Positive feedback mechanisms amplify responses and processes in biological organisms

  • the variable initiating the response is moved farther away from the initial set point, disrupting homeostasis

  • amplification occurs when the stimulus is further activated which initiates an additional response that produces system change

  • ex.

    • hypothalmus (brain) releases oxytocin

    • uterine walls contract

    • baby pushes against cervix

    • oxytocin continues to get released so long as baby is pushing against cervix (does not stop until baby is born)

Key Takeaways

1. feedback mechanisms are processes used to maintain homeostasis by increasing or decreasing cellular response to an event

2. negative feedback mechanisms maintain homeostasis for a particular condition by regulating physiological processes

3. positive feedback mechanisms amplify responses and process by regulating physiological processes

4.6: Cell cycle

• The cell cycle is a highly regulated series of events for the growth and reproduction of cells

  • the cell cycle consists of two highly regulated processes

    • interphase

      • growth and preparation

    • M phase

      • mitosis : division of the nucleus

      • cytokinesis : division of the cytoplasm

  • Interphase involves 3 sesquential stages

    • G1 : cell growth

    • S : copies of DNA are made

    • G2 : the cytoplasmic components are doubled in preparation for division

    • In interphase, the cell undergoes growth processes and prepares for cell division.

      

  In eukaryotes, cells transfer genetic infromation via highly regulated processes

  • mitosis plays a role in growth, tissue repair, and asexual reproduction

  • Mitosis ensures the transfer of a complete genome from a parent cell to two genetically identical daughter cells

  • Mitosis alternates with interphase in the cell cycle

  • Mitosis occurs in a sesquential series of steps (prophase, metaphase, anaphase, telophase)

  • Mitosis is followed by cytokinesis

    • cytokinesis ensures equal distribution of cytoplasm to both daughter cells

  • Cells can enter G0 phase where cell division no longer occurs, a cell can reenter the cycle with appropriate signals

  • Nondividing cells can exit the cell cycle or be held in a particular stage

Key Takeaways

1. the role of interphase is to allow newly divided cells the opportunity to grow, maintain normal cell function, and prepare for division

2. During interphase, cells grow, replicate DNA, and prepare for division

3. Mitosis plays a role in growth, tissue repaire, and asexual reproduction

4. During mitosis genetic information is transferred

5. Cytokinesis ensures equal distribution of cytoplasm to daughter cells

• Mitosis is a process that ensures the transfer of a complete genome to both daughter cells

  • daughter cells carry genomes exactly identical to the parent cell genome

• Prophase

  • nuclear envelope begins to disappear

  • DNA coils into visible chromosomes

  • fibers begin to move double chromosomes to the center of the cell

  • Separates the duplicated DNA and proteins contained in the nucleus

    

  Metaphase

  • fibers align double chromosomes across

  • The nucleus dissolves and the cells chromsomes condense / align at center of cell

    

  Anaphase

  • fibers separate double chromosomes into single chromosomes (chromatids)

  • chromosomes separate at the centromere

  • chromatids migrate to opposite sides of the cell

  • sister chromatids separate from eachother at centromere and pull to opposite sides of the cell by the spindle fibers (ensures that each daughter cell recieves a full set of chromosomes)

    

  Telophase

  • nuclear envelope reappears and establishes two separate nuclei

  • each nucleus contains a complete genome

  • chromosomes will begin to uncoil

  • the nuclear membrane reforms around the DNA and he spindle fibers disassemble

    

  Cytokinesis will separate the cell into two daughter cells, each with identical genomes

  • each daughter cell gets equal cytoplasm

    

Key Takeaways

1. DNA becomes visible and nuclear envelope disappears during prophase

2. Chromosomes are aligned across center of the cell

3. Double chromosomes are separated into single chromsomes and single chromosomes align at opposite sides of the cell

4. DNA uncoils and nuclear envelope reappears. Two new nuclei form and each nucleus contains a complete genome

5. Cytokinesis begins at the end of mitosis and separates the cell into two daugter cells

4.7: Regulation of cell cycle

• Internal controls or checkpoints regulate progression through the cycle

• G1 Checkpoint

  • at the end of G1 phase

  • cell size check

  • nutrient check

  • growth factor check

  • DNA damage check

• G2 checkpoint

  • at the end of G2

  • DNA replication check

  • DNA damage check

• M spindle checkpoint

  • fiber attatchment to chromosome check

• Interactions between cyclins and cyclin deprendent kinases control the cell cycle

  • Cyclins

    • a group of related proteins associated with specific phases of the cell cycle

    • different cyclins are involved in different phases of the cell cycle

    • Concentrations can fluctuate depending on cell activity

      • produced to promote cell cycle progression

      • degraded to inhibit cell cycle progression

    • Used to activate cyclin dependent kinases

      • cyclins are specific to the CDK they activate

  • Cyclin dependent kinases

    • group of enzymes involved in cell cycle regulation

    • requires cyclin binding for activation

    • phosphorylate substrates, promotes certain cell cycle activities

• Disruptions to the cell cycle can result in cancer and/pr apoptosis

  • cell goes through cell cycle repeatedly without going through checkpoints

Key takeaways

1. checkpoints are regulatory events in the cell cycle

2. checkpoints help determine whether the cell is ready to progress through the cell cycle

3. proteins are used to activate or inhibit cell cycle activites

4. apoptosis and/or cancer can occur when the cell cycle is disrupted