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LSU / Anatomy and Physiology / BIOL 1201 / What are biological molecules?

What are biological molecules?

What are biological molecules?

Description

School: Louisiana State University
Department: Anatomy and Physiology
Course: Biology for Science Majors I
Professor: Joseph siebenaller
Term: Spring 2017
Tags: JosephSiebenaller and BIOL1201
Cost: 25
Name: BIOL 1201 Week 3 Notes
Description: Lectures 3, 4, and 5 Quiz 2 and 3 Reviews Textbook/Lecture Notes Email me at ktrah18@lsu.edu for further questions!
Uploaded: 01/30/2017
16 Pages 76 Views 3 Unlocks
Reviews


BIOL 1201 Kristy Trahan


What are biological molecules?



Lecture 3

∙ Acids produce H+ ions

∙ Bases produce hydroxide (OH) ions  

∙ Salts produce neither  

∙ pH Scale  

o defined as the -log of the proton concentration  

o log base 10  

o the difference between pH 3 and pH 4 is a 10-fold difference in the concentration  of H+

o pH 3 and pH 5- a 100-fold difference  

o pH of 7 is neutral  

o below 7- acidic  


Why make large biological molecules from simple monomers?



o above 7- basic

o increasing the proton concentration???? decreasing the pH  

o the pH decreases by 1 unit, the proton concentration increases by 10 fold  ∙ pOH  

o defined as the -log of the hydroxide concentration  

▪ pH + pOH = 14  

∙ Neutrality  

o pH = pOH  

o Sum of pH and pOH is always 14

o pH 7, decrease proton concentration by a factor of 100, new pH is 9

∙ Buffers  

o Substances that maintain a constant pH  

∙ Solubility  


What is the endoplasmic reticulum?



o Solute- NaCl Don't forget about the age old question of What is the key feature of dual federalism?

o Solvent- water

BIOL 1201 Kristy Trahan

o The similarity of the solute and solvent determines the solubility of a molecule  o like dissolves like  

o Like in terms of polarity  

▪ Polar solutes dissolve in polar solvents  

▪ Non-polar solutes dissolve in non-polar solvents  

o Hydrophilic (water-loving) substances interact with water molecules  ∙ Biological Molecules  

o All except for water are built with carbon skeletons  

o Major Groups:  

▪ Water  

▪ Carbohydrates  

▪ Lipids  

▪ Proteins  

▪ Nucleic Acids  

o Functional Groups (know whether each group is polar/nonpolar)- charts attached  at end

▪ Hydroxyl- alcohols  

▪ Carbonyl- aldehydes (terminal carbon) and ketones (if within carbon  chain)

▪ Carboxyl- acid group  

▪ Amino- amines  

∙ Amino acids have one from the amino and one from the carboxyl  

▪ Sulfhydal- thiols  If you want to learn more check out What is a sample statistic?

▪ Phosphate- organic phosphates  

▪ Methyl- methylated compounds  

∙ Carbon Skeleton  

o Form the backbone of organic molecules  

o Covalently linked carbon molecules- has 4 valence electrons  

∙ Biological Molecules  

o Large molecules constructed from smaller molecules  We also discuss several other topics like What are the 3 classes of animal domestication that made my archaeozoologist?

o Polymers constructed from monomers

▪ Mers = units Don't forget about the age old question of What are the core financial statements?

▪ Mono = single  

▪ Poly = many  

o Synthesis of polymers- covalent bond formation between monomer units  ▪ Condensation (dehydration) synthesis  

∙ Proceeds with the removal of a water molecule  

o Breakdown of polymers- breaking the covalent linkage between monomer units  ▪ Hydrolysis reaction  

∙ Breaking the covalent bond linking the units of the polymer by the  addition of a water molecule  

o Why make large biological molecules from simple monomers?

▪ Flexible system

∙ Array of complex molecules from a few simpler molecules  

▪ Fewer enzymes to make biological molecules than if “starting from  scratch”

BIOL 1201 Kristy Trahan

∙ Need fewer catalysts  

∙ Carbohydrates  

o (CH2O) n We also discuss several other topics like What is tax abatements?

▪ General formula  

▪ n = 6, C6H12O6

▪ Starch in plants is a polymer of glucose  

▪ Glycogen in animals is a polymer of glucose

o Energy roles  Don't forget about the age old question of How will you define pure substance?

▪ 1. Metabolic Fuel (cellular metabolism)

▪ 2. Storage form (starch in plants and glycogen in animals)

▪ 3. Structural Roles

∙ Cellulose- plants  

∙ Chitin- animals

BIOL 1201 Kristy Trahan

BIOL 1201 Kristy Trahan

Lecture 4  

∙ Lipids

o Water-insoluble organic biomolecules  

▪ Because they are made up of nonpolar groups (like dissolves like and  water is polar)

o Structural components of cell membrane

o Storage and transport forms of fuel (store energy)

▪ Adipose tissue  

o Protective surface coating like in leaves  

o Cell component in cell recognition  

o Hormone- some hormones are lipids (all steroid hormones- testosterone, estrogen,  etc.)

o Different types of fat- saturated (butter) and unsaturated (canola oil)  

o Saturated- saturated with H, no double bonds between adjacent carbons  ▪ Bad because they raise the LDL cholesterol (the bad cholesterol)  

o Unsaturated- double bonds, lower melting/freezing point  

▪ The “good fat”

o Melting points differ:  

▪ Saturated fats are solids at higher temperatures than unsaturated fats  ▪ Acyl chains of unsaturated fats are kinky and therefore require a lower  temperature to become solid

o Compared to tropical fish, arctic fish oils have more unsaturated fatty acids ▪ Need a higher degree of fluidity  

o Polymers:  

▪ Triglycerides

∙ Made up of glycerol and two fatty acids

▪ Phospholipids

o Cholesterol (a steroid) has a series of ring structures  

o Fats (lipids) have more than twice the energy available per gram than  carbohydrates

▪ 1 nutritional calorie is 1 kcal  

o The more saturated, the more hydrogens (higher degree of saturation) ALL LIPIDS DO NOT DISSOLVE WELL IN WATER

∙ Comparison of lipids and Carbohydrates  

o Twice as much energy from fat  

o Stored without water

BIOL 1201 Kristy Trahan

o 1 g of glycogen is stored with 2 to 5 g of water  

o Disadvantage- not as rapidly mobilized as carbohydrates  

o Lipids metabolized in the mitochondria in the presence of O2

▪ Not ideal for short and quick bursts of energy

∙ Examples in the use of lipids:

o Camels- hump of the camel is filled with LIPIDS

▪ Up to 20% of body mass is fat when food is plentiful  

▪ Subcutaneous fat would cause thermoregulatory problems (get too hot) ∙ So, all the mass is accumulated as a hump on the back  

o Bears- hibernation 100 days without eating  

o Human-

▪ Normal weight- 40-day reserve of energy  

▪ Moderately obese- up to a year (why it’s so hard to lose it, so much energy  to burn)  

∙ Nucleic Acids  

o Nitrogenous heterocyclic bases  

o Pentose sugar  

o Phosphoric acids  

o Examples:  

▪ Coenzymes- NAD, NADP, FAD

▪ Genetic material- DNA, RNA  

▪ ATP- adenosine triphosphate  

∙ Proteins

o Excellent example of a polymer  

o Made of amino acids  

▪ 20 naturally occurring amino acids are L-isomers  

▪ Proteins vary in the number and sequence of the different kinds of amino  acids  

o Proteins are used in a variety of functions  

▪ Enzymes (proteins) work as catalysts

▪ Transport proteins move ions  

▪ Hormonal proteins help regulate things like insulin  

▪ Muscles are made up of primarily two proteins  

o Amino acids: the monomers, 20 different kinds  

▪ Central carbon that other groups are linked to  

▪ Amino group (covalently linked to carbon)

▪ Carboxyl group- characteristic of an acid

▪ Hydrogen  

▪ R group (20 different kinds of groups)  

∙ Makes the amino acid the particular amino acid it is  

o Different types of R groups  

▪ Some are polar (hydrophilic)  

▪ Some are non-polar (hydrophobic)

▪ Charged (+ or -)

o Nonpolar  

▪ No partial charges on the R groups

BIOL 1201 Kristy Trahan

▪ Hydrophobic (water is polar and like dissolves like)  

o 5 amino acids could potentially have a charge  

▪ Acidic (negatively charged)- aspartic and glutamic acid  

▪ Basic (positively charged)- lysine, histidine, arginine  

o Polar or electrically charged R groups  

▪ Interact with the partial + and – charges of water  

▪ Hydrophilic

BIOL 1201 Kristy Trahan

o The characteristics of the individual amino acids determine the protein they build o Covalent bond between amino acids is the peptide bond and is formed through  dehydration synthesis  

o The peptide bond- R group is not involved  

o The amino and carboxyl groups (common to all amino acids) are involved  o Proteins differ in the sequence and the length of the polypeptide chain o Primary structure:  

▪ Sequence of amino acids in a protein or peptide

▪ Determines what the protein will look like and how it functions  ▪ A single amino acid substitution in a protein chain causes sickle-cell  disease

∙ Causes the cell to be misshapen  

o Secondary structure: results from stabilization of hydrogen bonding involving  the peptide backbone (don’t involve the R group)

▪ Alpha helix

∙ Found in fibrous proteins (hair)  

▪ Beta pleated sheath  

∙ Found in core of many globules (silk)  

o Tertiary structure:  

▪ Folding into a 3 dimensional structure (globule)  

▪ Folding is due to the properties and interactions of the R groups (amino  acid side chains)  

▪ R groups  

∙ Hydrophobic and hydrophilic properties  

▪ Hydrophobic R groups  

∙ Buried in the interior of the protein  

▪ Hydrophilic R groups

BIOL 1201 Kristy Trahan

∙ Interact with one another on the surface  

▪ Stabilizing tertiary structures  

∙ Weak: hydrogen bonds, ionic interactions, hydrophobic and van  der Waals interactions  

∙ Strong: disulfide bridge (covalent bond)

∙ Disulfide bridges  

o SH groups of two cysteines form covalent bond  

▪ Stabilizes tertiary structure  

o Quaternary Structures

▪ Multiple polypeptide chains (subunits) fit together to form a larger protein  ▪ Collagen- made of multiple subunits of proteins  

▪ Hemoglobin- made of alpha and beta subunits  

o Sickle-cell hemoglobin mutation alters the primary, tertiary, and quaternary levels  of protein structure  

o Native and denatured Proteins  

▪ Native: properly fold and functional

▪ Denatured: not properly folded and nonfunctional

BIOL 1201 Kristy Trahan

Lecture 5

∙ Roles of Weak Bonds in Biological Systems  

o Easily made and broken at physiological temperatures  

o Provide specificity (make an enzyme for a specific substrate)

o If “weak” interactions were “strong”, would crystallize the contents of the cell o Attract and attach substrates and enzymes  

∙ Bonds responsible for primary structure- peptide and covalent

∙ Bonds responsible for secondary structure- hydrogen  

∙ H-bonding in secondary structure- atoms in peptide backbone

∙ Another look at SUPERCOOLING  

o The freezing problems confronting fish- putting a fish in supercooled water and  then introducing an ice cube will kill the fish  

o Fish in the ice- they accomplish this by using a sort of “anti-freeze”  

▪ Antifreeze peptides

∙ Small proteins (peptides) that depress the freezing point of  

solutions  

∙ Non-colligative freezing point depression  

∙ HAVE A HELICAL SECONDARY STRUCTURE  

▪ Colligative property  

∙ Depends on the number of particles (molecules) and not on the  

nature of the molecules

∙ Colligative concentration equivalent to 1 M glucose: 1 M sucrose  

or 0.5 M NaCl (dissociates)

∙ “Hysteresis proteins”- affect freezing point but not melting point  

o Decrease the freezing point  

o Does not affect the melting point  

o Freeze at -2°C, melt at 0°C

o Antifreeze molecules do to inhibit melting, only freezing

BIOL 1201 Kristy Trahan

o POLAR R GROUPS OF THE ANTIRFREEZE H-BONDS BONDS TO ICE  ▪ Antifreeze peptides H-bond with ice

∙ Requires more energy to add a water molecule to the curved  

surface of the ice crystal  

∙ Temperature must be lowered to add the molecule

∙ Decreased freezing point  

∙ Proteins gone bad- Mad Cow Disease  

o Transmissible Spongiform Encephalopathies  

▪ Scrapie- sheep  

∙ Only New Zealand and Australia are free of scrapie  

▪ CWD (chronic wasting disease)- muledeer and elk  

▪ BSE- cows  

▪ Human Spongiform Encephalopathies

∙ Genetic basis  

∙ Spread through medical procedures (using same equipment even  

after sterilization)  

∙ CJD (Creutzfeld-Jacob Disease)- typically onset at age sixty or  

later  

∙ Kuru- laughing disease in Papua New Guinea  

∙ vCJD- early variant of CJD (shows in much younger individuals

o eating meat from infected cows  

∙ vCJD in US  

o 3 cases  

o All epidemiologically linked to cattle (not US cattle)

∙ Chronology in the UK

o 1970’s- spread from sheep to cattle  

▪ Sheep meat and bones added to cattle feed  

o 1982- Prusiner discovers prions  

o 1986- Mad cow disease was identified  

o In 10, 165,000 cattle were affected  

o November 1989- British government banned animal additives in feed  ∙ Banned Feed  

o Sold in Europe and Asia  

o Sold for “use” in poultry  

∙ Unusual Diseases  

o Not caused by “germs”  

▪ Not a virus, bacteria, or fungus

▪ Not caused by organism with genetic material  

∙ Prions  

o Proteinaceous Infectious Particles  

o Mad cow diseases have a different secondary structure

∙ BSE in US  

o 4 cases of infected cows

o All these cows were imported

BIOL 1201 Kristy Trahan

∙ Normal Cellular form of the prion protein  

o Alpha helix  

▪ Present in all mammals

∙ Disease Form  

o Beta pleated sheet structure  

∙ Have the same amino acid sequence!!!

o Different secondary structures  

o Disease form converts the normal cellular form to the beta pleated sheet protein  

Cells

∙ Problems  

o Increased size

▪ Relatively less surface area for a unit of volume  

o Problem moving materials into and out of the cell  

o Problem controlling and coordinating metabolic processes  

∙ Overview- Cell Structure

o Keeping cell distinct from the environment  

o Organizing and coordinating metabolic processes  

∙ Two Categories Based on Structural Features

o Prokaryotes- lack a nucleus

▪ “before” the nucleus  

▪ No internal membrane-bound organelles  

▪ Prokaryotes (Bacteria and blue-green algae)

∙ 1. Cell wall of carbohydrates and peptides  

∙ 2. Ribosomes differ from eukaryotes in size and antibiotic  

sensitivity  

∙ 3. No nucleus or linear (histone-complexed) chromosomes  

∙ 4. No internal membranes  

o Eukaryotes- true nucleus  

▪ Have organelles bound by membranes  

▪ Eukaryotes (animals, plants, fungi, yeasts)

▪ Larger cell size  

∙ Need increased internal membranes  

∙ Problem of intake of nutrients

BIOL 1201 Kristy Trahan

∙ Problem of coordination and control of metabolism  

∙ More opportunities as a heterotroph (feeding on other organisms)  

o More potential food items  

∙ Chapter 6 Concepts/Review

o Biologists use microscopes ant the tools of biochemistry to study cells o Eukaryotic cells have internal membranes that compartmentalize their functions  o The eukaryotic cell’s genetic instructions are housed in the nucleus and carried  out by the ribosomes  

o The endomembrane system regulates protein traffic and performs metabolic  functions in the cell

o Mitochondria and chloroplasts change energy from one form to another  o The cytoskeleton is a network of fibers that organizes structures and activities in  the cell  

o Extracellular components and connections between cells help coordinate cellular  activities  

∙ Plasma Membrane  

o Present in prokaryotes and eukaryotes  

o Semi-fluid mosaic  

o Phospholipid

▪ Consists of a hydrophobic tail and a hydrophilic head group  

o Proteins  

o Semi-permeable barrier between contents of cell and environment  

▪ Selective of what crosses into the cell  

∙ Nucleus  

o present in eukaryotes  

o enclosed by nuclear envelope- a double membrane with pores  

o Contains linear chromosomes  

o Contains the nucleolus- region of nucleus where ribosomal subunits are  assembled  

o Genetic Material in eukaryotes

▪ Linear strands of DNA complexed with proteins (histones)  

o Genetic Material in prokaryotes  

▪ Circular strands of DNA

▪ “naked”- not complexed with histone proteins  

∙ Nucleolus  

o Region of the nucleus where ribosomal subunits are assembled  

o Also involved in the cell’s response to stress  

∙ Ribosomes  

o Present in prokaryotes and eukaryotes  

o Differ in size (prokaryotes have smaller ribosomes) and antibiotic susceptibility  o Two subunits of different size  

o Made of rRNA and protein  

o Site of protein synthesis  

o Occur free in cytoplasm or in association with rough ER

∙ Endomembrane System  

o Think of it like a process, not a structure

BIOL 1201 Kristy Trahan

o A dynamic pathway  

▪ We are identifying components of it  

∙ Endoplasmic Reticulum  

o Eukaryotes only  

o Internal membrane system  

o Mechanism of sorting material belonging in the cytoplasm from that which  doesn’t  

∙ Smooth Endoplasmic Reticulum  

o Lipid synthesis  

o Detoxification of water insoluble compounds  

o Sarcoplasmic reticulum- calcium store in muscle  

∙ Rough Endoplasmic Reticulum  

o Ribosomes on the cytosolic side  

o Prominent in cells synthesizing products destined for transport to other cells

Quiz 2 Review  

∙ Cells are surrounded by water, and cells themselves consist of about 70% to 95% water.  As a result, the temperature of living things tends to change relatively slowly, dissolved  substances can be easily transported within a cell or between cells in multicellular  organisms, a variety of nutrient molecules are readily available as dissolved solutes, and  waste products produced by cell metabolism can be easily removed.  

∙ The partial changes on a water molecule occur because of the unequal sharing of  electrons between the hydrogen and the oxygen atoms of a water molecule. ∙ The ability of water molecules to form hydrogen bonds with other molecules and water’s  ability to dissolve substances that have charges or partial charges are both caused by  water’s partial charges.  

∙ The amount of heat required to change the temperature of 1 g of any substance by 1 °C is  defined as the specific heat of that substance.  

∙ Sweating has a cooling effect because of water’s high heat of vaporization.  ∙ Water molecules have a higher boiling point than molecules of similar size, such as  ammonia and methane.  

∙ Because water molecules of water are farther apart in ice than liquid water, ice floats.  ∙ Water is a very versatile solvent because water molecules are polar.  

∙ Hydrophilic substances, but not hydrophobic substances, have charges and partial charges  to which water molecules can adhere.  

∙ A glass of grapefruit juice, at pH 3, contains ten times as much H+ as a glass of tomato  juice, at pH 4.

BIOL 1201 Kristy Trahan

Quiz 3 Review

∙ Hydroxyl is to alcohol as carbonyl is to aldehyde.  

∙ Which hydrocarbon has a double bond in its carbon skeleton? C2H4 

∙ Which functional group is not present in the molecule shown in this figure? Methyl  (amino acid model in figure)  

∙ Carbohydrates include monosaccharides, polysaccharides, starch, and disaccharides.  ∙ Nucleotides are to nucleic acids as amino acids are to proteins.  

∙ Which of the following statements about unsaturated fats is true? They have double  bonds in the carbon chains of their fatty acids.

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