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UCR / Biology / BIOL 5 / What is the biological medium on earth?

What is the biological medium on earth?

What is the biological medium on earth?

Description

School: University of California Riverside
Department: Biology
Course: Intro: Cell and Molecular Biology
Professor: Eugene nothnagel
Term: Winter 2016
Tags: Biology
Cost: 50
Name: Midterm 1 Study Guide: Chapters 1-7
Description: These notes cover what's going to be in our upcoming midterm. I've mainly focused on information provided directly in the textbook for chapters 1-7, including information not covered in lecture.
Uploaded: 01/26/2016
22 Pages 56 Views 2 Unlocks
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BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY


What is the biological medium on earth?



CONDENSED NOTES FOR MIDTERM 1

CHAPTER 1: EVOLUTION, THE THEMES OF BIOLOGY, AND SCIENTIFIC INQUIRY

Biology is the scientific study of life, with evolution, the process of change that has  shaped life from its origin on Earth to today’s diversity, as its organization principle. The properties and processes of life include highly ordered structure, evolutionary  adaptation, response to the environment, regulation, energy processing, reproduction,  and growth and development.  

1.1: The study of life reveals common themes 

Theme: New properties emerge at successive levels of biological organization ∙ biology today combines the strategy of reductionism, which breaks down complex  systems into simpler components, with systems biology, which studies interactions of the parts of a system and models the system’s dynamic behavior ∙ structural arrangements of and interactions among components at each level of  biological organization lead to emergent properties at the next level ∙ the form of a structure is well matched to its function at all levels of biological  organization


What is a major cell nutrient produced during photosynthesis, a raw material for other molecules?



Don't forget about the age old question of Why do companies go into advertising their products?

∙ the cell is lowest structural level capable of performing all the activities of life  ∙ the simpler and smaller prokaryotic cell, unique to bacteria and archaea, lacks a  nucleus to enclose its DNA and other membrane-enclosed organelles ∙ the eukaryotic cell-with a nucleus containing DNA, and numerous organelles-is  typical of all other living organisms Don't forget about the age old question of What are the activities involved in moving goods from producer to consumer?

Theme: Life’s processes involve the expression and transmission of genetic information  ∙ the genetic information of a cell is coded in DNA

∙ genes are units of inheritance that transmit information from parents to offspring.  They are located on chromosomes, long DNA molecules that replicate before cell  division and provide identical copies to daughter cells


What are the major cellular components?



∙ most genes program the cell’s production of proteins, and almost all cellular  structures and actions involve one or more proteins Don't forget about the age old question of Who elects the legislature in a parliamentary democracy?
If you want to learn more check out What is the function of the dermis?

∙ gene expression is the process by which a gene’s information is converted into a  cellular product. Genes also code from RNA’s that serve other functions: playing a  role in the cell’s protein manufacturing machinery and regulating gene expression

∙ the genetic instruction an organism inherits make up its genome  ∙ each of the two sets of chromosomes in a human cell contains about 3 billion  nucleotide pairs

∙ proteomes are whole sets of proteins encoded by a genome

∙ research developments contributing to genomics and proteomics:  1) “High throughput” technology that can analyze biological materials rapidly 2) Bioinformatics, which provides computational tools to process and analyze  the resulting data Don't forget about the age old question of Most carbon is locked in what areas?

3) interdisciplinary research teams with specialists from many diverse fields

Theme: Life requires the transfer and transformation of energy and matter  ∙ producers transform light energy to the chemical energy in sugars, which powers the cellular activities of plants

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∙ consumers eat plants and other organisms, using chemical energy in their foods to  power their movement, growth, etc

∙ in each use of energy to perform work, some energy is lost to the surroundings as  heat  

Theme: From ecosystems to molecules, interactions are important in biological systems ∙ molecular interactions within organisms are crucial to proper functioning  ∙ protein enzymes catalyze cell’s chemical reactions, which are often organized into  chemical pathways We also discuss several other topics like How can we reduce the impact of volcanoes?

∙ many biological processes are controlled through feedback regulation, in which  the product of a process regulates that process  

∙ in negative feedback, the response feeds back and reduces the original stimulus ∙ in positive feedback, an end product speeds up the process  

1.2: The Core Theme: Evolution accounts for the unity and diversity of life 

Classifying the Diversity of Life

∙ prokaryotes make up the domains Archaea and Bacteria

∙ all eukaryotes are placed in the domain Eukarya  

Charles Darwin and the Theory of Natural Selection  

∙ natural selection: individuals with traits best suited for the environment leave  more offspring; the mechanism of evolution based off of three observations 1) individuals vary in many heritable traits

2) the overproduction of offspring sets up a competition of survival  3) species are generally matched to their environments  

The Tree of Life

∙ diversity of species results from natural selection acting over millions of generations  as populations adapted to different environments  

1.3: In studying nature, scientists make observations and form and test hypotheses 

Science is an approach to understanding the natural world that involves inquiry, the  search for explanations of natural phenomena  

Making Observations

∙ data: recorded observations, quantitative and qualitative  

∙ using inductive reasoning to draw generalizations from collections of observations

Forming and Testing Hypotheses

∙ hypothesis: tentative answer to a question or an explanation of observations,  leading to predictions that can be tested

-must be testable

-cannot be proven to be true or incorrect  

-gains credibility when it is tested in various ways

∙ deductive reasoning uses “if…then” logic  

Theories in Science  

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∙ theory: broader in scope than a hypothesis, generates many specific hypotheses,  supported by a larger body of evidence. It can be modified and rejected when results and new evidence no longer support it

CHAPTER 2: THE CHEMICAL CONTEXT OF LIFE

2.1 Matter consists of chemical elements in pure form and in combinations called  compounds 

∙ Matter: anything that takes up space and has mass  

Elements and Compounds

∙ Elements: substances that cannot be chemically broken down to other types of  matter

∙ Compound: made up of two or more elements combined in a fixed ratio

The Elements of Life

∙ About 25 out of the 92 elements are essential to life

∙ Essential elements: needed for an organism to live and reproduce; Carbon,  Oxygen, Hydrogen, and Nitrogen make up 96% of living matter  

o Most of the remaining 4% consists of Calcium, phosphorus, potassium, and  sulfur

∙ Trace elements: elements required in very minute quantities such as Iron and  Iodine (Mn, Co, Ni, Cu, Zn, Mo, I)

*Hint: 99% of all living material consist of:

CHOPKINS CaFe Mg NaCl

(Carbon, Hydrogen, Oxygen, Phosphorus, Potassium, Iodine, Nitrogen, Sulfur)

Evolution of Tolerance to Toxic Elements

∙ Serpentine soil contains toxic elements but some plants exhibit evolutionary  adaptations that enable them to grow in such soils  

2.2 An element’s properties depend on the structure of its atoms 

Subatomic Particles

∙ Atom: smallest unit of matter retaining the properties of that element ∙ Uncharged neutrons and positively charged protons are packed tightly together to form the atomic nucleus of an atom

∙ Negatively charged electrons form a large cloud around the positively charged  nucleus

∙ Protons and neutrons have a similar mass of about 1.7 X 10^-24 gram or close to 1  dalton each

∙ Dalton: measurement unit for atomic mass

∙ Electrons have negligible mass

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CONDENSED NOTES FOR MIDTERM 1

Atomic Number and Atomic Mass

∙ Each element has a characteristic atomic number, or number of protons in each of  its atoms

∙ The mass number is equal to the number of protons and neutrons in the nucleus  and approximates the mass of an atom of that element in daltons

∙ Atomic mass: the total mass of an atom  

Isotopes

∙ Isotopes: a variance in the number of neutrons of a particular element; slightly  different mases but the same chemical behaviors

∙ Radioactive isotopes: unstable isotopes, spontaneously decay, giving off particles  and energy

o Fixed rate of decay, referred to as its half life: amount of years it takes for  50% of the parent isotope to decay into its daughter isotope  

o Radiometric dating: scientists use the ratio of different isotopes to estimate how many half lives have passed since a fossil or rock was formed  

The Energy Levels of Electrons

∙ Energy: the capacity to cause change, to do work  

∙ Potential energy: energy stored in matter as a consequence of its position or  structure

o Potential energy of an electrons increases as their distance from the positively charged nucleus increases

∙ Electron shells/energy level: an electron’s state of potential energy

Electron Distribution and Chemical Properties

∙ The chemical behavior of an atom is determined by the number of valence electrons  it has in its outermost electron shell or valence shell  

∙ Valence shell of eight electrons is complete, resulting in an unreactive or inert atom ∙ Atoms with incomplete shells are chemically reactive  

∙ Elements in each row or period of the periodic table of elements have the same  number of electron shells and are arranged in order of increasing number of  electrons

∙ Amount of energy necessary to remove an electron from its ground state is called  the ionization energy

o Greater the ionization energy, the more difficult it is to remove an electron o Increases from left to right and up from bottom to the top of the periodic table (except H, which has a very high ionization energy)

Electron Orbitals

∙ Orbital: 3D space or volume within which an electron is most likely to be found ∙ the first electron shell can contain two electrons in a single spherical orbital, 1s  orbital

∙ S –1 orbital –2 electrons

∙ P—3 orbitals—6 electrons

∙ D—5 orbitals—10 electrons

∙ F—7 orbitals—14 electrons

 2.3The formation and function of molecules depend on chemical bonding between  atoms 

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CONDENSED NOTES FOR MIDTERM 1

∙      Atoms with incomplete valence shells can share or transfer valence electrons with  certain other atoms

∙     These interactions usually result in atoms staying close together, held by attractions  called chemical bonds

Covalent Bonds

∙ Covalent bonds: when two atoms share a pair of valence electrons ∙ Molecule: two or more atoms held together by covalent bonds ∙ Electronegativity: attraction of a particular atom for shared electrons ∙ Nonpolar covalent bond: if the atoms in a molecule have similar  electronegativities and the electrons remain equally shared

∙ Polar covalent bond: if one electron is more electronegative, it pulls the shared  electrons closer to itself. The unequal sharing results in a polarity or separation of  charges  

Ionic Bonds

∙ if two atoms are very different in their attraction for valence electrons, the more  electronegative atom may completely transfer an electron from the other atom,  resulting in the formation of charged atoms called ions

∙ cation: positively charged, atom that lost an electron

∙ anion: negatively charged, atom that gained an electron  

∙ ionic bonds: holds cations and anions together because of the attraction of their  opposite charges

∙ ionic compounds/salts: 3D crystalline lattice arrangements held together by  electrical attractions

o number of ions present in a salt crystal aren’t fixed but the atoms are present  in specific ratios

o have strong ionic bonds when dry and dissolve in water

Weak Chemical Bonds

∙ Ionic bonds and other weak bonds may form temporary interactions between  molecules

∙ Weak bonds within many large molecules help create those molecules’ 3D functional shape

∙ Hydrogen bond: hydrogen atom that is covalently bonded to an electronegative  atom has a partial positive charge and can be attracted to a different nearby  electronegative atom  

∙ All atoms and molecules are attracted to each other when in close contact by  fleeting charge difference--van der Waals interactions

∙ Momentary uneven electron distributions produce changing positive and negative  regions that create van de Waals interactions

Hydrogen Bonds are weak bonds important in the chemistry of life

∙ Hydrogen bonds are attractive forces between polar molecules; when partial  opposite charges in different molecules attract each other

o Comparatively weak but collectively can be quite strong

o Where we see hydrogen bonds: between water molecules, helping to hold  DNA together, interactions between proteins

Molecular Shape and Function

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∙ Molecule’s shape and size affects how it interacts with other molecules ∙ In a covalent bond, the s and p orbitals may hybridize, creating specific molecular  shapes

∙ Biological molecules recognize and interact with each other with a specificity based  on molecular shape

∙ Molecules with similar shapes can have similar biological effects

2.4: Chemical reactions make and bread chemical bonds 

∙     Chemical reactions: the making or breaking of chemical bonds o Reversible

o Increasing concentrations of reactants can speed up the rate of a reaction  ∙     Matter is conserved in chemical reactions; same number of kinds of atoms are  present in both reactants and products, although the rearrangement of electrons  and atoms causes the properties of these molecules to be different  ∙     Chemical equilibrium: reached when the forward and reverse reactions processed  at the same rate, and the relative concentrations of reactants and products no  longer change

CHAPTER 3: WATER AND LIFE

∙ Water is the biological medium on Earth

∙ All living organisms require water more than any other substance ∙ Most cells are surrounded by water, and cells themselves are about 70-95% water o Red blood cells—60% water

o Muscle—75% water

o Plasma—92% water

∙ The abundance of water is the main reason the Earth is habitable  

Polar covalent bonds in water molecules result in hydrogen bonding ∙ The water molecules is a polar molecule: the opposite ends have opposite charges ∙ Polarity allows water molecules to form hydrogen bonds with each other  ∙ The hydrogen atoms pull towards the oxygen atom in water

∙ The unpaired electrons on a water molecule allow it to bond to other water  molecules

∙ A single water molecule can have up to 4 other water molecules bound to it ∙ The difference between the solid and liquid form of water is the formation of H bonds and the amount of kinetic energy present

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Emergent properties of water contribute to Earth’s suitability for life ∙     Some of water’s properties that facilitate an environment for life are: o Cohesive/Adhesive behavior

 Surface tension and capillary action

o Ability to moderate temperature, thermal stability

 Specific heat and heat of vaporization

o Expansion upon freezing

o Versatility as a solvent

o Colorless and transparent

o Low viscosity—compared to other liquids

Cohesion of Water Molecules 

∙     Collectively, hydrogen bonds hold water molecules together, a phenomenon called  cohesion

∙     Cohesion helps the transport of water against gravity in plants

∙     Adhesion is an attraction between different substances, for example, between  water and plant cell walls

∙     Surface tension: measure of how hard it is to break the surface of a liquid; related  to cohesion

o Detergents and heat lowers the surface tension of water so they can soak into our clothes. Washing in cold water requires a wetting agent in the detergent

Moderation of Temperature by Water 

∙ Water absorbs heat from warmer air and releases stored heat to cooler air  ∙ Water can absorb or release a large amount of heat with only a slight change in its  own temperature

Heat and Temperature

∙ Kinetic energy: energy of motion  

∙ Heat: the measure of the total amount of kinetic energy due to molecular motion ∙ Temperature: measures the intensity of heat due to the average kinetic energy of  molecules

Water’s High Specific Heat  

∙ The specific heat of a substance is the amount of heat that must be absorbed or  lost for 1 gram of that substance to change its temperature by 1 degree Celsius o Specific heat of water: 1 cal/g/degrees Celsius

∙ Water resists changing its temperature because of its high specific heat o Water heats slowly and cools slowly, it has a high heat of fusion ∙ Water’s high specific heat can be traced to hydrogen bonding

o Heat is absorbed when hydrogen bonds break

o Heat is released when hydrogen bonds form

∙ The high specific heat of water minimizes temperature fluctuations to within limits  that permit life

Evaporative Cooling

∙ Heat of vaporization: the heat a liquid must absorb for 1 gram to be converted to  gas

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o as liquid evaporates, its remaining surface cools, a process called  evaporative cooling (takes away heat)

o evaporative cooling of water helps stabilize temperatures in organisms and  bodies of water

o a liquid with a low heat of vaporization evaporates faster, such as alcohol

Floating of Ice on Water 

∙ ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making  ice less dense

∙ if ice sank, all bodies of water would eventually freeze solid, making life impossible  on Earth  

∙ ice occupies a larger volume because of its lattice structure but is less dense than  liquid water

Water: The Solvent of Life 

∙     solution: liquid that is a homogenous mixture of substances

∙     solvent: dissolving agent of a solution

∙     solute: substance that is dissolved

∙     an aqueous solution is one in which water is the solvent  

∙     water is a versatile solvent due to its polarity, which allows it to form hydrogen  bonds easily  

∙     when an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell

∙     water can also dissolve compounds made of nonionic polar molecules ∙     even large polar molecules such as proteins can dissolve in water if they have ionic  and polar regions  

Hydrophobic and Hydrophilic Substances

∙     hydrophilic substance is one that has an affinity for water

∙     hydrophobic substance is one that does not have an affinity for water o oil molecules are hydrophobic because they have relatively nonpolar bonds

Solute Concentrations in Aqueous Solutions

∙     most biochemical reactions occur in water

∙     chemical reactions depend on collisions of molecules and therefore on the  concentration of solutes in an aqueous solution

∙     molecular mass is the sum of all of the masses of all atoms in a molecule ∙     molarity (M) is the number of moles of solute per liter of solution  

Acidic and Basic Conditions Affect Living Organisms 

∙ a hydrogen atom in a hydrogen bond between two water molecules can shift from  one to the other

o the H atom leaves its electron behind and is transferred as a proton, or  hydrogen ion (H+)

o the molecule with the extra proton is now a hydronium ion (H3O+) o the molecule that lost the proton is now a hydroxide ion (OH-) ∙ water is in a state of chemical equilibrium in which water molecules dissociate at the same rate at which they are being reformed

∙ changes in concentrations of H+ and OH- can drastically affect the chemistry of a  cell

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CONDENSED NOTES FOR MIDTERM 1

∙ concentrations of H+ and OH- are equal in pure water

Acids and Bases 

∙ acid: any substance that increases the H+ concentration of a solution; ionize in an  aqueous solution. Proton donor

∙ base: any substance that reduces the H+ concentrati0on of a solution. Proton  acceptor

∙ Most biological fluids have a pH in the range of 6 to 8

∙ Acids and bases that ionize completely are considered strong acids and bases

Buffers 

∙ Buffers: substances that minimize changes in concentrations of H+ and OH- in a  solution  

o most buffers consist of an acid-base pair that reversibly combines with H+  

Acidification: A Threat to Water Quality 

∙     Human activities such as burning fossil fuels threaten water quality ∙     CO2 is the main product of fossil fuel combustion  

∙     About 25% of human-generated CO2 is absorbed by oceans

∙     CO2 dissolved in sea water forms carbonic acid; this process is called ocean  acidification  

∙     As seawater acidifies, H+ ions combine with carbonate ions to produce bicarbonate ∙     Carbonate is required for calcification by many marine organisms  

CHAPTER 4: CARBON AND THE

MOLECULAR DIVERSITY OF LIFE Organic Chemistry is the study of carbon compounds 

∙     Although cells are 70-95% water, the rest consists mostly of carbon based  compounds

∙     Organic compounds range from simple molecules to colossal ones ∙     Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are  all composed of carbon compounds  

Carbon atoms can form diverse molecules by bonding to four other atoms ∙     Electron configuration is the key to an atom’s characteristics ∙     Electron configuration determines the kinds and number of bonds an atom will form  with other atoms  

The formation of bonds with Carbon 

∙ Carbon can form 4 covalent bonds with a variety of atoms

∙ This tetravalence makes large, complex molecules possible

∙ In molecules with multiple carbons, each carbon bonded to 4 other atoms has a  tetrahedral shape

∙ However, when two C atoms are joined by a double bond, the molecule has a flat  shape

Molecular Diversity Arising from Carbon Skeleton Variation  

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∙ Carbon chains form the skeletons of most organic molecules

∙ Carbon chains vary in length and shape

∙ Hydrocarbons are organic molecules consisting of only carbon and hydrogen ∙ Many organic molecules, such as fats, have hydrocarbon components ∙ Hydrocarbons can undergo reactions that release a large amount of energy  

Isomers 

∙ Compounds with the same molecular formula but different structures and properties ∙ Structural isomers have different covalent arrangements of their atoms; same  chemical formula but different structures of atoms and bonds

∙ Geometric isomers have the covalent bonds to the same atoms, but differ in  spatial arrangement ( cis and trans)

∙ Enantiomers are isomers that are mirror images of each other o Important in the pharmaceutical industry

o Two enantiomers of a drug may have different effects

o Different effects of enantiomers demonstrate that organisms are sensitive to  even subtle variations in molecules

∙ Central carbon with 4 different groups bound to it is called the chiral center carbon;  present in amino acids

Functional groups are the parts of molecules involved in chemical reactions ∙ Distinctive properties of organic molecules depend not only on the carbon skeletons  but also on the molecular components attached to it

∙ Certain groups of atoms are often attacked to skeletons of organic molecules. These  functional groups have distinct chemical and physical properties

∙ Functional groups are the components of organic molecules that are most  commonly involved in chemical reactions  

o The number and arrangement of functional groups give each molecule its  unique properties

∙ the 7 functional groups that are most important in the chemistry of life: o hydroxyl group

o carbonyl group

o carboxyl group

o amino group

o sulfhydryl group

o phosphate group

o methyl group

______________________________________________ _________________

CHAPTER 5: STRUCTURE AND FUNCTION OF LARGE BIOLOGICAL MOLECULES How cells use organic compounds 

∙ Biological organisms use the same types of building blocks

∙ All macromolecules have specific functions in cells

∙ Other than water, macromolecules make up the largest percent mass of a cell Condensation and Hydrolysis 

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∙ Condensation/Dehydration synthesis

o two molecules combine with loss of water to form larger molecules o requires enzymes and energy; enzymatic reaction

o forms a strong covalent bond

o 1 OH and H removed by DNA polymerase

∙ Hydrolysis

o A molecule splits into two smaller ones with the addition of water o Breaks bonds

The Molecules of Life 

∙ Living cells synthesize:

o Carbohydrates

o Lipids

o Proteins

o Nucleic acids

*Large polymers form from smaller monomers. New properties emerge

Carbohydrates 

∙     Used as energy and structural molecules (structural polymers); backbone ∙     Are soluble in water to provide energy  

∙     Main types:

o Monosaccharides

o Disaccharides

o Polysaccharides

∙     Monosaccharides (CH2O)

o Major cell nutrient produced during photosynthesis, raw material for other  molecules

o 6 Carbon sugars (hexoses)

 Glucose, fructose, galactose

o 5 Carbon sugars (pentose)

 Deoxyribose, Ribose

∙     Disaccharides

o Sucrose (glucose + fructose); table/cane sugar

o Lactose (glucose + galactose); milk sugar, unabsorbed in intestines if individuals  lack lactase—leading to diarrhea

o Maltose (glucose + glucose); beer, formed during the hydrolysis of starch by  amylase

o Formed by condensation reactions (glycosidic linkages created) o Broken down by specific enzymes

∙     Polysaccharides (complex carbohydrates)

o 100s/1000s monosaccharides long

o Made of same subunit

o Energy storage

 Starch (amylose/amylopectin)

∙     Digestible

∙     In plants only

∙     Forms ring in aqueous solutions

 Glycogen (highly branched)

∙     In animals only  

o Structural support

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 Cellulose

∙     Forms rings in aqueous solutions

 Chitin

Lipids 

∙ Large hydrocarbons; insoluble in water

∙ Don’t form polymers

∙ Dissolve in nonpolar substances (chloroform, ether)

∙ Used for energy storage, structural, and chemical messenger

∙ Lipids with fatty acids

o Glycerides

o Phospholipids

o Waxes

∙ Lipids with no fatty acids

o Steroids

Fatty Acids

∙ Carbon backbone (4-24 carbon atoms)

∙ Carboxyl group (-COOH)

∙ Methyl group makes it nonpolar

∙ Unsaturated

o One or more double bonds in backbone

 Double bonds adds kinks

∙ Saturated

o All single bonds in backbone

Triglycerides

∙ Fats/neutral fats

o Three fatty acids and a glycerol molecule

o Condensation reactions forms ester linkage

o Most abundant lipid

o Non polar; contain no charged/polar functional groups

∙ Functions

o Energy storage in adipocytes

o Insulation  

Phospholipids

∙ Glycerol backbone

∙ Two fatty acid tails (hydrophobic)

∙ Phosphate-containing head (negatively charged therefore hydrophilic) ∙ Amphipathic (both hydrophilic and hydrophobic)

∙ Main materials of cell membranes

Sterols

∙ Steroids/sterols

o No fatty acid tails

o Four carbon ring

o In eukaryotic cell membranes

o Cholesterol in animal tissues

 Precursor to sex hormones and bile salts

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Waxes

∙ Long chained fatty acids linked to alcohols or carbon rings

∙ Cover plant parts (cuticle)

o Help conserve water

o Fend off parasites

∙ Animals

o Protect, lubricate, impart pliability to skin and hair

o Repel water (bird feathers, exoskeleton of insects)

Amino Acids and the Primary Structure of Proteins 

∙ Proteins

o Enzymes (metabolism); create reactions in a timely manner

o Structures (collagen and silk)

o Transport and movement (lipoproteins, hemoglobin, actin/myosin, tublin) o Nutritious (egg whites, casein)

o Hormones (chemical messengers, ex: insulin/growth hormone)

o Immune system (antibodies)

∙ Two classes: globular and fibrous

∙ Proteins are made from a pool of amino acids

Structure of Amino Acids

∙ Central carbon atom

∙ An amino group

∙ A carboxyl group

∙ A hydrogen atom

∙ One or more atoms “R group”

∙ Organisms use L form but not D

Peptide Bond Formation

∙ A type of condensation reaction

∙ DNA holds instructions for RNAs, mRNA determines order of amino acids

Protein Conformation

∙ Conformation (shape) is determined by genes and it determines function and is the  result of linear sequence of amino acids in a polypeptide

∙ Folding, coiling and interactions of multiple polypeptide chains create a functional  protein

∙ 4 levels of protein structure

o Primary

o Secondary  

o Tertiary

o Quaternary  

Primary Structure

∙ The unique, linear sequence determined by the mRNA

∙ A change in one a.a. can affect every other level of structure  

∙ One letter change may or may not have a change

Secondary Level of Protein Structure

∙ Hydrogen bonding occurs between amino and carboxyl groups of amino acids 13

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∙ Structures formed:

o Alpha helix. Common in fibrous proteins, creates elastic properties o Beta Sheet. Antiparallel chains form sheet

 Core of many globular proteins and inelastic fibrous proteins  

Tertiary Level of Protein Structure

∙ Additional folding of secondary structure and bonding between R groups o Hydrogen bonds

o Disulfide bridges (Strong)

o Hydrophobic interactions

o Ionic bonding  

Quaternary Level of Protein Structure

∙ Two or more polypeptide chains joined by  

o Weak bonds (H-bonds)

o Covalent bonds between sulfur atoms and R groups

 Collagen (3 helical polypeptides)

 Insulin (2 polypeptides)

 Hemoglobin (4 globular polypeptides)

Structural Changes by Denaturation

∙ Denaturation: altering a protein’s native conformation and activity o Usually at the secondary and tertiary structures

∙ Disruption of three dimensional shape of proteins

o Temperature: thermal agitation (increasing kinetic energy)

o pH and salts: additional H+/OH- or ions disrupts H-bonding, ionic and disulfide bridges

o non polar solvents: protein turns “inside-out”

∙ Some proteins have organic compounds attached

o Glycoproteins, lipoproteins (common on membranes)

Nucleotides and the Nucleic Acids 

∙     Nucleotides

o Sugar—ribose or deoxyribose

o Phosphate group

o Bases

 Single or double carbon rings with Nitrogen

∙     Subunits of coenzymes

o NAD+ and FAD

∙     ATP

o Energy source for chemical reactions

o Contains three phosphate groups

Nucleic Acids—DNA and RNA

∙     Building blocks

o Four kinds of nucleotides

o Differ only in component bases

Single Strand of Nucleic Acid

∙     A series of covalently bonded nucleotides

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DNA

∙ Double stranded

∙ Hydrogen bonds between strands

∙ Twisted helically

∙ Four kinds of nucleotide monomers (A, T, C, G)

∙ Encodes protein-building instructions

RNA

∙ Single stranded

∙ Four kinds of nucleotide monomers (A, U, C, G)

∙ Do not encode protein-building instructions

∙ Key players in the protein-building processes

∙ mRNA, tRNA, rRNA

CHAPTER 6: A TOUR OF THE CELL

Cells of Living Things 

∙ Prokaryotic

o Usually single celled, can form colonies

o No nucleus or membrane bound organelles

o Metabolism through aerobic and anaerobic means

o Genetic material localized (nucleoid)

o Most have cell wall composed of peptidoglycan

o No cytoskeleton—proteins move nutrients around

o Circular DNA, one form of RNA polymerase

 Bacteria and archaea  

∙ Eukaryotic  

o Kingdoms: lots in what used to be called Protista, Fungi, Plants, Animals o Nucleus membrane encloses DNA

o Organelles that have membrane

o RNA and protein synthesized in two different locations

o Linear DNA molecules with non coding introns

o More than one RNA polymerase

o Controlled—perfect at certain functions  

o Compartments—organelles  

Cell Size and Shape 

∙ Surface to volume ration limits size of cells. Large cells require more raw materials o Volume (V) = cm^3

o Surface Area (SA) = cm^2

o Restrictions on size and shape

∙ Cells compartmentalize to increase SA/V, specialize reactions within, localize  reactions where needed

Small Compartments 

∙ Isolate areas of the cell. Allows for varied conditions in different regions (pH,  concentration of solutes, etc)

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∙ Each smaller structure can be specialized ( a multi-departmental large company  versus small business)

o Allows for increase in complexity

o Leads to multicellularity  

∙ Provides surfaces for reactions (photosynthesis and respiration)

Basic Aspects of Cell Structure and Function 

∙ Plasma membrane

o Lipid bilayer—same basic architecture found in all membranous organelles o Proteins

 Channels, transport, pumps, receptors

∙ DNA-containing region

∙ Cytoplasm  

o Area between outer membrane and nuclear membrane. The cytosol is the  liquid/gel material containing water, gases, and macromolecules

Major Cellular Components 

∙ Nucleus

∙ Ribosomes

∙ Endomembrane system

o Endoplasmic reticulum, smooth and rough

o Golgi body

o Various vesicles

∙ Mitochondria/chloroplasts

∙ Cytoskeleton

Components of the Nucleus 

∙ Accounts for about 6-10% of total cell volume

∙ Membrane continuous with ER

∙ Nuclear envelope: surrounds nucleus

o Chromosomes: one DNA molecule and associated proteins, organized DNA o Chromatin: DNA molecules and histone proteins. Condenses to form  chromosome.

∙ Nucleolus: genes for rRNA that will be assembled into ribosomal subunits. Cells  may have more than one

The Nuclear Envelope

∙ Double membrane system

o Two lipid bilayers. 20-40nm thick

o Surrounds chromatin/nucleoplasm

∙ Nuclear pores regulate entrance/exit of ions and small proteins. Composed of a large number of proteins. It’s wider than it is thick. Passage through pore requires signal  proteins and GTP

∙ Nuclear lamina made of intermediate filaments, play a role in gene regulation

Ribosomes 

∙ Smallest, most numerous organelle. Composition slightly different in prokaryotic and  eukaryotic cells

∙ Composed of rRNA (60%) and proteins (40%). Synthesized by nucleolus  16

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o Large and small subunits

∙ Found free and bound to E.R. Differ only in what they are making ∙ Catalyzes formation of peptide bonds using RNA molecules

The Endomembrane System 

∙ Organelles in which lipids are assembled and proteins are produced and modified ∙ Are in direct contact or send vesicles (membrane-bound sacs)

∙ Occupy ½ of cell volume

∙ Nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, vacuole  

The Endoplasmic Reticulum

∙ Network of tubes and sacs that are continuous with nuclear membrane. Most  extensive membrane system

∙ Rough (ribosome studded) and smooth

o Rough: production of secretory proteins. Signal sequence on polypeptide  instructs ribosome to attack to ER

o Smooth: lipid production, CH2O metabolism, storage of ions (Ca+),  detoxification of drugs/alcohol

 Proteins in membrane or within lumen catalyze reactions

Golgi Bodies

∙ Enzymatic finished on proteins and lipids, and packaging in vesicles ∙ Cis (forming) face and trans (exit) face

∙ Forms glycolipids, glycoproteins through the modification of proteins produced by  ER. Enzymes in lumen catalyze addition/removal of parts

∙ Produce some polysaccharides and also pectin for plant cell walls ∙ Products of golgi leave as vesicles. From cisterna to another or out of cell

Lysosomes

∙ Membrane bound organelle that contains about 40 different hydrolytic enzymes  responsible for the digestion of macromolecules, autolysis, intracellular digestion ∙ Dead cells no longer able to maintain H+ gradient (uses H+ pump to maintain pH of  4.8), so organelle breaks down releasing contents  

∙ It works at low pHs because H+ is constantly be pumped by ATP; without it cells  would die

∙ Made by ER and Golgi

o Common in white blood cells

∙ Tay-Sachs is the result of faulty enzyme in lysosomes responsible for lipid breakdown in neurons

∙ Carries out hydrolysis; can break down:

o Nucleic acids with enzyme nuclease

o Proteins with enzyme protease  

o Lipids with enzyme lipase

o Carbohydrates to create usable monomers of macromolecules

Vacuoles

∙ Largest in plant cells

∙ Storage of water or ions, pigments, hold food, pump out water

∙ Are larger than vesicles from golgi/ER

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BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY

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∙ In plants it is enclosed by Tonoplast (membrane) and provides cell with hydrostatic  pressure

Peroxisomes 

∙ H2O2, bi-product of lipid production  

∙ Contain enzymes (catalase) that break down H2O2 formed during metabolism of  alcohols, fatty acids

∙ Specialized forms (glyoxysome) found in seeds and function during germination ∙ Self-replicating-imports proteins from cytosol  

Mitochondria 

∙ Production of ATP

∙ Double-membrane system

o Two distinct compartments

∙ Have their own DNA, maternal in origin

∙ Divide on their own, independent of cell

∙ Have ribosomes, produce enzymes necessary for ATP production  ∙ Endosymbiont theory describes proposed origin of both mitochondria and  chloroplasts

Chloroplast 

∙ Two outer membranes

∙ Semifluid stroma; site of carbon fixation  

∙ Inner thylakoid membrane system; converts light energy into chemical energy ∙ Photosynthetic pigments found in other plastids

Cytoskeleton 

∙     Protein fibers that support and give shape to a cell, involved in organelle movement  throughout cell, chromosome movement during cell division and large cell  movements (cell motility and cytokinesis)

∙     3 groups of fibers classified according to size:

o Microtubules (thickest)

o Intermediate filaments

o Microfilaments (thinnest)

Components of the Cytoskeleton 

∙ Microtubules  

o Alpha and beta tubulin subunits, form hollow tube

o Provide framework for cell, organized by centrosome from which they usually  originate  

o “rail” system for organelle transport

∙ Component of centriole

o Replicated prior to mitosis

∙ Form cilia and flagella  

o 9 + 2 arrangement (eukaryotic characteristic)  

Cilia and Flagella and the Structural Basis of Cell Motility

∙ Surrounded by plasma membrane

∙ Motor proteins (dynein toward – end; kinesin toward + end) on microtubules use ATP  to change shape and “ratchet” past one another

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∙ Movement causes bending of cilia/flagella

Microfilaments (actin filaments)

∙ Solid rope of two actin proteins

∙ Thinner and more flexible than microtubules

∙ Principle component of muscle fibers

∙ Provide mechanism to support cell shape. Found just inside the cellular membrane ∙ Enable cell movement, phagocytosis and cytokinesis  

Intermediate Filaments

∙ Tough and durable, made of keratin

∙ Mechanically strengthen/reinforce cells or cell parts that are under stresses o Provide structure to long cells

o Found in desmosomes

o Give nucleus shape (nuclear lamina)

Cell to Cell Junctions 

∙ Plants

o Plasmodesmata

 Perforations in cell wall that allow passage for water/solutes to  

adjacent cells

∙ Animals  

o Tight junctions: prevent leakage between cell (in stomach)

o Desmosomes: mechanically attach cells to each other, serve as anchoring  sites for interfilaments in cells

o Gap junctions: analogous to plasmodesma, function as common pathway  between cells. Cardiac muscle, nerves

Plant Cell Walls 

∙     Protect plants, allow for shape and prevent excess H2O uptake

o Composed of cellulose

∙     Plasmodesmata connect with neighboring cells when alive

∙     Secondary cell wall inside of primary wall, forms wood

∙     Cell secretions form pectin (polysaccharide glue) which acts as adhesive o Laid down in middle lamella to hold cells together

Extracellular Matrix (ECM) 

∙     Intricate network of proteins and polysaccharides that are organized into a  meshwork on the outside of cells

o Large polysaccharides and proteoglygans form a “gel-like” material that resist compression

o Proteins like collagen (most abundant protein in animals as part of bone and  skin) and elasin (stretch and recoil) provide structure and strength  ∙     Adhesive-like proteins (fibronectins and laminin) help cells attach to the appropriate  part of the ECM

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BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY

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CHAPTER 7: MEMBRANE STRUCTURE AND FUNCTION

∙ The plasma membrane is the boundary of life. Like all biological membranes, it  has selective permeability, allowing some materials to cross it more easily  than others. According to the fluid mosaic model, biological membranes consist of various proteins that are attached to or embedded in a bilayer of amphipathic phospholipids

The Fluidity of Membranes 

∙ Membranes are held together by weak hydrophobic interactions o Lateral movements of phospholipids is rapid

o Proteins move slower and in a directed matter (most are immobile because  they are attached to the cytoskeleton and extracellular membrane) ∙ Phospholipids with unsaturated hydrocarbon tails maintain membrane fluidity at  lower temperatures because the kinks in the hydrocarbon chain prevent  solidification

∙ Remains fluid until phospholipids solidify at lower temperatures ∙ Steroid more common in plasma membranes of animals, cholesterol, restricts  movement of phospholipids and thus reduces fluidity at warmer temperatures o Also prevents close packing of lipids and so it enhances fluidity at lower  temperatures

Evolution of Differences in Membrane Lipid Composition

∙ Variations in membrane-lipid composition and the ability to change the composition  in response to changing temperatures are evolutionary adaptations  

Membrane Proteins 

∙ Integral proteins: transmembrane proteins  

o Center is hydrophobic and outer edges are hydrophilic

o Have hydrophilic channels through the center

∙ Peripheral proteins: not embedded; loosely bound to integral proteins o Support for plasma membrane  

Functions of Proteins 

1. Transport

a. Hydrophilic channel

b. Change shape

c. Hydrolyze ATP to pump substances  

2. Enzymatic Activity

a. Membrane protein may be an enzyme with active site exposed

3. Signal Transduction pathway  

a. Membrane protein (receptor) has binding site with specific shape b. External messenger (signaling molecule) cause proteins to change shape  by binding to it

4. Cell to cell recognition  

a. Glycoproteins serve as identification tags specifically recognized by  membrane proteins of other cells

b. Short-lived

5. Intracellular joining

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a. Membrane proteins of adjacent cells hook through junctions

b. Long-lived

6. Attachment to cytoskeleton and extracellular membrane  

a. Microfilaments non-covalently bound to membrane proteins

b. Maintains cell shape and stabilized location of membrane proteins

Diffusion 

∙ Solutes move from a high concentration to a low concentration; down concentration  gradient due to thermal motion

∙ Diffusion of one solute is unaffected by the concentration gradient of other solutes ∙ Passive transport: diffusion of substances across biological membranes o Permits solute to move in either direction; net movement occurs down its  concentration gradient

H2O Balance of Cells Without Walls 

∙ Tonicity: ability of surrounding solution to cause a cell to gain or lose H2O o Depends on the solute concentration that cannot pass the membrane  ∙ Osmoregulation: control of solute concentration and water balance  

H2O Balance of Cells with Walls 

∙     Walls help maintain H2O balance  

∙     Turgor pressure: opposes further uptake of water

Facilitated Diffusion 

∙ Passive transport of polar molecules or ions aided by proteins (proteins speed  movement)

∙ Channel proteins—ion channels/aquaporin

o Gated channels  

∙ Carrier proteins change shape

∙ Ligand channels  

Active Transport 

∙ Pump a solute against its gradient

∙ Uses carrier proteins (allows cell to maintain a gradient different than its  surroundings)

∙ Cytoplasmic side is negatively charged and the extracellular side is positively  charged

∙ Membrane potential favors passive transport of cations into the cell and anions out ∙ Two forces drive the diffusion of ions:

o Chemical force (the ions’ gradient)

o Electrical force (effect of membrane potential on ions’ movement) ∙ Some membrane proteins that transport ions contribute to the membrane potential

Electrogenic Pump 

∙ Transport protein that generates voltage across membrane by active transport of  ions (stores energy for cellular work)

o Na-K pump (animals): maintains osmotic balance and establishes  electrochemical gradient

 Antiporter: results in net negative charge in cell, hydrolyzes ATP to  move ions

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BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY

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o Proton pump (plants, bacteria, fungi): actively transports H+ out of cell

Cotransport 

∙ Single ATP powered pump that transports specific solute and indirectly drives active  transport of other solutes

∙ Plants: load sucrose made by photosynthesis in leave veins

∙ Animals: helps with diarrhea (Na levels drop as too much waste is expelled. NaCl and glucose allos solutes to be taken up by the Na-Glucose cotransporters and pass into  the blood)

Exocytosis 

∙     Process by which the smooth and rough ER replace lipids and proteins lost from the  plasma membrane

∙ Cell secretes biological molecules by fusion of a vesicle with the plasma membrane ∙ Contents of vesicles spill to the outside of the cell, vesicle becomes part of the  plasma membrane  

∙ Does not move water and solutes out of the cell; only removes large, insoluble  particles

∙ Used by secretory cells to export products

o Delivers proteins and carbohydrates from the golgi body to outside of the cell  when making the plant cell wall

Endocytosis 

∙ Cells take in biological molecules and particulate matter by forming new vesicles  from the plasma membrane

∙ Means by which large protein molecules enter cells

∙ Small area of plasma membrane sinks inward, forms pocket and pinches in

Receptor Mediated Endocytosis

∙ Enables cells to acquire specific substances from the extracellular fluid ∙ Human cells taken in cholesterol for membrane and steroid synthesis o Cholesterol binds to LDL receptors on plasma membrane  

o Act like ligands: molecule that specifically binds to receptor site on another  molecule

Pinocytosis  

∙ Droplets of extracellular fluid are takin into the cell in small vesicles ∙ Uptake of water and solutes into the cell by formation of vesicles at the plasma  membrane

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