Bio 172 Exam 1 Content + Info

levels of biological organization

biosphere → ecosystem → communities → populations → organisms → organs and organs systems → tissues → cells → organelles → molecules

Common properties of living things

order

response to environment

reproduction

energy utilization

regulation/homeostasis

evolution and adaptation

growth and development

2 major themes of bio

1. diversity of life

2. unity of life

natural selection

species change over time and are related to one another

translation

convert information in their chromosomes to proteins

ribosomes

composed of rRNA and proteins

ALL living orgganiams…

• use DNA as genetic material

• do translation (convert info in their chromosomes to proteins)

Should closely related species have ribosomal RNA sequences more similar than those from distantly related species?

Yes!

• rRNA genes can be used to produce a phylogenetic tree showing evolutionary relationships

Tree of Life

Eukaryotes more closely related to archaea than bacteria

eukaryotes

all land plants lie on this branch

bacteria

most of life’s diversity, and so most of its deep evolutionary history, is microbial

archaea

animal diveristy lies on this branch of the tree

2 fundamental types of cells

Prokaryotes: bacteria, archaea

Eukaryotes: protists, plants, fungi, animals

what is a cell?

enclosed by a plasma membrane that regulates passage of materials in and out of the cell

ALL cells use DNA for their genetic info

2 major types: eukaryotic and prokaryotic

Eukaryotic cells

• Unicellular or multicellular

• contains organelles

• has nucleus that contains DNA

Prokaryotic

• unicellular only

• does NOT conatin organelles

• ex: bacteria and archaea

Atomic structure

• protons: positively charged particles (+1 charge)

• neutrons: neutral particles (0 charge)

• electrons: negatively charged particles (-1 charge)

protons & neutrons located in nucleus

electrons found in orbitals surrounding nucleus

• orbitals grouped into levels → electron shells

• valence electrons: electrons in outermost shell

atomic number

chracteristic number of protons in the nucleus

• atoms with same atomic number have same chemical properties and belong to same element

(bottom number of periodic table)

isotopes

forms of element with different number neutrons

atomic mass

number of protons + neutrons of most common isotope

(top number on periodic table)

valence

number of unpaired electrons in an atom

molecules

2 or more atoms held together by chemical bonds

octet rule

atoms most stable when outermost orbital has either 8 electrons or at least pairs of electrons

types of chemical bonds in cells

1. covalent

2. ionic:

3. hydrogen

4. hydrophobic

covalent bonds

• bonds hold molecules together in cells

• atoms share pairs of valence electrons

• ex: corbon has 4 unpaired valent electrons = “tetravalent”

Nonpolar

equal sharing of electrons

Polar

form when 2 atoms shre elctrons unequally

ex: oxygen has > electronegativity than H so partial charges exist on the O and H atoms in H2O molecules

Electronegativty

• Carbon abd hydrogen have approx equal eN

• oxygen most eN of biological molecules

• O>N,S,P>C,H

Hydrogen bonds

• weak bonds

• very important in chem of life

• formed as result of unequal sharing of electron pairs in covalent bonds

Oxygen more eN than hydrogen

ionic

• electron transfer

• cation (+) and anion (-)

• ionic copmpounds are salts

ions form when molecule gain or lose an electron

Van der. Waals or Hydrophobic

• small, when comapred to covalent and ionic and hydrogen bonds

• result from NON polar covalent bonds (equal sharing of electron pairs)

• carbon and hydrogen have approxiamtely equal electronegativities

• very important in chemistry of cells

transient “hot spots” of positive an dnegativ echarge in a molecule with non polar covalent bonds; creates wea interactions when molecules are very close

Properties of Water

Water is a great solvent (substances dissolve easily in it)

H—O bonds in water are polar covalent

hydrogen bonds between H2O and other polar molecules or ions help substances stay in solution

Nonpolar molecules do not easily dissolve in water

H2O molecules interact with other water molecules via hydrogen bonds

• cohesion and adhesion

• water has high surface tension

• in ice: water molecules form crystal lattice. in water: no crystal lattice forms. liquid water is denser than ice

hydrophilic

ater-loving, soluble in water

hydrophobic

water-hating, not dissolved in water

Chemical properties of water that support life

• cohesion (hydrogen bonds)

• moderation of temperature (hgh speciifc heat)

• insulation by floating ice (reduced density in solid)

• solvent for polar compounds

pH scale = -log[H+]

• acid increases [H+]

• base reduces[H+]

• buffer minimizes changes in [H+] and [OH-]

water has VERY high speciifc heat capacity

• bodies of water can absorb heat from sun and fly modestlyincrease in temperature

• at night (and during winter!) the warm ater will warm air

• coatsal areas have more moderate temperatures than inlands

• our bodies are over 60% water

biological macromolceules

Monomers v Polymers

• proteins. amino acids v polypeptide

• carbohydrates. monosaccharide v polysaccharides

• nucleic acids. nucleotides v nucleic acids

• lipids

larger molecules made of smaller molecules linked together with covalent bonds

proteins

chain of amino acids that’re linked together by a covalent bond

• 20 different types of amino acis

• each has carboxyl group and amino group

• differ in charge, polarity, size, and R group

do the work of the cell

function as enzymes, structural components, in transport, in signaling, in defense

Monomers

protein: amino acids

carbohydrates: monosaccharides

nucleic acids: nucleotides

polymers

protein: polypeptides (proteins)

carbohydrates: polysaccharides

nucleic acids: nucleic acids

functional groups affect reactivity

R groups differ in size, shape, reactivity, and interactions with water

• polar: hydrophilic, form hydrogen bonds, readily dissolve in water

• nonpolar: hydrophobic, don’t form hydrogen bonds, poorly dissolve in water

amino acids with hydroxyl, amino (polar), carboxyl (polar), or sulfhydryl (polar) functional groups in side chains can potentially form hydrogen or ionic bonds w/ other molcules and those w/ side chains composed of only carbon and hydrogen atoms (non-polar) potentially form hydrophobic interactions w/ other molecules

Polypeptides

synthesis of proteins

have a amino end and carboxyl end

peptide bond

Proteins are made of many amino acids linked together with a covalent bond that is an important enough covalent bond

amino acids linked between carboxyl & amino groups . . . to make a peptide bond

condensation

makes a peptide bond (lose h2o)

hydrolysis

breaks a peptide bond (add h2o)

• hydrolysis of phosphate groups off nucleotides RELEASES ENERGY

four levels of protein structure

primary structure

secondary structure

tertiary structure

quaternary structure

Primary. structure

linear sequence of amino acids in chain; amino acids are held together in a chain with peptide bonds

• held together by covalent bonds (peptide bonds) between amino acids

secondary structure

interactions between atoms in backbone

the 2D folding into beta-strands and alpha helices; held together by hydrogen bonds between the carbonyl and amide groups on amino acids of another

• a polypeptide must bend to allow these hydrogen, forming alpha-helices nd beta-strands/sheets

depnds onprimary strucrure

tertiary structure

the 3D shape of a protein/polypeptide; held together by bonds/interactions between atoms in the R-groups

• hydrophobic interactions

• hydrogen bonds

• ionic bonds

• covalent (disulfide bonds)

alpha helices

held together by hydrogen bonds that form between carbonyl and amide groups that are on every amino acid

-each carbonyl group in the backbone forms a hydrogen bond with an amide group 4 residues away

beta strands

held togetehr by hydrogen bonds between carbonyl groups in 1 polypepetide and mide groups in a different part of polypeptide

-adjacent strands can run in same direction (parallel) or in opposite directions (antiparallel)

can interact to make tertiary structure

quaternary structure

when multiple polypeptide chains (subunits) come together in a single complex

• held togetehr by covalent, ionic, hydrogen, and/or hydrophobic interactions

Denaturing

breaking of protein structure; loss of protein confirmation

can be done by changing conditions in cell

• temperature

• salts (ions)

• pH

inhibited by chaperones

*renaturstion - possible for some proteins

Folding aids

chaperone proteins which assist in folding other proteins

creates a sheltered enviornment to allow protein to adopt specific configuration

• helps with one of the biggest problems for parially unfolded or unfolded proteins - premature or inappropiate assocation of hydrophobic regions between denatured polypeptides

chemical reactions

allow proteins or molecules to do work

reactants → products *reactants must have more energy than products (for forward motion)

• energy comes from movement of electrons from high energy states to lower energy states

source of chemical energy

electrons = source of chemical energy

• changing bonds from non polar covalent to polar covalent releases energy

  • non-polar covalent bonds generaly have more potential energy than polar covalent bondsl

potential/free energy

capacity of. a molecule or object to do work

can be used to do work

• higher: less stable, more concentrated, more ordered (less entropy), greater work capacity

• lower: more stable, less concentrated, less ordered (more entropy), less work capacity

molecules tend to move from high free energy (more order) to lower free energy (less order)

kinetic energy

energy a molecule or object has while moving

Gibbs free energy

amount of free energy that molecules have

dellta G = Gibbs free energy change: Gproducts - Greactants

Change in free energy…

…determines chemical reaction chracteristics

energy-releasing reactions: expergonic (work), exothermic (heat) → SPONTANEOUS

energy-consuming reactions: endergonic(work), endothermic (heat) → NON-SPONTANEOUS

spontaneous reactions

delta G < 0; do NOT occur immediately or without kickstart

• requires activation energy

activation energy

energy required for reactants to reach transition states (unsatble intermediate)

• can be overcome by heat or catalysts (proetin enzymes - enzymes)

exergoic reactions

rectants have more potential/free energy than products

catalyst (enzyme) effect on reaction

doesn’t change amount of energy released

doesn’t change equilibrium constant Keq

does lower energy of activiation Ea

does increases rate of reaction

is not itslef changed by reaction

typical properties of enzyme catalysts

enzymes are proteins and substrate-specific

bring substrates together so that they can react

bidning involves interactions between enzyme’s R-groups and substrate

bidning destabilizes bond(s) in substrate

active site

region that binds substrate (reactant) on enzyme

whee catalysis occurs

amino acids that form active site are often far apart in linear sequence of unfolded enzyme; protein folding brings specific amino acids close to each other to form active site

• if you denature protein enzyme then active site doesn’t form and enzyme is NOT functional

what do enzymes do?

binding destabiilizes chemical bonds in substrate -→ lowers activition energy → reaction goas faster

induced fit

binding between enzyme and substrate can cause shape change in enzyme protein

enzyme efficiency is dependent on…

1. how well does the active site match shape and chemistry of substrate (hw good is enzyme at bidning to its substrate

2. how well does the enzyme drive catalysis for that substrate

When can enzymes catalyze reactions?

can only catalyze reactions that are ultimately “downhill” where delta G is negative

• sometimes 2 or more reactions need to be coupled so that overall delta G is negative

Reaction coupling

involveds at least 2 reactions:

• one that reeases energy (exergonic) that drives the energy consuming (endergonic) reaction

• together, reactionsa re spontaneous

enzymes can mediate reaction coupling

exergonic reactions are coupled to endergonic reactions

ATP

nucleotide commonly used by enzymes as a source of potential/free energy; high free energy molecule

much of the potential energy comes from 3 phosphate groups that are negatively charged and crowded together

• consists of 3 phosphate groups, ribose, and adenine

energy moving through biological systems

anabolic: building molecules; energy from ATP used to help build things

catabolic: breaking molecules down; ATP can be made

ADP + P → catabolism (- delta G) → ATP energy (more disorder/entropy, less chemical energy in bonds) → anabolism (+ delta G) → ADP + P (less disorder/entropy, more chemical energy in bonds

enzyme kinetics

substrate (S) + enzyme (E) →← ES (transition state) →← enzyme (E) + product (P)

• vary with substrate concentration

reaction rate

amount of product formed (or substrate used)/time

Velocity = product per unit time

factors that affect rate of reaction (ROR)

• substrate concentration

• enzyme concentration

• temperature

• pH (and the concentration of other ions)

concentration affects reaction rates

when concentration of reactants is high → more collisions occur, reactions should proceed more quickly

• for most reactions to proceed: 1. or more chemical bonds have to break; others have to form

• substances must collide in a specific orientation that brings electrons involved near each other

ROR increases as [S] increases to a maximum rate (velocity, V_max )

V_max

enzyme is processing substrate to product as fast it can (substrates are not limiting)

K_M

substrate concentration needed to get ½ V_max

• more efficient enzymes have lower K_M

described affinity of an enzyme for its substrate

• low: enzyme binds substrate tightly (high affinity) and is very efficint at converting to product

• high: enzyme binds substrate more loosely (lower affinity) and is less efficient at converting it to product

Enzyme concentration

less enzyme results in reduced V_max (fewer products in given time)

*K_M is unchanged

how to increase V_max?

increase enzyme concentration

• if we double number of enzymes, we have twice as many substrate molecules bound to active sites, so reaction rate would double

• doesn’t affect K_M; it would take the same amount of substrate to occupy ½ of enzyme’s active sites

V_max is proportional to enzyme concentration

how can enzyme activity be regulated in cells?

environemtal factors: temperature, pH, etc.

reversible inhibition/activators: competitive inhibitors; noncompetitive inhibitors and accelerators

how do temp, salts, and pH affect enzymes?

temeperature

• increase can break hydrophopbic interactions easily

salts (ions)

• can break ionic and hydrogen bonds

pH changes

• can break ionic and hydrogen bonds

Competitive inhibirtors

directly block enzyme’s active site

compete with substrate for active site of enzyme

often resemble substrate

• V_max is same

• K_M is greater K_M is ALWAYS changed

• affinity is less

at very high [S], substrate “out-competes” the inhibitor; V_max is same

Noncompetitive/Allosteric regulation

can be positive and negative

occurs when a regulatory molecule binds away from active site

• allosteric effectors": activators or inhibitors that activate or inhibit enzyme by chnagung its conformation

  • binds at site other than active site → regulatory site

  • alters properties of enzyme function (ALWAYS AFFECTS V_max)

  • **K_M can be unchanged, up or down

Can’t be overcome by excess substrate since regulator binds away from active site

Diffusion

if a molecule is small enough and uncharged, it can move through the membrane like the membrane is not there

simple diffusion

movement down a concentration gradient across

• small. non polar molceules can sometimes move across a membrane like its not even there

• no energy required

• not saturable

facilitated diffusion

movement down a concentration gardient through a transport protien

• transport proteings are specific for their cargo

• no energy required

• is saturable

• is necessary for molceules that are hydrophilic

ex: water movemnet across a membrane

example of facilitated diffusion: water movemment across a membrane

water moves across membrances through water channels

• aquaporins = channel proteins

• hypotonic: a solution that has LESS solutes than the surrounding media

• hypertonic: a solution with more solutes than the surrounding media

hypotonic

a solution that has LESS solutes than the surrounding media

hypertonic

a solution with more solutes than the surrounding media

active transport

movement against (up) a concentration gradient through a transport protein

• uses transport proteins

• requires energy

• is saturable

different types of active transport mechanisms

uniporter: moves molecules across the membrane across the membrane in one direction

antiporter: moves 2 molecules across the membrnce in opposite directions

symporter: moves 2 molecules across the membrane in the same direction

sodium-potassium pump

example of anti porter (still active transport!)

example of symporter (also called secondary active transport)

cell wants to bring in sucrose, but sucrose is in low concentration outside cell

can do so in 2 steps

• 1st: primary active transport uses ATP energy to move H+ ions from low to high concentration

• 2nd: can use high concentration of H+ ions on outside of cell to couple with the sucrose and then when the H+ comes into the cell, so will sucrose

summary of active transport

Carbohydrates

monosacchradies

disaccharides

polysaccharides

carbohydrate structure

basic formula: (CH₂)O_N

can be monosaccharides (mono sugars) or polysaccharides (many sugars)

names of most sugars end in -ose

vary in carbon number, position of carbonyl group, arrangement of atoms