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UT / Biology / BIOL 160 / What is Kinetic energy (thermal energy)?

What is Kinetic energy (thermal energy)?

What is Kinetic energy (thermal energy)?

Description

School: University of Tennessee - Knoxville
Department: Biology
Course: Cellular and Molecular Biology
Professor: John koontz
Term: Fall 2015
Tags:
Cost: 50
Name: BioExam1StudyGuide.pdf
Description: Comprehensive study guide of all material that could be covered by exam 1. *Water, carbon, bonding, nucleic acids, proteins, carbohydrates, and lipids*
Uploaded: 09/12/2015
15 Pages 7 Views 7 Unlocks
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Through Exam 1 (9/11)


What is Kinetic energy (thermal energy)?



Chapter 2- Water and Carbon

Molecules

∙ Formed when atoms bond to each other

∙ Water is most important to life

∙ Molecular weight is sum of mass of all the atoms in the  molecule

∙ One mole (6.022 x1023 molecules) has mass equal to  molecular weight in grams

∙ Concentration in molarity- moles/liter

Water

∙ Most important for life

∙ Highly polar, forms hydrogen bonds

o Oxygen is more electronegative than hydrogen o H gets partial +charge

o O gets partial –charge

∙ Polar molecules readily dissolve in water, nonpolar  molecules do not

∙ Cohesion- binding between water molecules o Leads to surface tension

∙ Adhesion- bonding between unlike molecules

∙ Crystal lattice in solid form- allows ice to float and allows  life

∙ Large capacity to absorb heat


What is the First Law of Thermodynamics?



o High specific heat and high heat of vaporization

Bonds

∙ Number per atom depends on valence

∙ Covalent

o Nonpolar- electrons are evenly shared and bond is  symmetrical  We also discuss several other topics like What are general methods used to treat depression?

o Polar covalent- symmetrically shared,  

∙ Electrostatic (ionic)

o Electrons transferred to one atom from another  ∙ Hydrogen

o Weak electrical attractions between H and an  electronegative atom with a partial –charge  

∙ Van Der Waals

∙ Hydrophobic

Atoms

∙ Protons- positive charge, 1 amu, in nucleus, gives atomic  number 

∙ Neutrons- no charge, 1 amu, in nucleus combines with  Protons for atomic weight 

∙ Electrons- negative charge, in orbitals  

Orbitals

∙ Electrons move in specific patterns around the nuclei  ∙ Grouped into levels called orbitals

∙ Outermost orbital are valence electrons 


What is the Second Law of Thermodynamics?



∙ Unpaired valence electrons are available for bonding 2

Reactions

∙ When a substance is formed or is broken down ∙ Have products and reactants

∙ Chemical equilibrium is when the forward and reverse  reactions happen at the same rate and the ratio of  products to reactants stays constant  

∙ Spontaneous if they lead to lower potential energy and  higher entropy

∙ Nonspontaneous if energy is input  

∙ Endothermic reactions need heat to continue, exothermic  reactions produce heat  

pH

∙ Based on proton (H+) concentration  

∙ pH of water is 7 (neutral)

∙ Acids have pH less than 7

∙ Bases have pH more than 7

∙ In acid-base reactions, a proton donor (acid) transfers a  proton to a proton accepter (base)

∙ Buffers- compounds that minimize changes in pH

Energy

∙ Capacity to do work or supply heat If you want to learn more check out What is the Law of Large Numbers?

∙ Potential energy- stored energy, energy of position

o Electrons in outer shells have more PE than internal  electrons

3

∙ Kinetic energy (thermal energy)- temperature, heat it  thermal energy transferred between two objects of  different temps

∙ First Law of Thermodynamics- energy is conserved (not  created or destroyed, only changed)

∙ Entropy (S) amount of disorder in a group of molecules ∙ Second Law of Thermodynamics- entropy always increases ∙ Gibbs Equation (ΔG) determines spontaneity  o ΔG=ΔH -TΔS

 H= potential energy (enthalpy)

 S= entropy (disorder) (becomes more  

important as temp increases) If you want to learn more check out What is the privileges and immunities clause?

o ΔG > 0 is exergonic spontaneous  

o ΔG < 0 endergonic and requires energy input o ΔG = reaction at equilibrium  

Chemical Energy

∙ Potential energy stored in chemical bonds

∙ Solar energy is converted into chemical energy by  photosynthesis  

∙ 9 calories/gram for fats and 4 calories/gram for  carbohydrates

Carbon

∙ most versatile atom on Earth  

4

∙ four valence electrons, can form many covalent bonds

Functional Groups

∙ Amino group- attract a proton, acts as a base (amines) o Nitrogen bonded to two H

∙ Carboxyl groups- drop a proton (Carboxylic acids) o C single bonded to –OH and double bonded to O

∙ Carbonyl groups- sites of reactions that link molecules into larger compounds [aldehyde (outside) or keytone  (internal)]

o C=O

∙ Hydroxyl groups- weak acids (alcohols)

o C-OH  

∙ Phosphate groups- two negative charges (organic  phosphates)

o P single bonded to three O (two negative charged,  one attatched elsewhere) and double bonded to one O

∙ Sulfhydryl groups- link together via disulfide groups  (Thiols)

o –SH

Chapter 3- Proteins

Proteins

∙ Cell functions depend on them We also discuss several other topics like What are the 6 PARTICULARLY important intermediates & their functions?

∙ Made of amino acids

∙ In cells, many are enzymes that act as catalysts  5

Structure

∙ Primary- amino acid sequence

∙ Secondary- alpha helices and beta sheets

∙ Tertiary- interactions between amino acids that dictate a  protein’s shape

∙ Quaternary- Interactions between polypeptides to form  one protein

∙ Denatured (unfolded) proteins can’t function ∙ Molecular chaperone proteins help proteins fold correctly ∙ Prions are improperly folded normal proteins

Amino Acids

∙ Only 20

∙ All have a central atom bonded to NH2, COOH, H, and an  ‘R’ group

o R group causes all amino acid variation  

o Hydrophobic- nonpolar R groups, no hydrogen  bonds

o Hydrophilic- polar R groups, hydrogen bonds,  dissolve in water

 Polar charged

 Polar uncharged (acids are negative, bases  

positive)

o R groups with hydroxyl, amino, carboxyl, or  sulfyhydral groups are more reactive than  

hydrocarbon side chains

∙ In the ionized form, the amine group takes an extra H and  the carboxyl loses an H

6

Monomers and Polymers

∙ mid-sized molecules (amino acids or nucleotides) are in  small monomers Don't forget about the age old question of what is Identity Theory?

∙ link together (polymerize) to form polymers ∙ Macromolecules are large polymers made of many  ∙ Polymerization is non spontaneous  If you want to learn more check out What are glasnost and perestroika?

∙ Monomers polymerize through dehydration synthesis  (condensation reactions where water is released)

∙ Hydrolysis is the opposite, polymers broken down by  adding water

∙ Amino terminus is the end amino group and the c terminus is the end carboxyl group

Peptide Bonds

∙ Condensation reactions bond the carboxyl group of an  amino acid to the amino group of another to form a  peptide bond

∙ Chain of amino acids liked by peptide bonds is a  polypeptide

o Less than 50 amino acids are oligopeptides  

o More than 50 are called proteins

Functions

∙ Catalysis- enzymes speed up reactions

o Most fundamental of functions

o Bring substrates together correctly  

o Decreases kinetic energy needed for reactions  (lowers EA) by lowering the free energy of the  

transition state

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o Do not change ΔG and aren’t consumed in the  reaction

o Reaction specific

o Steps of Enzyme Catalysis

1. Initiation- substrates are oriented correctly  

2. Transition State Facilitation- substrate and R  group interactions lower activation energy  

3. Termination- reaction products are released  

∙ Defense- antibodies

∙ Movement- motor and contractile proteins

∙ Signaling- convey signals between cells

∙ Structure- define shape and body structures

∙ Transport- transport proteins carry materials, membrane  proteins carry things in and out of the cell

Chapter 4- Nucleic Acids

Nucleotides

∙ Contain a sugar, a phosphate group, and a nitrogenous  base

∙ Ribo- form RNA, Deoxyribo- form DNA

∙ Nucleic acids form when nucleotides polymerize

∙ Phosphodiester linkage/bond form between the phosphate  on the 5’ C of one nucleotide and the –OH on the 3’ C of  another  

o Always written 5’  3’

∙ Polymerization is endergonic and uses enzymes 8

o Energy comes from the phosphorylation (transfer of  phosphate groups to a substrate) of nucleotides  

∙ Nucleoside triphosphates are reactants in polymerization  

DNA

∙ Primary structure- sequences of nitrogenous bases,  secondary is a double helix with parallel and opposite base pairing

∙ Allows organisms to store and replicate info needed to  survive

∙ Deoxyribonucleotides

∙ Watson and Crick

o Antiparallel configuration

o Double helix

o Bases on the inside

o Purines (A and G) pair with Pyrimidines (C and T) o A-T has two hydrogen bonds

o C-G has three hydrogen bonds

∙ Replication  

o Complimentary base pairing means each strand is a template for its compliment

o Steps

1. Separation of double helix

2. Hydrogen bonds between deoxyribonucleotides  with complimentary bases on original template  strand and phosphodiester bonds forming the  

new complimentary strand

∙ Stability makes DNA a poor catalyst  

9

RNA

∙ Primary structure is sequence of nitrogenous bases,  secondary is short double helices and hairpins

∙ Likely the first self replicating molecule

∙ Ribonucleotides

∙ First life-forms probably made of RNA

∙ One more –OH group than DNA, makes it more reactive  and less stable  

∙ Uracil instead of Thymine  

∙ Intermediate between DNA and proteins

∙ Can be information-containing and can self-replicate ∙ Can be catalytic

o Ribozymes are enzyme-like RNA

Temperature and Reactions

∙ Rate of reactions depends on number of collisions and  increased temp more collisionsfaster reaction

Chapter 5- Carbohydrates

Monosaccharides  

∙ Simple sugars that vary in four ways

1. Location of the carbonyl group  

a. Aldose- end of the monosaccharides

b. Keytose- middle of the monosaccharides

2. Number of carbons

a. 3- triose

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b. 5- pentose

c. 5- hexose

3. Spatial arrangement of hydroxyl groups

4. Linear or rings  

Polysaccharides- Complex Carbohydrates ∙ Polymers of monosaccharide monomers

∙ Simplest ones are disaccharides, made of two  monosaccharides

∙ Simple sugars form from condensation between hydroxyl  groups, causes glycosidic linkage

o Alpha is when –OH groups are on the same sides o Beta when not on the same side

Common Carbohydrates

∙ Glycogen and Starch- energy storage (animals, plants)

o Hydrolysis of alpha linkages in glycogen catalyzed  by phosphorylase

 Contained by most cells to provide glucose

o Alpha linkages in starch are hydrolyzed by amylase   Key role in carb digestion  

∙ Chitin and Cellulose- structure (animals, plants) ∙ Peptidoglycan- cell structure

Function

∙ Cell identity

o Glycoproteins are proteins covalently bonded to  carbs

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 Key in cell-cell recognition and signaling  

∙ Store energy

o Undergo reactions to form adenosine triphosphate  (ATP)

 Free energy in ATP is used for endergonic  

reactions

 Carbs have a lot of C-H bonds, so they have a  lot of free energy

∙ Fatty acids have even more

∙ Fibrous structure  

∙ Precursors to larger molecules  

Chapter 6- Lipids and Membranes

Lipids

∙ Mostly nonpolar and hydrophobic

∙ Hydrocarbons are nonpolar and only contain C and H ∙ Don’t dissolve in water due to fatty acids

o Hydrocarbon chain bonded to a carboxyl  

∙ Fatty acids and isoprene are primary components ∙ 3 Types

1. Triglycerides- energy storage

a. 3 fatty acids (ester linked) to a glycerol

b. formed by dehydration synthesis  

2. Phospholipids- membranes

a. Amphipathic  

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i. “head”- hydrophilic glycerol, phosphate, and  charged groups, highly polar covalent

ii. “tail”- two nonpolar fatty acid or isoprene  

chains

b. Allows membranes to form with heads outside and  tails inside

c. Do not dissolve in water

d. In water, spontaneously forms either

i. Micelles- heads face water, tails face each  

other

ii. Phospholipid bilayers

1. Selectively permeable- small or nonpolar  

molecules, affected by number of double  

bonds, length of tail, amount of  

cholesterol (decreases permeability),  

temperature  

2. Fluidity- individual phospholipids can  

move laterally, almost never flip across  

membrane

3. Steroids (Cholesterol)- membranes and metabolic  intermediates  

Solute Movement

∙ Passive transport no energy is added

∙ Active transport energy is needed

∙ Diffusion random movement of solutes

o Concentration gradient, spontaneous  

∙ Equilibrium once molecules are randomly dispersed  through the solution, still movement but no net movement

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∙ Osmosis movement of water to create equal  concentrations  

o Moves from low solute concentrations to high

o Only occurs across a selectively permeable  

membrane

Fluid Mosaic Membrane Model

∙ Proteins are inserted into the lipid bilayer

∙ Makes bilayer fluid, dynamic mosaic of phospholipids and  proteins

∙ Integral proteins- amphipathic so it can span the entire  membrane  

o Transmembrane – span entire membrane

 Transport proteins

1. Channels (passive)

a. Ion channels allow ions to flow across

the membrane down their  

electrochemical gradient  

b. Facilitated (passive) diffusion by  

channels that allows molecules that  

couldn’t pass otherwise

2. Carrier proteins/ transporters (passive)

a. Change shape during process

b. Down concentration gradient

c. Used to move glucose

3. Pumps (active)

a. Move ions or molecules AGAINST the  

gradient

b. Sodium-potassium pump

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c. Make cotransport possible

o Peripheral- one side of the membrane 15

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