BISC 1111 Exam Review Slides

Seven characteristics of life

1. cellular organization

2. ordered complexity

3. sensitivity

4. growth, development, and reproduction

5. energy utilization

6. homeostasis

7. evolutionary adaptation

Cellular organization

all life is composed of one or more membrane bound cells

Ordered complexity

molecules and cells making up an organism exhibit hierarchical, ordered complexity

Sensitvity

respond to stimuli

Growth, development, and reproduction

governed by molecules of heredity

Energy utilization

metabolism, take in energy that is used for work

Homeostasis

maintain relatively stable internal conditions different from external environment

Evolutionary adaptation

organisms interact with one another and their environment in ways that influence survival, and therefore, populations evolve to adapt to their environments

Theory to lay person

a theory to the general public usually implies uncertainty; a lack of knowledge or a guess

Theory to a scientist

• a proposed explanation for some natural phenomenon, often based on some general principle

• body of interconnected concepts, supported by scientific reasoning and experimental evidence, that explains the facts in some area of study

Deductive reasoning

applies general principles to predict specific results

• used to test validity of ideas in all branches of science, but especially in mathematics and philosophy

• can be used to infer the species of a specimen from its characteristics

Inductive reasoning

uses specific observations to construct a general set of principles (logic flow opposite of deductive reasoning)

• leads to generalizations that can then be tested

• Reductionism - A philosophical approach to understand a complex system by reducing it to its working parts. 

Hypothesis

suggested explanations that account for observed phenomena

• a set of propositions which might be true

Natural selection

the differential reproduction of genotypes; caused by factors in the environment; leads to evolutionary change

Chemical behavior is determined by

the distribution of electrons in the electron shells

Covalent bonds

the sharing of a pair of valence electrons by two atoms

• shared electrons count as part of each atom’s valence shell

Electronegativity

an atom’s attraction for the electrons in a covalent bond

Nonpolar covalent bond

the atoms share the electron equally

• always occurs if the atoms bonded together are the same element (H2, O2, N2) etc…

• form between two different atoms of similar electronegatives

Polar covalent bonds

one atom is more electronegative, and the atoms do not share the electron equally

• unequal sharing of electrons causes a partial negative or positive charge for each atom or molecule

Ionic bond

atoms strip an electron from their bonding partners—attraction of opposite electrical charges

• weaker than covalent bond, stronger than hydrogen bond

4 main mechanisms of evolutionary change

• mutation - introduction of new alleles

• gene flow - movement of genetic information from one population to another

• genetic drift - chance event changes allele frequencies 

• natural selection - the differential reproduction of genotypes; caused by factors in the environment; leads to evolutionary change

Chemical bonds

Reactions are influenced by 3 main factors: temperature

heating reactants increase reaction rates because reactants collide with one another more often

Reactions are influenced by 3 main factors: concentration of reactants & products

proceed faster when more reactants available for collisions. accumulation of product slows or reverses reactions

Reactions are influenced by 3 main factors: catalysts

a substance that increases reaction rates

• in living systems, proteins called enzymes catalyze most reactions needed for life… they do largely by bringing reactants into very close proximity

Water’s four emergent properties vital for life

• cohesive behavior

• ability to moderate temperature

• expansion upon freezing

• versatility as a solvent

Cohesive behavior

• hydrogen bonds collectively hold polar water molecules together

• results in surface tension and adhesive properties

• cohesion and adhesion (attraction between water and non-water substances)

Hydrogen bonds

forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

• in living cells, the electronegative partners are usually oxygen or nitrogen atoms

In the water molecule, the electrons of the _____________ spend more time near the oxygen than the hydrogen

polar covalent bonds

surface tension

a measure of how difficult it is to stretch or break the surface of a liquid

• cohesion results in a high __________

Adhesion

an attraction between different substances, for example between water and plant cell walls

• helps counter down pull of gravity → upward direction of water movement (transport) in plants

Water moderates temperature

• water absorbs heat from warmer air and releases stored heat to cooler air

  • can absorb or release a large amount of heat with only a slight change in its own temperature

    • because of water’s high specific heat

Specific heat

• the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1ºC

  • of water is 1 cal/(g * ºC)

Expansion upon freezing/solid less dense than liquid

• ice floats on water because it is less dense than liquid water

  • water molecules locked into crystalline lattice when freezing where the hydrogen bonds of adjacent molecules keep them far enough apart to make ice ~10% less dense than water

Universal solvent/solvent of life

• water is the best solvent because of its highly polar nature

• when an ionic compound is dissolved in water, each ion (whichever the electrical charge) is surrounded by a sphere of water molecules called a hydration shell

Hydrophilic substance

substance that has an affinity for water

• proteins, carbs, ionic compounds, etc… basically anything polar

Hydrophobic substance

substance that does not have an affinity for water

• alkanes, oils, fats, greases, etc… basically anything relatively non-polar

Water freely dissociates into…

hydroxide and hydronium

• hydrogen atom leaves its electron behind and is transferred as proton/hydrogen ion (H+)

  • hydroxide ion (OH-) - molecule at that lost the proton

  • hydronium ion (H3O+) - molecule with the extra proton, often represented as H+

Acid

a substance that increases the H+ concentration of a solution

• HCl → H+ + Cl-

• pH value less than 7

Base

a substance that reduces the H+ concentration of a solution

• NH3 + H+ → NH4+ (reversible)

• NaOH → Na+ + OH-

• pH value greater than 7

Buffers

substances that minimize changes in concentrations of H+ and OH- in a solution

• most solutions contain a weak acid and a corresponding base, which combine reversibly with H+ ions

Carbon skeleton variation generates molecular diversity

• Carbon skeletons vary in length

• The skeleton may have double bonds, which can vary in location

• Skeletons may be branched or unbranched

• Some skeletons are arranged in rings

Isomers

compounds with the same molecular formula but different structures and properties

Structural isomers

have different covalent arrangements of their atoms

Cis-trans isomers

(also called geometric isomers) have the same covalent bonds but differ in their spatial arrangements

Enantiomers

mirror images of each other

• Different enantiomers can cause certain antibodies to be ineffective

  • ie S-ibuprofen is effective while R-ibuprofen is ineffective

Functional groups

• are the components of organic molecules that are most involved in chemical reactions

  • The number and arrangement of functional groups give each molecule its unique properties 

Polymer

long molecule consisting of many similar building blocks

Monomer

repeating units that serve as building blocks

• monomers → polymerization → polymer

What are the structures and functions of the four important classes of biological molecules?

Macromolecules

large polymers—huge size

Build up & break down

Enzymes

specialized macromolecules that speed up chemical reactions

Dehydration reaction

when two monomers bond together via the loss of a water molecule

• synthesizes a polymer by a removing a water molecule

  • forms a new bond

Hydrolysis

polymers are disassembled to monomers

• breaking down a polymer through adding a water molecule & breaking a bond

• essentially the reverse of the dehydration reaction

Carbohydrates

• include sugars and polymers of sugars

  • simplest forms are monosaccharides, or simple sugars

  • carbohydrate macromolecules are polysaccharides

• (notes) many sugars form rings (though often drawn as linear skeletons)

Polysaccharides

polymers composed of many sugar building blocks

• have storage and structural roles

• architecture and function are determined by its sugar monomers and the positions of its glycosidic linkages

Monosaccharides

• have molecular formulas that are usually multiples of CH2O

• Glucose (C6H12O6) is the most common monosaccharide

• classified by the location of the carbonyl group (as ketose or aldose) & the number of carbons in the carbon skeleton

Disaccharide

formed when a dehydration reaction joins two monosaccharides

Glycosidic linkage

covalent bond between two monosaccharides

Starch

• storage polysaccharide of plants, consists of glucose monomers

• plants store surplus amounts as granules within chloroplasts and other plastics

• simplest form is amylose

Glycogen

• storage polysaccharide in animals

• stored in liver and muscle cells

  • hydrolysis of this in these cells releases glucose when the demand for sugar increases

Cellulose

• structural polysaccharide in the tough cell wall of plan cells

  • the most abundant organic polymer on Earth because it is the primary component of the cell wall of green plants, most algae, and many other organisms.

Cellulose vs Starch

• Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ

• The difference is based on two ring forms for glucose: alpha (α) and beta (β)

  • Enzymes that digest starch by hydrolyzing α linkages can’t hydrolyze β linkages in cellulose

• Some hydroxyl groups on the monomers of cellulose can hydrogen-bond with hydroxyls of parallel cellulose molecules

Fats/Triglycerides

constructed from two types of smaller molecules: glycerol and fatty acids

Glycerol

a three-carbon alcohol with a hydroxyl group attached to each carbon

Fatty acids

consists of a carboxyl group attached to a long carbon skeleton

Triglycerides (triacylglycerol)

• three fatty acids are joined to glycerol by an ester linkage

  • separate from water because water molecules hydrogen-bond to each other and exclude the fats

  • The fatty acids in a fat can be all the same or of two or three different kinds

Major function of fats (triglycerides, not all lipids)

energy storage—long term

Adipose tissue

• cushions vital organs and insulates the body

• humans and other mammals store their long-term food reserves in adipose cells

Saturated fatty acids

• have the maximum number of hydrogen atoms possible and no double bonds

• make saturated fats

  • solid at room temperature

  • most animal fats (not all though, like omega three fatty acids in fish/seafood)

• diet rich in saturated fats may contribute to cardiovascular disease, but they are still necessary in moderation

Unsaturated fatty acids

• have one or more double bonds

• make unsaturated fats

  • liquid at room temperature

  • usually plant fats and fish fats

Trans fats

• hydrogenation - converting unsaturated fats to saturated fats by adding hydrogen

• may contribute more than saturated fats to cardiovascular disease

• technically a subtype of unsaturated fat

Phospholipid

• two fatty acids and a phosphate group are attached to glycerol

• two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head

• (note) when added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward interior

  • bilayer forms boundary between cell and external environment

Steroids

lipids characterized by a carbon skeleton consisting of four fused rings

Cholesterol

• type of steroid

• a component in animal cell membranes

• precursor from which other steroids are synthesized

• high level in blood may contribute to cardiovascular disease

Polypeptides

unbranched polymers built from a set of 20 amino acids

Peptide bond

the covalent bond between amino acids

Protein

a biologically functional molecule that consists of one or more polypeptides

• polymers with 3-dimensional shape

Enzymatic proteins

• function: selective acceleration of chemical reactions

• example: digestive enzymes catalyze the hydrolysis of bonds in mood molecules

Defensive proteins

• function: protection against disease

• example: antibodies inactive and help destroy viruses and bacteria

Storage proteins

• functions: storage of amino acids

• examples: Casein, the protein of milk, is the major source of amino acids for baby mammals

Transport proteins

• function: transport of substances

• examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body

Hormonal proteins

• function: coordination of an organism’s activities

• example: insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration

Receptor proteins

• function: response of cell to chemical stimuli

• example: receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells

Structural proteins

• function: support

• example: Keratin is the protein of hair, horns, feathers, and other skin appendages. 

Amino acids are the monomers of proteins

• central carbon atom

• R side chain

• carboxyl group

• amino group

Polar vs nonpolar visually

• Polar - contain atoms like oxygen or nitrogen in functional groups (e.g., -OH, -NH2, -CONH2), making them hydrophilic and able to form hydrogen bonds with water and other polar molecules

• Nonpolar - consist mainly of carbon-hydrogen (CH) bonds, making them hydrophobic and tending to cluster away from water

Primary structure

• a protein’s sequence of amino acids

  • like the order of letters in a long word

  • determined by inherited genetic information (genes!)

Secondary structure

• coils and folds result from hydrogen bonds between repeating constituents of the polypeptide backbone (between carboxyl and amino groups)

  • typical structures are a coil called an α helix and a folded structure called a β pleated sheet

Tertiary structure

• the overall shape of a polypeptide, results from interactions between R groups, rather than interactions between backbone constituents

  • these interactions include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions

• strong covalent bonds called disulfide bridges may reinforce the protein’s structure

Quaternary structure

• results when two or more polypeptide chains form one macromolecule

• only proteins composed of two or more poly peptides can have quarternary structure

• (note) usually, quaternary structures of proteins are stabilized and sub-units held together by “weak” but numerous non covalent molecular interactions, like hydrogen bonds, Van der Waals, hydrophobic and ionic interactions, as mentioned before with tertiary structures.

Structure (thus function) gone wrong

• A slight change in primary structure can affect a protein’s structure and ability to function 

  • Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin

• The abnormal hemoglobin molecules cause the red blood cells to aggregate into chains and to deform into a sickle shape

Denaturation

• loss of a protein’s native structure

  • denatured protein is biologically inactive

• Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel

• (note) ex. Extremely high fevers can be fatal: proteins in the blood tend to denature at very high body temperatures

Cells fold proteins in several stages

• It is hard to predict a protein’s structure from its primary structure

• Most proteins probably go through several stages on their way to a stable structure

  • Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfolded proteins

Gene

• a unit of inheritance that programs the amino acid sequence of a polypeptide

  • consist of DNA

Nucleic acid

• made of monomers called nucleotides

• Deoxyribonucleic acid (DNA) & Ribonucleic acid (RNA)

  • DNA provides directions for its own replication

  • DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis

Polynucleotides

• nucleic acids are polymers called polynucleotides

• made of monomers called nucleotides

Nucleotide

• consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups

• portion of a nucleotide without the phosphate group is called a nucleoside

Nucleotide = nucleoside + phosphate group

• Nucleoside = nitrogenous base + sugar

• Two families of nitrogenous bases:

  • pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring

  • purines (adenine and guanine) have a six-membered ring fused to a five-membered ring

• ex. in DNA the sugar is deoxyribose; in RNA the sugar is ribose