Unit 1 Exam

List the characteristics that distinguish living organisms from non living organisms

Living things…

• contain nucleic acids, lipids, proteins, and carbohydrates

• composed of cells

• reproduce

• use energy and raw materials

• respond

• maintain homeostasis

Populations evolve and have adaptive traits

Properties of Life

Order

Evolutionary Adaptation

Regulation

Reproduction

Response to the Environment

Growth and Development

Energy Processing

List the levels of chemical/biological organization from complex to simple, and list a structure found at each level

1. Biosphere- Earth

2. Ecosystems- Forest

3. Communities- Deer, Tree, Fungi, Birds in a forest

4. Population- Herd of Deer

5. Organism- 1 Deer

6. Organs and Organ Systems- Circulatory System; heart and blood vessels

7. Tissue- Cardiac Muscle Tissue

8. Cell- Muscle Cell

9. Organelle- Mitochondria

10. Molecule- H20

11. Atom- Hydrogen

Explain the basic steps of the scientific process

Explain the major themes of biology

Organization- earth is organized into biological levels that help look at all systems of life

Evolution-

Information

Energy and Matter

Interactions

Organization

A major theme of biology

Earth is organized into biological levels that help look at all systems of life, creating hierarchy from complex to simple systems

Is a form of reductionism

• an approach that reduces complex systems to simpler components that are more manageable to study

• can give an incomplete view of life

Allows us to see what the emergent properties are at each level

• new properties that arise with each step upward in the hierarchy of life

• due to arrangement and interactions of parts as complexity increases

• explore emergent properties by combining reductionism and systems biology

  • exploration of biological system by analyzing interactions among its parts

  • used to study all levels of life

At each level there is a correlation btw structure and function

• analyzing biological structure help us learn about what living things do and how they work

• cell is the basic unit of structure and function

  • can perform all activities of life

Eukaryotic Cells

a type of cell with a membrane enclosed nucleus and membrane enclosed organelles

Has a nucleus

DNA is stored in the nucleus

Information

A Major theme of biology

Information is in genes which are located in DNA

• can be duplicated during cell division

DNA is stored in chromosomes where hundreds or thousands of genes are located

Genes encode info to build all molecules synthesized w/in a cell

• info gives cell it’s identity and function

Genetic info directs one’s development

Sequences of Nucleotides in genes encode info

Important in protein synthesis

Gene Expression

Genome

the genetic material of an organism or virus; the complete complement of an organism’s or virus’s genes along with its noncoding nucleic acid sequences

Genomics

the systematic study of whole sets of genes or other DNA and their interactions within a species as well as genome comparisons btw species

Bioinformatics

the use of computers, software, and mathematical models to process and integrate biological info from large data sets

Proteomics

The systematic study of sets of proteins their properties including their abundance, chemical modifications, and interactions

Gene Expression

the process by which information encoded in DNA directs the synthesis of proteins or in some cases RNAs that are not translated into proteins and instead function as RNS

Genes

a discrete unit of hereditary info consisting of a specific nucleotide sequence in DNA (or RNA in some viruses)

Prokaryotic Cells

a type of cell lacking a membrane enclosed nucleus and membrane enclosed organelles

NO nucleus

DNA is in the cytoplasm

2 Types

• Bacteria

• Archaea

Energy and Matter

a major theme of biology

the work needed to keep up cellular activities requires energy

• energy mostly comes from the sun

• energy is transformed from one form to another

  • photosynthesis- sun’s energy is converted into chemical energy

  • animals eating plants or other animals

• energy can be lost as heat

Energy is a cycle

• usually enters as light and exits as heat

• plants absorb light, consumers eat plants, consumers die and are decomposed back into the soil

Interactions

a major theme of biology

at all levels of organization interactions w/in the system ensure smooth function and integration

Molecules

• interact w/ organs, tissues, and cells

• works smoothly b/c feedback regulation

  • ability for process to self regulate because of interact

Ecosystem

• every organism interacts with other organisms

• symbiotic relationships

• organisms also interact w/ physical factors

  • roots break rocks as they grow

Evolution

Core theme of biology

a process of biological change in which species accumulate differences from their ancestors as they adapt to different environments over time

Explains that diversity is b/c heritable changes occurred a/f 2 species diverged from common ancestor

• 2 species will still shared some traits from common ancestor, unity btw them

Charles Darwin’s Idea

• Decent with modification- as species adapt to different environments over time they accumulate differences from their ancestors

• Natural Selection- individuals with inherited traits that are better suited to local environment are more likely to survive and reproduce

Feedback Regulation

regulation of a process by its output or end product

2 types

• negative feedback- response reduces the initial stimulus

• positive feedback- end product speeds up its own production

Domain bacteria

1 of 2 prokaryotic domains

the most diverse and widespread prokaryotes and are now classified into multiple kingdoms

Domain Archaea

includes multiple kingdoms

live in earth’s extreme environments

• salty lakes and boiling hot springs

Domain Eukarya

3 Kingdoms

• Plantae

• Fungi

• Animalia

Protists- unicellular eukaryotes, most numerous and diverse

Compare and Contrast the 3 domains of Life

Similarities

• Made of cells

• Use DNA or RNA to store genetic info

• use ribosomes to build proteins

• have a cell membrane

• divided into kingdoms

Differences

• Bacteria and Archaea are single cell prokaryotes

• Eukarya are eukaryotes

Review characteristics of life shared by viruses and what characteristics of life viruses lack

Have

• genetic material

• evolution and adaptation

• Reproduction

Don’t Have

• homeostasis

• metabolism

• cellular structure

• autonomous reproduction

Compare the physical properties (mass and charge) and locations of electrons, protons, and neutrons

Mass- space in which an object takes up

• Protons and Neutrons have mass

• Atomic mass= # of protons+ # of neutrons

Charge- occurs when # of electrons doesn’t = # of protons

• more protons = positive charge

• more electrons = negative charge

Partial Charges can occur in molecules when 1 atom is slightly more electronegative than others

• more electronegative atom pulls the electron to their direction more often causing a partial negative charge to that atom and a partial positive charge to the other atoms

• Ex. H20

Electrons are located in valence shells

Protons and Neutrons are located at center of atom

Explain how the valence electrons are related to chemical properties

Valence electrons determine the electronegativity of an atom which determines the chemical reactivity of an atom

• more electronegative= more chemically reactive

Relates to chemical properties by determining types of bonds an atom can create and its chemical reactivity

• atoms with almost empty or almost fully valence shells can create ionic bonds with each other

• atoms with same number of valence electrons have similar chemical behaviors

Compare and contrast covalent bonds (polar and non polar), hydrogen bonds, and ionic bonds

Covalent Bonds- electrons shared between atoms

• Polar- electrons are shared unequally due to high slightly higher electronegativity of one atom

  • creates partial charges

• Non Polar- electrons are shared equally

Hydrogen Bonds- bond formed between 2 molecules where H atom is covalently bonded to an electronegative atom

• When H atom has positive or partial positive charge and is a attracted to electronegative atoms

• individually weak but strong together

Ionic Bonds- transfer of electrons between atoms

• Results in Cation- atom that lost electron, and Anion- atom that gained electron

• Causes charges in atoms, cation=positive charge, anion=negative charge

• between highly electronegative atoms and atoms with little electronegativity

• cation and anion are attracted to each other and this attraction is the ionic bond

Explain how hydrogen bonds between adjacent water molecules govern the many amazing properties or water

Cohesion

• hydrogen bonds btw water molecules allows water to stick together

  • makes water more structured and has a higher surface tension

Moderation of Temperature

• Water’s High Specific heat allows it to be more resistant to temperature changes

  • needs more energy to change temp

  • Hydrogen Bonds cause this b/c heat is absorbed to break hydrogen bonds, but when hydrogen bonds reform they release heat

• High Heat of Vaporization

  • hydrogen bonds have to be broken to turn into water vapor

Expansion upon Freezing

• as water starts to freeze, molecules move too slow to break hydrogen bonds, so hydrogen bonds form in pattern that keeps molecules farther apart

  • less molecules in a space

Solvent of Life

• water molecules form hydrogen bonds with polar molecules which breaks down the molecule so it dissolves into the water

Explain how water ionizes; contrast acids and bases

Occurs when a hydrogen atom making a hydrogen bond btw 2 water molecules shifts from one molecule to the other

• aka Dissociation of water

• causes Hydrogen to leave its electron behind

  • Hydrogen only has 1 proton H+, no electrons

• water molecule that lost the H is now OH-

H+ and OH- are very reactive

in water # of H+ and OH- are equal

• creates pH scale

  • substances with more H+ are acidic

  • substances with more OH- are basic

  • substances that have equal amounts are neutral

    • water

Convert the hydrogen ion concentration of any solution to a pH value

Describe how buffers help minimize changes in pH

Buffers- a solutions that contains a weak acid and its corresponding base

• minimizes changes in pH by accepting H+ when in excess and donating H+ when depleted

What topics related to water interest you- internet research

Miller Urey Experiment

1. Water mixture in the “sea” flask was heated; vapor entered the “atmosphere” flask

2. “Atmosphere” contained a mixture of hydrogen gas (H2), methane (CH3), ammonia (NH3), and water vapor

3. Sparks discharged in atmosphere to mimic lightning

4. Condenser cooled the atmosphere, raining water, and dissolved molecules in sea flask

Results- found variety of Organic Molecules that are common in organisms

Conclusion- organic molecules may have been synthesized abiotically on Earth

Importance of valence electrons (COHN)

An atoms valence electrons determine the amount of other atoms it can bond too

• Carbon can form the most at 4

  • can form single or double bonds

• Oxygen 2

  • can form single or double bonds

• Nitrogen 3

  • can form single or double bonds

• Hydrogen 1

Isomers and enantiomers

Isomers- compounds with same # of atoms of the same elements but with different structures

• structure= functions

• 3 Types

  • Structural Isomers: differ in covalent arrangements (single and double bonds) of atoms

  • Cis Trans Isomers: carbons have covalent bonds to same atoms but atoms differ in spatial arrangement

    • double bond btw carbons

  • Enantiomers: isomers that are mirror images of each other and differ in shape b/c of asymmetric carbon

    • Left hand and Right hand

Hydroxyl group

OH

chemically reactive

hydrophillic

increase water solubility

polar due to electronegative oxygen

forms hydrogen bonds with water, helping dissolve compounds such as sugars

Compound name: Alcohol

Name usually ends in -ol

EX. Ethanol

Carbonyl group

C=O

chemically reactive

hydrophilic

increase water solubility

Compound Names

• Ketone groups- C=O is enclosed within carbon skeleton

  • Ketoses

• Aldehyde- C=O is at the end of carbon skeleton

  • Aldoses

EX. Acetone and Propanal

Carboxylic Acid

COOH (HO-C=O)

chemically reactive

hydrophilic

increase water solubility

acts as an acid (can donate H+) b/c covalent bond btw oxygen and hydrogen is so polar

Compound Name: Carboxylic Acid or Organic Acid

EX. Acetic Acid

Amino group

NH2

chemically reactive

hydrophilic

increase water solubility

acts as a base; can pick up H+ from the surrounding solution

Compound Name: Amine

Ex. Glycine

Sulfhydryl group

SH

chemically reactive

weakly increases water solubility

2 SH groups can react, forming a cross link that helps stabilize protein structure

Compound Name: Thiol

Ex. Cysteine

Phosphate group

OPO3 2-

chemically reactive

hydrophilic

increase water solubility

Contributes negative charge when positioned inside a chain of phosphates and when at the end

When attached, confers on a molecule the ability to react with water, releasing energy

plays role in ATP

Compound Name: Organic Phosphate

Ex. Glycerol Phosphate

Methyl group

CH3

not chemically reactive

Affects expression of genes when bonded to DNA or proteins that bind to DNA

Affects shape and function of male and female sex hormones

Compound Name: Methylated Compound

Ex. 5-Methylcytosine

Condensation synthesis and hydrolysis

Condensation synthesis- covalently bonds 2 molecules together by removing water

• connects a monomer to a monomer or polymer

Hydrolysis- breaks covalent bond btw 2 molecules by adding water

• disassembles polymers to monomers

  • H+ attaches to one monomer, OH- attaches to the other

Carbohydrates

Major macromolecule

a sugar (monosaccharide) or one of its dimers (disaccharide) or polymers (polysaccharide)

includes sugars and polymers of sugars

Monosaccharides

simplest carbohydrate, active alone or serving as monomer for disaccharides and polysaccharides

aka simple sugars

molecular formula usually ratio of CH2O

has carbonyl group and multiple hydroxyl groups

• location of carbonyl determines if it is a aldose or ketose

3-7 carbons long in carbon skeleton

Very diverse

• enclosed vs end carbonyl groups

• spacing of oxygen atoms

• length of carbon chain

major nutrient for cells

a part of cellular respiration

Ex. Glucose

Glucose

most common monosaccharide

hexoses- 6 carbon long- usually forms rings

Fructose is its isomer

Polysaccharides

macromolecules, polymers with few hundred- few thousand monosaccharides joined by glycosidic linkages

function: storage materials or building materials

• determined by monosaccharides and position of glycosidic links

2 types

• Storage Polysaccharides

• Structural Polysaccharides

Disaccharides

a double sugar, consisting of 2 monosaccharides joined by glycosidic linkage formed by a dehydration reaction

must be broken down to monosaccharides to energize organisms

Ex. Lactose and Sucrose

Sucrose

glucose+ fructose, table sugar

most common

helps plants transport carbohydrates from leaves to roots

Lactose

sugar in milk, glucose+ galactose

Lactase is enzyme that breaks it dwon

Storage polysaccharides vs. Structural polysaccharides

Storage

• plants and animals use to store sugars for later

• Starch- storage polysaccharide in plants

  • polymer of glucose

  • granulates within cellular structures known as plastids

  • enables plant to stock pile glucose

  • hydrolysis withdraws starch from stockpile

    • breaks bonds btw glucose monomers

  • mostly joined by 1-4 linkages

• Glycogen- extensively branched glucose found in the liver and muscle of animals

  • animals use for storage of sugars

  • breakdown occurs when energy demand increases

  • short life, depleted a/f a day

Structural

• helps organism build strong materials

• EX. Cellulose- structural polysaccharide of plant cell wall, made of glucose monomers, linked with glycosidic linkages

  • straight molecule

  • most animals including humans don’t have enzyme to breakdown cellulose

• EX. Chitin- carbohydrates used by arthropods to build their exoskeletons

Glycosidic Bond

a covalent bond formed btw 2 monosaccharides by a dehydration reaction

Lipids

group of biomolecules like fats, phospholipids, and steroids, that mix poorly with water

Hydrophobic b/c molecular structure

• mostly hydrocarbon regions with nonpolar CH bonds

vary in form and function

• most important biological are fats, phospholipids, and steroids

Fats

a lipid consisting of 3 fatty acids linked to 1 glycerol molecule; also called a triacylglycerol or triglyceride

not polymers but large molecules assembled by dehydration reations

• 3 different reactions b/c 3 fatty acids

• creates ester linage btw hydroxyl and carboxyl

Glycerol- an alcohol, 3 carbons each with a hydroxyl group

Fatty Acid- carboxylic acid with long carnon chain

• vary in length and # and location of double bonds

• 3 Fatty acids + 1 glycerol = Fat

  • triglyceride

• usually 16-18 carbons length

• contians 1 carboxyl gorup and lots of hydrocarbons

are hydrophobic

2 types

• Saturated

• Unsaturated

Major Function

• energy storage

• stores 2x of a storage polysaccharide

• animals need b/c use lots of energy

• stored in adipose cells

• also help insulate body and cushion organs

Saturated fats

no double bonds in all 3 fatty acids btw carbons in chain

no double bonds= as many hydrogen atoms possible bonded= flexible, allows fat molecules to pack tightly

solid at room temp

EX. butter and lard

Unsaturated fats

1 or more double bonds in carbon chain with fewer hydrogen bonds

most have cis double bond

• cause a kink

  • kink= less flexible= can’t be packed closely to solidify

liquid at room temp

Phospholipids

lipid made up of glycerol joined to 2 fatty acids and a phosphate group

hydrocarbon chains of fatty acids act as nonpolar, hydrophobic tails

hydrophilic head

cells could not exist w/o

• makes up cell membrane

differs from fats b/c only 2 fatty acids with a phosphate group

• phosphate gives negative electrical charge

amphipathic- both polar and non polar

• bilayer created so heads on outside, tails on inside

Steroids

lipids characterized by carbon skeleton of 4 consistent rings, distinguished by chemical group attached to rings

EX. Cholestrol

Ester Bond

a type of covalent bond formed by a condensation reaction between a hydroxyl group (–OH) of an acid (such as a carboxylic acid or phosphoric acid) and a hydroxyl group of an alcohol

Proteins

biologically functional molecule made up of 1 or more polypeptides, each folded and coiled into a specific 3D structure

account for 50% of dry mass in most cells and are instrumental in almost all organisms do

Functions

• speed up chem reactions, defense, storage, transport, cell communication, movement, and structural support

Enzymes

• most important proteins

• are catalysts (speed up chem reactions)

• can perform over and over

• workhouse that keep cell running

Structured by 20 different aminos acids

• linked in unbranched polymers

• peptide bonds

• structure= function

Amino Acids

an organic molecule with both an amino group and a carboxyl group

• all share a common structure

  • alpha carbon: asymmetric carbon atom in the center

    • connect to hydroxyl, carboxyl, H atom, and various R groups

      • R group differs with each amino acid, so determines characteristics and functional role

• bonded together with peptide bonds to form polypeptides

monomer of proteins

Peptide bonds

bond btw amino acids, covalent bond

bonds that make polypeptides

dehydration reaction btw carboxyl of one AA and amino group of another AA

Polypeptide

polymer of amino acids

Polypeptide backbone- N-C-C-N-C-C…

one end will have free amino group, other will have free carboxyl group

Primary structure

protein’s sequence of amino acids

determined by inherited genetic info

20 different amino acids make up in varying length and order

Secondary structure

polypeptide chain coils and folds due to hydrogen bonds btw polypeptide backbones

O atoms have partial negative charge and H atoms have partial positive charge, create hydrogen bonds btw H and O atoms

• bonds individually weak, but many = strong

alpha helix: delicate coil held together by hydrogen bonds

beta pleated sheet: 2 or more segments of polypeptide chain lying parallel

• connected by hydrogen bonds

• core of globular proteins

Tertiary Structure

overall shape of polypeptide stabilized by interactions btw R groups (side chains)

3D

Hydrophobic interactions- amino acids with non polar side chains fold into the core of the protein to be shielded from water

hydrogen and ionic bonds btw positive and negative charge R groups stabilize tertiary structure

Disulfide Bridges- covalent bonds btw 2 cysteine monomers that have Sulfhydryl groups in R groups

Quaternary Structure

association of 2 or more polypeptides

EX. Hemoglobin

Nucleic Acids

polymers of nucleotides

DNA belongs to them

contain genes

• determine AA sequence in proteins

2 types

• DNA

• RNA

Nucleotides

monomers of nucleic acids

building block of nucleic acids, made up of a 5 carbon sugar covalently bonded to a nitrogenous base and 1-3 phosphate groups

• 2 phosphate groups are lost during polymerization process

condensation reactions link nucleotides to form polynucleotides

• joined by phosphodiester linkages

  • consists of phosphate group covalently bonds to sugar group of another nucleotide

    • creates sugar phosphate backbone

DNA

deoxyribonucleic acid: nucleic acid molecule, usually double stranded helix, in which each polynucleotide strand consists of nucleotide monomers w/ deoxyribose sugar and nitrogenous bases (ATGC)

capable of being replicated and determining inherited structure of cells proteins

provides its own replication

directs RNA synthesis and controls protein synthesis through RNA, aka gene expression

genetic material organisms inherit from parents

stored in chromosomes

copied during cell division

holds info of all cells activities

antiparallel structure

• one runs 5’-3’, other runs 3’ to 5’

2 strands are complementary

• allows DNA to be copied during in cell division

RNA

ribonucleic acid: type of nucleic acid consisting of a polynucleotide made up of nucleotide monomers with a ribose sugar and nitrogenous bases (AUGC)

usually single stranded

functions in protein synthesis, gene regulation, and as genome of some viruses

Ribose vs. Deoxyribose

Ribose

• sugar in RNA

• containing O on 2nd C in ring

Deoxyribose- sugar in DNA that lacks O atom on 2nd C ring

Purine vs. Pyrimidine

Pyrimidines- has 1 six ring of C and N atoms

• Cytosine and Thymine and Uracil

Purines- 2 six ring structures of C and N atoms

• Adenine and Guanine