Bio 12 - Exam Review

Electron Arrangement

Electron Arrangement

• Orbitals (Max 2 Electrons each)

• First Orbital = spherical (1s)

• Second Orbital= either 1 spherical shaped (2s) or 3 dumbbell shaped ones (2p)

Polar Covalent Bond

occurs when electrons are not equally shared between atoms, because of ELECTRONEGATIVITY.

Electronegativity

a measure of the tendency of an atom to attract another atoms e-

Dehydration (condensation) reaction

• Covalent bond between subunits formed by the removal of H+ and OH- from the functional groups of adjacent subunits

• energy is absorbed

• water is released

• anabolic metabolism (smaller to bigger molecules)

• Example: Peptide Bonds, Glyosidic Linkages

Hydrolysis Reaction

• “water breaking”

• energy is released

• water is used to break a covalent bond

• catabolic metabolism (bigger to smaller molecules)

Neutralization Reaction

• when an acid and a base react to form a salt and water. The acid and base neutralize each other.

• NaOH + HCl ⇢ NaCl + H2O

• ex: HCl from the stomach is neutralized by sodium bicarbonate  (NaHCO3) from the pancreas

Oxidation-Reduction reactions

• this combination of reactions is called REDOX reactions

• the atom that loses the electron is the reducing agent (it reduces the other molecule but gets oxidized itself)

• the oxidizing agent gains the electron (gets reduced)

• L.E.O (loss of electrons OXIDIZED), the lion goes G.E.R (gain of electrons REDUCED)

• as electrons move closer to a more electronegative atom it loses E, usually as heat

High Specific Heat Capacity

• Requires large amounts of E to break the H-bonds (that keep reforming) AND additional energy to increase the temperature of the water.

• high specific heat = lots of energy is required to heat water 1Celcius

• high heat of vaporization = evaporating mlcl has the most kinetic E, thus leaving low E mlcls behind (called evaporative cooling).

• Benefit: Living organisms can continue living and not vaporise

Freezing

• Water has a greater density as a liquid than as a solid, ice floats in water, due to H bonds.

• As water molecules slow down, each mlcl H-bonds with 4 others to form crystalline lattice that takes up more space.

• Benefit: ice floats, therefore it will not crush the living organisms in the water when forming

Cohesion

• H-bonds between water molecules

• Benefit: Insects + Lizards that can walk on water

Adhesion

• H-bonds between water and polar material

• Benefit: The plants xylem

Acid

• a substance that ionizes to form H+ ions when dissolved in water, proton (H+) donor.

• pH is less than 7 because [H+] > [OH-]

• sour taste, conducts electricity

• e.g. HCl: HCl(aq) + H2O(l) 🡪 Cl-(aq) + H3O+(aq)

Base

• a molecule or ion that can i) release OH- or ii) combine with H+ from water or another molecule, proton acceptor.

• pH is greater than 7 because [H+] < [OH-]

• bitter taste, slippery feel, conducts electricity

e.g.  a)  NaOH(s) 🡪 Na+(aq) + OH-(aq)

pH in the ocean

• Ocean pH is 8 but is dropping due to excessive CO2 from the burning of fossil fuels.  This impacts calcifying species including oysters, clams and corals as the available calcium carbonate for making shells is reduced as pH drops.

• The lower pH causes carbonate ions to form bicarbonate, this pulls carbonate ions AND Ca2+ from shelled creatures that use Ca2+ to make their shells.

Buffers

• Carbonic acid H2CO3 is a weak acid that regulates blood pH, as it rapidly absorbs or releases H+ as needed, thus it acts as buffer.

Why Carbon is the fundamental element of life (3 Reasons)

• Can form long chains and ring structures

• Can form up to 4 covalent bonds

• Can form single, double and triple bonds

Hydroxyl

• -OH

• In alcohols, lipids, amino acids

• POLAR

Carbonyl

• -CHO

• In lipids & sugars(linear)

Carboxyl

• -COOH

• In lipids and amino acids

Amino Groups

-NH2

-In amino acids

Phosphate Groups

• P surrounded by oxygens

• In DNA, RNA, ATP

Sulfhydryl

-SH

-In many cellular molecules (amino acids)

Monosaccharides

• Simple Sugars

• Dissolve into water & taste sweet

• Glucose, Fructose, Galactose

• Alpha Glucose & Beta Glucose are ISOMERS

Disaccharides

• 2 Monosaccharides joined by a glyosidic linkage

• Glucose + Glucose = Maltose (Alpha 1-4)

• Glucose + Fructose = Sucrose (Alpha 1-2)

• Glucose + Galactose = Lactose (Beta 1-4)

Polysaccharides

• 100’s or 100’s of monosaccharides

• Mix with water but don’t dissolve

• Don’t taste sweet

• Structural or Energy

Monomers

repeating units. example glucose in starch

Polymerization

• Repeated Linkages

• Produced a polymer

Cellulose

• Formed by plants

• Cannot be digested by animals

• Beta 1-4 Glyosidic Linkage

• Structural component in plant cell walls

Starch

• Formed by plants

• Storing energy

• Contains Amylose (Chains of Alpha 1-4 linkages)

• Contains Amylopectin (amylose but w/ branches bc of alpha 1-6 bonds)

Glycogen

• Made by animals

• Similar to starch but with MORE amylopectin

• can be digested into monomers and absorbed by animals

Fatty Acids

• Long Hydrocarbon chain with a carboxyl at the end (acid)

• If H are missing, double bonds are formed btwn C’s. It is unsaturated

  • liquid at rt

  • in plants & fish (live in cold conditions)

  • healthy to eat

• if max # of H are attached, then it is saturated

  • solid at rt

  • Found in animal fats & butters

  • unhealthy to eat

Glycerol

• 3 Carbons with hydroxyl groups on 1 side

Triglycerides

• Energy Storage

• 3 Fatty Acids & 1 Glycerol

• dehydration rxns form ESTER bonds (bonds between hydroxyl and carboxyl groups)

Phospholipids

• 1 Glycerol, 2 Fatty Acids, 1 Phosphate Group attached to Choline

• Double Layer forms the phospholipid bilayer in the cell membranes

Protein

Polymer of amino acids

Structure of Proteins

• a backbone of N-C-C with an amino group, carboxyl group and R-group

• Amino acids are characterized by their R-group. There are 20 different types, some charged, some polar, many have reactive functional groups

Functions of Proteins

• Structural - bones, muscles, hair, hooves

• Functional - enzymes (biological catalysts that speed up chemical rxns without being consumed)

• Transporters - embedded in cell membranes and act as 'gate-keepers' by allowing certain material to move in and out of the cell, also systemic transport (Hb to carry oxygen)

• Messengers - both within cells and between cells (hormones).

Peptide Bond

• Amino Acids join through a dehydration reaction between the carboxyl and amino group

• Amino acids are added at the C-Terminus

Primary Structure of Protein

• Polypeptide

• A long strand of Amino Acids

• Not functional

Secondary Structure of Proteins

folds or coils of a polypeptide (α-helix and β-pleated sheets) created by H-BONDS between adjacent amino acids.

Tertiary Structure of Proteins

• side chains interact to fold the polypeptide in a unique way.

• Major bonds include ionic bonds, hydrophobic interactions, disulfide bridges (S-S covalent bonds) and H-bonds \n

Quaternary Structure

• a cluster of more than one polypeptide (example: Hemoglobin)

Denaturation

• loss of shape and function of a protein due to heat, changes in pH, salt, etc.

• bonds broken

Nucleic Acids

Composed of nucleotides joined together to form DNA (deoxyribonucleic acid) or RNA (ribonucleic acid)

DNA

• deoxyribonucleic acid

• stores the genetic information for the cell

RNA

• ribonucleic acid

• copies information from DNA and carries it to the cytoplasm where it can be used to produce a protein.

Nucleotides

• Composed of a pentose sugar attached to 1 to 3 phosphate groups and a nitrogenous base.

Glycine

• Non Polar

Methionine

• START codon (AUG)

• Non-Polar

Disulfide Briges

• Strong chemical side bonds formed when the sulfur atoms in two adjacent protein chains are joined together.

Purines

• Bases with a double-ring structure.

• Adenine and Guanine

Pyrimidines

• Bases with a single ring structure

• Cytosine, Thymine, Uracil

Phosphodiester Bonds

• Nucleotides link together between the phosphate of one nucleotide and the 3' carbon of the sugar in an adjacent nucleotide

• forms the sugar-phosphate backbone of the polynucleotide

Adenine and Thymine

• 2 H Bonds

• Forms the TATA Box in transcription

• Easily Broken by Helicase

Cytosine and Guanine

• 3 H Bonds

• Harder to break by helicase so it is not the promotor region in transcription

This happens after an enzyme is finished

Enzyme returns to it's regular shapes and is free to bind to other substrates and repeat the reaction

Cofactors

• Minerals (inorganic), like Zn2+ or Mn2+

• Help Enzyme Activity

• Attach to enzyme or substrate

Coenzymes

• Vitamins, eg B3

• Help Enzyme Activity

• Attach to enzyme or substate

Effect of Substrate concentration on Enzyme Function

• More enzymes speed up the reaction.

• Adding more substrate will increase the rate of reaction until saturation is reached

Competitive Inhibitors

block the active site, preventing substrate from attaching.

Noncompetitive inhibitors

bind to enzyme at a location other than the active site causing a change in the shape of the enzyme’s active site and thus reducing enzyme activity.

Allosteric Regulation

• can be activators or inhibitors of enzyme activity, noncompetitive and reversible.

• Activator or Inhibitor bind to allosteric site and change the shape of the active site

Feedback Inhibition

the product of a reaction (or series of reactions) allosterically inhibits the enzyme, continual on/off process tightly controls amount of product made.

Effect of pH on Enzyme Function

• Shifts in pH can influence the bonds that are responsible for the tertiary structure of proteins and lead to denaturation.

• Too Acidic = Denaturation

• Too Basic = Denaturation

Effects of Temperature on Enzyme Function

• If T° is too cool, protein shapes tend to be too rigid for catalysis.

• If T° is too warm, certain bonds in protein are too weak to maintain the required position for catalysis, eventually denaturation occurs.

• Work optimally between 35 and 40ºC (in humans)

Nucleoplasm

• Similar to Cytosol

Nucleolus

dense region of rRNA and ribosome proteins

Nuclear Envelope

double membrane with transporters and pumps

Rough Endoplasmic Reticulum

• extensions of the nuclear envelope

• ribosomes attached, synthesize proteins that enter the ER

Smooth Endoplasmic Reticulum

• Extension of the nuclear envelope

• doesn’t make proteins, processes proteins (enzymes) to make/modify lipids, carbs, drugs, etc.

Ribosome

• Composed of proteins and rRNA

• Synthesizes new proteins in translation

Vacuole

• disposes waste and toxins

• stores ions and dissolved material

• in plants, maintains cell shape

Chloroplast

• Site of Photosynthesis

• Double Membrane, interior has liquid STROMA and THYLACOIDS (membranous sacs)

Secondary Cell Wall

• Closest to cell membrane

• Thick and Firm

Primary Cell Wall

• Type of Extra Cellular Matrix

• Thin and Pliable

Plasma Membrane

• Regulates movement of material in and out of the cell

Mitochondria

• Site of ATP Synthesis

• Liquid interior is matric, space between double membrane is the intermembrane space

Vesicle

• transports material, has enzymes to digest fatty acids and amino acids (these vesicles are called PERIXISOMES)

Golgi Apperatus

• receives material from vesicles to further process proteins, lipids etc and produces vesicles to send to the cell membrane or other locations in the cell.

Extracellular Matrix

non-living, fibrous protein and polysaccharides to support and anchor the cell

Cell Junctions

-structures that connect adjacent cells

-allows flow of ions, molecules and signaling molecules

Chromoplasts

• type of plastid for pigment storage, ex. carotenoids.

Amyloplasts

• type of plastid for starch storage, unpigmented

Endomembrane System

• interconnection and flow of material between organelles using direct connections and vesicles - builds and delivers lipids and protein and recycles waste or destroys toxins.

Cytoskeleton

filamentous proteins that provide support, allow movement of material in the cell and cell movement (ex spindle fibres)

Cytosol

the liquid portion of the cytoplasm

Cell Membrane

• selectively permeable

• composed of two layers of phospholipids.

Influences on the density of phospholipids

• saturated fatty acids are straighter and can be more tightly packed

• decreasing temperature causes the mlcls to slow down and become closely packed (cool butter vs warm).

• the presence of other mlcls in the membrane (ex sterols)

Fluid Mosaic Model

• describes the properties and composition of the cell membrane

• cell membranes are composed of a mosaic of material including lipids and  many different types of proteins

• the lipids and proteins do not sit in place but drift and flow laterally

Integral Proteins

• embedded in the membrane with one portion interacting with the hydrophobic regions

• Mostly transmembrane (span the membrane)

• Usually has both hydrophobic and hydrophilic regions

Sterols (Cell Membrane)

• stabilize membranes particularly as temperatures change so membrane doesn't become too fluid (when hot) or rigid (when cold).

• Ex: Cholesterol

  \n

Peripheral Proteins

• loosely held on the surface of the membrane, usually on the cytosol side and often interact with the cytoskeleton to hold proteins and/or cytoskeleton in place.

Function of Membrane Proteins

• Transport material across membrane

• are enzymes

• signalling

• intracellular and extracellular attachment

• cell-to-cell recognition.

Glycolipids and Glycoproteins

short strands of carbohydrate attached to phospholipids or to proteins in the membrane, used to identify the cell as self or foreign (ex. in the immune system)

Passive Transport

• No cellular energy needed

• Occurs by diffusion

• The random movement of material until even distribution results and the solution reaches DYNAMIC EQUILIBRIUM

• diffusion, osmosis, facilitated diffusion

Active Transport

• Cellular energy needed

• Molecules move AGAINST their concentration gradient (low to high)

• Dynamic Equilibrium is not reached

• Concentration gradient established

• includes endocytosis and exocytosis

Simple Diffusion

the movement of very small molecules through the membrane, including non-polar O2 and CO2, also water and glycerol.

Facilitated Diffusion

• For larger and Charged mlcls that can’t pass through the hydrophobic interior of the phospholipid bilayer

• Rely on transport proteins. Each mlcl is moved by one type of protein, from high to low concentration.

Channel Proteins

• 'gates' through membrane, include ion channels

Carrier Proteins

Binds to the molecule and changes shape to transfer the molecule across the membrane