BIOL 190

How are strands connected?

Professor Angela M. Cox

FINAL EXAM REVIEW SHEET

Unit 1 Review 

Lecture 1 (8/30/16) – DNA Introduction

∙ Each DNA strand is made up of repeating nucleotide subunits o Strands oriented in opposite direction

o Nucleotide (repeating subunit):

 Sugar (deoxyribose)

 Phosphate group

 Nitrogenous Base (Can be A, T, C, or G)

o How are strands connected?

 Complementary base pairing

∙ A with T

∙ C with G

∙ Connected with 2 or 3 Hydrogen Bonds

 Complementary = Always go together, “complete”  each other

o What aspect of DNA structure allows it to carry the coded  information?

What aspect of dna structure allows it to carry the coded information?

 Sequence of bases on each strand (what makes each DNA molecule unique)

Lecture 2 (9/1/16) – DNA Structure and Function

∙ Back then, scientists knew…

o Genetic material was in the nucleus

o Pieces of genetic material were chromosomes

o Chromosomes were made of protein and DNA

∙ Hershey and Chase, 1952

o Question Asked: Where is the genetic material contained in the nucleus?

o DNA was made up of 4 nucleotides, but they thought that it was too simple of a makeup for the genetic material to be  contained in it

o Proteins, on the other hand, were made up of 20 amino  acids, so it seemed a lot more likely that that was where  the genetic material would be found

Where is the genetic material contained in the nucleus?

o Used a Phage (or Bacteriophage) as an illustration – The  phage must get its genetic material into the cells somehow because it infects bacteria We also discuss several other topics like Compare your acoustic analysis results between these two speakers' speech production in terms of duration, speech rate, pitch, and averaged syllable duration.

o Process:

 Used radioactive Phosphorus and incorporated it into  the groups of DNA

 Used radioactive Sulfur and incorporated it into the  proteins (NOT the DNA)

 Radioactive DNA, not radioactive proteins, were  

found in the infected cells

o Summary?

 The injected DNA contained all of the genetic info  needed for directing synthesis of new virus particles  The protein part of the phage didn’t enter the  

bacterial cells (meaning it’s not needed for infection)  Conclusion? DNA, not protein, is the genetic  

molecule!

∙ DNA Structure

o Erwin Chargaf

 Determined that for any sample of DNA…

∙ The number of A is equal to the number of T

∙ The number of C is equal to the number of G

o Rosalind Franklin

 Helical shape We also discuss several other topics like How is music meaningful?

 2nm wide

 Complete turn every 3.4nm

o Watson and Crick

 Double stranded

 A pairs with T

 C pairs with G

 Complementary molecule If you want to learn more check out Define electrophoresis.

o Summary – DNA is…

 Double helix shape

 Contains a Phosphate group

 Contains a 5-carbon sugar

 Contains a Nitrogenous base

 Strands are oriented in opposite directions

 Complementary molecule

o Pyrimidines (Single Ring)

 Thymine

 Cytosine

o Purines (Double Ring)

 Adenine

 Guanine

 Think: Pure As Gold

o Carbon attached to the PH group is the 5’ end

o Carbon attached to O group is the 3’ end We also discuss several other topics like Who went to holland until jesus was overthrown?

∙ Genes  Proteins

o If a gene is expressed, it is used to direct the synthesis of a protein

o Epigenome:

 Relates the control function of DNA

 From Greek (epi=above); “Above” the genome

 Environmental efect on expression (lifestyle choices)  Influence whether or not a gene is expressed

o DNA Methylation

 Direct efect on DNA

 Methyl groups attach to DNA in specific places

 Turn genes of/on

o Chemical tags on proteins (histones associated with DNA)  Indirect efect on DNA

Lecture 3 (9/6/16) – DNA Replication (DNA Synthesis or Copying) ∙ 2 Major functions of DNA

o Heredity – Complete copy of genetic info physically passed  from generation to generation during reproduction

 DNA MUST be replicated

 Copies passed to daughter cells when a cell divides  DNA passed from parent to ofspring during sexual  reproduction

o Control – DNA controls cell function and structure

 DNA codes for proteins

 Proteins for a cell determine it’s structure and  Don't forget about the age old question of Why symmetry?

function

 All of the cells in an organism determine the  

structure/function of the organism

∙ DNA Replication (SEMI-CONSERVATIVE)

o Proteins bind free-floating nucleotides to the DNA

(Labeled diagram for Replication can be found here)

o DNA Helicase

 Unwinds and separates the DNA strands

o DNA Polymerase

 Has two responsibilities

∙ Covalently links the free nucleotides to the 3’  

end of the newly forming daughter strand  

(ALWAYS occurs in the 5’  3’ direction)

∙ Proofreads – Fixes mismatched base pairs

- Before proofreading, 1 in 10,000 base pairs  

are mismatched

- After proofreading, 1 in 1 billion base pairs are

mismatched

- For each replication event, approx. 3 mistakes

remain (mutations) – Raw materials for  

evolution

o DNA Primase

 Adds primers to the template strand

o DNA Ligase

 Bind together the DNA fragments on the lagging  We also discuss several other topics like What is the definition of lobbying?

strand

o Leading strand vs. Lagging strand?

 Leading strand the replication is continuous

 Lagging strand the replication is discontinuous

∙ Synthesized pieces called Okazaki fragments

o ALL steps of Replication:

1. Helicase unwinds and separates DNA strands

2. Primers are added to the single stranded template  strands

3. Free deoxyribonucleotides form H-bonds with the  

nucleotides of the newly forming strand

4. DNA Polymerase covalently links the free nucleotides to the 3’ end of the newly forming strand

5. The leading strand is synthesized in fragments  

(discontinuous)

6. Primers are removed and replaced with  

deoxyribonucleotides

7. Ligase covalently links the fragments

8. DNA polymerase proofreads and fixes mistakes  

(along with DNA ligase)

(A video animation on DNA Replication can be found here - Please  ignore exonuclease as we do not need to know that enzyme)

Lecture 4 (9/8/16) – Protein Synthesis (Transcription and Translation) ∙ DNA vs. RNA

o DNA

 Deoxyribonucleic Acid

 Deoxyribose sugar

 Bases A, T, C, G

 Double stranded

 Found in the nucleus

o RNA

 Ribonucleic Acid

 Ribose sugar

 Bases A, U, G, C

 Generally single stranded

 Found in the cytoplasm

∙ What are genes?

o Segments of DNA in each chromosome

o Each chromosome has a diferent set of genes

o Each gene is 1,000s to 100,000s of base pairs long  (sequence of bases)

o Code for a specific gene product

 Mostly protein; some RNA

 Often separated by non-coding regions of DNA

∙ Transcription (DNA  RNA – Synthesis of RNA under the direction  of DNA)  

o Promoter

 Where transcription begins (start)

 Binding site for RNA polymerase

 Determines which strand will be used as a template  for transcription

o Coding Sequence

 Series of codons (three base code for an amino acid) o Terminator

 Where transcription ends

 RNA polymerase detaches

o Initiation

 RNA polymerase binds to promoter

 DNA strands unwind

o Elongation

 RNA polymer (strand) gets longer

o Termination

 The “terminator” region of the gene is reached

o After termination, everything goes back

o ~10% of genes are transcribed into either Ribosomal RNA  (rRNA) or Transfer RNA (tRNA)

o ~90% of genes are transcribed into Messenger RNA  (mRNA)

 Translated into a polypeptide (protein)

o What happens to RNA after it is released?

 rRNA  

∙ rRNA + “imported” proteins = ribosomal  

subunits (made in the nucleolus)

∙ 1 Ribosome which is ~60% RNA, ~40% protein  

(made in cytoplasm)

 tRNA

∙ H-bonding between complementary  

ribonucleotides results in 3-D “L” shape with  

the amino acid at one end and an anticodon (3  

ribonucleotides that can pair with mRNA  

codons) at the other end

 mRNA

∙ Cap and tail added

∙ Introns removed

∙ Exons spliced together

o The Genetic Code

 Triplet

 Redundant

 START codon – AUG (ALWAYS)

 STOP codons – UAA, UAG, UGA

 One codon – Three ribonucleotides

 The amino acids are specified by these codons

∙ Translation (RNA  Polypeptide (Protein) – Synthesis of proteins  under the direction of RNA)  

o Initiation

 mRNA binds to small subunit of ribosome

 tRNA binds to START codon AUG (methionine)

 When the large ribosome subunit binds to the small  unit, initiation is complete

o Elongation

 Another tRNA binds to the next codon in A site

 tRNA in P site emptied of amino acid when the amino acids covalently link (peptide bond)

 mRNA moves through the ribosome

o Termination

 STOP codon reached

 Polypeptide released

 mRNA released

∙ Mutations

o Silent Mutation – Mistake in the DNA, but the protein ends  up staying the same

o Point Mutations

 Wrong protein

 Truncated (cut of early) protein

o Frame Shift Mutation – One more or one less letter added  or subtracted from the code sequence

(Video animation for transcription and translation can be found here –  Start the video at 0:30 and end at 6:30 – It’s a little longer than it really needs to be. Ignore these three terms as we do not need to know  them: Spliceosome, E site, and release factor)

UNIT 2 REVIEW 

Lecture 1 (9/20/16) – Chemistry

∙ Matter

o What everything is made of

o Atoms – Tiny pieces of matter

o Elements – Diferent kinds of atoms

 Hydrogen, oxygen, carbon

o Compounds – Two (or more) kinds of atoms stuck together  Water, Methane

o Anything that occupies space and has mass

 States of matter: Solid, liquid, gas

o Composed of elements

 92 occurring elements

 25 essential to life

∙ Oxygen, carbon, hydrogen, nitrogen

∙ Calcium, phosphorus, potassium, sulfur,  

sodium, chlorine, magnesium

∙ 14 trace elements

o Elements combine to form compounds

 Compounds have diferent characteristics than their  elements

o Atoms made of protons (+), neutrons, and electrons (-)  Protons and neutrons in nucleus

∙ Atoms

o Smallest unit of matter that till retains the properties of an  element

o Composed of subatomic particles

 Proton – Single unit of positive charge

 Electron – Single unit of negative charge

 Neutron - Neutral

o Protons and neutrons in nucleus – Have nearly identical  mass (Daltons)

o Electrons – Circle around the nucleus

o Element symbol – Internationally recognized symbol for an  element

o Atomic # - # of protons

o Mass # - # of protons and neutrons

o Mass # – Atomic # = # of neutrons  

∙ Molecule

o A combination of atoms

o Held together with covalent bonds

o Similarities

 All have C and H

 This makes them organic molecules

∙ Chemical Bonding

o Electrons determine how an atom bonds

 Electrons are organized into orbitals

 Atoms combine to obtain a full outer orbital

∙ Stable (happy) – 8 electrons (except for 2 H)

 Atoms can gain, lose, or share electrons (whatever it  takes to get to a stable state)

∙ Covalent Bonds

o Atoms bonded by sharing electrons

o Electrons spend time around both atoms

o Polar Molecule – Has opposite charges on opposite ends of  the molecule

 Has poles on the molecule (like a magnet)

 Electrons aren’t shared equally – Negatively charged  electrons spend more time around one atom (the O  atom in water)

 Gives this end a negative charge

∙ Ionic Compounds (Salts)

o Ionic Bonds – Attraction between oppositely charged ions  Ions – Atoms with a positive or negative charge

∙ Have gained or lost an electron

∙ Hydrogen Bonds

o Weak electrical attractions between polar molecules  (electrons not moving between molecules)

o Important to the properties of water

∙ Water’s Life Supporting Properties

o The polarity of water molecules and the hydrogen bonding  that results explain most of water’s life-supporting  

properties

 Water molecules stick together (cohesion)

 Water has a strong resistance to change in  

temperature

 Frozen water floats

 Water is a common solvent for life sustaining  

reactions

∙ Does “Carbon-based” mean there’s more carbon than any other  element?

o No – Carbon forms the “skeleton” of molecules

o Carbon Skeletons

 Hydrocarbons (only C and H)

 All nonpolar (hydrophobic)

∙ CHNOPS (Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus,  Sulfur)

o Big elements

o More complex organic molecules

∙ Chemical Groups = “Functional Groups”

o Groups of atoms found in organic molecules

o Influence the water solubility of hydrocarbons

o Influence the function of the molecule

∙ Macromolecules

o Very large organic molecules

o Hundreds to million of atoms

o Common in cells

o Carbohydrates, nucleic acids, proteins, lipids

Lecture 2 (9/22/16) – Polymers and Monomers

∙ Polymer – Long chain of monomers

o Broken up by hydrolysis

 Chemical process of breaking down polymers

 Water added

 Process requires an enzyme  

∙ Dehydration Synthesis

o Builds polymers from monomers

o Chemical process

o Water removed

o Enzyme required

Link to dehydration synthesis chart can be found here ∙ Sugars take on ring form in water

o Glucose (an aldose)

o Fructose (a ketone)

∙ Glucose monomers link together with a covalent bond called a  glycosidic bond to for a disaccharide

o Maltose (glucose and glucose) – used to produce liquor,  malted items

o Sucrose (glucose and fructose) – table sugar

o Lactose (glucose and galactose) – sugar found in milk o Monosaccharides and disaccharides dissolve in water  easily – HYDROPHILIC

 Classified by location of carboxyl and number of  

carbons

∙ Polysaccharides

o Many sugars

 Linked together by dehydration synthesis

o Ex.

o Starch – Energy storage molecule for plants

 Plants store surplus starch as granules with  

chloroplasts and other plastids

 Have alpha linkages

o Glycogen – Energy storage molecule for animals

 Humans and other vertebrates store glycogen  

mainly in liver and muscle cells

 Have alpha linkages

o Cellulose – Structural polymer in plants

 Hydrophilic – Water sticks to the surface:  

absorbent

 Diferent patterns of bonds in cellulose vs. starch  and glycogen

 Humans cannot digest cellulose (Beta Linkages):  lack enzyme to hydrolyze bonds

 Another name: “Dietary fiber” listed on nutrition  labels

 Many herbivores have symbiotic relationship with  microbes that can digest cellulose

o Chitin

 Also a polymer of glucose monomers

 Makes up insect and crustacean exoskeletons

∙ Lipids

o Fats and oils (triglycerides)

 Glycerol: “Head” region

 Fatty acid “tails”

 Triglycerides (fats vs. oils)

 Fat molecules contain much more energy than carb  molecules

 Saturated and unsaturated fats  

∙ Number of bonds in the hydrocarbon chain in a  

fatty acid

 Saturated Fats

∙ Generally bad for you  

∙ Animal fats (Lard, butter, shortening)

∙ Pack well – Solid at room temp. (Hll single  

bonds)

 Unsaturated Fats (Fewer hydrogens)

∙ Generally good for you

∙ Plant fats and fish (olive oil, cod liver oil) high  

in unsaturated fats

∙ Liquid at room temperature (have one or more  

double bonds)

 Hydrogenation

∙ Adding hydrogens to unsaturated fatty acids

o Makes them saturated

 Fatty Acids

∙ Monomer of fat/oil/phospholipid molecules

∙ Unsaturated fatty acids can be cis or trans

o Phospholipids

 Major component of the cell membrane

∙ Membrane structure (bilayer)

∙ Separation of water-filled cells from watery  

environments

o Steroids

 Cholesterol

∙ Important component of cell membranes

∙ Can attach to blood vessel walls and cause  

them to thicken

∙ Cell sin our liver produce almost 90% of  

circulating cholesterol

 Steroid hormones

∙ Estrogen

∙ Testosterone

o Waxes

 Strongly hydrophobic

 Protection

 Prevent dehydration

o All hydrophobic (non-polar)

o Store energy

Lecture 3 (9/27/16) - Proteins

∙ Many, many diferent proteins

o Each cell contains thousands of diferent proteins o Diferent types of cells produce diferent proteins ∙ Polymers of amino acids

o There are 20 amino acids

o Main structure

 Amino group

 Carboxyl group

 Central carbon

 Hydrogen atom

 R-group (side chain)

o Non-polar R-groups

 Decrease water solubility

 Hydrophobic

o Polar R-groups

 Increase water solubility

 Hydrophilic

∙ Amino Acids – Linked together by peptide bonds o Polypeptides

 Polymer of polypeptides

∙ Structure (Proteins)

o A functional protein consists of one or more polypeptides  twisted, folded, and coiled into a unique shape

o Primary Structure

 Unique sequence of amino acids

o Secondary Structure

 Local patterns/structure held together by H-bonds  Coils (alpha helix) and folds (beta pleated sheets) o Tertiary Structure

 Overall 3-D structure of the protein held together by  chemical bonds between side chains (R-groups)

 H-bonds, ionic bonds, hydrophilic interactions

 Strong covalent bonds called disulfide bridges

o Quaternary Structure  

 Two of more polypeptide chains bonded together ∙ The ability of R-groups to interact with water and/or with each  other influences the formation of structure

o Non-polar R-groups internalize to minimize interaction with  water

 Polar and charged R-groups position themselves

∙ On the exterior where they will interact with  

water OR in positions to interact with each  

other

o Hemoglobin (alpha) (quaternary)

 4HHB

 Protein found in red blood cells that helps transport  oxygen through the body

o Hexokinase (alpha) (tertiary)

 1 CZA

 Enzyme that helps to break down glucose

o Glucagon (alpha) (secondary)

 Raises blood sugar if level gets too low

 Opposite efect from insulin

 Pancreatic hormone

o Transthyretin (beta and alpha) (quaternary)

o K+ (alpha) (qyaternary)  

 Channel (hole) in the middle

o SHAPE DETERMINES FUNCTION

 Butterfly

 Donut

 Globular

 Long fiber

∙ Protein Structure

o Tertiary structure determines shape and function o Binding pockets – To bind a target molecule

 Lactase – Protein that breaks down lactose (shape  

fits lactose)

Lecture 4 (9/29/16) – Denaturation, Biomolecules, Cell Theory ∙ Denaturation

o Loss of 3-D “native confirmation”

o Caused by excessive heating or salt, pH change

o Mutations can also change the shape of proteins

o Prions

 Proteinacious infections particles

o Consequences of flawed/misfolded proteins at cellular level  Generally reduced function

 Sometimes flawed proteins are destroyed

∙ Never get to final cellular destination

∙ Never perform intended function

 Sometimes flawed proteins form clusters in cell

∙ Whole or after inappropriate breakdown into  

pieces

∙ Interfere with normal cellular function

∙ Similarities b/w four classes of biomolecules

o Organic

o Contains one or more chemical groups

 Specific number, combination and arrangement of  

these groups characterize each type of molecule

o Fabrication of monomers (repeating subunits)

 Same chemical reaction (dehydration synthesis)

 Requires enzyme

 Degradation of monomers

o Degradation of monomers  

 Same chemical reaction (hydrolysis)

 Requires an enzyme

Biomolecular Class

Monomers

Polymers

Nucleic Acids

Nucleotides

Polynucleotides

Proteins

Amino Acids

Polypeptides

Carbohydrates

Monosaccharides

Polysaccharides

Lipids

Fatty Acids/Glycerol

Triglycerides/Phospholip ids

∙ Diferences

o Interactions with water (hydrophilic/hydrophobic)

o DNA has phosphates

o DNA and proteins have Nitrogen, sugars and lipids don’t o Which atoms are present?

 Nucleic Acids: CHNOP

 Proteins: CHNO and a little S

 Carbohydrates: CHO in 1:2:1 ratio (in the monomer)  Lipids: CH and a little O (in phospholipids, only some  N and P)

o What chemical groups are present?

 Nucleic Acids: PO4 (charged), OH (polar) on  

backbone, various (polar) on bases

 Proteins: COOH (charged), N H2 (charged), variety  of R-groups ranging from polar to non-polar

 Carbohydrates: Lots of OH (polar)

 Lipids: Mostly hydrocarbon and C H3 (non-polar) o Which are hydrophilic/hydrophobic?

 All but lipids are hydrophobic

 What makes them this way?

∙ Their chemical groups

∙ Cell Theory

o What is a cell?

 All living things are made up of one or more cells  All cells came from pre-existing cells

 Cells are the basic unit of structure and function in  living things (basic unit of life)

o Least complex to most complex: Atom, molecule,  organelle, cell, tissue, organ, organ system, organism o Cells are the lowest level or biological organization that  exhibit all of the characteristics of life

∙ Characteristics of Life

o Organized

o Contain DNA

o Reproduce (like begets like)

o Grow and develop (controlled by DNA)

o Process energy

o Respond to environment

o Regulate internal conditions (homeostasis)

o Adapt

o Beneficial traits become more common in a population  over time

∙ Structures present in all cells

o Cell membrane  

 Outer limiting boundary

 Separates living cell from the non-living environment o Cytoplasm

 Cytosol – Gel like fluid

 Internal structures

o DNA

 Genetic instructions

 Heredity and cellular control functions

o Ribosomes

 Role in protein synthesis

o Based on their structure, we can categorize cells into two  

groups

 Prokaryotes

∙ Domain bacteria

∙ Domain archea

∙ “Pro” = before, “karyon” = kernel/nucleus

 Eukaryotes

Lecture 5 (10/4/16) – Bacteria, Archea, Eukaryotes, Multicellular  Organisms

∙ Bacteria

o Hidden life

o Ex. E. coli

o Human Microbiome

 The body contains 10 times more bacteria, fungi, and

other micro-organisms than human cells

∙ Archea

o Can live in harsh environments

∙ Eukaryotes

o “eu” = true, “karyon” = kernel/nucleus

o 1 Domain, 4 kingdoms

 Protists

 Plants

 Fungus

 Animals

o Epithelial cells line our cavities and cover flat surfaces

o Fibroblast cells are found in connective tissue, they secrete

collagen and ECM

Diferences between prokaryotic and eukaryotic cells

Prokaryotic

Eukaryotic

Smaller (1-10 μm)

Larger (10-100 μm)

No membrane bound internal components (organelles)

Many membrane bound internal compartments (organelles)

Small ribosomes

Large ribosomes

DNA

o Single circular molecule

o Not membrane enclosed

o “Nucleoid Region”

DNA

o Linear molecule

o Many (chromosomes)

o Look alike “pairs”

o Membrane enclosed

o Nucleus

∙ Why no huge cells? Surface Area vs. Volume ratio

∙ Plant vs. Animal Cells

o Animal Cells

 No cell wall

 Contain lysosomes and centrosomes

o Plant Cells

 Have cell walls

∙ Diferent than prokaryotic cell wall

 Few sperm cells have flagella

 Central vacuole – stores water, other chemicals

 Have chloroplasts

 Have plasmodesmata

∙ Multicellular Organisms

o Animals (humans too) and plants

 All eukaryotic

 Contain many diferent types of specialized  

(diferentiated) cells

∙ Animals: Muscle, RBC, Keratinocyte, fibroblast

∙ Plants: Mesophyll, guard, epidermis

 All originated from the same single fertilized egg (aka

Zygote)

 Process by which these cells formed: Cellular  

Diferentiation

∙ Cellular Diferentiation

o Normal process by which immature undiferentiated cells  

develop distinct structures and functions of specialized  

cells

o Underlying mechanism: Diferential expression of genes in  the DNA

 Certain genes turned on (expressed)

 Others turned of (silenced)

o Result: Change in the number and type of proteins (the  

proteome) in the cell

 Defines morphology

 Defines specialized function

 >200 diferent kinds of specialized cells in human  

body, all begin with an undiferentiated cell (stem  

cell)

∙ Advantages of compartmentalization in eukaryotes

o Increased surface area

o Increased concentration of reactants used in chemical  

reactions

 Higher concentration, higher rate

o Separation of incompatible reactions/reaction  

environments

 Synthesis vs. degradation

 Reactions that need diferent environments

o Separation of products based on what they are for internal  or external use

 Internal

∙ Inside a membrane-enclosed organelle, e.g.  

enzyme in a lysosome

∙ Free-floating in the cytoplasm, e.g. enzyme  

needed for glycolysis (cytoplasm)

 External (export)

∙ E.g. collagen of ECM, insulin, digestive  

enzymes – e.g. trypsin – for use in intestines

∙ Ribosomes: Free and bound

o Free: In cytoplasm

 Translation of proteins used in cytoplasm

o Bound: Attached to RER

 Translation of membrane-associated proteins

∙ Proteins to be inserted into phospholipid  

bilayers of membranes

∙ Proteins for export from cell by exocytosis

∙ Proteins for membrane enclosed cellular  

organelles

Lecture 6 (10/6/16) – Cell Structures

∙ Lysosomes

o Round, membrane-enclosed, acid-filled vesicles that  function as garbage disposals

∙ Microfilaments (Actin filaments)

o Function = Cell shape; while cell movement (e.g. amoeboid movement)

o Easily disassembled and reassembled

o Function in cytokinesis

∙ Intermediate Filaments

o Generally not disassembled and reassembled

o Function = cell shape; reinforcement of cell junctions,  organelle placement, especially nucleus

∙ Microtubules – Tubulin Proteins

o Hollow tubes; can be disassembled and reassembled o Functions: Arrangement of organelles; cell motility (e.g.  flagellum of sperm); intracellular transport (along with  accessory transport, e.g. kinesin)

∙ Membrane Functions

1. Barrier

 Cell membranes are gatekeepers

 Regulate what goes in and out

 Limiting boundary

2. Regulates Transport

 Passive transport (no energy required) is the  

spontaneous difusion of molecules across a  

membrane

∙ Osmosis

o Passive difusion of water across a  

membrane

o One of the most important substances to  

cross is water

o Body is 60% water

o There is water in and around cells

∙ Difusion (high to low)

o Solutes – Particles being dissolved

o Solvents – Substance doing the dissolving

o Solution – Combination of solute and solvent

o Facilitated Difusion – Most molecules can’t  

get through membranes on their own;  

carrier molecules – transport proteins

 Active transport – Requires ATP

∙ Molecules flow against their concentration  

gradient

∙ Needs energy

∙ Protein required

∙ Usually ions or small molecules

∙ Ex. Na+/K+ pump

 Bulk Transport

∙ Endocytosis and exocytosis

∙ Exocytosis – Transport of cell via vesicles that  

fuse with plasma membrane

∙ Endocytosis – Transport into cell via vesicles

o Phagocytosis – Engulfs large particles

o Pinocytosis – Cells taking in dissolved  

particles and liquid

o Receptor-Mediated – Bind to receptor  

proteins in the membrane

3. Communication

4. Recognition/Identification

5. Anchor

 Cell attachment via “junctions”

∙ Adjacent cells in many animal tissues are often  

directly connected by cell junctions consisting  

of specific proteins

o Tight Junctions – Keep things in the cell from

body

o Anchoring Junctions – Anchors to the cell;  

holds together

o Gap Junctions – Used to transport molecules

between cells

∙ Additional Cell Boundaries

o Cell wall made of cellulose

∙ Cell Membrane Structure

o Every cell is bordered by a plasma membrane

o Fatty acid tails hydrophobic because they are made of  carbon and hydrogen

o What’s there?

1. Phospholipids – Barrier that prevents the difusion of  most material in and out of the cell

2. Proteins – Maintain cell shape; receptors; enzymes;  cell to cell recognition; intercellular junctions;  

transport

3. Carbohydrates – CHO layer on external surface of cell (hooked onto lipids – glycolipids; hooked onto  

proteins – glycoproteins); recognition/identification’  

interaction with other ECM and other cells

4. Cholesterol – Stabilizes the membrane; keeps it  

flexible (not too flexible at warm temps.; not too rigid

at cold temps.)

UNIT 3 REVIEW 

Lecture 1 (10/13/16) – Energy

∙ Energy we take in is originally from the sun

∙ Matter

o Material that takes up space and has mass or weight o Atoms, molecules, macromolecules, cells

∙ Energy

o Ability to do work

 Ability to move matter

 Ability to change the arrangement of matter

o Potential Energy

 Stored energy

 Energy derived from position or arrangement

 Ex. Water behind a dam, roller coaster cresting,  

chemical bond energy

o Kinetic Energy

 Energy of movement

 Ex. Light, random motion of atoms and molecules  (heat), molecules or ions flowing down a  

concentration gradient

o Thermodynamics – The study of energy transformations  First Law of Thermodynamics

∙ The total amount of energy in the universe is  

constant – energy can’t be created or  

destroyed, but it can change forms

 Second Law of Thermodynamics

∙ The quality of energy in the universe is NOT  

constant

o The amount of useful energy declines  

spontaneously

o Energy transformations are not 100%  

efficient

o At each transformation, some useful  

energy is lost as heat – the lowest quality

of energy

o Energy Conversions

 Only ~1% of the energy released by the sun that  earth receives is captured and converted by plants

∙ Converted into chemical bond energy

o Entropy

 Measure of DISORDER

 Increases spontaneously

 Ex. Leaves changing

o Corollary of the 2nd Law of Thermodynamics

 In the universe as a whole, processes that increase  entropy occur spontaneously

o Cells

 Highly organized

 A cell needs to obtain and use energy in order to  maintain this level of organization

 Chemical reactions allow a cell to obtain and use  energy

o Changing the arrangement of atoms in molecules is a  chemical reaction

∙ Metabolism

o All of the chemical reactions in a cell or organism  Released or stored

 Exergonic Reactions – Release energy

∙ Catabolic

∙ Releases energy (makes energy available to  

cell)

∙ ΔG = “Change in free energy” – Differences in  

PE of substrates and products

 Endergonic Reactions – Require an input of energy  and store energy

∙ Anabolic

∙ Consumes energy (requires energy input from  

cell)

∙ ΔG = amount of energy consumed

∙ Energy put into bonds (stored)

o Catabolism

 Breakdown, degradation

 Releases energy, making energy available for the cell  Ex. Hydrolysis

o Anabolism

 Synthesis

 Requires energy

 Ex. Dehydration Synthesis

Lecture 2 (10/18/16) – Energy Pt. 2: Enzymes

∙ Metabolism – All of the chemical reactions n a cell or organism o Catabolic – Break down, degradation (exergonic)

o Anabolism – Synthesis, building (endergonic)

∙ Chemical Reactions

o Re-arranging atoms in molecules

o Activation Energy

 Energy of Activation ( EA) – Kinetic energy needed  for reactions to reach transition state (start)

 Transition State – Point at which reactant bonds break and product bonds start to form (high energy point)

∙ Metabolic Pathways – A series of chemical reactions in which the  product of first reaction becomes substrate of next reaction o Linear Pathways (ex. Glycolysis)

o Cyclic Pathway (Ex. Krebs Cycle – Citric Acid Cycle) ∙ Enzymes speed up the cell’s chemical reactions by lowering  energy barriers

o Catalysts – Speed up chemical reactions about 106 x o Lower activation energy

o Facilitate chemical reactions by making it easier to reach E¿ (transition state)

o Enzymes – Biological catalysts (do not add/provide energy) ∙ Each chemical reaction needs a unique enzyme

∙ Enzyme are very specific – Their active site will only bind specific substrates (shape determines specificity)

o Substrate – The specific reactant that an enzyme acts on o Active Site – A region of the enzyme the substrate fits into ∙ An enzyme can reduce the activation energy in a variety of ways o By stressing, bending, or stretching critical chemical bonds o By directly participating in the reaction

o By creating a microhabitat that is conducive to the reaction o By simply orienting or holding substrate molecules in place so that they can be modified

∙ Catalytic Cycle

1. Enzyme available with empty active site

2. Substrate binds to enzyme with induced fit

3. Substrate is converted to products

4. Products are released

∙ How do cells control enzyme activity?

1. Make more/fewer copies of the enzyme

 Increase/decrease temperature

 Increase/decrease pH

2. Location (keeping things contained – Ex. Lysosomal  enzymes)

3. Activate when needed (Ex. Trypsin in its inactive form is  trypsinogen – has a tag that if applied, keeps the enzyme  from working)

4. Inhibitors (stop the enzyme from working)

 Chemical that interferes with an enzyme

 Competitive inhibitors

o Block substrates from entering the active site

o Reduce an enzyme’s productivity

 Noncompetitive Inhibitors

o Bind to the enzyme somewhere other than the  

active site

o Change the shape of the active site

o Prevent the substrate from bonding

 Feedback Inhibition

o Enzyme inhibitors are important n regulating  

cell metabolism

o Product acts as an inhibitor of one of the  

enzymes in the pathway that produced it

o Ex. Thermostat (stops at a certain point)

 Many drugs, pesticides, and poisons are enzyme  inhibitors

o Many beneficial drugs act as enzyme inhibitors

 Ibuprofen – Inhibits enzyme involved in  

production of prostaglandins  

(pain/inflammation signal)

 Some blood pressure medicines

 Some antidepressants

 Many antibiotics

 Protease inhibitors used to fight HIV

o Enzyme inhibitors have also been developed as

 Pesticides

 Deadly poisons for chemical warfare

Lecture 3 (10/20/16) – Energy Pt. 3: Energy Carriers

∙ Induced Fit – Stressing/straining of bond to be broken o Allows for better fit between enzyme and substrate o Makes it EASIER to form products = lower activation energy o Ex. Chemotrypsin (pancreas, hydrolyzes proteins)

∙ Some enzymes require a cofactor in order to function o “Helper molecules”

o Complete the shape of the active site

o NOT proteins

o Inorganic Cofactors

 Minerals (iron, magnesium, manganese)

o Organic Cofactors

 Derived from vitamins

 Small

 “Coenzymes”

∙+¿

NAD¿ 

∙ FAD

∙ CoA

∙+¿

NAD¿ and FAD are electron carrying enzymes

∙ Alcohol Dehydrogenase

o Enzyme in liver and stomach

o Protects us from the toxic efects of alcohol

 Detoxifies about one drink/hr

∙ LEO GER

o Lose Electrons = Oxidized

o Gain Electrons = Reduced

o+¿

NAD¿ – Empty, depleted/oxidized

o NADH – Full, energized/ reduced (electrons used to make  ATP)

∙ ATP molecules are like free floating rechargeable batteries in all  living cells

o Usable form of energy for cells

o Cycled constantly ADP/ATP

o Transfers energy from one reaction to another  Acts like an energy shuttle

o Only used within a cell – Not long term energy storage  molecule

o Adenosine Triphosphate

 A molecule of Adenine and ribose with a tail of 3  phosphate groups

o Pop of the third phosphate group

 ATP  ADP and phosphate group and energy release o Releases energy the cell uses to do work

 ADP – Adenosine diphosphate (2 phosphates) o The cell then uses energy harvested from food to convert  ADP back to ATP (cellular respiration)

o Phosphate groups

 Negatively charged

 A lot potential energy

 Popped of phosphate = inorganic phosphate o Energy Coupling

 Use of an exergonic process to drive an endergonic  one

∙ Mediated by ATP

o Coupling exergonic reactions to endergonic reactions o A cell does three main kinds of work

 Chemical – Reactants  Product formed

∙ Substrate activated/energized from gained  phosphate group

∙ Transfer of a phosphate group called  

phosphorylation

∙ Phosphate group released

∙ Phosphorylation of reactant provides enough  energy to synthesize the product

 Transport – Transport protein  Solute transported ∙ Solute binds to transport protein

∙ Transport protein phosphorylated when it  

changes shape

∙ Original transport protein returns to original  shape when phosphate group detaches 

solute moves against the gradient

 Mechanical – Motor protein  Protein moved  ∙ Phosphorylation of motor proteins (myosin in  muscle cells)

∙ Protein changes shape and pull on protein  

filaments

∙ Makes the cell contract

∙ Ex. Muscle contraction

∙ Glucose Catabolism

o Aerobic

 With oxygen (oxygen = electron acceptor)

 Aerobic glucose catabolism = Cellular respiration

o Anaerobic

 Without oxygen

 Fermentation

∙ Mitochondria

o Cellular respiration

o Energy from glucose is transferred to ATP

o Matrix – Thick fluid

o Cristae – Membrane folds

 Increase surface area for energy production

∙ Electron Transport Chain (ETC)

o Series of electron transport proteins inserted in  

phospholipid bilayer of inner mitochondrial membrane o Each protein passes electrons to next protein in series,  gradually releasing energy

o Must be an electron donor at the start and a final electron  acceptor at the end of the chain

o Like a staircase

Lecture 4 (10/25/16) – Energy Pt. 3: Glycolysis (and photosynthesis and fermentation)

∙ Photoautotrophs

o Feed us

o Clothe us (think cotton)

o House us (think wood)

o Provide energy for warmth, light, transport, and  

manufacturing

∙ Photosynthesis – Captured energy from the sun to make food o CO2+ H2O →C6 H12O6+O2+ ATP

o Three inputs

 Light

 Water

 Carbon dioxide

o Two products

 Oxygen

 Sugar

o Light Reaction – Chlorophyll converts solar energy to  chemical energy

 Into ATP and NADPH

 Water is split – Oxygen is given of and hydrogens  

(and electrons) are transferred to +¿

NAD P¿ (Oxygen  

= byproduct)

o Calvin Cycle – Uses the products to make sugar

 ATP and high energy electrons in NADPH for the  

reduction of carbon dioxide to glucose

 Series of chemical reactions

 Occurs in stroma

 Carbon dioxide form the air is put together to build  

sugars

 A carbon from a carbon dioxide molecule is added to  a 5-carbon sugar

 This is broken into two 3-barbon sugars

∙ Glyceraldehyde 3 Phosphate (G3P)

 Some are recycled

o Molecules that gain electrons gain energy

o About 50% of the carbs made are consumed in the  

mitochondria of plant cells

 Store in excess in roots, tubers, seeds, and fruits

o Sugars

∙ Heterotrophs

o Must consume other organisms for food

∙ Chemical Cycling

o Producers use the sun to make glucose and oxygen

 Stores energy in chemical bonds

o Consumers eat the plants and break up the glucose  

releasing carbon dioxide and water

 The producers use the carbon dioxide and water to  

build more organic compounds

∙ ATP Synthesis in glucose catabolism

o Glycolysis – Always the first pathway

o Cellular Respiration (aerobic)

 OR

o Fermentation (anaerobic)

∙ Glycolysis

o Harvests chemical energy by oxidizing glucose to pyruvate o Uses 2 ATP, produces 4 (net gain of 2)

o Three of ten steps yield energy

 Quickly harnessed to make ATP

o High energy electrons are transferred to NADH (electron  carrier)

o A 6-carbon sugar (glucose) molecule is double  

phosphorylated (costs 2 ATP)

o It is broken down into two 3-carbon sugars converted to  pyruvate

 Each produces 1 NADH

 Each produces 2 ATP

o This happens in the cytoplasm (whether or not oxygen is  present)

∙ Substrate-level Phosphorylation

o An enzyme transfers a phosphate group to ADP to make  ATP

∙ There are alternative pathways to energy acquisition ∙ Characteristics of glycolysis indicate that it is an ancient metabolic  pathway

o Functions in BOTH fermentation and aerobic glucose  catabolism

o Does not require oxygen

o Does not occur in membrane bound organelle

∙ Fermentation

o Occurs when the energy needs of the cell are greater than  can be produced with the amount of oxygen supplied

o Fermentation relies only on glycolysis to produce ATP o Glycolysis does not require oxygen (requires NAD+  NADH transfers electrons to the pyruvic acid and restoring NAD+, creating lactic acid or ethanol)

∙ Lactate Fermentation (produces Lactate)

o Animal cells

o Some bacteria

o Glycolysis  Lysis of glucose, ATP generated, anaerobic o Fermentation  No ATP generated, NAD+ produced

o Without oxygen, pyruvate begins to accept electrons from  NADH, producing NAD+

∙ Alcohol Fermentation (Produces Ethanol)

o Yeast cells

o Plant cells

o Some bacteria

o Glycolysis  Lysis of glucose, ATP generated, anaerobic o Fermentation  No ATP generated, NAD+ produced

o Without oxygen, pyruvate is converted to acetaldehyde,  which accepts electrons from NADH to form NAD+, and  carbon dioxide is released

Lecture 5 (10/27/16) – Energy Pt. 4: Aerobic Glucose Catabolism (and  Oxidative Phosphorylation)

∙ Cellular Respiration

o Glycolysis

 Breaking up of glucose into two pyruvic acid  

molecules

 Present in all living cells

o Krebs (Citric Acid) Cycle

 Completes the breakdown by converting pyruvic acid to carbon dioxide

 Produces

∙ Per pyruvate: 1 NADH, 1 Carbon Dioxide

∙ Per glucose: 2 NADH, 2 Carbon Dioxides

 Takes place in mitochondrial matrix

 Takes acetic acid, breaks apart the carbons, and  

produces 2 carbon dioxide, ATP, NADH, and FAD H 2 

 Completes the oxidation of organic molecules

 Payof

∙ Completes the breakdown of sugar

Per Pyruvate

Per Glucose

ATP

1

2

NADH

3

6

FAD H 2

1

2

CO2 (given of as a byproduct)

2

4

o After glycolysis and the Krebs Cycle, the cell has gained 4  ATP, 10 NADH, and 2 FADH 2 

o Harvest the energy banked in NADH and FADH 2 

 High energy electrons shuttled to Electron Transport  Chain

o Cellular Respiration: ATP is built in the ETC

 Proton gradients and potential energy

∙ The force of the flow of hydrogen ions fuels the

attachment of free-floating phosphate groups  

to ADP to produce ATP

 Takes place in the inner mitochondrial matrix

o Electron Transport Chain (ETC)

 Redox reactions that are used to make ATP

 Releases energy slowly

 NADH and FADH 2 transfer their electrons to the  

ETC

 The energy lost by the “falling” electrons is used to  

pump hydrogen ions across the inner mitochondrial  

membrane

∙ The oxygen receptor pulls the electrons down  

the chain

o Receives 2 electrons (with 2 hydrogens)  

= water!

 Hydrogen is concentrated on one side then flows  

through ATP Synthase creating 34 ATP

 Think: Bowling ball/catapult analogy

o Most ATP production occurs by oxidative phosphorylation o Chemiosmosis

 Hydrogen difuses back across the inner membrane,  through ATP Synthase complexes, driving the  

synthesis of ATP

Unit 4 Review 

Lectures 1 and 2 (11/3/16 and 11/8/16) – Cell Cycle and Mitosis ∙ A cell is the smallest unit of life

∙ One characteristic of life = Reproduction!

∙ Why do cells reproduce (divide)?

o Allows some organisms to reproduce (Mitosis – Asexual  Reproduction)

 Ofspring are from a single parent

 They are genetically identical to each other and to  the original cell

o Allows an organism to maintain and repair tissues

o It’s the basis for growth and development

o Both prokaryotic and eukaryotic cells divide

 Prokaryotic Cells

∙ Binary fission

 Eukaryotic Cells

∙ Cell cycle including…

o Interphase (preparation)

o Karyokinesis (nuclear division)

o Cytokinesis (separation of cytoplasm)

∙ Life-Cycle of a Cell (Eukaryotic)

o Interphase

 ~24-48 hrs

 G1  Growth of cell

∙ Doubling of organelles

∙ Synthesis of proteins, lipids, CHOs

 S  DNA Synthesis/Replication

∙ Copying of each DNA molecule

∙ Full compliment of genetic information for each

daughter cell

 G2  Further preparations for division (growth,  organelle duplication, macromolecule synthesis…) o Mitosis and Cytokinesis

 ~20-60 min

 Mitosis (Karyokinesis)  Nuclear division

 Cytokinesis  Division of cytoplasm

∙ In animal cells – Plasma membrane pinches in,  separating the two daughter nuclei (cleavage  

furrow)

∙ In plant cells – Vesicles filled with cellulose  

accumulate between the daughter nuclei

 Each cell within a tissue may be in a diferent stage  of the cell cycle

 Job of Mitosis: Get one copy of each DNA molecule  into each daughter cell

∙ Problems

1. DNA is very long and thin – Could get  

tangled

2. The cell needs to move chromosomes  

around in the cell and to each pole

3. The nuclear membrane will get in the  

way of moving the chromosomes to the  

poles of the cell

o All problems are overcome during  

prophase (Mitosis stage 1)

∙ Packaging the ~6 ft of DNA in each of your  

cells to move it around without damage during  division

o Compact it into chromosomes

o DNA wraps around proteins called  

histones to form chromosomes  

(condensed)

o Happens at the beginning of Mitosis,  

prophase

1. The cell needs to move chromosomes around  in the cell and to each pole

2. Interphase – Chromatin

∙ Prophase/Prometaphse – Chromatin to  

chromosome conversion

∙ Metaphase – Chromosome alignment at center ∙ Anaphase – Centromere division allows sister  chromatids to separate

∙ Telophase and Cytokinesis – Cytokinesis is  

diferent in plant cells because the rigid cell  

wall does not allow pinching in of cytoplasm

3. The nuclear membrane will get in the way of  

moving the chromosomes to the poles of the  

cell at anaphase

o Fragment the membrane at start of  

mitosis (prophase)

o Re-form the membrane after  

chromosomes have been separated  

(telophase)

∙ Prophase

o Nuclear membrane disassembled

o DNA condensed into chromosomes

o Mitotic spindle is formed

∙ Metaphase

o Sister chromatids line up at the center of  

the cell

∙ Anaphase

o Sister chromatids come apart and  

become daughter chromosomes (done by

mitotic spindle)

∙ Telophase

o Chromosomes begin to uncoil as nuclear  

membrane reassembles

o Cell begins to pinch in two

∙ MITOSIS IS ABOUT CREATING GENETICALLY  

IDENTICAL CELLS

Lectures 2 (cont.), 3, and 4 (11/8/16, 11/10/16, and 11/15/16) – Cell  Cycle Control and Meiosis

∙ Cell cycle control involves both internal and external signals o Regulatory proteins coded for by cell’s DNA

o Growth factors and other signals from the outside

∙ These signals function in each stage of cycle (G1, S, G2, and M)  and together act as “checkpoints” during the cycle

∙ Signal Transduction Pathways

o A signal transduction pathway – Series of molecular  changes

 Convert a signal on the target cell’s surface to a  

specific response within the cell

o Signal transduction pathways are crucial to many cellular  functions

∙ Cell Cycle Checkpoints

o Stop or go decisions

o Default = Stop

o G1 Checkpoint (Pass checkpoint if all these factors are met)  Sufficient nutrients

 Growth factors present (usually protein hormones  that stimulate cell division)

 Cell size is appropriate

 No DNA damage

 Environment favorable

o Quiescence

 G0

 A non-dividing state

 Response to a lack of growth factors

 Mature (fully diferentiated)/adult body cells

 Reversible – Depending on cell type

∙ Mature nerve or heart muscle cells will most  likely remain in G0

∙ Lymphocytes (white blood cells) can be  

stimulated to re-enter the cell cycle

∙ Skin cells are not likely to enter G0 at all

o G2 Checkpoint (Pass checkpoint if all these factors are  meant)

 DNA replication successful

 No DNA damage

 Environment favorable

o Apoptosis

 Cell suicide

∙ Programmed cell death

∙ Response to DNA damage

∙ No necessarily bad, can be used for growth (ex. Human hand)

o Cell Senescence

 Irreversible loss of ability to divide

 Response to DNA damage

 Alternative to apoptosis

 Related to changes associated with aging

o M Checkpoint (Pass checkpoint if all these factors are  present)

 All chromosomes attached to spindle and correctly  aligned

 Kinetochore = Proteins found on either side of the  centromere that attach to the spindle fibers

o Length of cell cycle can vary depending on…  Cell Type

∙ Intestinal cells divide 2x and day

∙ Mature nerve and muscle cells usually do not  

divide

 Conditions

∙ Liver cells divide 1x a year on average

∙ If damaged – Liver cells divide every 1-2 days

∙ Why is understanding this important?

o Important that cells divide only when needed

∙ Several Genes Involved

o Normal Genes

 Proto-Oncogene – Codes for proteins that stimulate  cell division

∙ Growth factors or proteins that respond to  

growth factors

∙ Helps to regulate cell cycle

 Tumor Suppressor Gene – Codes for proteins that  help prevent uncontrolled cell division

∙ Blocks expression of gene(s) needed for cycling

∙ Detects DNA damage (initiates repair or  

apoptosis if not repairable)

∙ Ex. BRCA1 and BRCA2

o Mutated Genes

 Oncogene – Gene that causes tumors

∙ Formed when a proto-oncogene is mutated,  

over-expressed or involved in a chromosomal  

translocation

 Mutated Tumor Suppressor Gene

∙ Results in a non-functional protein product

∙ Ex. Mutated BRCA1 and BRCA2 associated with  

breast and ovarian cancers

∙ Mutations accumulate?  Cancer

∙ Uncontrolled cell division can result in…

o A benign condition if the abnormal cells stay in their  original location

 Psoriasis

 Benign tumor (not cancer)

o A malignant tumor if the abnormal cells spread from their  original location

 Cancer

∙ Continued cell division depends on…

o Cell type

 Frequent Division – Skin, lining of digestive tract

 Infrequent Division – Heart muscle, nerve, liver

o Chemical Factors

 Growth factors (proteins) – Stimulate cell division  Nutrient availability

o Physical Factors

 Density – When a cell population reaches a certain  density, the amount of required growth factors and  nutrients available to each cell becomes insufficient  to allow continued cell growth

 Anchorage – For most animal cells to divide, they  must be attached to the extracellular matrix of a  

tissue

∙ Meiosis

o Ploidy refers to the number of haploid chromosome sets  present in a cell

 Where N = the # of chromosomes in a cell (the  

haploid #)

∙ Humans N = 23

∙ Grasshoppers N = 12

∙ Dogs N = 12

 Polyploidy (more than two sets) is common in plants,  rare in animals

o Diploid Cells (2N)

 All cells except for sperm and egg

 Somatic – Ordinary body cells

 Contain two copies of each distinct type of  

chromosome (two complete sets)

o Sister Chromosomes – Identical

o Homologous Chromosomes – Not identical, but carry same  set of genes

 Look alike

∙ Centromere location

∙ Length

 Same sequence of genes

 Diferent “versions” of genes

 Not to be confused with sister chromatids

∙ Two identical DNA molecules

∙ The product of DNA replication

∙ Joined at a centromere

o Haploid Cells (N)

 Sperm in men and eggs in women (or pollen and  eggs in plants)

 “Gametes”

 Contain one copy of each distinct type of  

chromosome (one complete set)

o Unlike mitosis, meiosis has two consecutive nuclear  divisions, M1 and M2

 Mitosis produces to diploid daughter cells from one  

diploid parent cell

∙ Daughter cells have same amount of DNA as  

parent cell (go through cycle again)

 Meiosis produces four haploid daughter cells from  

one diploid parent cell

∙ Daughter cells have half the amount of DNA as  

parent cell

∙ Gametes don’t divide  Either die or fuse with  

another parent gamete

o Interphase

 A pair of homologous chromosomes in a diploid  

parent cell

 A pair of duplicated homologous chromosomes

o Meiosis 1

 Homologous chromosomes separated in M1

o Meiosis 2

 Sister chromatids are separated in M2

o Germ cells in human males are called primary  

spermatocytes

 In testes

 Diploid

 Divide by meiosis to produce sperm that are haploid

o Germ cells in human females are called primary oocytes  Inside ovary

 Diploid

 Divide by meiosis to produce eggs (ova) that are  

haploid

o Meiosis  Reduction division (because they have half as  many chromosomes)

o Meiosis 1

 Prophase 1 – Crossing over

∙ Homologous chromosomes exchange some  

genetic information

 Anaphase 1  

∙ Sister chromatids migrate in pairs

o Meiosis 2 (no DNA replication before)

 Cell division separates the sister chromatids

 Produces four haploid daughter cells (not identical)

Asexual Reproduction

Sexual Reproduction

All genetic information from one

Genetic information from two

parent

parents

Mitosis = Asexual reproduction

Meiosis = Allows for gamete formation in each parent,

fertilization required

Parent doesn’t exist after

reproduction

Parents still exist after

reproduction

Ofspring identical to parent (mutations rare)

Ofspring unique (mutations rare; DNA mixed)

∙ Sources of genetic variation

o Gene Mutation (rare)

 In the germ line, i.e. in cells that divide by meiosis to  become gametes

o Chromosomal Aberration (rare)

 In the germ line

 Aneuploidy

∙ Too few or too many chromosomes (46±1)

 Change in the structure and/or number of  

chromosomes in a cell

 Can afect many genes

 Random errors during meiosis, usually not passed  

from one generation to the next

 The result of nondisjunction or mistakes during  

crossing over

∙ Nondisjunction  

o Error in chromosome/chromatid  

separation in meiosis 1 or 2

o Results in an incorrect number of  

chromosomes

∙ Trisomy (Autosomal Chromosomes)

o Result of fusion of…

 Gamete (N+1) with 24  

chromosomes (from nondisjunction

event)

 Gamete (N) with 23 chromosomes  

(normal)

o Most autosomal trisomies are lethal

 Embryo/fetus dies in utero  

(miscarriage)

o A few are viable (2N+1)

 Trisomy 21 (Down Syndrome)

 Trisomy 13 (Patau Syndrome)

 Trisomy 18 (Edwards Syndrome)

∙ Trisomy (Sex Chromosomes0

o XXY Males (“Super males”)

o XXX Females (“metafemales”)

o XXY (Klinefelter Syndrome – males)

∙ Monosomy (Sex of autosomal chromosomes) o Result of fusion of…

 Gamete (N-1) with 22  

chromosomes (from nondisjunction

event)

 Gamete with 23 chromosomes  

(normal)

o Turner Syndrome (female)

 XO

o Monosomies are lethal embryo/fetus dies  

in utero (miscarriage)

o Single exception

 Turner Syndrome, individuals are  

2N-1

 Chromosome Breakage

∙ Rearrangements

o In gametes produce genetic disorders

o Cancer in somatic cells

∙ Deletion – Loss of a chromosome segment

∙ Duplication – Repeat of a chromosome  

segment

∙ Inversion – Reversal of a chromosome segment ∙ Translocation – Attachment of a segment to a  nonhomologous chromosome

o Translocation my be reciprocal

o Sexual Reproduction (common)

 Meiosis

∙ Crossing over (prophase 1)

o Exchanging genetic material

 Non-sister chromatids

 1-3 times per tetrad

o Creates more variation in gametes

o Non-sister chromatids, within a tetrad,  

swap DNA

∙ Independent Assortment (metaphase 1)

o Side-by-side orientation of each  

homologous pair of chromosomes is a  

matter of chance

o Every chromosome pair orients  

independently of the others during  

metaphase 1

 Results in diferent combinations of

chromosomes in gametes

 Fertilization

∙ Random fusion of gametes

∙ Egg  1 in 8.4 million possibilities

∙ Sperm  1 in 8.4 million possibilities

∙ 70 trillion possible combinations in one mating  

pair

Lecture 5 (11/17/16) – Inheritance and Mendelian Genetics ∙ Gene – Segment of DNA at a particular location on a particular  chromosome  

o Codes for a specific protein

∙ Allele – A unique version of gene

o Diferent alleles for the same gene difer by at least one  nucleotide

o We use diferent formats (upper and lower case) of the  SAME letter for diferent alleles of the SAME gene

 Ex. H and h

o New alleles arise when mutations occur in existing alleles o Can be dominant or recessive

 Dominant (uppercase) – Always show up in  

phenotype if present

 Recessive (lowercase) – Will be masked/hidden by  dominant allele if both are present  

∙ Only show up in the phenotype if homozygous

∙ Phenotype – Appearance or characteristic that results from the  expression of the alleles in the genotype

∙ Genotype – Combination of alleles present in a diploid  cell/organism

∙ Gamete – Haploid sperm or egg cell

∙ Blending  

o The accepted theory of inheritance in the mid 1800s ∙ Menedlian Genetics

o Mendel worked with pea plants because they reproduce  sexually

 Easy to maintain and breed

 Quick generation time

 Many ofspring

 Easily categorized traits

∙ Green or yellow seeds

∙ Round or wrinkled seeds

∙ Purple or white flowers

∙ Nothing in between

 Developed true breeding lines – ofspring always  carried the same phenotype as the parents

o Monohybrid Cross – Parents difer in only one characteristic (ex. Flower color)

 Involve one gene that controls one phenotypic  characteristic

 Alleles are diferent versions of the same gene o A dominant trait masks the efect of a recessive trait o Dihybrid Cross  

 Consider two diferent genes that control two  diferent phenotypic characteristics

 Mendel wondered if diferent characteristics would  always be inherited together

o Laws of Inheritance

 Law of Gene Segregation

∙ In each (diploid) individual, there are two  

alleles for each trait, that reside on  

homologous chromosomes

∙ These alleles are segregated into separate  

gametes during gamete formation

 Law of Independent Assortment

∙ Pairs of alleles on diferent chromosomes  

assort independently of each other during  

gamete formation

∙ That means that a particular gamete may end  up containing the maternal copy of gene A but  the paternal copy of gene B

o A trait’s mode of inheritance is not always completely  obvious

 Some traits may not show complete dominance  Many traits are influences by the environment  Genes with multiple alleles

∙ Some genes have more than two alleles  

(versions)

∙ Ex. Blood Type

∙ Multiple alleles make it impossible to predict  phenotypic frequencies of ofspring

 Genes that exhibit incomplete dominance

∙ Two alleles for a gene are neither fully  

dominant nor fully recessive to each other

∙ The heterozygote has an intermediate  

phenotype

 Genes that exhibit codominance

∙ Two alleles for a gene are BOTH fully expressed

when present together

 Polygenic Inheritance

∙ A characteristic is determined by two or more  

genes

∙ Results in a gradation of traits

 Epistasis

∙ One gene afects the expression of another  

gene, resulting in unique phenotypes

 Pleiotropy

∙ One gene controls several apparently unrelated

characteristics

 Environmental efects on gene expression and  

inheritance

∙ Phenotype can be afected by the environment  

in which the gene is expressed

 Sex-linked Genes

∙ X-Linked

o Expressed more frequently in males

 Passed from mother to son

o Y-Linked

 Only in males

∙ Passed from father to son

∙ Can be used to trace male  

lineage

∙ A gene is located on a sex chromosome

o Females – have two copies of X

o Males – have one X and one Y

∙ Sex linked recessive alleles

o Located on X chromosome

o Red-green color blindness, muscular  

dystrophy, hemophilia

∙ Males only have one copy – no back up allele

o Genes inherited in simple Mendelian inheritance patterns  Autosomal

 Two alleles – one dominant and one recessive

 F two of more genes are being considered, they are  located on diferent chromosomes

o Testcross – To determine unknown phenotype

Unit 5 Review 

Lectures 1, 2, & 3 (11/29/16-12/8/16) – Ecology and Evolution

∙ Ecology – A sub-discipline of biology defined as the study of the  interactions between organisms and their environments ∙ Levels

o Individual – One living organism

o Population – Collection of individuals of the same species  that live in a defined area at the same time

 Species

∙ Latin = Appearance

∙ A group of individuals that can successfully  

breed with one another (produce viable, fertile  

ofspring)

 Mutations can accumulate in isolated populations ∙ They can no longer successfully breed

∙ Now have two species

 Prezygotic Barriers

∙ Temporal isolation (no mating attempt)

∙ Habitat isolation (no mating attempt)

∙ Behavioral isolation (no mating attempt)

∙ Mechanical isolation (after mating attempt)

∙ Gametic isolation (after mating attempt)

 Postzygotic Barriers

∙ Reduced Hybrid Viability – Feeble ofspring

∙ Reduced Hybrid Fertility (ex. Horse-donkey

mule)

∙ Hybrid Breakdown

o Community – All of the populations (many species) living in a defined area

o Ecosystem (Biome) – Interaction between community  (biotic) and abiotic components of the environment (soil,  air, water, etc.)

o Biosphere – All of the ecosystems on earth

∙ Things that influence ecosystems

o The distribution of solar energy

o Formation of rain shadows

o Modern landscapes influence weather

o Ocean circulation patterns

∙ Evidence for environmental change

o Long Term

 Plate tectonics

∙ Pangaea

o Short Term

 Secondary succession (replacement)

∙ Mt. St. Helens – Soil already present

 Primary succession

∙ Start without soil

∙ Population ecology

o Important because populations evolve

o Study of factors afecting population

 Size – Number of individuals

 Density – Number of individuals per unit of area

 Structure – How many individuals in each age group  Growth Rate – How fast the population is growing ∙ Influenced by

o Exponential growth rate of species

o Population limiting factors

o Carrying capacity

∙ Limiting Factors

o Biotic

 Infectious disease

 Predators

 Pathogens

 Competition

 Parasites

o Abiotic

 Flood, fire, tornado

 Temperature

 Available water

 Pollution

 Climate change

∙ Carrying capacity – The max. population size  

that an environment can sustain

o Depends on available resources

o Each species in a particular environment  

has its own carrying capacity

o Application

 Conservation

∙ Estimate populations of endangered species

∙ What is limiting population growth?

∙ Why they are endangered?

 Sustainable Resources

∙ Maintain a population high enough to restore  

the population after harvesting

 Pest management

 Invasive species

∙ Non-native species introduced to an  

environment that spread uncontrolled

o Rabbits in Australia

o Asian Shore Crab

o Kudzu

∙ Cause extinction of native species

∙ Economic damage

∙ Human Population Growth

o Growth rate peaked in 1962 and has started to decline o Should peak between 7.96 and 10.46 billion

o About half of the people on earth live in extreme poverty ∙ Ecological Footprint

o Resource management tool, can help us answer that  question

o Estimates what is required to support an individual or a  population (nation)

o Need to compare it with what is available (ecological  capacity) to predict whether or not CC is being exceeded o Amount of land and water required to produce all of the  needed resources and absorb all the weight

o Difers by individual and nation

 U.S. requires 9.4 gha/person

 BUT we have only about 5 gha/person

∙ So we import from other countries

o The global human footprint must be less than or equal to  ecological capacity for our population to remain at or below carrying capacity

o Today, the ecological footprint of humanity is 23% larger  than what the planet can regulate

o It takes one year and two months for the earth to  regenerate what we use in one year!

o Goal = sustainability

o A balance between society’s demand on nature and  nature’s capacity to meet the demands

∙ Microevolution

o Lamarck (1809)

 Inheritance of acquired characteristics

 Correct

∙ The environment is a factor

∙ First to propose evolution

 Incorrect

∙ Phenotypic changes that occur in the lifetime  

of one individual are not passed down!

o Darwin

 South America

∙ Organisms diferent than the organisms in  

Europe

∙ More related to each other than to organisms  living in similar climates elsewhere

∙ Fossils found were similar to the organisms  

living there now

 Galapagos

∙ Volcanic islands and relatively new (540 miles) ∙ Some animals are unique

o Resemble animals on the mainland

∙ Finches

o Darwin thought he had collected many  

diferent types of birds, but they were all  

just diferent types of FINCHES

∙ Recognized

o There is variation within populations

o The overproduction of ofspring

o A struggle for existing

o Diferential survival and reproduction

o Natural selection

 The mechanism for evolution

 Organisms with certain inherited  

characteristics are more likely to  

survive and reproduce than are  

individuals with other  

characteristics

o Five primary lines of evidence for evolution

 The fossil record

∙ Documents the process of natural selection

∙ Fossils – Imprints or remains of organisms that  lived in the past

∙ Older fossils are deeper than newer ones

o Reveals he appearance of organisms in a  

historical sequence

∙ Each stratum (layer) contains a specific set of  fossils

∙ Transitional Fossils

o Extinct animals that have a form  

between an earlier and more recent  

animal

o Fossilization is very rare

o Evolution can be rapid if the selection is  

great

 Biogeography

∙ Distribution of species reflects evolutionary  

history

∙ The animals in a particular place (like South  

America or Australia) aren’t found elsewhere

∙ Marsupials in Australia

o Placental mammals can live there

∙ Hippos only in Africa

 Comparative anatomy and embryology

∙ Common anatomy and embryology = common  

origins

∙ The comparison of body structure between  

diferent species

∙ Evolution is a remodeling process

o Works with what is already there

∙ Homologous Structures – Features that have  

diferent functions but are structurally similar,  

due to common ancestry

o Adult organisms

o Embryos

∙ Vestigial Structures – Remnants of features that

served a purpose in an ancestor

 Molecular Biology

∙ Common genetic sequences link all life forms

∙ All life uses the same genetic language

o DNA and proteins

∙ Similar animals have similar genes

o Closer common ancestor

 Laboratory and field experiments

∙ You can watch evolution in progress

∙ Evolution

o Genetics

 Population – Smallest biological unit that can evolve ∙ Individuals of a population are more related to  

each other than other individuals of another  

population

∙ Gene Pool

o Total collection of alleles in the  

population

o Allele – A form of a gene

 Blue and brown eyes

o Microevolution

 Small Scale – Within a population

 A change in the allele frequency in a population over  many generations

 Pocket mice, tortoises, bacteria

 Causes

∙ Natural Selection

∙ Genetic Drift

∙ Gene Flow

∙ Mutations

∙ Non-random Mating

o Macroevolution

 Large Scale – Above the level of population or  species

 Major evolutionary trends, patterns in the history of  life on earth

 Origin of mammals, extinction events

o Biological Evolution

 Change in the genetic make-up of a population over  (generational) time

o Natural Selection

 Unequal reproductive success of individuals in a  population based on the “match” between their gene based phenotype and the prevailing environmental  conditions

 Leads to adaptations – Characteristics that enhance  survival/reproduction

 Selection due to diferential survival and reproduction  NOT RANDOM

 Fitness

∙ How well an individual is suited to its  

environment

∙ Leads to higher reproductive success

 Directional Selection – Individuals with one extreme  from the range of variation in the population have  higher fitness

 Stabilizing Selection – Individuals with intermediate  phenotypes are most fit

 Disruptive Selection – Individuals with extreme  phenotypes have highest fitness

∙ Those with intermediate have lowest benefits o Genetic Variation

 Mutation – Source of variation (new alleles)

∙ Sickle Cell Disease

 Rarely mutations can improve the adaptation of the  individual to its environment

∙ Increased reproductive success

 Chromosomal Duplication – Extra copies can mutate,  can lead to new functions

o Non-Random Mating

 Sexual selection

∙ Selection for traits that increase reproductive  success

∙ Certain traits make an individual more likely to  obtain mates

o Sexual Dimorphism – Diferences  

between males and females

 Size diference, antlers, manes,  

coloring

o Not associated with survival

o These traits are associated with overall  

health

o Contests

 Physical combat

 Ritual

 Artificial Selection

∙ Used by animal breeders and farmers to  

increase favorable traits

o Genetic Drift

 Chance events change allele frequencies

 Most likely to happen in small populations

 Bottleneck Efect – Loss of genetic diversity when a  population is greatly reduced

 Founder Efect – When a small number of individuals  colonize a new habitat, they will have diferent allele  frequencies than the parent population

o Gene Flow

 Gain or loss of alleles when individual move into or  out of a population