bio101

the study of life, the chemical context of life, water and life

biology

• scientific study of life and living things

• organizational ladder

biological ladder

1. atom

2. molecule

3. cell

4. tissue

5. organ

6. organ system

7. organism

8. population

9. community

10. ecosystem

11. biosphere

basic characteristics of life

1. living things require materials and energy

2. living things maintain homeostasis

3. living things respond to their environment

4. living things reproduce and develop

5. living things adapt and evolve

living things require materials and energy

• Energy goes to the consumer

• Decomposition last part of the cycle, the dead organism goes into the ground and becomes nutrients for the flower to grow and be eaten

• Metabolism = sum of all chemical reactions

• Organisms must acquire materials from their environment and convert it to energy

• chemical cycling and energy flow is essential

living things maintain homeostasis

• examples of constant states: temperature, moisture levels, sugar levels, pH, etc.

living things respond to their environment

• Appropriate responses ensure the survival of the organism and allow it to carry on its daily activities

• Responses focus on maintaining homeostasis.

• Behaviors = Collectively the activities conducted in response to the environment

living things reproduce and develop

• genes = how living things pass along their genetic info to offspring

• mutations to genes increase diversity

• living things start as an underdeveloped form

living things adapt and evolve

• Organisms adapt to make them more able to function in a particular environment.

• evolution = result of s series of adaptations over time that lead to changes in a population

• Evolution is driven by Natural Selection.

all living things have/are/do/need

• D = DNA

• O = organized

• G = grow

• S = stimulus response

• R = reproduce

• E = energy

• A = adapt

• C = cells

• H = homeostasis

taxonomy

• organisms are grouped into categories using this method

• groups are divided based on shared traits/characteristics across organisms

• carl linnaeus

taxonomic levels

1. domain (largest)

2. kingdom

3. phylum

4. class

5. order

6. family

7. genus

8. species (smallest)

dear king philip came over from Germany sick

domains

1. bacteria

2. archaea - extremophiles

3. eukarya

kingdoms in eukarya domain

1. protista

2. fungi

3. plantae

4. animalia

scientific method

• observation

• hypothesis

• experimentation

• conclusion

process of scientific method

• problem/question

• research & observations

• hypothesis

• design the experiment

• run the experiment

• results

• conclusion

• communicate

variables

things that change in an experiment

• independent - what the investigator changes

• dependent - what the investigator measures

control

a test group that is not exposed to experimental conditions (not affected)

allows for a comparison

constants

conditions that are kept the same in all experimental groups

goal of scientific method

• form theories (how or why something happens)

• form laws (predict what will happen under certain conditions - backed by math)

atoms

• Atoms consist of subatomic particles

  • protons

  • neutrons

  • electrons

• protons positively charged

  • identify the element

• neutrons

  • Identify the isotope

• electrons are negatively charged

  • create the chemistry

electrons and electron shells

• constantly moving

• cant identify precisely where they are

• Move in shells that surround the nucleus

  • Each shell has an average distance away from the nucleus

  • Electrons are somewhere in the shell at least 90% of the time

• electrons in shells further away from the nucleus have more potential energy than electrons closer to the nucleus

• Electrons fill the shells beginning close to the nucleus

• The more electrons, the more shells are needed to hold them all (and the bigger atom)

• The first shell holds 2 electrons

  • Simplifying, subsequent shells hold 8 electrons

• The outermost shell of any atom is called the valence shell

  • this is where the chemistry happens

chemical bonds

• 2 or more atoms close together create a molecule when they bond together

• bonds involve electrons

• 2 main types that make a molecule

  • ionic bonds

  • covalent bonds

electronegativity

• the attraction of a given atom for the electrons in a covalent bond

• the more electronegative an atom, the more strongly it pulls shared electrons towards itself

ionic bonds

• When 2 atoms interact, the more electronegative atom strips a valence electron away from the less electronegative atom

• pulled together and stay together bc opposites attracting

• the more electronegative atom now has one extra electron and carries a negative charge

  • called an anion (a negative ion)

• the less electronegative atom now has one less electron and carrier a positive charge

  • called a cation (cats are ‘paw’sitive)

• atoms can be held together by their electrostatic interactions

• compounds with ionic bonds are ionic compounds or salts

• salts

  • NaCl

  • CaClsub2

  • KCl

  • MgClsub2

covalent bonds

• strongest bonds

• occurs when 2 atoms share a pair of valence electrons

• as 2 atoms of hydrogen approach each other the electron that orbits the nucleus of one atom becomes attracted to the neighboring atom’s nucleus

electronegativity: non-polar bonds (=)

• Non-polar covalent bond: attraction for the electrons by the nuclei in a covalent bond is equal

  • the paired electrons will spend an equal amount of time in the orbitals of both atoms

electronegativity: polar bonds (not =)

• polar covalent bond

  • attraction for the electrons by the nuclei in a covalent bond is unequal

    • the paired electrons will spend more time in the orbital of the nucleus of the more electronegative atom

• the more electronegative atom carries a partial negative charge (delta -)

• the less electronegative atom(s) carry a partial positive charge (delta +)

polar vs. non-polar

• Oxygen and nitrogen are very electronegative and form polar covalent bonds with carbon and hydrogen

• carbon and hydrogen are approximately the same electronegativity

  • They form non-polar covalent bonds with each other

• Sulfur forms covalent bonds with carbon and hydrogen

hydrogen bonds

• extremely important in biology

  • hold many complex molecules together

  • Though each h-bond is weak, there are often many of them working together

• Hydrogen atoms in a molecule that carry a partial positive charge are attracted to electronegative atoms to which they are not covalently bonded

• This is an interaction between molecules not within molecules

water

• polar molecule

• form hydrogen bonds

  • Form and break with high-frequency

  • Water molecules are constantly forming new hydrogen bonds

• emergent properties

  • Hydrogen bonding that orders water molecules into a high level of structural organization

    • no hydrogen bonds in atoms, just molecules

  • Cohesion/adhesion

    • Hydrogen bonds between water molecules increase the cohesion of water

    • Cohesion is the linking together of %%like %%molecules

    • adhesion is when water molecules form hydrogen bonds with non-water molecules which leads to adhesion, the clinging of one substance to another

    • cohesion contributes to the transport of water and dissolved nutrients against gravity

    • adhesion of water to cell walls helps counter the downward pull of gravity

  • moderation of temp by water

  • floating ice on liquid water

  • water is an excellent solvent

• surface tension

  • measure of how difficult it is to stretch or break the surface of a liquid

    • hydrogen bonds between water molecules give water a high surface tension

  • at the interface between water and air

    • ordered arrangement of water molecules

    • hydrogen bonded to one another and to the water molecules below

emergent properties of water: moderation of temperature

• water moderates air temperature by:

  • absorbing heat from air that is warmer

  • releasing stored heat to air that is cooler

• heat

  • energy measure of the matter’s total kinetic energy due to the motion of its molecules

  • heat depends on the matter’s volume

• temperature (not energy)

  • measure of heat intensity that represents the average kinetic energy of the molecules

  • temperature does NOT depend on the matter’s volume

measuring heat

• 1 cal: amount of heat it takes to raise the temperature of 1g of water by 1 degree celsius

  • So, when 1g of water cools by 1 degree celsius it releases 1 calorie of heat

• 1 kilocal: amount of heat necessary to raise the temperature of 1kg of water by 1 degree celsius

• 1gal: 4L

• 1ml: 1g

• 1L: 1kg

• Room temp: 70 degrees F / 21 degrees C

• Boiling: 100 degrees C / 212 degrees F

• specific heat

  • amount of heat that must be absorbed or lost for 1g of a substance to change its temp by 1 degree C

  • water: 1 cal/g degrees C

  • alcohol: 0.6 cal/g degrees C

  • glass: 0.2 cal/g degrees C

  • aluminum: 0.2 cal/g degrees C

  • iron: 0.1 cal/g degrees C

  • gold: 0.03 cal/g degrees C

    • Water’s high specific heat is due to hydrogen bonding because a lot of energy is needed to break a hydrogen bond

      • As water absorbs heat, the kinetic energy is used to break the hydrogen bonds between the water molecules before the individual water molecules can speed up

    • energy is released in the form of heat to form hydrogen bonds

      • as water cools and the water molecules slow down, more hydrogen bonds form and release heat, slowing cooling process

temperature moderation of water

• oceans moderate coastal climates by absorbing or releasing heat

• cool ocean reduces coastal air temperatures by absorbing heat

• ~75% of the earth is covered in water which keeps the av temp on earth in a habitable range

  • absorbs heat during the day and releases it at night

• evaporative cooling keeps organisms cool

  • when water molecules evaporate, the remaining liquid water is cooler

  • the molecules with the most kinetic energy (hottest) leave the liquid phase (evaporate/transform into water vapor)

  • av kinetic energy of the remaining molecules is lower

emergent properties of water: floating ice on liquid water

• most elements’ solid phase is denser than the liquid phase because molecules are packed more closely together

• water is unusual because the solid phase is less dense than the liquid phase

  • when ice forms, the hydrogen bonds between the water molecules cant break

  • just above freezing the hydrogen bonds can break and reform which allows the molecules to pack tightly

• floating ice insulates water below and helps prevent it from freezing which is good for organisms living in the water

emergent properties of water: water is an excellent solvent

• solution

  • liquid that is a homogenous mix of 2+ substances

• solvent

  • dissolving agent of a solution

• solute

  • substance that is dissolved in a solution

• solute dissolves in a solvent to make a solution

• The polarity is what makes water molecules a powerful solvent, especially for salts (ionic compounds)

• Negatively charged oxygen atoms are attracted to cations

• water dissolves things that are charged

• positively charged hydrogen atoms are attracted to anions

• water molecules will form a hydration shell that encapsulates each ion of the salt

water can dissolve other molecules

• some amino acids (building blocks of proteins) have positive or negative charges

• water will interact with the charged surface of a protein, providing a hydration shell

hydrophobic vs. hydrophilic

• hydrophilic

  • water loving

  • salts, charged molecules and polar molecules (amino acids)

  • will dissolve in water

• hydrophobic

  • oils, non-polar amino acids

  • molecules that are nonionic, nonpolar, or cannot form hydrogen bonds

  • will not dissolve in water

• amphipathic molecules

  • Large biological molecules that usually have both hydrophobic and hydrophilic regions

acid, bases, buffers, pH

• Sometimes a water molecule breaks apart to create ions like a salt

  • A hydrogen atom participating in a hydrogen bond between 2 water molecules can shift from one molecule to the other

    • When it shifts, it leaves its electron behind so it actually transfers an H+ ion

    • Now, the water molecules that lost their proton a hydroxide ion

H+ and OH- ions

• rare event

  • only one water molecule in every 10 mil dissociates into ions

• neutral

  • concentration of H+ and OH- ions in pure water is 1 x 10^-7 (mol/L)

acids and bases

• acid

  • substance that increases the hydrogen ion (H+) concentration of a solution

    • HCl dissociates into H+ and Cl- in water which increases the concentration of H+

• base

  • substance that reduces the hydrogen ion (H+) concentration

    • NaOH dissociates into Na+ and OH- in water

    • the OH- can react with H+

• basic solution

  • 2:7

  • H+ : OH-

• neutral solution

  • equal

  • 5:5

  • H+ : OH-

• acidic solution

  • 7:2

  • H+ : OH-

pH

• pH scale developed because H+ and OH- concentrations of solutions can vary by a factor of 100 trillion

• scale compresses the range of H+ and OH- concentrations by using logarithms

• each pH unit represents a tenfold difference in H+ and OH- concentrations

  • x10 up 1 number, x10 up another number, etc.

  • when the pH of a solution changes slightly, the actual concentration of H+ and OH- in the solution changes drastically

• pH of a solution defined as the negative logarithm (base 10) of the [H+]

  • pH = -log [H+]

  • neutral water: pH = -log [10^-7]

  • pH = 7

• acids ahve higher [H+], so a lower pH (1-6)

  • -log [10^-4] = 4

• bases have lower [H+], so higher pH (8-14)

  • -log [10^-8] = 8

• pH is a log scale

  • solutions with a different of 1 pH value actually have a 10-fold difference in the concentration of H+ ions

  • solution with a pH of 3 has 10x as many H+ molecules as a solution iwth a pH of 4

• scale starts from 0 at the top and goes to 14 at the bottom

• acids donate H+ in aqueous solutions

• bases donate OH- or accept H+ in aqueous solutions

buffers

• prevent rapid change in pH when an acid or base is added to a solution

• compounds that readily accept or donate H+ ions

• carbonic acid

  • important buffer

  • can lose 2 H+ to form:

    • biocarbonate

      • 1 H+ lost

    • carbonate

      • 2 H+ lost

reaction is reversible

• if extra H+ ions, reaction reverses

  • carbonate accepts an H+ to become bicarbonate

  • bicarbonate accepts an H+ to become carbonic acid

carbonic acid buffers blood

• Blood transports CO2 produced by our cells in theform of carbonic acid.• In the lungs, carbonic acid is converted back toCO2 and expelled

• In the blood, carbonic acid keeps pH = 7.4

  • Adding 0.01 mol of a strong acid to water drops the from 7 to 2

  • Adding 0.01 mol of a strong acid to blood drops the from 7.4 to 7.3

ocean acidification

• ongoing decrease of ocean’s pH cause by uptake of CO2 from the atmosphere

• to reach equilibrium, come CO2 reacts with H2O to form H2CO3 aka carbonic acid

• some carbonic acid dissociates into HCO3 aka bicarbonate and H+

• the excess H+ therefore increases the acidity of the ocean

macromolecules

• monomer

  • Small subunits that makeup polymers

• polymer

  • larger molecules made up of smaller monomers

• biological macromolecules

  • carbs

    • polymer

  • lipids

    • not polymer

  • proteins

    • polymer

  • nucleic acids

    • polymer

• synthesis and breakdown of polymers

  • each polymer is comprised of different monomers

  • the mechanisms cells use to break down and make polymers is the same

    • Dehydration/condensation

      • build polymers and a water molecule is produced

      • monomers connected by covalent bonds (sharing electrons) through the loss of a water molecule

      • each monomer contributes part of the H2O molecule that is lost

        • 1 provides the OH

        • 1 provides the H

    • hydrolysis

      • breaks polymers by adding water molecules

      • each monomer receives part of the H2O molecule

        • 1 receives OH

        • 1 receives H

      • reverse dehydration

carbohydrates

• sugars or polymers of sugars

• monosaccharide

  • sugar monomer

  • monomers from which carbs are built

• structure

  • carbon chains with attached:

    • hydroxyl groups

      • oxygen hydrogen

    • one carbonyl group

      • carbon double bonded to an oxygen

  • 3-7 carbons in the chain

    • most commonly 5 or 6 carbons

  • Multiples of CH2O

    • ribose

      • C5H10O5

    • glucose

      • C6H12O6

      • most common monosaccharide

  • when glucose forms a ring, hyroxyl group on first carbon located either below (α) or above (β) the ring

  • for every C, twice as many H’s and the same number of o’s

carbohydrates: aldose and ketose

• aldose

  • carbonyl group at end of the carbon chain or 1 in from the end

  • a sugar can be an aldose sugar

    • aldehyde sugar

      • glyceraldehyde

      • ribose

      • glucose

      • galactose

• ketose

  • carbonyl group in middle of carbon chain

  • found off second carbon

  • a sugar can be a ketose sugar

    • ketone sugar

      • dihydroxyacetone

      • fructose

      • ribulose

• linear vs rings

  • in 5 and 6 carbon sugars the caronyl group can react with a hydroxyl group, forming a 4 or 5 carbon ring

    • oxygen also in the ring

    • some carbons in the ring some out

    • start at oxygen and go clockwise

carbohydrates: disaccharides

• double sugars

• 2 monosaccharides joined by a covalent bond

  • joined by dehydration reaction

  • maltose

    • 2 glucose molecules

      • brewing beer

  • sucrose

    • one glucose and one fructose

      • table sugar

  • lactose

    • one glucose and one galactose

      • milk sugar

    • intolerant people do not have the enzyme to break down polymers

carbohydrates: polysaccharides

• many sugars

• Many monosaccharides joined by covalent bonds

• energy stores

  • glycogen

    • Animals store glucose as glycogen

      • Highly branched polymer

      • liver and skeletal muscles in humans

  • starch

    • polymers of glucose monomers

    • plants use amylose and amylopectin

      • stored in plastids within the cells

• Structural material for organisms

  • cellulose

    • Plant cell walls

  • chitin (kie-tin)

    • structural polysaccharide

    • produced by arthropods and some fungi

      • Exoskeletons in many bugs and crustaceans

carbohydrates: starch vs. cellulose

• starch

  • contains only α glucose monomers

  • 2 forms

    • amylose

      • unbranched and helical

    • amylopectin

      • branched and helical

  • animals have enzymes that digest starch \n (α glucose)

• cellulose

  • contains only β glucose monomers

    • monomers are “upside down”

  • linear molecule

    • bundle several molecules together to form a microfibril

    • hydroxyl groups on glucose monomers in adjacent fibers can hydrogen bond giving the myofibril strength

  • very few organisms have enxymes that can digest cellulose (β glucose)

  • dietary fiber

lipids

• not a true polymer

  • doesnt have repeating units of monomers

• smaller macromolecules life starch

• made of C, H, and O

  • no set ratio

• common trait: hydrophobic

  • property of repelling or not mixing with water.

  • In the context of lipids, inability to dissolve in water bc nonpolar

lipids: fats

• combination of glycerol and 3 fatty acids

• is an alcohol

  • contains 3 hydroxyls

• fatty acids

  • hydrocarbon chains of 16-18 carbons

  • end of carbon has a carboxyl group

• use a dehydration reaction to link fatty acids to glycerol

lipids: fats and hydrophobicity

• referred to as a triacyglycerol

  • or a triglyceride

  • triacyl

    • 3 fatty acids

    • linked to a glycerol molecule

• covalent bond (ester bond) between:

  • hydroxyl group

    • in glycerol

  • carboxyl group

    • in fatty acid

• fats separate form water because the water molecules hydrogen bond to one another and exclude the fats

lipids: saturated vs. unsaturated fatty acids

• refers to degree of hydration of carbons in the fatty acid components of the fat

  • hydration refers to atoms of hydrogen

lipids: fats saturated with hydrogen

• if all carbons have as many hydrogens covalently bonded as it possibly can have

lipids: fats unsaturated (not saturated with hydrogen)

• One or more double bonds formed by the removal of hydrogen atoms

• maximal of hydrogen is not covalently bonded

lipids: cis vs. trans fatty acids

• double bonds in unsaturated fatty acids

  • cis or trans orientation

  • refers to placement of hydrogen atoms around the double bond

lipids: fat and diet

• diet rich in saturated or trans fats

  • contribute to cardiovascular disease

    • atherosclerosis

      • deposits called plaques develop in walls of blood vessels, causing inward bulges that impede blood flow and reduce resilience of vessels

lipids: phospholipids

• essential for cells

  • make up the cell membrane

• similar to a fat molecule

  • only 2 fatty acids attached to glycerol

• 3rd hydroxyl group of glycerol attached to a phosphate group

• additional small molecules usually charged/polar can be linked to phosphate group for variety

lipids: lipid bilayer

• Phospholipids self organize into bilayers

  • hydrophobic (nonpolar) tails associate together

  • hydrophilic (polar) heads associated with an aqueous environment

• all cell membranes and organelles have a lipid bilayer

lipids: steroids

2 types of chemistry

• organic

  • contain carbon

  • specialized in carbon compounds

  • mostly make up living things

• inorganic

  • do not contain carbon

  • some compounds essential for living

carbon

• has the ability to form 4 covalent bonds

• typically bonds with (most abundant elements in living things)

  • other carbons

  • hydrogen

  • nitrogen

  • oxygen

  • phosphorus

  • sulfur

• carbon skeletons vary in shape

  • changing shape = changing function

• atomic number of 6

  • so 6 electrons

  • 2 in first shell

  • 4 in second shell

    • can hold 8 in this shell

  • usually valence shell is completed by sharing electrons (covalent bonds)

• valence = electrons available for chemical bonding

• carbon is tetravalent

  • carbon can branch off in 4 directions

    • makes 4 bonds so valence = 4

  • oxygen can branch off in 2 directions

    • makes 2 bonds so valence = 2

  • hydrogen can branch off in 1 direction

    • makes 1 bond so valence = 1

• carbon bonded to 4 atoms forms a tetrahedron

  • angles = 109.5 degrees

  • double bonded

    • causes all bonds in the carbon to fall into the same place

• major atomic component of organic molecules

  • carbon

    • valence of 4

  • oxygen

    • valence of 2

  • hydrogen

    • valence of 1

  • nitrogen

    • valence of 3

• CO2

  • carbon joined by 1 oxygen atoms by double covalent bonds

    • each line represents a pair of shared electrons

• hydrocarbons

  • compounds that only contain carbon and hydrogen

  • important for life

    • fat, gasoline made from hydrocarbons

  • good way to store energy

  • hydrophobic

    • most of their bonds nonpolar carbon to hydrogen linkages

• fat

  • large hydrocarbon chains attached to non-hydrocarbon component

• carbon skeletons

  • refers to chain of carbon atoms in a compound’s structure

    • each different arrangement/length is a different compound

  • number and arrangement of chemical groups give molecules unique properties

• isomers

  • compounds that have:

    • same number of atoms

    • same electrons

    • different structures and properties

  • 3 types:

    • structural

      • differ in the covalent arrangement of their atoms

    • cis-trans

      • cis = same side

      • trans = opposite side

      • must have a double bond in the compound

      • The arrangement of atoms around the double bond differs between the isomers

    • enantiomers

      • isomers that are mirror images of each other

      • contains an asymmetric carbon; a carbon bonded to 4 different atoms

• functional groups

  • specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and involved in chemical reactions

  • hydrophilic and

    • increase the solubility of organic compounds in water:

      • hydroxyl

      • carbonyl

      • carboxyl

      • amino

      • sulfhydryl

      • phosphate

    • not reactive but often act as recognizable tag of biological molecules

      • methyl

cell theory

• all organisms are composed of cells

• cells are the basic unit of structure and function in an organism

• all cells come from pre-existing cells (self-reproducing)

all cells have:

• plasma membrane (cell membrane)

  • membrane at the boundary of every cell

  • selective barrier

  • regulates the cell’s chemical composition

• cytoplasm

  • contents of the cell within the plasma membrane

  • in eukaryotes: the portion inside which excludes the nucleus

• chromosome(s)

  • organizing units of DNA

• ribosomes

  • protein synthesis factories

cellular basis of life

• cell is simplest unit necessary for all the activities of life

• introduction to parts of the cell

  • cell size

  • cell types

    • prokaryotic/eukaryotic

    • nucleus

    • endomembrane system

    • mitochondria and chloroplasts

    • cytoskeleton

    • extracellular matrix

cells are genetically very small

• most plant and animal cells are less than 100 μm in size

  • 1 micron = 1 μm = 0.001 mm

• most bacterial cells are less than 10 μm in size

• oxygen/nutrients need to diffuse across the plasma membrane into the cell and wastes need to diffuse out of the cell

• as a cell grows, the volume of the cell increases faster than the surface area

  • volume = cm³ vs. surface area = cm²

• cells must maintain a high surface area to volume ratio to function

  • more surface area provides cells with more contact points with the environment

  • important in cells that exchange a lot of material with their surroundings (secrete/absorb)

• larger organisms does not mean larger cells but more cells

• ALL cells are either prokaryotic or eukaryotic

• prokaryotes (pro no… nucleus/organelles)

  • single cell

  • no nucleus or other organelles

    • DNA concentrated in a region that is not membrane-enclosed: nucleoid

  • 2 of 3 domains of life

    • bacteria

    • archea

      • microorganisms that sometimes live in extreme conditions like deep sea thermal vents: extremophiles

• eukaryotes (eu do… have nucleus/organelles)

  • plants, animals, fungi

    • have a nucleus and other internal membrane-bound organelles

    • can be unicellular

  • endosymbiotic theory

    • eukaryotic cells evolved from a symbiotic relationship between different types of prokaryotic cells… mitochondria and chloroplasts were once free-living bacteria that were engulfed by a larger host cell. Over time, these bacteria became mutually beneficial to the host cell, eventually evolving into organelles with specialized functions. This theory provides an explanation for the presence of DNA in mitochondria and chloroplasts, as well as their ability to replicate independently within the cell.

nucleus

• nuclear envelope

  • membrane that surrounds the nucleus

  • double membrane

  • contains nuclear pore complexes

  • contains structural proteins

    • nuclear lamina

      • lines inner surface

      • helps maintain shape

    • nuclear matrix

      • extends throughout nuclear interior

• nuclear pore

  • small holes that allow transport into and out of the nucleus

• inside the nucleus

  • chromatin

    • contains most DNA material

    • some DNA in mitochondria and chloroplasts

    • evidence of endosymbiotic theory

    • complex of DNA and proteins that make up eukaryotic chromosomes (stringy)

  • chromosomes

    • where nuclear is organized

    • chromosome = ONE very long DNA molecule

    • made of chromatin

  • nucleolus

    • condensed region in the center of the nucleus that produce ribosomes

    • makes and assembles ribosomes

      • ribosomes are then transported to the cytoplasm to make proteins

  • ribosomes

    • small bodies that produce proteins (free and membrane-bound)

    • complexes made of RNA and protein

    • cellular components that carry out protein synthesis

      • cells with high rate of protein synthesis have a very large number of ribosomes

      • free ribosomes are suspended in the cytosol

        • cytosol is a semifluid portion of the cytoplasm

      • bound ribosomes are attached to the outside of the ER or nuclear envelope

    • free and bound ribosomes are structurally identical

      • can alternate between both roles

      • both come from the same pool of ribosomes in the cytoplasm

    • free ribosomes make soluble proteins

    • bound ribosomes generally make protiens that are destined for insertion into membranes, packaging within organelles, or export from the cell

• endomembrane system

  • the collection of membranes inside and surrounding a eukaryotic cell, related either through direct physical contatc or by the transfer of membrane vesicles

    • plasma membrane

    • nuclear envelope

    • endoplasmic reticulum

    • golgi apparatus

    • lysosomes

    • vesicles

    • vacuoles

  • tasks:

    • synthesis of proteins

    • transport of peoteins into membranes and organelles or out of the cell

    • metabolism and movememtn of lipids

    • detoxification of poisons

    • removal of cellular waste

    • acquisition of large materials from outside the cell

• endoplasmic reticulum

  • endoplasmic:

    • within the cytoplasm

  • reticulum:

    • fine network / netlike structure

  • extensive membranous network in eukaryotic cells, continuous with the outer nuclear membrane

  • very extensive

    • accounts for over half of the membrane material in a cell

  • interior of the ER is separate from the cytosol

    • called the lumen or cisternal space

  • synthesis and transport of proteins and lipids

• rough ER

  • has ribosomes attached to its surface

  • secretory proteins are made from the attached ribosomes

    • as polypeptide chain grows from bound ribosome, its threaded into the ER lumen through a pore

    • as it enters the ER luman, it folds into its native shape

  • proteins inside the lumen can be modified by enzymes located there

    • addition fo carbs (glycoproteins)

  • after secretory protein is formed, AER membrane keeps them separate from cytosiolic proteins

  • secretory proteins travel form the er via transport vesicles (escape pods)

• smooth ER

  • site for lipid synthesis

    • including steroids

  • metabolism of carbs

  • detoxification of drugs and poisons

  • storage of calcium ions

  • amount of smooth ER in a cell will depend on the particular function of that cell

    • ovaries prodice steroid hormones, or ovarian cells have more smooth ER than toher cell types

• golgi apparatus

  • shipping and receiving center

  • products of the ER are modified and then sent to other desinations

  • golgi apparatus is especially extensive in cells specialized for secretion

  • made of flat stacks of membrane celled cisternae

  • like the ER, the membrane of each cisterna separates its internal space from the cytosol

• vesicles

  • how materials move from roganelle to organelle

  • from ER to golgi to be processed and packaged

  • from golgi to plasma membrane to be secreted

• lysosomes

  • only in animal cells

  • a membranous sac of hydrolytic enzymes used to digest macromolcules

  • lumen of lysosome is acidic

  • intracellular ddigestion

    • can digest material broght into ecll via phagocytosis

    • can recycle material from inside the cell: autophagy

  • sugars and amino acids tht are produced by digestion in the lysosome pass into the cytosol to be used by the cell

  • help cell continuously renew itseld

  • dugestion products:

    • simple sugars

    • amino acids

    • other monomers used as nutrients

  • damage organelle in a vesicle fuses with the lysosome for digestion

  • recycling of the cell’s organic material: autophagy

• phagocytosis

  • amoebas and other protists eat by engulfing smaller organisms or toher food particles

  • macrophages

    • type of white blood cell

    • engulf bacteria and other invaders to help defend the bodu

    • produces a phagosome: vesicle formed aorund an engulfed bacteria

    • phagosome fuses with a lysosome to form a phagolysosome

    • some dugested prodtcs may be useful to the cell and are moved into the cytoplams

      • others are exported as waste via exocytosis

• vacuoles

  • storage sacs in cells

  • found in plants, fungi, and animal cells

  • many small vacuoles in animal cells

  • large ones in plants and fungi

  • variety of functions depending on the cell:

    • food vacuoles

      • formed by phagocytosis

    • contractile vacuoles

      • expel excess water

      • —central vacuoles (plants)

        • grow with the cell

        • absorb water and store ions like potassium and chloride

        • plant cells englarge as their vacuoles absorb water

        • enables their cell to become larger with minimal investment in new cytoplasm