VCU BIOL 151: Introduction to Biological Sciences Exam 1 Notes PDF

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Summary

Professor: Merk
Topics Covered:
Introduction to Life
Atoms, Bonds, and Water
Carbon and Organic Molecules
Molecules & Membranes
Comparing Components of Cells...

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Bio 151 Study Guide #1 Introduction to Life Earth has been around for a hecking long time - 4.5 billion years o First true cells = prokaryotes from 3.9 billion years ago o Has water – important for life, required for life to exist  Early Earth was too hot for liquid water, it had to cool down first  Ice = potential for life  Came from icy comets New life followed water o Earliest cells = fossils found in Australia from 3.5 billion years ago  Similar to cyanobacteria – photosynthetic organism  Prokaryotic, small and simple – no complex parts  Able to live in hostile environment Larger cells came 500 million years ago, plants and animals o Humanoids came 2.5 million years ago o Anatomically modern humans – 200,000 years ago Life – things all living things have in common o Cells o Adaptation o Reproduce o Organized o Growth o Metabolism o Homeostasis o Response to Stimuli Order + Cells o All life organized on inside  Specific to carry out jobs o All life consist of one or more cells  Atoms  molecules  cells  organelles  Amoebas are single-celled  Bigger things consist of many cells  Specialized  Form stuff like tissue  organs  organ systems o Failure of organization = bad Response to stimuli o Stimulus: Anything the organism can detect and respond to o Organisms sense surroundings, responds accordingly  Ex: Venus fly trap Reproduction o Single cells just divide and make identical copies (same DNA)  Mitosis  Makes a copy of the DNA  One cell splits into two identical cells  Variation comes from mutations o Multi-celled  sexual reproduction  Involves the passing down of DNA from parent to offspring  Offspring are similar (but not identical) to parents  Combining parent’s DNA  Diverse offspring  allows species to evolve more  Genetic diversity = required for evolution Adaptation – organisms are well adapted to their environment due to natural selection o Some traits  more common because allows organism to thrive in environment Growth and Development - Organisms grow & develop according to their genes o Genes – recipe for proteins  makes everything  Gene: Segment of DNA containing information for a protein  Provides instructions for each species’ unique traits o Most individuals share traits within a species Homeostasis: Steady state internally so everything functions properly o Maintaining constant internal conditions

Organisms evolved to maintain homeostasis in certain environments  Ex: Temp, pH, concentration of chemicals  Not all organisms regulate body temperature  Ex: Camels with humps, polar bears, panda bears  Not always beneficial if environment is rapidly changing Energy – needed for metabolic processes o Attained from eating or photosynthesis (sun) o Various chemical processes taking place in cells of organism Adaptation + Energy - Making use of food available o Ex: Koalas and eucalyptus leaves, anteater and ants, sloth and leaves o Digestive system – determines what can be digested and how efficiently o Behavior – ways to get food o Anatomical Structures  Ex: Anteater and nose o Metabolism - How much energy you could use  If the energy supply is limited, metabolic reactions proceed more slowly o

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Atoms, Bonds, and Water Everything is made of atoms o Atoms: Tiny particles that consists of protons, neutrons, and electrons o 3 Main particles  Protons = +1, weighs 1  Neutrons = 0, weighs 1  Electrons = -1, weighs essentially nothing o Most of an atom’s volume is empty space  Nucleus = size of a pea Particles gives characteristics to an atom o Protons determine atom identity o Electrons determine bonding behavior – interaction with other atoms  Bond types – sharing or taking electrons o Neutrons affect mass, no effect on identity Element: Substance made of one atom type o 94 = naturally occurring, 25 = made in lab o Organized on periodic table based on atomic number (protons)  Electron number = same as proton number  No +/- = neutral  Can figure out number of neutrons from mass  subtract mass from protons  Decimal point – due to variation in neutron number depending on element o Has different properties - chemical and physical Working with CHNOPS – makes up 96% of mass of all living organisms Neutrons determine mass o Atomic mass: Number of protons + neutrons o Proton number will be smaller than atomic mass Isotope: Atom with different neutron number o Essentially the same but different mass o Ex: Carbon  Used to track things o Radioisotope: Unstable (radioactive) isotopes  Used for carbon dating – older fossils have different carbon makeups Electrons are found in orbitals outside nucleus o Orbitals: Regions around nucleus where we expect to find electrons  Each orbital holds 2 electrons  Can have various shapes o Bigger atoms have more electrons, fills more orbitals o Columns in periodic table based on orbitals o Fill orbital in sequence, moving farther away from the nucleus  Located at different distances from nucleus  First shell fits 2  Second fits 8  3rd shell and beyond fits 8 – doesn’t really matter in bio

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Important because electrons determine bonding o How many electrons found in outermost shell = important  Number of electrons in the outermost shell ( valence shell) determines reactivity of an atom o Atoms form bonds to fill outer shell, wants full valence  Exception = hydrogen  Can gain/lose electrons or share with other atoms  Depends on atom Molecule: Atoms held together by bonding o Can contain multiple atoms of same type o Compounds: Molecules consisting of different elements Ionic Bonds: Electrons are transferred between atoms o 1 or more electrons will go from an atom to another  One atom steals the outermost electron(s) from the other  Changes charge  Ion: Charged atom/molecule o Why it’s called ionic bond o Opposites attract – the 2 atoms stick together and are bonded  One atom will most likely have 1 or 2 electrons, other will have 6 or 7  They both end up with 8 in their valence shell  The metal’s original valence shell is now empty, but the new valence shell has 8 electrons o Formed between metal and nonmetal  Metals on left will have 1 electron in outer shell  2nd column have 2 electrons  Last column = noble gases – has full shell o Very strong in a solid state, dissolves in water though  Not very useful or biological stuff Covalent Bonds: Sharing valence electrons o H-Bonds = result of covalent bond o Occurs between atoms that want to share  Strongest type of bond in biology  Both think the shared pair is theirs, which brings them up to 8  2 in the case of hydrogen o Forms between nonmetals o 2 kinds  Nonpolar Covalent: Equal sharing of electrons  Typically between same type of atom  Refers to ends of the bond  Polar Covalent: 2 different atoms sharing electrons unequally  Stranger atom pulls the electron closer to itself o Makes one side partially negative and partially positive  Most things in cells = polar because cell is made of water Hydrogen Bonds: Attractions between 2 polar molecules or 2 polar regions of a molecule o Don’t change electrons o Happens between H & F, O, N o Very polar bonds o Many of water’s special life-giving properties are due to extensive H-bonding between water molecules o Individually weak, but collectively strong Electronegativity: How strongly an atom pulls electrons towards itself o Ex: Water – oxygen is more electronegative, has partial negative charge o Polar molecules have a partial negative and partial positive side due to covalent bonds  The stronger atom (high EN) will have a slight – charge while the other will have a slight + charge  More polar if bigger difference in electronegativity  Lots of O, N, and F = polar  Considered nonpolar if 2 atoms are similar in electronegativity – basically neutral  H-C = nonpolar o Upper right of periodic table = most electronegative

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 Bottom left is least electronegative o Polarity affects whether a molecule can dissolve in water Like dissolves like o Hydrophilic: polar, dissolves in water; water loving o Hydrophobic: nonpolar, doesn’t dissolve in water Water = important for life, different from other liquids o All its unique properties are due to H-bonds o Solid water is less dense than liquid water  H-bonds locked in a lattice in solid water  Molecules further apart in ice than liquid water  Why ice floats  Water under ice doesn’t freeze – life can still continue  Less heat needed to melt the icy surface o High Specific Heat: How much energy is required to raise 1g of a substance by 1 degree C  Takes a lot of energy to warm and cool water  H-bonds must be broken before heat can increase molecular movement  Helps keep temperatures constant o High Heat of Vaporization: Takes lots of energy for water to evaporate  H-bonds must be broken  Need lots of heat from environment to evaporate – molecule breaks off and leaves  Takes heat from environment, cools environment down when evaporating  Ex: Sweating o Cohesion: Water sticks to water o Adhesion: Water sticks to other things  Cohesion + adhesion = why water moves through plants – xylem o High Surface Tension: Makes it hard for things to break through water  Water molecules are tightly bonded to each other  Minimize surface area  Water resists force that depresses the surface o Good solvent for dissolving polar things/charged things  Why ionic bonds come apart in water Carbon and Organic Molecules Carbon = important o Has 4 atoms in outer shell, can form 4 covalent bonds  More than most atoms  4 electrons in its valence shell  Wants 4 more o Can form double and triple bonds  Shares 2 or 3 electrons o Versatile – life atom, all molecules in cells have carbon 4 main groups of organic molecules o Organic Molecules: Molecules based on carbon  Proteins  Carbohydrates  Lipids  Nucleic Acids o Polymers: Large molecules built of many small monomers  Repeating units  Aka macromolecules because they can get very large (MW over 1000 g/mol) Macromolecules have chemical functional groups attached o Functional Group: Small groups of atoms frequently found in biological molecules o Can change molecule’s shape, polarity, and charge  Know if a molecule is polar/not if adding groups o Adding functional groups  more likely to form H-bonds o Affect how the molecule interacts with other molecules, and with water SHAPE INFORMS FUNCTION o The function of a macromolecule depends on its 3D shape and chemical properties o Disrupting shape disrupts function o The same molecule in different organisms usually has a similar function

Conserved – when something useful evolved once, it was inherited by later organisms  Evolution from a common ancestor  Allows us to eat each other and utilize similar molecules o Affects interactions with other molecules Condensation Reactions (Dehydration Synthesis): Form covalent bonds to link monomers o H & OH bond to form water, other monomers bond together  Release a water molecule in the process o Requires energy input  Building bigger things require energy, breaking them releases energy Hydrolysis: Breaking water molecule and bonds between monomers o Reverse of condensation o Releases energy Proteins o Very diverse in chemical properties and function – important o Monomers = amino acids (20 different types)  Like Legos  A protein consists of one or more linear chains of amino acids  Amino acids linked together, folded up to form 3D structure o The sequence of different amino acids in a chain determines the protein o A protein consists of one or more linear chains of amino acids o Have core structure and R-group  Amino group + carboxylic acid + alpha-carbon + side chain (R-group)  Different R-groups affect overall polarity and charge o Cell knows to add which one because of genes o Central Dogma – transcription and translation o Peptide bonds: Bonds that link amino acids  Formed by condensation reaction  Connected by alpha-carbon and nitrogen on other amino acid  Protein = polypeptide basically o Protein Structure: Sequence polypeptide  3D shape  Primary Structure: Sequence of amino acids in the chain  Secondary: Backbone of amino acids interacting with each other  Folding of the polypeptide chain as a result of Hydrogen bonding between amino acid “backbones”  Interactions between non-R groups o R groups are not directly involved  Produces 2 structure types o Alpha helix: Coil with R-groups extending outward from the helix o Beta sheet: Two parts of a polypeptide chain aligned and held together by H-bonds  Easily formed because backbone lends itself  Useful for forming pores in membrane for membrane transport  Tertiary: 3D folding of the chain due to interactions between R-groups  H-bonds can form between R groups  Charged R-groups can form ionic bonds  Hydrophobic R-groups turn inside to avoid water  Covalent “disulfide bridges” can form between sulfurs of two cysteine R-groups  Most are done at this point, now functional  Quaternary: Multiple polypeptide chains joined together to carry out function  Subunit: Each polypeptide chain o Ex: Hemoglobin o The function of a given protein is determined by:  Final shape = VERY important  Misfolding/mutation  nonfunctional protein  If it wants to interact with a molecule, that molecule has to “fit”  Exposed R-groups determine interactions  Must be complementary to bond o Can be affected by internal conditions  Denatured: When a protein loses its 3D structure  Increased temperature  denatures proteins 

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 Rapid molecular movement disrupts H-bonds and hydrophobic interactions  Breaks bonds and unraveled proteins now not functional  Change in pH causes denaturing  Affects which R-groups form ions  Can disrupt ionic interactions  Change in polarity affects solvents interacting with R-groups  Can disrupt H-bonding and/or hydrophobic interactions o Chaperone Proteins: Provide a suitable environment for new (or sometimes denatured) proteins to fold into the correct shape  Protein that needs folding goes inside and lid goes on top  Heat shock proteins o Spongiform Encephalopathies: Diseases caused by abnormal folding of proteins (prions) in the brain  Abnormally folded prions trigger normal prions to change their shape as well  Accumulate and kill brain cells  Prion aggregates lead to large-scale cell death: sponge-like appearance of brain  Progressive neurodegeneration; always fatal  Ex: Mad cow disease (BSE), Creutzfeld-Jacob Disease/Kuru (human), Scrapies (sheep) Carbohydrates: CnH2nOn; can have other things attached, Carbon chains with –H and –OH linked to them o Used for energy and structural material  Produce certain amino acids  Can be used for other things o Molecular weight = 100-100,000 Daltons o Monomers = monosaccharides (aka simple sugars)  Ex: Glucose – most common, found in all organisms o Typically in ring structure under physiological conditions  Looks like a mouse LMAO  Hexose: All 6-carbon monosaccharides  Pentose: All 5-carbon monosaccharides o Polymers = Disaccharide and polysaccharides linked together via a condensation reaction  Ex: Sucrose = disaccharide, consists of glucose and fructose  Glycosidic bond, glyco = sugar o Polysaccharide: Consists of many (hundreds or thousands) of monosaccharides linked together  Can be used for energy directly by breaking down or build bigger polysaccharides  Some have branches – easier to break down  Starch: Energy storage in plants o Consists of glucose monomers o Food source for baby plants that can’t photosynthesize yet  Form aggregates called starch grains in seeds o Branched – can break glucose off in many directions  Cellulose: Structural material for plants, found in cell wall o Linear molecules that run parallel to each other  Not branched o The most abundant of all macromolecules o Glucose monomers o More chemically stable than starch  Won’t break down under harsh environmental conditions = great structural material o Fiber – can’t break down when we eat it  Why celery has negative calories o Some animals can break it down  Glycogen: Short-medium term energy in animals o Highly branched o Stores glucose in liver and muscles  Breaks off and goes into bloodstream when we hunger  Flight/fight response o Glucosamine: Important constituent of joint fluid, cushions joints  Monosaccharide

 Glucose with amine group on it Chitin: Derivative of glucosamine, makes up exoskeletons of insects and shells  Glucose + N-acetyl group  Polysaccharide  Structural material  Indigestible to humans Lipids: Fats o Insoluble – nonpolar and not water soluble o Hydrocarbon, mainly hydrogens and carbons o Triglyceride: Long-term energy storage; fats and oils  Composed of 3 fatty acid tails + glycerol molecule  Fatty Acid: Long chain of hydrogens and carbons with polar head o Very nonpolar  Saturated Fatty Acid: No double bonds in its chain o Has as many hydrogens and carbons it can o Straight, can pack together tightly o Solid at room temperature  Unsaturated Fatty Acid: 1 or more double bonds in carbon chain o Holds both members more rigidly  kink  Can’t pack together o Liquids at room temperature o Phospholipid: Forms cell membranes  Only has 2 chains and a phosphate group at the head  Amphipathic: Has polar and nonpolar regions  Has to form phospholipid bilayer  Nonpolar tails inside, polar heads on outside  Rescales itself if the cell has damage o Carotenoids: Pigments that absorbs light, makes yellow foods  Makes vitamin A – good eyesight  Also in green leaves but masked by chlorophyll o Steroids: Signals cells in body, multiple carbon rings linked together  Cholesterol: a cell membrane component  2 types of hormones – some are proteins, some are lipids  Steroid hormones are synthesized from cholesterol  Not all hormones = steroids o Waxes: Nonpolar, malleable at room temperature  Plant leaves have waxy surface  Minimize water loss, keep pathogens out  Secreted by glands in the skin of birds and mammals to coat hair or feathers  Repel water, keep hair/feathers pliable Nucleic Acids: Polymers specialized for the storage and transmission of genetic information o Used for storing and transmitting information o 2 types:  DNA: Long term, encodes hereditary info and passes it from generation to generation  Negatively charged molecule  RNA – short term, used to make proteins from DNA o Monomers = nucleotides  Made of a sugar, nitrogenous base, and a phosphate group  Nitrogenous Base: Adenine, guanine, cytosine, thymine o Uracil instead of thymine in RNA o Contain nitrogen  Linked via phosphodiester bonds o 2 anti-parallel strands of DNA are held together by pairs of bases, linked by hydrogen bonds  Base pairs – A&T, C&G  Complementary o DNA – double helix shape, all DNA visually looks the same  Information stored in sequence of base pairs o RNA – Single stranded, copy of one gene  Shorter than DNA  Made of sugar + phosphate + base o

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Can base pair to itself – like fold over and pairs with itself  A & U, C & G o New cells need the DNA when replicated  DNA Replication: Makes an exact copy of the original DNA  Passes on the genetic info to the new cell  Transcription: Creates an RNA copy, happens all the time  Makes a protein based on the info in that gene  Transcription  Translation  DNA replication only happens when they need DNA copies o Adenosine Triphosphate (ATP): Energy carrier and storage  Can be used during translation  Sometimes GTP used – GTP has G base instead of A o Cyclic adenosine monophosphate (cAMP): Transmits information within cells Viruses can have DNA and RNA o No lipids because no proteins o Have some properties of living organisms 

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Molecules & Membranes Cell membranes composed of phospholipid bilayers ...