Biology Study Guide #2

Common Chemical Components and Structures:

• Living organisms are composed of common chemical components such as water, ions, small molecules, proteins, carbohydrates, lipids, and nucleic acids

• They also exhibit similar structures, including cells, which are the basic units of life

Cellular Composition

• Cells are the basic structural and functional units of life

• There are two main types of cells: prokaryotic and eukaryotic

• Eukaryotic organisms can be unicellular or multicellular

• Cells reproduce through cell division, passing along a complete copy of their genome to each new cell

• All cells come from pre-existing cells

Energy Acquisition and Metabolism

• Living organisms acquire molecules and energy from their environment to build new molecules and perform biological work

• They obtain energy from their environment and transform it into other forms of energy through enzymes and metabolic pathways

• Organisms capture and transform energy from their environment to perform various biological funcitons

Genetic Information

• Living organisms contain genetic information that determines their structure, growth, physiology, and reproduction

• They use a common genetic code, with DNA nucleotides (A, G, C, T) forming the genetic alphabet

• The genome, containing genetic information, is faithfully copied and passed to offspring

The Scientific Method

• Involves several steps

  • Asking questions

  • Looking for sources to answer questions

  • Developing hypotheses

  • Designing experiments to test hypotheses

  • Predicting experiment outcomes based on hypotheses

  • Collecting and analyzing data

  • Developing explanations for results

  • Revising hypotheses based on findings

  • Designing new experiments

  • Sharing findings with other scientists

Deductive Reasoning

Used to create testable predictions based on supported hypotheses

Inductive Reasoning

used to form hypotheses based on specific observations or data

Chemical Composition and Structure

Living organisms share common chemical components and structures, including cells

Cellular Basis

Cells are the basic unit of life, reproducing and passing along genetic information

Energy Acquisition and Metabolism

Organisms acquire energy and molecules from the environment for biological work

Genetic Information

Living organisms contain genetic information, using a common genetic code

Scientific Method

Science employs a methodical approach involving questioning, hypothesis formation, experimentation, data analysis, and sharing findings

Reasoning in Science

Deductive reasoning is used to make predictions, while inductive reasoning forms hypotheses based on observations

Atoms

• Consist of protons, neutrons, and electrons

• Each element has a unique number of protons

Isotopes

• Have different numbers of neutrons

• Radioisotopes are unstable and spontaneously break down, releasing energy

Chemical Bonding

atoms with full outer electron shells are stable

Covalent bonds

form when atoms share electrons, creating stable molecules

Polar covalent bonds

result from unequal sharing of electrons, while nonpolar bonds involve equal sharing

Ionic bonds

form through the transfer of electrons from one atom to another, resulting in oppositely charged ions

Van der Waal interactions

occur between oppositely charged atoms in nonpolar molecules

Hydrophobic interactions

involve the exclusion of water molecules by nonpolar substances

Biological Energy Transformation

• Living organisms acquire and transform energy for various functions

• Energy transformations in cells are linked to chemical reactions in metabolism

• Energy changes forms during biological processes, with potential energy stored in chemical bonds and kinetic energy associated with movement

Anabolic reactions

build complex molecules, requiring energy input, while catabolic reactions break down complex molecules, releasing energy

First Law of Thermodynamics

States that energy is neither created nor destroyed, only converted from one form to another

Second Law of Thermodynamics

Suggests that energy conversions are not 100% efficient, and some energy becomes unavailable for work, leading to an increase in entropy

Chemical reactions involve

energy changes, with some energy becoming unavailable for work, contributing to entropy increase

Biological energy transformations

follow the laws of thermodynamics, with energy changes occurring in pathways and entropy increasing at each step

Total Energy in Reactions

• Total energy consists of usable (free) energy and unusable energy (entropy), expressed as enthalpy (H) = free energy (G) + entropy (S)

• Changes in free energy (ΔG) during reactions determine whether energy is released or consumed

Chemical reactions

• Involve the combination or alteration of atoms and their bonding partners

• Energy differences between reactants and products, along with changes in entropy, determine the direction and magnitude of energy changes

Chemical transformations

require activation energy (Ea) to initiate reactions by breaking covalent bonds in reactants

Exergonic

Release energy

Endergonic

Require energy

Equilibrium and Reversible Reactions

• Reactions may reach equilibrium, where forward and reverse reactions occur at equal rates, and ΔG = 0

• Equilibrium depends on the concentrations of reactants and products

Living Organisms and Thermodynamics

• Living organisms maintain order despite the second law of thermodynamics by utilizing constant energy inputs

• Organisms capture and convert energy from their environment, coupling endergonic reactions with exergonic reactions in metabolic pathways

Closed systems

Have no exchange of matter or energy with their surroundings, while open systems exchange energy but not matter

Living organisms are ___________, requiring a constant supply of energy to maintain order and carry out metabolic processes

Open systems

Macromolecules

Large molecules composed of smaller units called monomers

Polymers

Formed when monomers are joined together through covalent bonds, often defined by functional groups, such as polarity, acidity, or basicity

The essential building blocks of living organisms

Amino acids, Phospholipids, Sugars, Nucleotides

Amino Acids

monomers of proteins

Phospholipids

Components of cell membrane

Sugars

Monomers of carbohydrates

Nucleotides

Monomers of nucleic acids

Carbohydrates

• Or polysaccharides, have the general formula Cn(H2O)n and are categorized based on size

• Monosaccharides, disaccharides, oligosaccharides, and polysaccharides (i.e. starch, glycogen, cellulose) serve various functions, including energy sources, carbon skeletons, and cell recognition signals

Nucleic acids (DNA, RNA)

polymers of nucleotides

Nucleotides consist of

pentose sugar, phosphate group, and nitrogenous base

DNA stores ________ in its specific sequence of nucleotides, while RNA participates in ________

genetic information; protein synthesis

DNA’s structure

includes two antiparallel chains of nucleotides with complementary base pairing (A-T, G-C), crucial for replication and transcription

Function of DNA

• carries essential information for an organism’s structures and functions

• It undergoes replication, transcription, and translation processes, ensuring the continuity of life and specifying the sequence of amino acids in proteins

Function of Nucleotides

Like ATP, GTP, and cyclic AMP serve as energy carriers and signal transducers in biochemical reactions and cellular processes

Special Cases of Proteins

Glycine, Cysteine, Proline

Proteins

• Exhibit remarkable diversity in structure and function, serving essential roles in living organisms

• Composed of 20 different amino acids (AAs), which vary in side chain composition and size

Amino acids are linked by ________ to form polypeptides, which can vary in length from a few AAs to thousands

Peptide bonds

Amino Acids

• The side chains (R-groups) of amino acids determine the unique properties and functions of proteins

• Electrically charged with hydrophilic side chains

• Hydrophilic amino acids with polar but uncharged side chains form hydrogen bonds (serine, threonine, asparagine, glutamine, tyrosine)

• With nonpolar hydrophobic side chains (alanine, isoleucine, leucine, methionine, phenylalanine, tryptophan, valine)   

• Special cases (glycine, cysteine, proline) 

Protein synthesis

occurs through condensation reactions between amino acid monomers

Polypeptides grow from the _______ to the ________, with each additional AA joined to the _______ of the previous one

N-terminus; C-terminus; C-term

Primary Structure (I)

the linear sequence of amino acids, determining the composition and order of AAs

Secondary Structure (II)

Regular, repeated patterns such as a-helices and B-pleated sheets, formed by hydrogen bonding between AAs

Tertiary Structure (III)

Unique three-dimensional shape resulting from interactions between R-groups, including ionic bonds, hydrogen bonds, and hydrophobic interactions

Quaternary Structure (IV)

The association of two or more polypeptides to form a functional protein, not present in all proteins

Protein Stability

refers to a protein’s tendency to maintain its native conformation, essential for proper function

Factors of stabilizing protein conformation

disulfide bonds, hydrogen bond, hydrophobic interactions, ionic interactions, and van der Waals forces

Protein Denaturation

occurs when a protein loses its native 3D structure, leading to loss of function

Environmental factors that disrupt protein folding and stability

temperature, pH changes, and exposure to denaturing agents

Factors influencing protein folding

• may fail under certain conditions, such as extreme temperatures or pH levels, affecting protein stability and function

• Denatured proteins can sometimes renature spontaneously to regain their biologically active conformation

Enzymes facilitate chemical reactions by _____ the ______ required to initiate them

Lowering; activation energy

Activation energy

is the energy input needed to start a reaction by breaking bonds in reactant molecules

Reduction in activation energy

allows reactions to proceed more rapidly at physiological temperatures, where kinetic energy is relatively low compared to high-temperature conditions

By decreasing the energy barrier

enzymes enable reactions to occur within the cellular environment, where conditions are conducive to life processes

Enzymes exhibit _______ for their substrates, recognizing and binding them at specific regions called ______

high specificity; active sites

Substrate Specificity and Active Site

• The specificity arises from the precise three-dimensional arrangement of amino acid residues in the enzyme’s active site, which complements the shape and chemical properties of the substrate

• This “lock and key” fit ensures that only the correct substrate can bind to the enzyme, preventing non-specific interactions and enhancing catalytic efficiency

Enzymes facilitate reactions by _______ the _______ required for the transition state, the intermediate stage between reactants and products

lowering; energy barrier

Energy Barrier Lowering

• this reduction in activation energy enables more reactant molecules to reach the transition state, thereby increasing the rate of reaction

• By stabilizing the transition state, enzymes make it easier for chemical bonds to break and form, promoting the conversion of substrates into products

Mechanism of Catalysis

• Enzymatic catalysis involves the formation of an enzyme-substrate complex (ES), where the enzyme binds reversibly to the substates

• The binding interaction between enzyme and substrate leads to conformational changes in both molecules, known as induced fit

• Induced fit facilitates the alignment of reactive groups int he enzyme and substrate, promoting the catalytic reaction

• Enzymes catalyze reactions without altering the overall thermodynamics of the process, meaning they do not affect the equilibrium constant or change the free energy of the reaction

Induced fit

facilitates the alignment of reactive groups in the enzyme substrate, promoting the catalytic reactions

Enzyme activity is influenced by

ligand binding, cofactor presence, and protein conformational changes

Ligand binding

such as substrate or allosteric regulator binding induces conformational changes in the enzyme that affect its catalytic activity

Cofactors

including metal ions or coenzymes, may be required for enzyme function, serving as essential cofactors in catalytic reactions

Protein conformational changes

such as induced fit or allosteric modulation, alter the active site’s shape or accessibility, regulating enzyme activity

Enzyme kinetics depend on ___________, with reaction rates reaching a maximum when all enzyme molecules are bound to substrate

substrate concentration

Inhibitors modulate enzyme activity by

interfering with substrate binding or catalytic function

Competitive Inhibitors

compete with the substrate for binging at the active site

Noncompetitive inhibitors

Bind to alternative sites, altering enzyme conformation or activity

Enzymes regulation ensures that

metabolic pathways maintain homeostasis, balancing catabolic and anabolic processes to meet cellular demands

Enzymes

play a critical role in metabolic pathways, coordinating the sequential reactions that convert substrates into products

Feedback inhibition and allosteric regulations

regulate enzyme activity within metabolic pathways, ensuring that reactions proceed at appropriate rates

Feedback inhibition

occurs when the end product of a pathway inhibits an earlier enzyme, preventing the over-accumulation of intermediates

Allosteric regulation

involves the binding of regulatory molecules to allosteric sites on enzymes, modulating their activity and controlling pathway flux

Enzyme activity is influenced by

pH, temperature, and substrate concentration

pH affects enzyme activity

by altering the ionization state of amino acids residues in the active optimal activity occurring within a narrowing temperature range

Temperature influences enzyme activity

by affecting protein stability and conformation, with optimal activity occurring within a narrow temperature range

Changes in substrate concentration affect reaction rates

with enzyme kinetics exhibiting saturation kinetics at high substrate concentrations

Lipid Diversity

• Comprise a diverse group of molecules characterized by their hydrophobic nature and nonpolar covalent bonds

• Triglycerides, phospholipids, sterols, and other lipids classes serve various functions in cellular structure, energy storage, and signaling

Fatty Acid Properties

• Fatty acids are long hydrocarbon chains with a carboxyl group at one end, imparting amphipathic properties

• Saturates fatty acids contain only single bonds between carbon atoms, while unsaturated fatty acids have one or more double bonds, affecting their physical properties and biological functions

Triglycerides

consist of glycerol and three fatty acid chains, serving as energy storage molecules in adipose tissue

Phospholipids

are key components of cell membranes, comprising a glycerol backbone, two fatty acid tails, and a phosphate head group that confers amphipathic properties

Lipoproteins

facilitate the transport of lipids in aqueous environments, including cholesterol and triglycerides, between tissues and organs

Steroid hormones

derived from cholesterol, serve as chemical messengers that regulate various physiological processes, including metabolism and reproduction

Waxes

provide waterproofing and protective barriers in plants and animals, preventing desiccation and microbial invasion

Carotenoids

act as pigments in photosynthetic organisms, absorbing light energy for photosynthesis and providing antioxidant properties