BIO 121 Ch 2-5 Exam

Structure of an Atom

Positively charged nucleus (protons and neutrons) with negatively charged electrons attracted to the nucleus

Neutrons

- Particles with neutral charge and a mass of ~1 amu - Located in nucleus - May vary in number in an element (isotopes)

Protons

- Particles with relative charge of +1 and a mass of ~1 amu - Located in nucleus - Characteristic number for each element

Atomic number

Number of protons; number on the bottom

Mass number

Number of protons and neutrons; number on the top

Average weight

Average of the mass numbers of the isotopes, weighted by abundance

Radioactive isotopes

Unstable isotopes; additional neutrons can create instability

Electron shells

- Clouds around the nucleus occupied by electrons - Each shell has a characteristic energy; the farther from the nucleus, the higher the energy

Valence electrons

- electrons in the outer (valence) shell - interact with other atoms; give rise to chemical properties

Orbitals

- Certain regions around the nucleus where we have a high probability of finding an electron - each orbital can hold up to two electrons; more electrons = more orbitals

Valence

- the number of electrons that are unpaired and available to participate in bonding - elements in the same group/column have the same valence and similar chemical properties

Molecule

Two or more atoms bonded together

Compound

Any molecule composed of two or more distinct element

Covalent Bonding

- Arises from sharing electrons - Most common way of stabilizing atoms - Very stable

Nonpolar covalent bonding

- Electrons are shared equally between two atoms, located halfway between the two - Very stable - Contain a lot of potential energy

Polar covalent bonding

- Arises from a difference in electronegativity between the two bonded atoms - influenced by the size of the nucleus as well as the distance between the nucleus and the outermost shell

Electronegativity

- the pull of an atom on electrons - tends to increase as you move left to right and down to up

Ion formation

- very electronegative atoms will "steal" an electron from not-very electronegative atoms, resulting in an ion with a full positive charge (cation) and an ion with a full negative charge (anion) - anion and cation form ionic bond from the electrostatic attraction between the ions - often results in a crystalline structure

Properties of water

- Excellent solvent - Cohesion, adhesion, surface tensions - High specific heat - High heat of vaporization - Water is denser as a liquid than solid

Water as a solvent

- arises from water's partial positive and negative charges - forms a hydration shell around hydrophilic (ionic or polar covalent) compounds - nonpolar substances do not dissolve in water - critical to life's ability to use aqueous solutions to transport nutrients and wastes

Adhesion

- water molecules adhering to other surfaces - arises from water's polarity/partial charges - contributes to plants’ ability to transport water against gravity from roots to leaves - causes the meniscus in like a test tube

Cohesion

- water molecules adhering to each other - arises from water's hydrogen bonds - contributes to plants’ ability to transport water against gravity from roots to leaves

Surface tension

- water's tendency to minimize surface area - arises from cohesion

High specific heat

- amount of energy it takes to raise the temperature of 1 g of a liquid by 1 degree C - makes water resist changes in temperature - arises from high amount of hydrogen bonds in water; bonds must be broken before temperature raises - allows life to maintain temperature homeostasis

High heat of vaporization

- the amount of energy it takes to turn 1g of liquid into a gaseous state - reason behind the efficacy of evaporative cooling (sweat) - also arises from the high amount of hydrogen bonds in water

Density of ice

- Unlike most solids, ice is less dense than water (liquid) - Arises as the water molecules cool/slow down; hydrogen bonds crystallize to form a hexagonal lattice - an important quality of life; if ice was denser than water, the oceans would freeze from the bottom up and wouldn't be able to support life

Molarity

Number of moles per liter of solution

Dissociation of water

- h2o dissociates into OH- and H+ randomly - rare but biologically relevant - Adds more charge to the water

Acid

- a solution that donates hydrogen ions to a solution; lowers the pH

Base

- a solution that accepts hydrogen ions in a solutions; raises the pH

pH formulas

pH = -log[H+] or [H+] = 10^-pH [H+] = concentration of hydrogen ions each pH unit represents a tenfold difference in OH- and H+ concentrations

Buffers

- Substances that minimize or resist changes in pH; help solutions maintain homeostasis - Usually comprised of a weak base and weak acid; accept H+ in excess and donate H+ in excess of OH- - biologically important, since maintaining pH homeostasis is crucial to all living systems - Carbonic Acid: an important buffer in human blood and other biological solutions

Organic molecules

- Contain carbon bonded to other elements - Carbon based; since carbon is not strongly or weakly electronegative, it can form four very stable/not super polar covalent bonds

Amino Acids

- building block of proteins - Central carbon, amino group (left), carboxyl group (right) - runs N—> C terminus - R group attached to central carbon; varies - ionize in water; amino group attracts a hydrogen (NH3+) and carboxyl group loses a hydrogen (COO-) —> helps amino acids stay in solution and makes them more reactive

Side chains

- can be charged (acidic/basic; full charge), polar (side chain contains an oxygen), or nonpolar - interactions between them contribute to proteins’ unique 3D shapes

Condensation (dehydration) reactions

- the mechanism by which monomers polymerize - forms between an —OH and an —H or —OH; produces water as byproduct

Hydrolysis

Reverse reaction of condensation; breaks polymers apart by adding a water molecule

Unique characteristics of polymers

- monomer type (monosaccharides, amino acids, nucleotide) - polymer length: influences polymer's ability to do things and its structural strength - Bonds between monomers (type and location); affects function and structure

Peptide bonds

- connect amino acids between the carboxyl group of one amino acid and the amino group of another - electron sharing between the N and the O gives the peptide (C—N) bond the characteristics of a double bond, although they are not bonded - contribute to formation of peptide bond backbone in amino acid chains

Flexibility of amino acid chains

Since the peptide backbone is comprised of single bonds, the peptide backbone can flex and rotate around bonds; important quality for the formation of secondary structure

Primary structure (proteins)

- sequence of amino acids in a polypeptide chain - held together/stabilized by peptide bonds - fundamental to the higher levels of protein folding; a single amino acid change can radically alter a protein's structure and function

Secondary structure (proteins)

- arises from the formation of hydrogen bonds from partially positive charged hydrogens (bonded to N) and partially negatively charged oxygen as the polypeptide backbone bends so that the groups are close together - stabilized by hydrogen bonding between the functional groups - α-helixes or β-pleated sheets

Tertiary structure (proteins)

- 3D shape of a polypeptide - arises from interactions between a polypeptide's R-groups and/or its backbone - hydrogen bonding - hydrophobic interactions (stabilized by van der Waals interactions) - ionic bonding - covalent bonding (disulfide linkages; strongest interaction) —> only occurs for cysteines

Quaternary structure (proteins)

- several polypeptide units stabilized by interactions between their R groups and/or backbones - not all proteins have a quaternary structure, but many do

Protein folding

- normal folding is essential for function; each protein has a characteristic folded shape that leads to its function - many proteins are regulated by regulatory molecules that bind or unbind to a protein to signal when it should be in its ordered, active conformation

Molecular chaperones

- special proteins that can facilitate protein folding; are present in high concentrations after proteins experience a denaturing event (such as high heat, which is why they belong to a class of proteins called heat-shock proteins) - recognize unfolded proteins by binding to hydrophobic regions that would not normally be accessible in a properly folded protein - prevents unfolded proteins from folding together, allowing them to fold into the shape specified by their primary sequence

Prions

- infectious misfolded proteins (unlike viruses or bacteria, do not contain a genome) that can induce properly folded proteins to misfold - have higher resistance to proteases, temperature, and harsh chemicals - have aggregates (waxy tendrils/amyloids) that surround the prions, making it difficult to break down - ALL prion illnesses are fatal

Protein functions

- catalysis, defense, movement, signaling, transport, structure

Catalysis

- protein function - enzymatic function; speed up chemical reactions - might be the most important protein function - active site; the location on an enzyme where substrates bind and react - Substrates: the reactants in enzyme-catalyzed reactions; each enzyme usually only binds with one substrate - Enzymes are good catalysts because they bring substrates together in a precise orientation that makes a reaction more likely to occur

Defense (proteins)

- protein function - antibodies

Movement (proteins)

- actin and myosin (muscles) - cilia (intestines, stomach, ears) - flagella (sperm)

Signaling (proteins)

- communication between cells - neurotransmitters and other cell signaling molecules can bind to cell membrane proteins

Support/structure (proteins)

- keratin (hair, etc) - collagen, elastin: form structural support matrix in connective tissues (tendons, ligaments, etc)

Transport (proteins)

- hemoglobin (transport oxygen) - Sodium-potassium ion pump

Nulceic acids

- polymer of nucleotide monomers - polymerize via condensation reactions to form phosphodiester linkages/bonds - information storage molecules

Nucleotide

- monomers of nucleic acid - composed of a phosphate group, a five-carbon sugar (ribose or deoxyribose), and a nitrogenous base

Guanine

- nitrogenous base - purine (nine-carbon ring) - contains a double-bonded oxygen - bonds with cytosine

Adenine

- nitrogenous base - purine - does not contain an oxygen - bonds with thymine or uracil

Cytosine

- nitrogenous base - pairs with guanine - only contains one O - pyrimidine

Thymine

- nitrogenous base - binds with adenine in DNA - has two Os - pyrimidine

Uracil

- nitrogenous base - pairs with adenine in RNA - Contains two Os - pyrimidine

Phosphodiester linkage/bond

- occurs between the phosphate group on the 5' carbon of one nucleotide and the hydroxyl group on the 3' carbon of another - phosphodiester bonds between nucleotides forms phosphodiester backbone

Ribonucleic acid (RNA)

- single-stranded - reactive (ribozymes) - sugar is ribose (2 —OH groups) - uracil - secondary structure forms loops and stems - negatively charged - can self-replicate

Deoxyribonucleic acid (DNA)

- double-stranded helical structure - very, very stable (has never been known to catalyze reactions) - sugar is deoxyribose (only has one —OH) - negatively charged - thymine - requires enzyme catalyzation

Chargaff's Rule

- A pairs with T or U, G pairs with C

DNA Secondary Structure

- double helix - hydrogen bonding between nitrogenous bases - twisting to shield hydrophobic region in middle (nitrogenous bases) from polar water - forms a major groove and the minor groove

DNA Tertiary Structure

- 3D structure of compacted DNA - DNA strands wrap around proteins (histones), which further condense to radial loop domains, which further condense to heterochromatin, which finally condense to chromosomes with distinctive x-shapes - DNA would not be able to fit in nuclei without this condensation

DNA function

- information storage contained in the sequence of the bases

DNA replication (basic)

- strands separate when hydrogen bonds between complementary bases are broken by an enzyme moving 5' —> 3' - new free nucleotides hydrogen bond on the antiparallel strand's 3' end - New strands polymerize to form a sugar-phosphate backbone, secondary structure is restored

RNA primary structure

- chain of nucleotides (single-stranded)

RNA secondary structure

- formation of loops and stems due to hydrogen bonding between nucleotides of the same strand

RNA Tertiary structure

- forms when secondary structures fold to form a wide variety of distinctive 3D shapes, such as tRNA, mRNA, etc

Carbohydrates

- macromolecules composed of carbon, hydrogen, and oxygen atoms - Formula: C.n(H.2O).n - most carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group (H—C—OH) - OH makes the carbohydrates hydrophilic and capable of hydrogen bonding (important for its biological functions as structural material)

Monosaccharides

- simplest sugars - can be classified several different ways (based on the position of the carbonyl group; based on the number of carbon atoms; based on the spatial arrangement of their atoms) - each has a unique structure and function

Ketose

- carbonyl group is located in the interior of the chain, not at the end of the carbon chain - carbonyl group is a ketone

Aldose

- carbonyl group is located at the end of the carbon chain - carbonyl group is an aldehyde

Triose

3 carbon sugar

Pentose

- 5 carbon sugar - numbered around the ring starting at the little appendage thing outside the ring

Hexose

- 6 carbon sugar - numbered around the ring ending at the little appendage thing outside the ring

Linear and alternative ring forms (sugars)

- sugars spontaneously form ring structures in aqueous solutions; it's rare for sugars with more than 6 carbons to be found in linear form

Disaccharides

- two sugars linked together when a condensation reaction occurs between two hydroxyl groups

Glycosidic linkage

- covalent bond that forms due to condensation reactions between two sugars - can be broken by hydrolysis reactions - α-glycosidic linkage: —OH groups are orientated on the same side of ring; easily hydrolyzed (glycogen—phosphorylase, starch—amylase, etc) - β- glycosidic linkage: —OH groups are oriented on opposite sides of the ring * note: β-glycosidic linkages can look like α-glycosidic linkages if the sugars are flipped alternatively

Polysaccharides

- carbohydrates made up of many monosaccharides - may have cell identity, structural or energy storage function

Starch

- glucose linked by α-1,4-glycosidic linkages (unbranched straight chain: amylose) and/or α-1,6-glycosidic linkages (branched chain: amylopectin) - branched forms have branches about 1 every 30 monomers - energy storage

Glycogen

- highly branched glucose polymer; branches occur about every 10 monomers - can be hydrolyzed to break into glucose monomers for energy - stored in liver and muscle cells

Cellulose

- formed of straight chains of β-1,4-glycosidic linkages that are alternatively flipped - chains are held together by hydrogen bonding between the CH2OH's and OH's of the glucose monomers - structural component of plant cell walls - very difficult to hydrolyze; the fibers are so tightly packed that water has difficulty accessing the hydrogen bonds to break the monomers apart

Chitin

- formed of β-glycosidic linked N-acetylglucosamine (NAG), which is like a glucose with a NHCOCH3 group - found in the cell walls of fungi and the exoskeletons of arthropods like lobsters and insects - strands of NAG are held together by hydrogen bonding just like cellulose

Peptidoglycan

- formed of β-glycosidic linked NAG and N-acetylmuric acid (NAM), which contains a chain of 4 amino acids - stabilized by the formation of peptide bonds between the terminal amino acid on the downward-facing chain and the third amino acid on the upward-facing chain

Carbohydrate functions

- structural (cellulose, chitin, peptidoglycan) —> tend to be β-1,4-glycosidic linked because they are not easy to hydrolyze - energy storage (starch, glycogen; photosynthesis of glucose) —> carbohydrates are good energy storage molecules because they have a lot of C—C and C—H bonds, which are high in potential energy and release a lot of potential energy when broken - cell identity (carbohydrates are attached to the surfaces of cell membranes and act as "tags" for cell-cell recognition and cell-cell signaling; glycoproteins = carbohydrates attached to proteins; glycolipids = carbohydrates attached to lipids

Enzymes

- proteins that speed up chemical reactions by lowering activation energy and creating an ideal environment