Studied by 10 people
Biology
the study of living organisms and their environments at various levels of organization
what are the levels of biological organization (in order)
atoms, molecules, macromolecules, cells, tissues, organs, organism, population, community, ecosystem, biosphere
organism
living things of a species
(levels of biological organization)
population
organisms of the same species that occupy the same environment
(levels of biological organization)
community
populations of different species
(levels of biological organization)
ecosystem
formed by the interactions of a community of organisms with their environment
(levels of biological organization)
biosphere
all the places on earth where organisms exist
(levels of biological organization)
evolution
diversity of life evolved through mutation, natural selection, and genetic exchange
(core concepts of biology)
structure and function
basic units of structure defining the function of all living things
(core concepts of biology)
information flow, exchange, and storage
traits and behavior of organisms that happen to some extent from the control by the expression of genetic information
(core concepts of biology)
pathways and transformations of energy and matter
biological processes based on pathways transforming chemicals and governed by laws of thermodynamics
(core concepts of biology)
systems
living systems interconnected and interacting
(core concepts of biology)
Unity (mechanism of evolution)
all life displays a common set of characteristics (ex: homeostasis, cellular organization, ability to reproduce)
united by a shared evolutionary history
evolution (mechanism of evolution)
heritable change in genetic material in a population of organisms from one generation to the next
the genetic material mostly composed of DNA
DNA provides a blueprint for traits and function
DNA is heritable
lead to diversity to form in diverse environments
genome
the complete genetic material of an organism
segments of DNA
govern the traits of organisms
most genes are transcribed into mRNAs
most mRNAs are translated into a polypeptide
a protein may compose more than 1 polypeptides
genomics
the study of genomes and many if not all genes at the same time
characteristics and importance of a model system
a species that is straightforward to study where knowledge gained can potentially be useful for understanding other species
hypothesis
a proposed explanation for a phenomenon
based on prior knowledge
must be testable (can be shown to be correct or incorrect)
support/reject with evidence
never proven with certainty
ex: Maple trees drop their leaves in autumn because of shorten hours of sunlight.
theory
a broad explanation of aspects of the natural substantiated by a large body of evidence
allows us to make many predictions
can never be proven true
due to overwhelming evidence, very likely to be true
ex: DNA is the genetic material
discovery based hypothesis
inductive reasoning
data → patterns → conclusions
ex: test candidate drugs to look for action against disease
ex: sequence genomes and proteomes
hypothesis-based science
deductive reasoning
purpose of controls in experiments
increase the reliability of results and also to eliminate errors and bias
control group
the group that does not receive the new treatment being studied
experimental group
the group that does receive the new treatment being studied
synthesizing life-like systems (grand challenges in biology)
Can we construct systems with characteristics of life that are capable synthesizing materials or carrying out functions as yet unseen in natural biology? (This is why it’s challenging)
understanding the brain (grand challenges in biology)
the human brain may be nature’s most complex system. Just how do all the neurons and synapse work together and contribute to brain functions?
predicting characteristic based on DNA (grand challenges in biology)
Ultimately, the blueprint for form and function lies in an organism’s DNA sequence. How can DNA be used to predict forms and functions? (This is why it’s challenging)
interactions of the earth, its climate, and the biosphere (grand challenges in biology)
how do these processes operate on much different scales of time (fractions of a second to many years) and space (microscopic to the global) unfold? (This is why it’s challenging)
atom
the smallest functional units of matter that form all chemical substances
cannot be further broken down into other substances by ordinary means
2 or more bonds bonded together to form molecules
each specific type of atom is a chemical element
structure of an atom
dense nucleus that contains protons and neutrons surrounded by a “cloud” of electrons
orbitals
regions surrounding the nucleus in which the probability of finding electrons is high
a central nucleus surrounded by cloudlike orbitals
picture:
7 protons and 7 electrons
2 protons fill the 1st shell
2 in the 1s orbital
5 electrons in the 2nd shell
2 fill the 2s orbital
1 in each of the three 2p orbitals
electrons in the outer shell available to combine with other atoms are called valence electrons
about 12C, which of the following is correct?
a) it has 12 protons
b) it has 12 electrons
c) it’s 2p orbitals contains 4 electrons
d) it has 4 valence electrons
D
a) it has 12 protons (actually has 6)
b) it has 12 electrons (actually has 6)
c) it’s 2p orbitals contain 4 electrons (actually has 2 electrons bc the electron configuration is 1s1 1s2 2s1 2s2 2p1 2p2)
d) it has 4 valence electrons (6-2 = 4… 6 is from carbon’s atomic number and 2 is from helium’s noble number)
results of Rutherford’s experiment
Rutherford conducted the gold foil experiment where an alpha particle is shot to a gold foil surrounded by a detection screen. Most of the alpha particles went straight through the gold foil (undeflected), some slightly deflected, and very few alpha particles bounced back. Through this experiment, it was proven that atoms are mostly composed of mostly empty space with positive charges in a small volume (the nucleus)
elements that make up most of living organisms
oxygen, carbon, hydrogen, and nitrogen
hydrogen and oxygen occur primarily in water
nitrogen is found in proteins
carbon is the building block of all living matter
most oxygen and hydrogen atoms in living things are from water (2H and 1O). Why does the enrichment numbers differ so much from 2-to-1 ratio?
because 1) the atomic masses differ by 16x between O and H, 2) in addition to water, H is predominantly associated witH C in macromolecules
molecule
more than 2 atoms bonded together
compound
a molecule composed of 2 or more elements
free radicals
molecules containing an atom with a single, unpaired electron in its outer shell (oxidized)
can form by exposure to radiation and some toxins
highly reactive
can “steal” an electron from other molecules
can cause cell damage
can kill invading bacteria
benefits of antioxidants
covalent bonds
electrons are shared to fill valence shells, and can be polar or nonpolar
atoms share electron pair(s)
between atoms with unfilled outer electron shells
strong chemical bond
can share:
1 electron pair: single bond
2 pairs double bond
3 pairs: triple bond
atoms are stable when their outer shell is full (8 valence electrons)
for many atoms, the outer shell is filled with 8 electrons (“the octet rule”)
any exception is HYDROGEN, which fills its outer shell with just 2 electrons
hydrogen bonds
hydrogen atom from one polar molecule attracted to an electronegative atom from another molecule
small molecules may bind to enzymes through hydrogen bonds
ex: bonds between DNA strands, small molecules and enzymes
ionic bonds
electrons are transferred, forming ions that are attached to each other
forms when differences in electronegativities are large between 2 atoms
Nonpolar covalent bond
similar electronegativities between atoms connected by the bond (equal sharing of electrons)
δ: attraction to electrons
no charge difference across molecules
ex: C-C, C-H (they have very similar electronegativities)
polar covalent bond
different electronegativities between atoms connected by the bond (unequal sharing of electrons)
electronegative side (more electrons) and electropositive side (less electrons)
since one atom is more electronegative, it will attract more of the electrons, causing the unequal sharing of electrons
ex: O-H, N-H
ion
an atom or molecule gained/lost one or more electrons
solvent
liquid
solute(s)
dissolved substances
solvent + solute(s) =
solution
water + hydrophilic molecules
aqueous solution
hydrophilic
water loving
solutes are molecules that are:
ionic and/or with polar covalent bonds
hydrophobic
water fearing
solutes are molecules that are:
nonpolar like hydrocarbons, oils
amphipathic
both hydrophilic and hydrophobic
solutes are molecules that are:
both polar/ionized and nonpolar at the same time, like detergent
cohesion (property of water)
water molecules stick to other water molecules
hydrogen bonds make water molecules stick to one another
adhesion (property of water)
water molecules are attracted and stick to other substances
hydrogen bonds allow water molecules stick to other substances
surface tension (property of water)
allows it to resist an external force, due to the cohesive nature of its molecules
molecules at liquid surface attract each other
capillary action (property of water)
the upward motion against gravity
depends on the attraction between water molecules and the glass walls of the tube (adhesion), as well as on interactions between water molecules (cohesion)
water molecules are more strongly attracted to the glass than they are to other water molecules (because glass molecules are even more polar than water molecules)
acids
releases H+ in solution
strong acids releases more H+
ex: human stomach acid → pH= ~2
ex: undiluted orange juice → pH= ~4
bases
lowering the [H+] by releasing OH- and/or binding to H+
ex: baking soda → pH= ~9
ex: bleach → pH= ~12
buffer
maintains a constant pH by removing H+ or releasing H-
molecules can be __ and ____
inorganic and organic
organic molecules
contains carbon that tends to be abundant in living organisms
small organic molecules
macromolecules
vitalism
19th-century concept that organic molecules were created by and imparted with a vital life force within a plant or animal’s body
believed organic compounds could not be synthesized
later disproven—organic compounds can be synthesized
carbon contains how many electrons and how many valance electrons?
6 electrons and 4 valence electrons
how many bonds can carbon form while the molecule created does not carry charges?
4
can be polar or nonpolar bonds!!
molecules with polar bonds are water-soluble
molecules with nonpolar bonds (like hydrocarbons) are not very water soluble
functional group
an atom or group of atoms within a molecule that has similar chemical properties whenever it appears in various compounds
ex: methyl group
ex: carboxyl group
isomers
molecules with identical molecular formula but different structures
allows more diversity in chemical structure even though the atomic compositions are the same
structural isomer
same atoms, different bonding relationships
stereo-isomer
identical bonding relationships, different spatial arrangements
cis-trans isomers
enantiomers
cis-trans isomers
different positioning around double bond or rings
enantiomers
mirror image molecules
difference in orientation leads to different binding abilities
enzymes that recognize one enantiomers usually do not recognize the other
condensation/dehydration (top)
a molecule of water is removed each time a new monomer is added (that’s why it’s called a “dehydration” reaction)
the process repeats to form long polymers
a polymer can consist of thousands of monomers
dehydration is catalyzed by enzymes
hydrolysis (bottom)
a molecule of water is added back each time a monomer is released
the process repeats to break down a long polymer
hydrolysis is catalyzed by enzymes
what are the four major types of organic molecules
DNA/RNA (nucleic acids), proteins, lipids, carbohydrates
3 properties of nucleic acids
storage, expression, and transmission of genetic information
3 components of a nucleotide
phosphate, 5 carbon sugar (either ribose or deoxyribose), base (single or double ring of carbon and nitrogen atoms)
components of nucleotides in DNA
phosphate
sugar: deoxyribose
base: cytosine
double helix
nucleotides: dA, dG, dC, dT (thymine)
components of nucleotides in RNA
phosphate
sugar: ribose
base: uracil
single strand
nucleotides: A (adenine),G (guanine),C (cytosine),U (uracil)
in DNA, adenine pairs with
thymine
in DNA, cytosine pairs with
guanine
purines
adenine (A) and guanine (G)
pyrimidines
cytosine (C) and thymine (T)
is this amino acid side chain polar (charged or un-charged) or non polar
nonpolar
is this amino acid side chain polar (charged or un-charged) or non polar
polar un-charged
is this amino acid side chain polar (charged or un-charged) or non polar
polar charged
how do amino acids form polypeptides and proteins
amino acids are joined together by dehydration reactions
chains of amino acids
polymers of amino acids known as polypeptides
proteins may be formed form one or several polypeptides
protein primary structure
the free amino group of a polypeptide is the N-terminal
the free carboxyl end is the C-terminal
carboxy + amino forms peptide bond
protein secondary structure
folded structures that form within a polypeptide due to hydrogen bonds between atoms of the backbone
gene expression (protein functions)
RNA polymerase: synthesize RNA using DNA as a template
polymerase: an enzyme which brings about the formation of a particular polymer, especially DNA or RNA.
motor (protein functions)
myosin: contractile force of muscles
defense (protein function)
antibodies: destroy pathogens
metabolism (protein function)
hexokinase: phosphorylate glucose
signal transduction
taste receptors: taste molecules in food
stucture (protein functions)
actin: shape to the cytoplasm of plant and animal cells
transporter (protein functions)
glucose transporters: move glucose from outside to inside cells
monosaccharides
one sugar molecule
disaccharides
2 monosaccharides joined by dehydration/condensation
ex: sucrose, maltose, lactose
polysaccharides
many monosaccharides linked together to form long polymers
ex: starch & cellulose
features of lipids
composed of hydrogen, carbon, and some oxygen
nonpolar, so very insoluable in water
classes of lipids: fats, phospholipids, steroids, waxes
comprises about 40% of the organic matter in the average human body
fats (a class of lipid, also called triglycerides)
formed by bonding glycerol to 3 fatty acids
joined by dehydration; resulting bond is an ester bond
important for energy storage
fatty aids:
saturated
unsaturated
cis
trans
saturated fatty acids
all carbons have the maximal amount of hydrogens
tend to be solid at room temperature
Note 
Flashcard (30)