AGENDA Hand in Homework 1 l Hand in

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AGENDA Hand in Homework #1 l Hand in in-class work from last class l

AGENDA Hand in Homework #1 l Hand in in-class work from last class l Questions / Concerns? l Lecture Quiz #2 l l REMINDERS: l l l Pre-lab #3 due at beginning of lab period Lab quiz #2 during lab 1 st four Microworlds due at end of lab today

Reminder: Exam next class! l l Weeks 1 -3 Chapters 1 -3, 10. 1

Reminder: Exam next class! l l Weeks 1 -3 Chapters 1 -3, 10. 1 -10. 5

Study Hints l l l Study in several shorter sessions Write down answers to

Study Hints l l l Study in several shorter sessions Write down answers to the Course Objectives for the chapters 1 -3. Answer them IN YOUR OWN WORDS using Vital Vocab (to be posted) Make flash cards for Vital Vocab Review the powerpoints and highlight Vital Vocab and definitions

Important Points from Lecture #2 Atoms are made up of protons, neutrons and electrons.

Important Points from Lecture #2 Atoms are made up of protons, neutrons and electrons. l The number of protons, neutrons and electrons give atoms their properties. l Molecules are made from atoms linked together by bonds l

Lecture 3 Summary l Three bond types: l l l COVALENT - share electrons,

Lecture 3 Summary l Three bond types: l l l COVALENT - share electrons, strong IONIC - transfer electrons, medium HYDROGEN - form between partial charges (polar molecules), weak

Lecture 3 Summary l Properties of water: l l l Polar (hydrophobic sand demo)

Lecture 3 Summary l Properties of water: l l l Polar (hydrophobic sand demo) “Sticky” - surface tension, capillary action Ice floats High specific heat Universal solvent Importance in body

Polar and Nonpolar l l Polar = charged regions “Like dissolves like” l l

Polar and Nonpolar l l Polar = charged regions “Like dissolves like” l l polar wants to be near polar Non-polar wants to be near non-polar

Organic Compounds CARBON l HYDROGEN Is stable with how many bonds? Structural formula l

Organic Compounds CARBON l HYDROGEN Is stable with how many bonds? Structural formula l Is stable with how many bonds? Ball-and-stick model Space-filling model Methane The 4 single bonds of carbon point to the corners of a tetrahedron.

Organic Compounds CARBON l Is stable with how many bonds? Ethane Propane Carbon skeletons

Organic Compounds CARBON l Is stable with how many bonds? Ethane Propane Carbon skeletons vary in length.

Organic Compounds CARBON l Is stable with how many bonds? 1 -Butene 2 -Butene

Organic Compounds CARBON l Is stable with how many bonds? 1 -Butene 2 -Butene Skeletons may have double bonds, which can vary in location.

Organic Compounds CARBON l Is stable with how many bonds? Cyclohexane Benzene Skeletons may

Organic Compounds CARBON l Is stable with how many bonds? Cyclohexane Benzene Skeletons may be arranged in rings.

Why is the structure of carbon important? l Almost infinite variety of possible structures

Why is the structure of carbon important? l Almost infinite variety of possible structures for biological molecules HYDROCARBONS – composed of only hydrogen and carbon 12

Exact structure of molecules is important l l Structure = Function ANIMATION: Campbell Ch

Exact structure of molecules is important l l Structure = Function ANIMATION: Campbell Ch 4 – L_dopa_A

Functional Groups l l l Groups of atoms attached to the carbon skeleton of

Functional Groups l l l Groups of atoms attached to the carbon skeleton of molecules Determine the properties of organic compounds Part of molecule that participates in chemical reactions

Functional Groups l Five main functional groups in biology: l l l Hydroxyl group

Functional Groups l Five main functional groups in biology: l l l Hydroxyl group Carbonyl group Carboxyl group Amino group Phosphate group These groups are all polar and make compounds containing them hydrophilic

WHAT ATOMS MAKE UP FUNCTIONAL GROUPS? WHY IS EACH OF THESE FUNCTIONAL GROUPS POLAR?

WHAT ATOMS MAKE UP FUNCTIONAL GROUPS? WHY IS EACH OF THESE FUNCTIONAL GROUPS POLAR?

Atoms in the Functional Groups l Stable with how many bonds? l l l

Atoms in the Functional Groups l Stable with how many bonds? l l l OXYGEN NITROGEN PHOSPHOROUS (atomic # 15)

Chemical Building Blocks of Living Systems l Organic compounds l l l Contain at

Chemical Building Blocks of Living Systems l Organic compounds l l l Contain at least one CARBON atom Hydrocarbon + functional group Small molecules combine to form large molecules (macromolecules) Organic Macromolecule Small Molecule

Monomers vs Polymers Monomer • Monomer (1 small molecule) usually has 1 functional group

Monomers vs Polymers Monomer • Monomer (1 small molecule) usually has 1 functional group • Polymer has many functional groups: • Can interact with many other things • Can perform a more complicated function

Connecting and Un-connecting l Dehydration synthesis l l Hydrolysis l l l removal of

Connecting and Un-connecting l Dehydration synthesis l l Hydrolysis l l l removal of a water molecule Connects two monomers Forms COVALENT BOND addition of a water molecule Disconnects two monomers http: //science. nhmccd. edu/biol/dehydrat/dehy drat. html

Connecting Unlinked monomer Short polymer Dehydration reaction Longer polymer New COVALENT bond

Connecting Unlinked monomer Short polymer Dehydration reaction Longer polymer New COVALENT bond

Un-connecting Hydrolysis Broken COVALENT bond

Un-connecting Hydrolysis Broken COVALENT bond

Four major classes of organic macromolecules Carbohydrates l Nucleic acids l Proteins l Fatty

Four major classes of organic macromolecules Carbohydrates l Nucleic acids l Proteins l Fatty Acids (lipids) l

Carbohydrates Monomer = monosaccharide l Structure l l carbon, hydrogen, oxygen (C 1 H

Carbohydrates Monomer = monosaccharide l Structure l l carbon, hydrogen, oxygen (C 1 H 2 O 1)n Contains hydroxyl and carbonyl groups

Carbohydrates Structural formula Abbreviated structure Simplified structure

Carbohydrates Structural formula Abbreviated structure Simplified structure

Carbohydrates l Functions l l l Store and release energy (glucose, starch) Structural support

Carbohydrates l Functions l l l Store and release energy (glucose, starch) Structural support (cellulose) Examples = glucose, sucrose, lactose

Carbohydrates l l MONOSACCHARIDE = one monomer of a carbohydrate DISACCHARIDE = two monomers

Carbohydrates l l MONOSACCHARIDE = one monomer of a carbohydrate DISACCHARIDE = two monomers TRISACCHARIDE = three monomers POLYSACCHARIDE = many monomers Connected by WHAT kind of bond? ANIMATION: Campbell Ch 3 - Disaccharides

Polymer = Polysaccharides Cellulose: Structure • Polysaccharides connected to form strands with hydrogen bonds

Polymer = Polysaccharides Cellulose: Structure • Polysaccharides connected to form strands with hydrogen bonds Starch: Energy storage • Glucose connected together to form a long chain

Structure = Function l Sweetness of sugars depends on the structure of the polysaccharide

Structure = Function l Sweetness of sugars depends on the structure of the polysaccharide

Polarity l l Are these sugars polar or non-polar? What do sugars do in

Polarity l l Are these sugars polar or non-polar? What do sugars do in water?

Lipids l VARIOUS TYPES l l Triglycerides Phospholipids Waxes Steroids

Lipids l VARIOUS TYPES l l Triglycerides Phospholipids Waxes Steroids

Lipids - Triglycerides l l Monomer = 3 fatty acids + glycerol Structure: l

Lipids - Triglycerides l l Monomer = 3 fatty acids + glycerol Structure: l l Fatty Acids: Long hydrocarbon chains Glycerol: hydrocarbons with hydroxyl (OH) groups

Lipids - Triglycerides l Function: Stores energy long-term

Lipids - Triglycerides l Function: Stores energy long-term

Polarity l l Is a lipid polar or non -polar? Does fat dissolve in

Polarity l l Is a lipid polar or non -polar? Does fat dissolve in water?

Saturated vs Unsaturated l l l Maximum number of hydrogensattached to carbons No double

Saturated vs Unsaturated l l l Maximum number of hydrogensattached to carbons No double bonds between carbons More flexible Straight Packs tightly More solid at room temperature

Saturated vs Unsaturated l l l Some carbons connected via double bonds Fewer than

Saturated vs Unsaturated l l l Some carbons connected via double bonds Fewer than maximum number of hydrogens Less flexible (double bonds are stiffer) Kinked Does not pack tightly Less solid at room temperature

Saturated vs Unsaturated ANIMATION: Campbell Ch 3 - Fats

Saturated vs Unsaturated ANIMATION: Campbell Ch 3 - Fats

Trans fats l Unsaturated fat made by partially hydrogenating an oil

Trans fats l Unsaturated fat made by partially hydrogenating an oil

Trans fats l l Which will pack more tightly, a “cis” unsaturated fat or

Trans fats l l Which will pack more tightly, a “cis” unsaturated fat or a “trans” unsaturated fat? Which will be more solid at room temp? “cis” unsaturated fat “trans” unsaturated fat

Trans Fats - why are they bad? l Enzyme in the body that digests

Trans Fats - why are they bad? l Enzyme in the body that digests fats is less effective on trans unsaturated fats

Lipids - Phospholipids l Structure – Glycerol connected to TWO fatty acids and a

Lipids - Phospholipids l Structure – Glycerol connected to TWO fatty acids and a phosphate group POLAR OR NONPOLAR?

Phospholipid structure

Phospholipid structure

Lipids - Phospholipids l Lipid bilayer: Function: Makes up membranes in cells (phosphoplipids)

Lipids - Phospholipids l Lipid bilayer: Function: Makes up membranes in cells (phosphoplipids)

Membrane structure

Membrane structure

Lipids - Waxes – – STRUCTURE: Consist of a single fatty acid linked to

Lipids - Waxes – – STRUCTURE: Consist of a single fatty acid linked to an alcohol FUNCTION: Form waterproof coatings

Lipids - Steroids l l l STRUCTURE: Have backbones bent into rings FUNCTION: Are

Lipids - Steroids l l l STRUCTURE: Have backbones bent into rings FUNCTION: Are often hormones or the basis of hormones EXAMPLE: Cholesterol

Lipids - Steroids l Naturally found in living things l l l Testosterone Estrogen

Lipids - Steroids l Naturally found in living things l l l Testosterone Estrogen Progesterone Corticosteroids (regulate metabolism) Found in other organisms - Insects have them

Lipids - Steroids l Anabolic Steroids – natural and synthetic versions of testosterone l

Lipids - Steroids l Anabolic Steroids – natural and synthetic versions of testosterone l Build up bone and muscle mass

Lipids - Steroids l Anabolic Steroids – natural and synthetic versions of testosterone l

Lipids - Steroids l Anabolic Steroids – natural and synthetic versions of testosterone l l Build up bone and muscle mass Can cause serious health problems

Proteins l l l Monomer = amino acids There are 20 different amino acids

Proteins l l l Monomer = amino acids There are 20 different amino acids Protein structure is determined by order of amino acids Leucine (Leu) Hydrophobic Serine (Ser) Aspartic acid (Asp) Hydrophilic

Amino Acid Structure l Structure: l Central C

Amino Acid Structure l Structure: l Central C

Amino Acid Structure l Structure: l l Central C Amino group

Amino Acid Structure l Structure: l l Central C Amino group

Amino Acid Structure l Structure: l l l Central C Amino group Carboxyl Group

Amino Acid Structure l Structure: l l l Central C Amino group Carboxyl Group

Amino Acid Structure l Structure: l l Central C Amino group Carboxyl Group R

Amino Acid Structure l Structure: l l Central C Amino group Carboxyl Group R group

Amino Acid Structure l l Structure of R group determines the properties of each

Amino Acid Structure l l Structure of R group determines the properties of each amino acid Hydrophobic or hydrophilic Charged or uncharged Small or large

Amino Acid Structure l Hydrophilic or Hydrophobic? l Polar or Non -polar?

Amino Acid Structure l Hydrophilic or Hydrophobic? l Polar or Non -polar?

Amino Acid Structure l Hydrophilic or Hydrophobic? l Polar or Non -polar?

Amino Acid Structure l Hydrophilic or Hydrophobic? l Polar or Non -polar?

Amino Acid Structure l Hydrophilic or Hydrophobic?

Amino Acid Structure l Hydrophilic or Hydrophobic?

Amino Acid Structure l Hydrophilic or Hydrophobic?

Amino Acid Structure l Hydrophilic or Hydrophobic?

Protein Structure l How are amino acids connected together? DEHYDRATION SYNTHESIS PEPTIDE BOND =

Protein Structure l How are amino acids connected together? DEHYDRATION SYNTHESIS PEPTIDE BOND = What type of bond?

Protein Structure l l Very complicated Described as four levels: l l Primary Secondary

Protein Structure l l Very complicated Described as four levels: l l Primary Secondary Tertiary Quaternary

Protein Primary Structure l l The unique sequence of amino acids forming the polypeptide

Protein Primary Structure l l The unique sequence of amino acids forming the polypeptide Amino acids connected by peptide (covalent) bonds ANIMATION: Campbell Ch 3 – Primary Structure

Protein Secondary Structure l Levels of Protein Structure The coiling or folding of the

Protein Secondary Structure l Levels of Protein Structure The coiling or folding of the chain, stabilized by hydrogen bonding between O and H of backbone l l Alpha helix Beta pleated sheet Amino acids Hydrogen bond Alpha helix Pleated sheet

Alpha Helixes

Alpha Helixes

Beta Pleated Sheets ANIMATION: Campbell Ch 3 – Secondary Structure

Beta Pleated Sheets ANIMATION: Campbell Ch 3 – Secondary Structure

Protein Tertiary Structure Levels of Protein Structure l The overall threedimensional (globular) shape of

Protein Tertiary Structure Levels of Protein Structure l The overall threedimensional (globular) shape of the polypeptide Amino acids Hydrogen bond Alpha helix Polypeptide (single subunit of transthyretin) Pleated sheet

Protein Tertiary Structure l Determined by: l l Hydrogen Bonds Ionic Bonds Hydrophobic /

Protein Tertiary Structure l Determined by: l l Hydrogen Bonds Ionic Bonds Hydrophobic / hydrophilic interactions Disulfide bonds – covalent bonds between S atoms ANIMATION: Campbell Ch 3 – Tertiary Structure

Protein Quaternary Structure Levels of Protein Structure l l The association of two or

Protein Quaternary Structure Levels of Protein Structure l l The association of two or more polypeptide chains Not found in all proteins ANIMATION: Campbell Ch 3 – Quaternary Structure Amino acids Hydrogen bond Alpha helix Polypeptide (single subunit of transthyretin) Transthyretin, with four identical polypeptide subunits Pleated sheet

Proteins: 3 D Structure

Proteins: 3 D Structure

Protein Structures Insulin Snake Venom

Protein Structures Insulin Snake Venom

Protein Structures DNA Binding protein Bacterial protein of undetermined function

Protein Structures DNA Binding protein Bacterial protein of undetermined function

R groups and interactions determine structure l “World’s largest protein”

R groups and interactions determine structure l “World’s largest protein”

Specific Shape Determines Function 1. ENZYMES: perform chemical reactions

Specific Shape Determines Function 1. ENZYMES: perform chemical reactions

Metabolic Pathways

Metabolic Pathways

Specific Shape Determines Function 2. Structural: hair, cartilage, muscle, cell cytoskeleton TUBULIN

Specific Shape Determines Function 2. Structural: hair, cartilage, muscle, cell cytoskeleton TUBULIN

Specific Shape Determines Function 3. Contractile: producers of movement in muscle and other cells

Specific Shape Determines Function 3. Contractile: producers of movement in muscle and other cells ACTIN / MYOSIN in muscles

Specific Shape Determines Function 4. Immune system: marker proteins identify self vs other; antibodies

Specific Shape Determines Function 4. Immune system: marker proteins identify self vs other; antibodies ANTIBODY

Specific Shape Determines Function 5. Transport: carry other molecules CHANNEL PROTEIN

Specific Shape Determines Function 5. Transport: carry other molecules CHANNEL PROTEIN

Specific Shape Determines Function 6. Signaling: hormones, membrane proteins

Specific Shape Determines Function 6. Signaling: hormones, membrane proteins

Specific Shape Determines Function 7. Gene Regulatory: control whether a gene is active or

Specific Shape Determines Function 7. Gene Regulatory: control whether a gene is active or not

Proteins: 3 D Structure l DENATURATION: chemical or physical changes that can cause proteins

Proteins: 3 D Structure l DENATURATION: chemical or physical changes that can cause proteins to lose their shape and thus their specific function ANIMATION: Cain Ch 4 – Ch 04 a 06

Nucleic Acids Monomer = nucleotides l Structure = three parts: sugar, phosphate, and nitrogen-containing

Nucleic Acids Monomer = nucleotides l Structure = three parts: sugar, phosphate, and nitrogen-containing base l

Functions l l Nucleotide monomers can be used as “energy currency” Examples = ATP

Functions l l Nucleotide monomers can be used as “energy currency” Examples = ATP / ADP

Functions l l Stores genetic information (traits and inheritance) Examples= DNA, RNA

Functions l l Stores genetic information (traits and inheritance) Examples= DNA, RNA

Nucleotide Structure l Nucleotides – the building blocks of nucleic acids l Made of:

Nucleotide Structure l Nucleotides – the building blocks of nucleic acids l Made of: Phosphate Sugar Nitrogenous Base 1. 2. 3.

Sugar-Phosphate Backbone l l Nucleotides connected together with what type of bond? Alternating sugars

Sugar-Phosphate Backbone l l Nucleotides connected together with what type of bond? Alternating sugars and phosphates

Nitrogenous Bases l Four bases: l l Adenine (A) Thymine (T) Cytosine (C) Guanine

Nitrogenous Bases l Four bases: l l Adenine (A) Thymine (T) Cytosine (C) Guanine (G)

Base Pairing l Bases form hydrogen bonds with each other l l A with

Base Pairing l Bases form hydrogen bonds with each other l l A with T C with G PURINE with? PYRIMIDINE with?

DNA Structure l DNA nucleotides are linked together by covalent bonds into a single

DNA Structure l DNA nucleotides are linked together by covalent bonds into a single strand l l phosphates are bonded to sugars are bonded to N Bases

DNA Structure l DNA bases are bonded together with hydrogen bonds to form a

DNA Structure l DNA bases are bonded together with hydrogen bonds to form a double stranded molecule

3 -D DNA Structure l Based on the angle of the bonds (remember what

3 -D DNA Structure l Based on the angle of the bonds (remember what a C with 4 bonds looks like), DNA forms a DOUBLE HELIX

DNA Structure l l l Hydrogen Bonds occur between Nucleotide Bases the bonds between

DNA Structure l l l Hydrogen Bonds occur between Nucleotide Bases the bonds between which 2 bases are stronger? thousands of bases, thousands of bonds, thousands of big twists

Polarity l Is DNA polar or nonpolar?

Polarity l Is DNA polar or nonpolar?

Determining that DNA is the Genetic Material l l GRIFFITH: 1928 "Transforming factor”

Determining that DNA is the Genetic Material l l GRIFFITH: 1928 "Transforming factor”

Determining that DNA is the Genetic Material l l HERSHEY – CHASE: 1952 Determined

Determining that DNA is the Genetic Material l l HERSHEY – CHASE: 1952 Determined that the heredity material was DNA not protein Studied the bacteriophage T 2 Head DNA Tail fiber 300, 000 l

Determining that DNA is the Genetic Material Phage Bacterium Radioactive protein DNA Batch 1

Determining that DNA is the Genetic Material Phage Bacterium Radioactive protein DNA Batch 1 Radioactive protein Mix radioactively labeled phages with bacteria. The phages infect the bacterial cells. Batch 2 Radioactive DNA Empty protein shell Phage DNA Radioactivity in liquid Centrifuge Agitate in a blender to separate phages outside the bacteria from the cells and their contents. Pellet Centrifuge the mixture Measure the so bacteria form a radioactivity in pellet at the bottom of the pellet and the test tube. the liquid. Radioactive DNA Centrifuge Pellet Radioactivity in pellet

Determining the Structure of DNA l l CHARGOFF: 1949 Different species have different amounts

Determining the Structure of DNA l l CHARGOFF: 1949 Different species have different amounts of A, T, C, G A always equals T C always equals G

Determining the Structure of DNA l l FRANKLIN and WILKINS: 1950’s X-ray crystalographic determination

Determining the Structure of DNA l l FRANKLIN and WILKINS: 1950’s X-ray crystalographic determination that DNA is a double helix

Determining the Structure of DNA l l WATSON and CRICK: 1953 Double helix structure

Determining the Structure of DNA l l WATSON and CRICK: 1953 Double helix structure of DNA

Determining the Structure of DNA

Determining the Structure of DNA

Determining the Structure of DNA l http: //www. pbs. org/wgbh/nova/photo 51/

Determining the Structure of DNA l http: //www. pbs. org/wgbh/nova/photo 51/