Biology Midterm: Lectures 1-8 and 27 Flashcards
What is biology the study of
life
characteristics of life (7)
- reproduction
- ability to metabolize
- growth and development
- homeostasis
- sense + respond to stimulus
- has order/organization
- adaptation
reproduction
the ability to generate offspring with new combinations of (parent) DNA
ability to metabolize (2 types)
- catabolism: break down molecules to yield energy
- anabolism: building up of molecules by using energy
growth and development
- growth: size
- development: maturation
homeostasis
the ability to maintain a controlled internal environment
sense + respond to stimulus (2 types)
- immediate: fight or flight, phototropism
- overtime: evolutionary adaptations that do not just occur in 1 individual
has order/organization
made up of at least one cell that has chemical structure and cellular processes
adaptation
changes that occur over time due to natural selection and mutation
are viruses living?
no, because they require a host to reproduce
Classification of Living Organisms (9)
- domain (most inclusive and least genetically identical)
- kingdom
- phylum
- class
- order
- family
- genus
- species
- sub species/strain (least inclusive and most genetically identical)
How were domains discovered and how many are there?
- discovered by woese and fox
- sequenced 165 rRNA genes and found 3 different types
- 3 domains of life
What are the 3 domains and their characteristics?
-Archaea: prokaryotes single celled extremophiles no nucleus -Bacteria: prokaryotes -Eukarya eukaryotes have a nucleus
What organisms are classified as Archaea?
- methanogens (organisms that produce methane)
- extreme halophiles (salt loving)
- extreme thermophiles
What organisms are classified as bacteria?
- gram positive (thick cell walls of peptidoglycan)
- gram negative/proteobacteria (thin cell walls of peptidoglycan)
- cyanobacteria (photosynthesis bacteria)
What organisms are classified as eukarya
- protista
- fungi
- plantae
- anamalia
what is the organism naming system called
binomial nomenclature
what are the 5 unifying themes of life
- organization
- information
- energy and matter
- interactions
- evolution
What is organization
heirarchy used to organize the study of life
what is the order of the heirarchy of life
- biosphere
- ecosystem
- community
- population
- organism
- organs
- tissues
- cells
- organelles
- molecules
biosphere
all life on eart and all of the places where life exists
ecosystem
all the living things in a particular area, along with all of the nonliving components that life interacts with
community
the array of organisms that live in an ecosystem
population
all of the individuals within a species that live in a certain area
organism
individual living thing
organs
a bodypart made up of multiple tissues, with a specific function
tissues
a group of cells that works together to perform a function
cells
lifes fundamental unit, the smallest unit of organization that can perform all activities required for life
organelles
functional components of cells
molecules
a chemical structure consisting of two or more atoms
reductionalism
reduces complex systems to simpler components that are more manageable to study
emergent properties
new properties emerge at each level that are absent from the one before because complexity increases at higher levels of organizations
systems biology
exploring biological systems by analyzing interactions among its parts
how do structure and function corralate
you can analyze a structure to find clues about how it’s function works
cell theory
all living organisms are made up of cells-and the actions of organisms are based on the activities of cells
what are the differences between eukaryotic cells and prokaryotes
EUKS -membrane bound organelles -has a nucleus PROKS -lack a nucleus -no membrane bound organelles -generally smaller than euks
where is DNA contained
chromosomes
what does DNA contain
genes
what are genes
units of inheritance, code the info necessary to build all molecules synthesized in a cell (identity and function)
structure of DNA
2 chains arranged in a double helix
what are nucleotides
they make up the strands of the double helix
chemical building blocks A,T,C,G
specific sequences of nucleotides encode info in genes (many times it is making protein)
producers
photosynthetic organisms that consumers feed on
consumers
organisms that feed on other organisms, or their remains
what happens when an organism uses chemical energy to do work
some of that energy is lost to the surroundings, in the form of heat
how does energy flow through an ecosystem
- in 1 direction
- usually enters as light and exits as heat
how are chemicals recycled in an ecosystem
when chemicals that the plant absorbs have passed through the host’s body, the plants re-uptake the chemical again
why is feedback regulation important
- interactions between components that make up organisms are crucial to smooth operation
- the output or product of a process is what regulates the process
negative feedback loop
the response reduces the initial stimulus
positive feedback loop
the response increases the initial stimulus
which feedback loop is most common
negative feedback loop
3 types of organism interactions
- mutually beneficial
- one species benefits, the other doesn’t
- both are harmed
relationship between organisms and their environment
organisms help their environments and the environment helps the organisms
climate change
a directional change to the global climate that lasts for 3 decades or more
evolution
a process of biological change in which species accumulate differences from their ancestors as they adapt to different environments over time
the order of naming organisms
- genus (which the species belongs to)
2. unique to the species within the genus
what are the 3 domains of life
bacteria
archaea
eukarya
domain bacteria
most diverse and widespread prokaryotes
domain archaea
live in the earth’s most extreme environments (prokaryotes)
kingdoms in domain eukarya
- plantae
- fungi
- animalia
- protists
kingdom plantae
multicellular eukaryotes that carry out photosynthesis (usually live on land)
kingdom fungi
characterized by the nutritional mode, which absorbs nutrients from outside of their bodies
kingdom animalia
multicellular eukaryotes that ingest other organisms
protists
mostly unicellular eukaryotes and simpler, multicellular relatives
what is used to distinguish most of the kingdoms in domain eukarya
nutrition
what are the 2 main points in Charles darwin’s “On the Origin of Species by Means of Natural Selection”
- species adapt to different environments over time, and accumulate differences from their ancestors (descent with modification)
- natural selection is a primary cause of descent with modification
what are darwin’s 3 observations of nature
- individuals in a population vary in their traits, many of which seem to be heritable
- a population can produce far more offspring than can survive to produce offspring of their own (more individuals than the environment can support=competition)
- species are generally suited to their environments (adapted to circumstances)
what individuals are more likely to survive and reproduce
individuals with inherited traits that are better suited to the local environment, opposed to those who are less well-suited
corralation between time and suitable traits
over generations, a higher and higher proportion of individuals in a population will have the advantageous trait
darwins proposal of descendant species
-one population of organisms became fragmented into several populations
-b/c they were isolated in different environments
-1 species radiated into multiple species and adapted to the different environments
(galapagos finches)
genomics
large scale analysis of the DNA sequences of a species
bioinformatics
using computational tools to deal with huge volumes of sequences data
compound
made of atoms, joined by bonds
what does number of protons determine
determines and atoms identity
what does electron distribution determine
ability to form bonds
what does a compound’s properties depend on
its atoms and how they are bonded together
matter
- organisms are composed of it
- anything that takes up space and has mass
- matter is made up of elements
- consists of chemical elements in pure form and in compounds
element
a substance that cannot be broken down to other substances by chemical reactions
how many elements occur in nature
92
compound
a substance consisting of 2 or more different elements combined in a fixed ratio
what percentage of the 92 naturally occuring elements are essential
20-25%
essential elements
organisms need these to live and to reproduce
what are the top 4 essential elements and the % of living matter that they make up
oxygen carbon hydrogen -nitrogen 96%
what are the top 4 trace elements and the % of living matter that they make up
calcium phosphorus potassium sulfur 4%
Atom
smallest unit of matter that still retains the properties of an element
subatomic particles
what atoms are composed of…
- protons (+)
- electrons (-)
- neutrons
what 2 subatomic particles are almost identical in mass
protons and neutrons (about 1 dalton)
characteristics of the atomic nucleus
- protons and neutrons are tightly packed
- electons are moving rapidly
- electrons form a “cloud” of negative charge
- the attraction between the opposite charges keep the electrons near the nucleus
what is a Dalton
named after John Dalton who helped develop the atomic theory, and is used to measure atoms/subatomic particles (amu)
atomic number
the number of protons unique to that element (bottom)
mass number
total number of protons and neutrons in the nucleus of an atom (top)
how do you find the # of neutrons
atomic number - mass number (bottom-top)
atomic mass
total mass of the atom
isotopes
- when all atoms of a given element have the same number of protons
- buttt some of the atoms have more neutrons (and a greater mass)
- essentially are different forms of the same element
radioactive isotope
- nucleus spontaneously decays => gives off particles of energy
- isotopes are unstable, nuclei lose subatomic particles
what happens when radioactive decay causes a change in the number of protons in an isotope
the atom transforms to that of another element
radioactive tracers
used to follow chemical processes of an organism and diagnose problems (but is dangerous)
radiometric dating
used to measure radioactive decay of fossils in order to date them
half life
when a parent isotope decays into its daughters isotope at a steady rate (time it takes for 50% of the parent isotope to decay)
when 2 atoms approach eachother during a chemical reaction, how do their nuclei behave
they do not interact because they do not come close enough to. most of an atom is empty space
what subatomic particle is directly involved in reactions
electrons
what is energy and how does it relate to electrons
energy is the capacity to do work. electrons of an atom vary in energy levels
what is potential energy and how does it relate to electrons in the nucleus
- energy that matter has because of its location or structure
- matter tends to move towards the lowest area of potential energy
- potential energy results from an electrons distance from the nucleus
- the further away the electrons are from the nucleus, the greater the potential energy (takes for work to keep them further away)
energy levels
electrons exist at specific energy levels
- closer to the nucleus = less energy
- further away from the nucleus = more energy
what are electron shells
electrons live here, each shell has a unique distance and energy level
can electrons move from one shell to another? if so, how?
yes, BUT only by absorbing or loosing energy equal to the difference of PE between positions
- absorbing energy = moving out
- loosing energy = moving in
how is chemical behavior determined?
by the distribution of electrons in the electron shells (mostly the outer shell)
periods on the periodic table
elements are arranged in 3 rows, and they correspond to the number of electron shells in their atoms
1st shell
this is the lowest electron shell (2 electrons)
3rd shell
highest electron shell (up to 18)
how many electrons does the 2nd shell hold
8
valence electrons
electrons in the outermost shell
valence shell
the outermost electron shell
electron orbitals (definition)
the 3D space where an electron is found 90% of the time
what is the reactivity of an atom dependant on
unpaired electrons
atoms with incomplete valence shells…
can interact with certain other atoms so that it can complete its valence shell
methods of completing a valence shell (2)
sharing or transfering valence electrons
strongest kinds of bonds (for covalent and ionic)
- covalent=in molecules
- ionic=dry ionic compounds
covalent bonds
the sharing of a pair of electrons by 2 or more atoms
double bonds
when atoms form a molecule and share TWO pairs of valence electrons
bonding capacity
when an atom has a full valence shell of electrons (usually equal to the number of electrons needed to complete it)
electronegativity
attraction for a particular atom for the electrons of a covalent bond
the more electronegative an atom is . . .
the stronger is pulls on shared electrons towards itself
when is electronegativity the same in both atoms?
non polar covalent bonds, because they share electrons
polar covalent bonds
when bonds are not shared equally and one atom is more electronegative
polar covalent bonds
when bonds are not shared equally and one atom is more electronegative
ionic bonds
when 2 atoms are so unequal in the attraction for their valence electrons that the more electronegative one strips an electron away from its partner
ions
the 2 resulting, oppositely charged atoms after an ionic bond
cation
+ ion
anion
- ion
cation+anion
attracted to eachother, form ionic bonds
what are the advantages of weak bonds (ones that arent covalent between molecules)
they can effect eachother, but then seperate
important weak interactions
hydrogen bonds, vanderwaals interactions, ionic bonds in water
hydrogen bonds
- an H+ ion covalently bonds to an electronegative atom
- partial + charge of H+ attracts a negative charge and a noncovalent attraction occurs
- usually takes place between oxygen or nitrogen in living cells
van der waals interactions
when electrons are not evenly distributed => can accumulate by chance in one part of a molecule
- ever-changing regions of postive/negative charge that allows atoms+molecules to stick to one another
- only occurs when atoms/molecules are very close together
how are molecules aranged when there are 2 or more of them
they are always linear
how are shapes of molecules determined
by the positions of the atom’s orbitals
what happens to the atoms when a covalent bond is formed
the orbitals in the valence shell undergo rearrangement
what happens when molecules with atoms in both s and p orbitals form covalent bonds
4 new hybrid orbitals shaped like teardrops extend from the nucleus (tetrahedron with a triangle base)
why is molecular shaoe important
it determines how biological molecules recognize and respond to one another
chemical reactions
the making and breaking of chemical bonds => changes in composition of matter
reactants
starting materials
products
resulting materials
how far out can the point of equilibrium be
some are so far out that reactions almost go to completion
is water polar or nonpolar
polar
what types of charges do O and H have
- o has a partial negative charge
- H has a partial positive charge
how is water bonded and why
water forms hydrogen bonds because the weak attractions between oppositely charged O and H
how does water bond in the liquid form
hydrogen bonds are constantly breaking and reforming, which allows molecules to slip closer together
how does water bond in the solid form
- hydrgen bonds are stable
- water molecules are further apart
- ice is less dense than liquid and floats
what does floating ice do to the water below
insulates it, promoting aquatic life
what are polar covalent bonds
b/c oxygen is more electronegative than hydrogen, electrons of the covalent bond spend more time closer to the oxygen
why is water a polar molecule
b/c the electrons are unequally shared and the molecule is V shaped
-overall charge is unevenly distributed
properties of water
properties arise from the attraction between oppositely charged atoms of different water molecules
- held together by hydrogen bonds
- in liquid form, bonds are very fragile
- bonds break and reform VERY often
What are the 4 emergent properties of water
- cohesion
- high surface tension
- cohesion and the transport of water against gravity in plants
- adhesion
cohesion of water molecules
hydrogen bonds hold water together collectively
high surface tension
hydrogen is bonded to one another and to the water below but not to the air above
-the asymmetry gives high surface tension
cohesion and the transport of water against gravity in plants
water goes from the roots to the leaves through a network of water conducting cells
- water evaporates from the leaf, leaves the veins to tug molecules further down because of the hydrogen bonds
- an upward pull is transmitted through the water conducting cells to the roots
adhesion
the clinging of one substance to another
-because of the H+ bonds in water, adhesion of water to the molecules of a cell wall helps counter the downward pull of gravity in cohesion transport
photosynthesis, reactants and products
process that is the foundation of life
reactants: 6CO2 + 6H2O
products: C6H12O6 + 6O2
are all chemical reactions reversible?
theoretically, all chemical reactions are reversible
the greater the concerntration of reactant molecules…
the more frequently they collide and react to form products
what happens as products in chemical reactions accumulate
collisions resulting in reverse reaction become more frequent
chemical equillibrium
when reactions/reverse reactions offset eachther
how does water moderate air temp
by absorbing heat from air that is warmer and releasing stored heat to air that is cooler
kinetic energy and the relationship with molecules
the faster molecules move, the greater their kinetic energy
thermal energy
the kinetic energy associated with the random movement of atoms/molecules. passes from warmer to cooler until the 2 reach the same temp
temperature
represents the average kinetic energy of the molecules in a body of matter
difference between thermal energy and temperature
thermal energy reflects the TOTAL kinetic energy, temperature reflects AVERAGE kinetic energy
heat
when thermal energy is transfered from one body of matter to another
calorie
amount of heat it takes to raise the temp of 1g of H2O by 1* C
-also the amnt of heat that 1g of H2O releases when it cools by 1*C
kilocalorie
1kg=1*C (same as calorie but in kgs)
joule (cals and joules conversion)
equals .239 cals
1 cal=4.184 J
Waters specific heat
the amount of heat that must be absorbed or lost for 1 g of that substance to change its temp by 1 degree
-H2O changes its temp less often because much of the heat is used to disrupt hydrogen bonds before the water molecules can begin moving faster
what happens when the temp of water drops slightly
H bonds form and release energy in the form of heat
evaporative cooling
stabilizes the temp of H2O
how does evaporative cooling work
- molecules moving fast enough to overcome attraction can depart the liquid and enter the air as gas
- some evaporation occurs at any temperature, but when liquid is heated the average KE of molecules increases and the liquid evaporates more rapidly
heat of vaporization
the quanitity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas
heat of vaporization of water
1g of H2O @ 25*C needs 580 cals of heat
why does H2O have a high heat of vaporization
due to the strength of hydrogen bonds
why does ice float on liquid water
water expands when it solidifies instead of contracting/becoming denser
solution
a mixture (homogenous) of 2 or more substances
solvent
dissolving agent
solute
the substance that is dissolved
aqueous solution
solute is dissolved in water
why is water a versitile solvent
because of its polarity
hydration shell
a sphere of water molecules around each dissolved ion
what can be dissolved in water
anything, as long as the molecules have an ionic and polar region
hydrophilic
likes water
hydrophobic
scared of water, nonpolar, nonionic
are hydrophilic substances dissolvable
not always ex) cotton towels
how are hydrophobic substances bonded
nonpolar covalent bonds
molarity
of moles of solute per liter of solution (and unit of concentration for aqueous solutions
mole
number of molecules in a substance
buffer
an acid-base pair that combines reversibly with hydrogen ions, allowing it to resist pH changes
ocean acidification
fossil fuels are burned => increase CO2 => CO2 dissolves in ocean
carbon chemistry
specializes in the study of carbon
electrons in carbon
2 in first shell 4 in second shell 4 empty electron spots in second shell valence number = 4 total electrons = 6
what are carbon’s bonding patterns
carbon shares electrons with other atoms to complete its outer shell (very little tendency to gain or lose electrons/form ionic bonds)
hydrocarbons
organic molecules consisting of only carbon and hydrogens
isomers
compounds that have the same molecular formula but different structure and therefore have different properties
what are the 3 classes of isomers
- structural isomers
- geometric isomers
- enantiomers
structural isomers
differ in the arrangements of their atoms
geometric isomers
cis-trans
entantiomers
mirrored
functional groups
components of organic molecules that are most commonly involved in chem reactions (bonded to carbon skeleton)
6 functional groups
hydroxyl carbonyl carboxyl amino sulfhydryl phosphate methyl
hydroxyl
- OH
- ex)alcohols
- polar (O is electroneg)
- water is attracted to these
carbonyl
=O (double bond)
- aldehyde (on end of carbon skeleton)
- ketone (in middle of carbon skeleton)
- polar
carboxyl
- COOH
- carboxylic acids
- have acidic properties because H+ tends to dissociate
- covalent bond between H and O are VERY polar
amino
- NH2
- amines
- act as bases
- commonly attract H+ ions, giving it a + charge
sulfhydryl
- SH
- thiols
- stabilizes the structure of proteins
phosphate
- PO4-
- important for the transfer of energy between organic compounds
methyl
- CH3
- methylated compounds
- nonpolar
- adding a methyl group to DNA affects gene expression
what makes carbon the basis for all biological molecules
- can form 4 bonds (with other atoms/groups of atoms)
- can bond to other carbons (carbon skeleton)
what does ccarbon commonly bond with
- hydrogen
- oxygen
- nitrogen
organic chemistry
- carbon containing compounds = organic
- study of these
what kind of bonds do carbons form
a covalent bond
what kind of molecules does carbon form and why
- large, complex molecules
- b/c molecules can branch out from a carbon in as many as 4 directions
what shape will carbon be in 4, singular&covalent bonds
tetrahedron
what shape will carbon be in for 2, double bonds
both carbons will be in the same plane (molecule is flat)
shapes of carbon skeletons
- vary in length
- straight
- branched
- closed ring
what constitutes carbon’s molecular complexity in living matter
-some have double bonds that vary in number and location => variation in carbon chains
hydrocarbons
organic molecules consisting of only carbon and hydrogen
how are hydrocarbons bonded
covalently
characteristics of hydrocarbons
- hydrophobic
- do not dissolve in water
characteristics of a cis-trans isomer
- atoms differ in spacial arrangement due to the inflexibility of double bonds
- single bonds allow atoms to rotate freely without changing the compound
- double bonds to not rotate
characteristics of an enantiomer
- 4 groups can be arranged in space around asymmetric carbon in 2 different ways, which forms mirror images
- only 1 is usually biologically active (only that 1 form can bond to specific molecules)
why are phosphate groups key to molecular function
- because ATP!
- ATP is made up of an adenosine attached to a string of 3 phosphate groups
monomer
1 building block of a polymer
-small repeating molecules
polymer
more than 1 monomer joined together to make a large molecule
-long molecules consisting of many identical or similar building blocks linked by covalent bonds
polymers and their monomers (biological molecules)
- proteins/amino acids
- carbohydrates/monosaccharides
- lipids/fatty acids+glycerol
- nucleic acid/nucleic acids
dehydration reactions
removes a water to form a new bond
hydrolysis
adds a water to break a covalent bond
- chemical reactions responsible for the disassembly of polymers
- reverse if dehydration reactions
carbohydrates
main source of energy in living organisms
types of saccharides (4)
- monosaccharides
- disaccharides
- trisaccharides
- polysaccharides
what is the general structural formula of monosaccharides
(CH2O)n
pentose
5 carbon sugar
ribose
RNA (has extra oxygen from the hydroxyl group at its 2nd carbon)
deoxyribose
DNA (only hydrogen at the 2nd carbon)
how are disaccharides bonded
glycosidic linkage (covalent bond)
structure of disaccharides
2 glucose molecules and a loose H2O molecule
what are the 3 important disaccharides
- maltose
- sucrose
- lactose
maltose
glucose+glucose
sucrose
glucose+fructose
lactose
glucose+galactose
starch
energy storage form of glucose in plants
cellulose
major component of plant cell walls
lipids
3 fatty acids and 1 glycerol
lipids
3 fatty acids and 1 glycerol
saturated fatty acid
only single bonds
unsaturated fatty acids
1 double or triple bond in the chain
polyunsaturated fatty acid
more than 1 double or triple bond in an ester linkage
biologically relevant lipids
phospholipids and steroids
in a condensation/dehydration reaction, how do the molecules contribute to the loss of a water molecule
- one molecule contributes the -OH group
- one molecule contributes the -H group
carbohydrates
main source of energy: sugars (saccharides)
what are the 3 types of saccharides
mono
di
poly
about monosaccharides
- simple sugar
- general structure (CH2O)n
hexose
monosac
6 carbon sugars
pentose
monosac
5 carbon sugar
glucose
C6H12O6
aldose sugar
fructose
C6H12O6
ketose sugar
disaccharides
two simple sugars joined together
glycosidic linkages
a covalent bond formed between 2 monosaccharides by a dehydration reaction
sucrose
(disac)
glucose+fructose
maltose
(disac)
glucose+glucose
lactose
glucose+galactose
polysaccharides
more than 2 simple sugars joined together
what are the biologically important polysaccharides
- starch
- glycogen
- cellulose
- chitin
starch
storage form of glucose in animals
alpha glucose=(-OH group of C1 is down)
1-4 linkages
glycogen
storage form of glucose in plants
alpha glucose=(-OH group of C1 is down)
1-4 and 1-6 linkages
cellulose
major components of plant cell walls
polymers of beta glucose (-OH group on C1 is up)
1-4 linkages
chitin
component of arthropod exoskeleton (invertabrates), and the cell wall of some fungi
beta-glucose (-OH group on C1 is up) with nitrogen appendages
fatty acids
the building blocks of lipids: long chains of carbon atoms with associated hydrogen
saturated fatty acids
chains of carbons with single bonds
unsaturated fatty acids
chains of carbons with one double or triple bonds (makes a kink in the chain)
polyunsaturated fatty acids
chains of carbons with more than one double or triple bonds
long chains of hydrocarbons and their relationship with water
no affinity for water
basic structure of lipids
- 3 fatty acid chains bonded by an ester linkage (long carbon skeleton of 16-18 carbons in length
- 1 glycerol (3 carbon alcohol)
structure of phospholipids
- 2 fatty acid chains and a phosphate group joined to a glycerol
- amphipathic (both hydrophilic and hydrophobic parts)
what is the charge and polarity of the phosphate group in phospholipids
negative charge, polar
what is the charge and polarity of fatty acid groups
uncharged and nonpolar
micelles
aggregate of phospholipids that form when they are put into an aqueous solution
phosphate heads
exposed to water
carbon tails
are shielded from the water
importance of phospholipids
they form cell membranes/lipid bilayers
steroids
lipids characterized by a carbon skeleton consisting of 4 fused rings
- different steroids have different functional groups attached to the rings
- vertebrate sex hormones
cholesterol
common component of animal cell membranes, precursor from which other steroids are synthesized
proteins
made of amino acids joined together by peptide bonds
how many amino acids are there that make up proteins
20
amino acid structure
- amine group
- carboxyl group
- R group (gives each amino acid different chemical properties, like polar/nonpolar/acid/base)
what are 2 amino acids bonded together called, and how are they bonded
dipeptide, bonded by peptide bonds
what is it called when many amino acids are bonded together
polypeptide
primary structure
a linear sequence of amino acids
secondary structure
- alpha helix
- beta pleated sheets
primary structure
a linear sequence of amino acids
secondary structure
- alpha helix
- beta pleated sheets
alpha helix
forms dur to hydrogen bonding every 4th amino acid in primary structure
beta pleated sheet
due to hydrogen bonding between 2 sections of the primary structure that are aligned parallel to eachother
tertiary structure
irregular contortions from bonding between R-groups of the various amino acids
hydrophobic interactions
amino acids with non-polar R-groups tend to cluster in the center of the protein
how do hydrogen bonds form in tertiary structure
between polar side chains
how do ionic bonds form in tertiary structure
between positive (base) and negative (acid) charged R-groups
what force is betwee R-groups in tertiary reactions
vanderwaals forces
disulfide bridges
covalent bonds between sulfur groups in the R-group of amino acid cystein
quaternary structure
overall protein structure that results from the aggregation of polypeptide units
collagen
3 polypeptides that aggregate to form a triple helix
hemoglobin
consists of 2 kinds of polypeptide chains, with 2 of each kind per hemoglobin molecule
what are the 2 classes of proteins
structural proteins
functional proteins
function of structural proteins
cell structure
clases of functional proteins
- enzymes
- transport proteins
- hormones
- receptor proteins
- contractile/motor proteins
- defense proteins
what determines protein conformation
a polypeptide chain of a given amino acid sequence can spontaneously arrange itself into a 3D shape maintained by the above interactions
-also depends upon the physical and chemical conditions of the proteins environment (pH, salt concentration, temp)
denaturation
unraveling of protein structure due to adverse environmental conditions, the protein is said to be inactive
Nucleic acids
DNA
RNA
structure of nucleic acids
- composed of chains of monomers called nucleotides
- pentose sugar (deoxyribose/ribose)
- nitrogenous base: pyrimidine (6 membered ring fused to a 5 member ring) (adenine and guanine)
- phosphate group
nucleosides
pentose sugar + nitrogenous base
nucleotides in DNA
GATC
nucleotides in RNA
GAUC
polynucleotide structure
anti-parallel double helix (5’/3’ ends)
- base pairing via hydrogen bonds (DNA=A-T G-C) (RNA= A-U G-C)
- 2 H bonds between A and T and 3 H-bonds between C and G
organelles
tiny sacs and compartments bounded by membranes
what characteristics do both euks and proks share
- outer plasma membrane
- internal region of DNA
- cytoplasm
plasma membrane
forms boundaries between cell and external environment
- phospholipid bilayer
- contains sterols(cholesterol)
- contains proteins for transport and recognition
phospholipid bilayer
- hydrophilic end
- hydrophobic end
fluid mosaic model
plasma membrane is a fluid structure with a mosaic of various proteins embedded in it
the fluid nature of the membrane allows the proteins and phospholipids to move in the horizontal plane without losing the membrane’s integrity
nucleus
contains DNA organized into chromosomes, existing in the form of chromatin (a DNA histone complex)
- membrane
- nuclear pores
- nucleoli
- nucleoplasm
membrane in nucleus
bound by a double lipid bilayer-nuclear envelope
nuclear pores
highly selective to protect chromosomes
nucleoli
synthesis of ribosomes
nucleoplasm
cytoplasm of nucleus
characteristics of cytoplasm
- within plasma membrane but outside of nucleus
- cytosol (the watery substances supporting organelles
- contains metabolic machinery (organelles, enzymes, etc)
mitochondria
energy center (powerhouse of the cell) -forms ATP through the electron transport system
how many membranes does the mitochondria have
2, one outer and one inner that folds and forms cristae
why are cristae important
they increase the surface area of the membrane to permit increased ATP production
what does the double membrane in mitochondria create
matrix-space inside the inner membrane
intermembrane space-space between the inner and outer membrane
ribosomes
- composed of rRNA and r-proteins
- used to make protein from DNA
endoplasmic reticulum
circulatory system of the cell
smooth ER
lipid assembly/modification and transport
- carbohydrate metabolism
- detoxification of drugs and poisons
rough ER
protein assembly/modification and transport
- bounded by ribiosomes
- stores proteins
golgi apparatus
recieves protein from ER (cis end) and further modifies
-packages proteins for transport either within or external to cell (trans end)
lysosomes
- contains hydrolytic enzymes that digest macromolecules
- bind with vesicles containing ingested materials (food, bacteria) and break it down
- autophagy
autophagy
recycling of cells own organic materials derived from damaged materials
peroxisomes
- contains enzymes that transfer hydrogens from (usually toxic) substances to oxygen creating hydrogen peroxide
- detoxifies alcohol
- converts hydrogen peroxide to water because hydrogen peroxide is toxic
vacuoles/vesicles
- vesicles are smaller vacuoles
- transport, storage
cytoskeleton
gives mechanical support to the cell, anchors organelles in the cytoplasm
- aids in cellular molarity
- helps to maintain its shape
- made up of 3 types of fibers
what are the 3 types of fibers in the cytoskeleton
- microtubules
- microfilaments
- intermediate filaments
microtubules
shape and support the cell and serve as tracks along which the organelles can move
microfilaments/actin
bear tension within the cell
-help support the cell’s shape and are involved in cell motility
intermediate filaments
-specialized for bearing tension and fixing the position of organelles, especially the nucleus
centrosomes
- microtubules organizing center for cell division
- composed of 2 centrioles (9 triplet microtubules) arranges in a ring
what organisms lack centrosomes
-plant and yeast cells lack centrosomes
flagella
- composed of microtubules
- external to plasma membrane
- provide motility
cilia
- composed of microtubules
- shorter and more numerous than flagella
- used in movement of protozoa (single celled euks)
how do cilia work in humans
ciliate cells move mucous and materials past the cell for expulsion
pseudopodia
- false feet
- composed of microfilaments
- projections of cytoplasm which creates ameboid movement
- used in human phagocytes to engulf foreign material
what are the organelles that are specific to plants
chloroplast central vacuole tonoplast cell wall protoplast plasmodesmata middle lamella
chloroplast
- site of photosynthesis
- envelope of 2 phospholipid bilayers (inner and outer), separated by an intermembrane space
structures in the chloroplast
stroma thylakoid membranes grana chlorophyl thylakoid space
stroma
space between the envelope and the thylakoid membrane
thylakoid membranes
“pancake stacked” membranes that separate the stroma from the thylakoid space (or lumen)
grana
the “pancake stacks” that increase surface area
chlorophyll
resides in the thylakoid membranes
thylakoid space
space inside the thylakoid membrane
central vacuole
contains sap; nounded by the tonoplast
tonoplast
membrane that regulates the traffic of molecules between the sap and the cytosol
cell wall
external to the plasma membrane
primary cell wall
all plant cells have; secreted as the cell grows and develops
secondary cell wall
produced by certain specialized plant cells; closer to the protoplast than the primary wall because it forms after the cell has stopped growing: provides protection and support
protoplast
are spherical naked plant cells produced by the removal of the cell wall with digestive enzymes
plasmodesmata
cytoplasmic channels that pass through pores in the cell walls allowing the protoplasts of neighboring cells to be connected
middle lamella
adhesive layer that cements together the cell walls of the adjacent cells
prok cell structure
- bacteria and archeae are considered proks
- unicellular
- smallest of all organisms (viruses are smaller but acellular)
- bacteria
shapes of bacteria
- coccus
- bacillus
- vibro
- spirillum
- spirochete
- pleiomorphic
coccus
spheres
bacillus
rods/coccobacillus (in between the 2)
vibrio
comma shaped
spirillum
cork skrew with flagella at one end or both ends
spirochete
cork skrew with internal flagella
pleiomorphic
bacteria exhibiting many shapes
patterns of bacteria
cocci and bacilli
types of cocci
- diplococci
- staphylococci
- streptococi
- tetrad
- sarcinae
diplococci
pairs
staphylococci
clusters
streptococci
chains
tetrad
4 cell cube
sarcinae
8 cell cube
types of bacilli
bacillus and palisade
bacillus
chains
palisade
bacilli side-by-side
cell/plasma membrane function/structure kinda
forms boundary between cell and external environment
-contains proteins for transport
what does the bacterial cell membrane lack
sterols (cholesterol) but they contain sterol-like molecules called hopanoids
characteristics of the cell wall
- lies outside the cell membrane
- porous
- maintains integrity of cell shape
- main component is peptidoglycan (murein)
cross linking
a bond that links 1 polymer chain to another
what type of amino acid can not be broken down by common enzymes
stereoisomers of common amino acids
gram +
thick peptidoglycan wall
gram -
thin peptidoglycan wall
characteristics of the outer membrane of prok cells
- gram -
- attached to the cell wall and lipid bilayer
- contains lipopolysaccharide (LPS)
- core polysaccharide
- o antigen
lipid A
embedded in the outer membrane
-stabalizes outer membrane structure
abt O antigen
displays antigen variation
periplasmic space
- gap between the cell membrane and the cell wall
- includes peptidoglycan, enzymes, and proteins which makes up the periplasm
- serves as a site for transport of nutrients protection
protoplasts and spheroplasts
-the cell wall protects bacteria from osmotic lysis when they are in a hypotonic solution
what does digestion of cell wall in gram + yield
protoplasts
what does digestion of cell walls in gram - yield
spheroplasts
cytoplasm
- watery substance in the cell
- contains metabolic machinery like proteins and DNA
- determines cell shape
nuclear region (nucleoid)
contains compacted DNA with some associated protein (not histones) and RNA
plasmids
extra chromosomal DNA
types of plasmids
- conjugative plasmids
- col plasmids
- virulence plasmids
- metabolic plasmids
conjugative plasmids
F plasmids and R plasmids
col plasmids
produce bacteriocins
virulence plasmids
encode virulence factors
metabolic plasmids
encode degradiative enzyme
cytoskeleton
homologs of all 3 eukaryotic cytoskeletal components have recently been identified in bacteria (microtubules, microfilaments and intermediate filaments)
functions of the cytoskeleton
- participate in cell division
- localize proteins to certain sites within the cell
ribosomes
- RNA & protein structures that ain in synthesizing protein
- euks: 80S
- proks: 70S
what does “S” mean
suedberg unit; sedimentation coeficcient measure of sedimentation velocity in a centrifuge
inclusion granules
storage pools of required metabolites
- stores glycogen and glucose
- stores volutin and polyphosphate
capsule
well organized and not easily washed off
slime layer
more diffuse and can easily be removed
similarities of the capsule and the slime layer
both are external to the cell wall and can be called glycocalyx
functions of the capsule and the slime layer
- prevents phagocytosis
- aids in adherance to host tissues
pili/fambriae
-hollow projections
what are the 2 types of fili/fambriae
conjugation pili and attachment pili
conjugation pili
transfer of genetic material
attachment pili/fambriae
attach to surfaces like cells and water
flagella
- external to cell wall
- provide motality
key base word of flagella
trichous
flagella prefixes
- mono: 1
- amphi: 1 at each end
- lopho: 2 or more at one or both ends
- peri: all over surface
- a:none
clockwise flagella movement
direct movement
counter clockwise flagella movement
random movement
chemo movement
move toward (positive) or away (negative) from chemical substances
photo movement
toward or away from light
aero movement
toward or away from oxygen
osmo movement
move toward or away from osmotic pressure
vegetative cells
cells that are actively metabolizing
spore formation
occurs under harsh conditions
dormant state
form within the cell
endospores
highly resistant to environmental conditions, contains little water, resistant to heat
sporulation
when conditions are right, the spores will germinate=begin to develop into vegetative cells again
cell-cell recognition
a cells ability to distinguish one type of neighboring cell from another
oligosaccharides
are on the external side of the plasma membrane, they vary from cell to cell and species to species
what enables oligosacs to function and how do they function?
the diversity of molecules and their location on the cell’s surface. the oligosacs function as markers that distinguish one cell from another
enzymatic activity
a protein embedded into the membrane with enzymatic activity
what happens when there are several enzymes in a membrane
enzymes are ordered as a team that carries out sequential steps of a metabolic pathways, like in the mitochondria
signal transduction
membrane protein with a b inding site for a chemical messenger such as a hormone
what happens upon the protein bonding to a messanger
a signal is transmitted to the interior of the cell
extracellular matrix (ECM)
the substance in which animal tissue cells are embedded
- consists of proteins and polysaccharides
- helps to maintain cell shape, anchor cells in a specific location, stabilizes membrane proteins
what are the functions of plasma membrane proteins
- cell/cell recognition
- enzyme activity
- signal transduction
- intracellular joining (gap junctions, etc)
- attachment to cytoskeleton and extracellular matrix
- transport
semi permeable membrane
ability of membranes to selectively permit certain substances to cross it over other substances
hydrophobic phospholipid tails
core of the membrane. is the main barrier for transport across the plasma membrane
molecules that can cross the plasma membrane
-hydrophobic molecules: dissolve into the hydrophobic core of the membrane, enabling them to cross it ex) -hydrocarbons -CO2 -O2
molecules that cannot cross the plasma membrane
-hydrophilic molecules
ex)
-charged ions
-polar molecules
-large, uncharged and polar molecules (too big)
ex)
carbs
proteins
transport proteins
proteins that span the membrane that permit the transit of ions, polar molecules and larger molecules across the membrane
what type of structure do transport proteins usually have
hydrophilic channels
aquaporins
transport proteins that transport water
diffusion
the tendancy for molecules of any substance to spread out into available space from a high to low concentration (downhill)
concentration gradient
a gradient of different concentrations of a solute in a solutions
dynamic equilibrium
occurs when the concentration of solutes is equal access a membrane. There is no net charge in solute movement across the membrane but the solutes are still moving
what must NOT happen in order for diffusion to occur
NO WORK must be done to make diffusion happen, it is a spontaneous process and delta G is negative
passive transport
the diffusion of substances across a biological membrane
what does the cell NOT do in passive transport
the cell does NOT expend energy
facilitated diffusion
the passive transport of ions and polar molecules that cannot cross the semipermeable membrane on their own
what is required in facilitated diffusion
a transport protein is required, it just serves as a hydrophilic channel
osmosis
diffusion of water across a semi-permeable membrane (aka the passive transport of water)
hypertonic solution
the solution has a higher solute concentration that the animal cell
what happens in a hypertonic solution
water exits the cell and the cell shrinks
hypotonic
a solution that has a lower solute concentration than the animal cell
what happens in a hypotonic solution
the cell gains water and the cell could lyse
isotonic
both solutions have the same solute concentration
how do water molecules move
from a hypotonic solution to a hypertonic solution
if a cell is placed in a hypertonic solution, what happens to its membrane?
plasmolysis: as the plant cell shrivels, the plasma membrane pulls away from the cell wall
if a cell is placed in a hypotonic solution, what happens to its membrane
turgid-the cell takes up water until it is full and the turgid cells give a plant its structure
what happens to the membrane when a cell is placed in an isotonic solution
it is flaccid and there is no net movement of water, so the membrane becomes limp and wilts
active transport
the transport of solutes against their concentration gradients
what does active transport require
active transport requires energy
transport of large molecules
exocytosis, endocytosis
exocytosis
fusion of vesicles derived from the golgi apparatus with the plasma membrane => extrusion of macromolecules
ex) hormones, insulin
endocytosis
the taking in of macromolecules by forming vesicles derived from the plasma membrane through the process of phagocytosis, pinocytosis, receptor-mediated endocytosis
phagocytosis
uptake of particles by wrapping pseudopodia around it and packaging it within a vacuole
pinocytosis
the cell gulps droplets of extracellular fluid in tiny vesicles
receptor mediated endocytosis
endocytosis of specific molecules that bind to membrane bound receptors
steroids
4 fused hydrocarbon rings
why is cholesterol important
b/c it is important in cell membrane structure
what is the precursor molecule for all other human steroids
cholesterol
how are proteins made in euk cells
DNA => mRNA => ribosomes +cytoplasm
occurs mostly in the nucleus
how are proteins made in prok cells
everything occurs in the cytoplasm because theres no membrane bound organelles
when do H bonds occur
every 4th amino acid, below the polar R-groups,
what do H bonds do to the helix structure
stabilizes the alpha helix structure
folding
FOLDING IS NOT RANDOM, it is due to the amino acids in the polypeptide
what are the types of bonds that hold tertiary structure together
- hydrophobic interactions
- hydrogen bonding between R groups
- ionic bonds below acidic + charges
- disulfide bridges
hydrophobic interactions
amino acids with non polar R-groups will cluser inside of the globular protein
disulfide bridges
covalent bonds below R groups of cystein amino acids
4 prime structure
multiple 3 prime proteins are bound together to create a large functional protein molecule
chaperonin
helps 2 prime => 3 prime and 3 prime => 4 prime
what are chaperonins made by
other chaperonins
what are the types of functional proteins in a cell
- enzymes
- receptor proteins
- transport proteins
- structural proteins
- motor proteins
- defense proteins
- hormones
what determines protein structure
environment and function
denaturation
process by which protein structure unfolds. this is irreversible, protein is nonfunctional b/c there is no chaperonins or DNA
mRNA
codes for proteins
RNA
carries amino acids to ribosomes to make a protein
rRNA
structural components of the ribosome
central dogma
DNA => RNA => protein
purines
adenine and guanine
perimadines
thymine, cytosine and uricil
nucleosides
sugar + base w/o phosphate group
what type of bond holds nucleotides together
phosphodiester
characteristics of DNA
- double stranded
- antiparallel
- 3’ and 5’ end
- 2 different strands are oriented in opposite directions
a-t
2 hydrogen bonds
c-g
3 hydrogen bonds
characteristics of RNA
- single stranded (mRNA)
- tRNA + rRNA have regions of double strandedness
characteristics of RNA
- single stranded (mRNA)
- tRNA + rRNA have regions of double strandedness
functions of cell to cell recognition (plasma membrane proteins)
- used to help cells recognize eachother
- human immune response (recognizing the difference between self and non self)
enzymetic activity
plasma membrane proteins that have metabolic functions
signal transduction
enables cells to monitor environment + respond
metabolism
the totality of an organisms chemical processes
catabolic pathways
the metabolic pathways responsible for the breakdown of complex molecules into simpler ones
- energy is released
- cellular respiration
cellular respiration
glucose => CO2 + H2O + ATP
anabolic pathways
- the metabolic pathways responsible for the build up of complex molecules from simpler ones
- energy is consumed
- photosynthesis
photosynthesis
synthesis of a protein from amino acids
bioenergetics
study of how organisms manage their energy resources
energy
the capacity to do work
thermodynamics
study of energy transformations that occur in a collection of matter
the first law of thermodynamics
energy can be transferred and transformed, but it can not be created nor destroyed
the second law of thermodynamics
every energy transfer or transformation increases the entropy of the universe
how do organisms process energy
an organism takes in organized forms of energy from the surroundings and replaces them with less ordered forms of energy
free energy
the portion of a system’s energy that can perform work when the temperature is uniform throughout the system (=potential energy of the system)
-the energy that is available to do work
what are the 2 components of free energy (g)
H: potential + kinetic energy
S: the systems of entropy (randomness)
T: absolute temp in Kelvin units
what is the equation for G free energy
G= H-TS
chemical rections are of 2 types
- spontaneous
- nonspontaneous
spontaneous reactions
occur spontaneously because the starting materials have either high energy (unstable) or low entropy (not random) or both
- complex macromolecules
- catabolic reactions
nonspontaneous reactions
require energy to occur. they do not occur spontaneously because the starting materials have either low energy (stable) or high entropy (random) or both
- monomers
- anabolic reactions
free energy in spontaneous reactions
the free energy of a system decreases by either giving up energy (usually in the form of heat) or by increasing randomness
what must free energy be in order for a spontaneous reaction to occur
change in G must be NEGATIVE
what happens to free energy when chemical reactions reach equilibrium
free energy G = 0
exergonic reactions
reactions that occur spontaneously, free energy is negative, and free energy is released (catabolic)
endergonic reactions
reactions that do not occur spontaneously, free energy is positive, and free energy is absorbed for the reaction to occur (anabolic)
metabolic disequilibrium
because free energy = 0 when the system reaches equilibrium, the system can do no work.
what happens when all of the chemical reactions within a cell reach equilibrium
the cell would be dead
how do cells prevent equilibrium
use the products of the chemical reactions as quickly as they are produced
energy coupling
use of an exergonic process to drive an endergonic one
what is responsible for mediating most energy coupling reactions within cells
ATP
what happens when the bonds between the phosphate groups are broken by hydrolysis
yields an inorganic phosphate molecule and ADP
what does hydrolysis of the high energy phosphate bonds do (exergonic)
releases energy that can be used to drive endergonic reactions
how can ATP be regenerated
by the process of cellular respiration
enzymes
catalytic proteins that lower the free energy of activation of chemical reactions
catalyst
chemical reagent that changes the rate of reaction without being consumed or changed
free energy of activation
the initial investment of energy for starting a reaction (the energy that is required to break bonds in the reactant molecules)
enzymes and their relationship to substrates
enzymes are substrate specific (lock and key)
active site
site on the enzyme in which the substrate interacts (usually through week interaction) and the catalytic reaction occurs
stretching and bending of chemical bonds
helps break the bonds that must be broken for the enzyme to bind to the substrate
environment for active site
active site may have a specific microenvironment that may be suitable for the reactions (acidic R groups, basic R groups etc)
inducible fit
as the substrate enters the active site of the enzyme, it induces the enzyme to change its shape slightly so that the active site fits even more snugly around the substrate
factors that affect enzymatic activity
- concentration
- temp
- pH
- cofactors
- enzyme inhibitors
concentration
the more enzymes present, the more enzymatic activity (and vice versa)
temperature
up to a point, the velocity of an enzymatic reaction increases with increasing temp, partly because substrates collide with active sites more frequently when the molecules move rapidly
high temp’s affect on enzymatic activity
denaturation (loose structure) of proteins
low temp’s affect on enzymatic activity
reaction rate decreases because there are less collisions
pH affect on enzymatic activity
6-8 is usually optimal
cofactors affect on enzymatic activity
non-protein helpers for catalytic activity (vitamins)
co-enzymes affect on enzymatic activity
organic molecules that serve as co-factors
competitive inhibitors
enzymatic inhibitors that resemble the substrate. they bind the active site and reversibly inhibit the enzyme
noncompetitive inhibitors
do not bind to active site, instead bind to another part of the enzyme and causes the enzyme molecule to change its conformation so the substrate can no longer interact with the active site
reversible reactions
if inhibitors can be removed
irreversible reactions
suicide inhibitor
bioenergetics
the study of how organisms manage their energy resources
what do biological systems want to do with energy
want to decrease the amount of energy lost as heat because heat can not be used to run chemical reactions. they want to harvest NG as ATP
what defines whether or not a chem reaction is spontaneous or nonspontaneous
the characteristics of the starting materials
spontaneous reactions
- catabolic
- high energy
- unstable
- low entropy
- organized
- starting materials are polymers
nonspontaneous reactions
- anabolic
- starting materials are monomers
- low energy
- stable
- high entropy
- random
activation energy
required in all reactions
initial investment of energy ensuring all reactants are close enough for their bonds to react
what do enzymes do to activation energy and why
lower it because they serve as “landing pads” to bring substrate molecules together in 1 place and to expose bonds that need to be worked on to create products
