BS 181H Exam 1

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

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* 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

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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

* # of protons = # of electrons (unless the atom is charged)
* # of protons = atomic number

orbitals

regions surrounding the nucleus in which the probability of finding electrons is high

* a central nucleus surrounded by cloudlike orbitals

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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?**

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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

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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

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* 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

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solutes are molecules that are:

* ionic and/or with polar covalent bonds

hydrophobic

water fearing

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solutes are molecules that are:

* nonpolar like hydrocarbons, oils

amphipathic

both hydrophilic and hydrophobic

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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

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* 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

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* 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

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* 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

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* double helix
* nucleotides: dA, dG, dC, dT (thymine)

components of nucleotides in RNA

* phosphate
* sugar: ribose
* base: uracil

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* 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

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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

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fatty aids:

* saturated
* unsaturated
* cis
* trans

saturated fatty acids

all carbons have the maximal amount of hydrogens

* tend to be solid at room temperature