General Biology unit 1

What are the 5 fundamental characteristics all living organisms share

1. Cells

2. Replication

3. Information

4. Energy

5. Evolution

Theory

• a big idea that explains why or how something happens.

• It’s based on a lot of evidence and has been tested many times.

Cell theory

• What are organisms made of? Where do organisms come from?

• states that all organisms are made up of cells and that cells come from preexisting cells

Theory of evolution by natural selection

• How are organisms related to one another?

Chromosomes theory of inheritance

• How is hereditary information transmitted from one generation to the next?

Robert Hooke

• devises microscope with 30x magnification

• observed small compartments invisible to naked eye and named them “cells”

Anton van Leeuwenhoek

• devised microscope with 300x magnification

• observed single called organisms named “animalcules”

Hypothesis

• Testable statement that explains something observed

Experiment

• allows researchers to test effect of a single, well-defined factor on particular phenomenon

Prediction

• what you think will happen in an experiment

• measurable to observable results

• must be correct if hypothesis is valid

Spontaneous generation

• was an alternative hypothesis for the cell theory

• The belief that organisms could arise spontaneously under certain conditions

Louis Pasteur’s experiment

Louis’s hypothesis: cells arise from cells and cells do not arise by spontaneous generation

Experiment:

• Two glass flasks:

• Both flasks had nutrient broth

• One flask had swan neck open to the air

• Concluded that all-cells-from-cells hypothesis was correct

Chromosomal theory of inheritance

• Proposed by Sutton and Boveri

• Heredity or genetic information is encoded in genes

• Genes are units located on chromsomes

What was found of in the 1950s

• chromosomes are molecules of deoxyribonucleic acid (DNA)

• DNA is the hereditary material

• Genes are segments of DNA that code for cell products

Double helix

• Each strand is made up of four building blocks: A,T,C, and G

  • Adenine (A) pairs with Thymine (T)

  • Cytosine (C) pairs with Guanine (G)

• D N A carries, or encodes, information needed for an organism’s growth and reproduction

• James Watson and Francis Crick proposed that D N A is a double-stranded helix

The central dogma

• Describes flow of information in cells

• Dogma means framework for understanding

• DNA codes for ribonucleic acid (RNA) which code for proteins

RNA

• Molecules that carry out specialized functions in cells

• Messenger RNA (mRNA) is read to make proteins

Proteins

• molecules that help cells do their jobs.

• they build cell structures and speed up chemical reactions that keep the cell alive.

Why is DNA copied

• to pass genetic information from cell to cell or from one organism to its offspring

• Copying DNA is highly accurate

What happens if a mistake is made when DNA is copied?

• A change in DNA can cause changes in proteins

• Proteins determine how we look and how our bodies function

• DNA changes can be passed down and create differences between living things, leading to diversity

What do cells need to carry out chemical reactions?

• Chemical reactions inside cells require energy

• Organisms have two main nutritional needs:

  • Energy in the form of ATP (adenosine triphosphate)

  • Molecules used as building blocks for DNA, RNA, proteins, and other cell parts

• How organisms get energy is a key reason life is so diverse

Plants and bacteria

• Can produce sugar using energy from sunlight

• Use sugar to make A T P or store it in energy-rich molecules

• Can use molecules absorbed by environment as food

What is evolution?

• the process by which living organisms change over generations.

What did Darwin and Wallace say about how species change?

• All species are related because they come from common ancestors

• Traits can change from one generation to the next

• Darwin called this process descent with modification

What did Darwin learn from the finches on the Galápagos Islands? (ex of natural selection)

• Different islands had finches with different beak shapes

• Beak shape matched the type of food available on the island

• Birds with beaks best suited for their food survived and reproduced more

• Over generations, this led to descent with modification — changes in traits based on survival needs

Population

• Group of individuals of same species

• Living in the same area at the same time

Natural selection

• explains how evolution occurs

• Two conditions must be met for natural selection to occur in a population:

1. Individuals must vary in characteristics that are heritable—can be passed onto offspring

2. Within an environment, certain versions of these heritable traits help individuals reproduce more than other versions

How does natural selection work?

• Traits that help organisms have more offspring become more common

• Natural selection affects individuals

• Evolutionary changes happen in populations over time

• When populations change enough, new species can form (speciation)

Fitness

• Ability of individual to produce offspring:

• Individuals with high fitness produce many more surviving offspring than do others in population

Adaptation

• Trait that increases fitness of individual in particular environment

Tree of life

• depicts evolutionary history

• family tree of organisms

• describes genealogical relationships among species with single ancestral species at its base

• Phylogeny: actual genealogical relationships among all organisms

How is genetic variation analyzed

• Biologist study RNA and DNA from different organisms

• compare sequences or building blocks (A,T,C,G)

• Fewer sequence variations between two species may indicate closer relationships

What are the three major groups of organisms indicated by the tree of life

• Eukaryotes (have nucleus) = Eukarya

• Two groups of prokaryotes (lack nucleus) = Bacteria and Archaea

Taxonomy

• Taxonomy: the effort to name and classify organisms

• Taxon: a named group of organisms

• Domain: highest taxonomic level, created by Woese

  • Three domains: Bacteria, Archaea, Eukarya

• Phylum: a major lineage within a domain

What did Carolus Linnaeus contribute to classification?

• Created the classification system still used today (1735)

• Gave each organism a unique two-part scientific name: genus + species

• Genus: group of closely related species

• Species: individuals that regularly breed together or have distinct characteristics from other species

Rules for naming a species

• An organism’s genus and species designation is called its scientific name or Latin name:

  • Scientific names are always italicized

  • Genus names are always Capitalized

  • Species names are not capitalized:

• For example, Homo sapiens

Null hypothesis

• the idea that nothing is happening.

• It says there is no difference, no effect, or no relationship.

Food competition hypothesis

• Argues that long necks evolved because those with long necks can reach food unavailable to other mammals

• Simmons and Scheepers tested this

• Predictions:

• Neck length variable among giraffes

• Neck length in giraffes heritable

• Giraffes feed high in trees

The sexual competition hypothesis

• giraffes evolved long necks because:

  • Longer-necked males win more fights than shorter-necked males

  • Longer-necked males can then father more offspring

• Data support this hypothesis

• Data refutes food competition hypothesis

• Question is not closed—all hypotheses must be tested rigorously

Important characteristics of good experimental designs

• must have a control group

• experimental conditions must be constant

• repeating test essential

• use large sample size

Independent variable

what’s being tested or manipulated

Dependent variable

what is observed/measured

Chemical evolution

• how life started from non-living chemicals.

• Simple chemicals slowly formed more complex carbon-based molecules

• These molecules eventually formed one that could copy itself

• Once that happened, life began and biological evolution started

What are the four types of atoms make up 96% of matter in organisms

Hydrogen, carbon, nitrogen, and oxygen

Basic Atomic Structure

• The nucleus is in the center and has:

  • Protons (positive charge +1)

  • Neutrons (no charge)

• Electrons move around the nucleus:

  • Negative charge −1

• If an atom has the same number of protons and electrons, the charges cancel out

➡ The atom is electrically neutral

Atomic and Mass number

Elements: Consist entirely of a single type of atom

Atomic number:

• Characteristic number of protons in nucleus of any atom

• Written as subscript left of its symbol

Mass number:

• Sum of protons and neutrons in atom

Subtract mass and atomic numbers to find neutron number

Dalton (Da)

• Each proton and each neutron has a mass of one dalton (D a)

• Mass of electron so small that it can be ignored

• Therefore, mass of atom is equal to its mass number

what is an isotope

• The number of protons never changes

• The number of neutrons can change

• Same element + different neutrons = isotope

• Isotopes have different masses

• Example: All carbon atoms have 6 protons

What is atomic weight

• The average mass of all the element’s naturally occurring isotopes

• Based on how common each isotope is

• Example: Carbon’s atomic weight is 12.01 because carbon-12 is most common

How are electrons arranged in an atom?

• Electrons move in orbitals around the nucleus

• Each orbital can hold 2 electrons

• Orbitals are grouped into electron shells (1, 2, 3…)

• Smaller numbers = closer to nucleus

• This arrangement affects how elements behave

What are electron shells?

• Shells hold orbitals

• 1 orbital → 2 electrons, 4 orbitals → 8 electrons

• Electrons fill inner shells first, then outer shells

What is the valence shell and valence electrons?

• Valence shell = outermost electron shell

• Valence electrons = electrons in the valence shell

• Valence of an atom = number of unpaired electrons

• Different atoms have different numbers of unpaired electrons

How do atoms become stable?

• Atoms are most stable when their valence shell is full

• Shells can be filled by forming chemical bonds

• Covalent bonds = sharing unpaired valence electrons between atoms

• Atoms connected by bonds form a molecule

How do hydrogen atoms become stable?

• Hydrogen’s valence shell isn’t full (needs 2 electrons)

• Two hydrogen atoms share electrons

• Sharing fills their outer shells → more stable

What are compounds and how do electrons behave in them?

• Compounds = molecules made of different elements

• Electrons in covalent bonds are not always shared equally

• Atoms pull electrons toward themselves differently → called electronegativity

What is electronegativity?

• how strongly an atom pulls electrons toward itself

• Depends on:

  • Number of protons (more protons → stronger pull)

  • Distance of valence shell from nucleus (closer → stronger pull)

• Trend: increases up and to the right on the periodic table

• 6 most abundant elements in the body: C, H, N, O, P, S

What are the differences between nonpolar covalent, polar covalent, and ionic bonds?

• Nonpolar covalent bond: electrons shared evenly, bond is symmetrical

• Polar covalent bond: electrons shared unevenly, bond is asymmetrical

• In polar bonds, electrons spend more time near the more electronegative atom

• Ionic bond: electrons transferred from one atom to another → creates charged ions that attract each other

what are ions?

Ion: atom or molecule with a charge

• Cation: loses electron → positive charge

• Anion: gains electron → negative charge

How do unpaired electrons determine bonds?

• Each unpaired electron can join with another electron to make a covalent bond.

• Number of unpaired electrons = number of bonds an atom can make

• More than one unpaired electron → double or triple bonds

EX: Oxygen has 2 unpaired electrons → can form 2 bonds (like in H₂O).

How are molecules represented?

• Molecular formulas: show types and numbers of atoms (e.g., H₂O, CH₄)

• Structural formulas: show which atoms are bonded and if bonds are single, double, or triple

• 3D models: ball-and-stick or space-filling show molecule’s shape

Why is water important for life?

• Cells are ~75% water

• Water is an excellent solvent → can dissolve many substances

• Substances react more easily when dissolved in water

What makes water unique

• Small size

• Bent shape

• Highly polar covalent bonds

• Overall polarity

Why is water a polar molecule and what are hydrogen bonds?

• Water is polar:

  • Oxygen = partial negative (δ−)

  • Hydrogen = partial positive (δ+)

• Water has bent shape

• Hydrogen bonds = weak attractions between positive hydrogen of one water and negative oxygen of another

How does water dissolve substances

• Water can stick to polar or charged molecules using hydrogen bonds

• Molecules that mix well with water are called hydrophilic

• This is why many polar or charged substances can dissolve in water

What are hydrophobic molecules?

• Hydrophobic = “water-fearing”

• Uncharged and nonpolar → do not dissolve in water

• Stick together through hydrophobic interactions

• Van der Waals forces help keep them stable when clustered

What happens in a chemical reaction?

• Substance can be combined or broken down

• Bonds are broken and new bonds form

• Reactions are shown using chemical equations

What happens when water dissociates?

• Water (H₂O) can split into H⁺ (proton) and OH⁻ (hydroxide)

• The reaction goes both ways:

  • H₂O ⇌ H⁺ + OH⁻

• This is chemical equilibrium because the reaction happens both ways at the same time.

What are acids and bases?

• Acids: give up protons (H⁺) → increase hydronium (H₃O⁺) in solution

• Bases: take in protons (H⁺) → decrease hydronium (H₃O⁺) in solution

What is a mole

• a set amount of atoms or molecules

• 1 mole of an element weighs its atomic weight in grams

  • Example: Carbon = 12 → 1 mole = 12 g

Molecular weight: add up the atomic weights in a molecule

• Example: H₂O = 1 + 1 + 16 = 18 g per mole

Molarity (M)

• how concentrated a solution is

• measures how many moles of a substance are in 1 liter of solution

pH

• pH tells if a solution is acid (low pH) or base (high pH)

• Measures how many hydrogen ions (H⁺) are in the solution

• Each pH number is 10 times more or less H⁺ than the next number

What do pH numbers mean and what are buffers?

• Acid: pH less than 7

• Base: pH greater than 7

• Neutral: pH = 7 (like inside cells)

• Buffers: help keep pH stable → important for homeostasis

Why is carbon important in living things?

• Most molecules in organisms (except water) contain carbon

• Carbon has 4 valence electrons → can form 4 bonds

• Organic compounds = carbon + other elements

• Can make many shapes with single and double bonds

Functional groups in organic molecules

• Amino group: attracts proton → acts as base

• Carboxyl group: drops proton → acts as acid

• Carbonyl group: helps join molecules together

• Hydroxyl group: weak acid

• Phosphate group: has two negative charges

• Sulfhydryl group: forms bonds between molecules

What are macromolecules and polymers?

• Macromolecules: big molecules made of smaller subunits (monomers)

• Polymer: many monomers linked together

• Polymerization: the process of joining monomers to make a polymer

How are polymers made and broken?

• Condensation (dehydration) reaction: joins monomers → loses a water molecule

• Hydrolysis: breaks polymers → water is used to split the bond

What roles do carbohydrates play in cells?

Cell structure, cell identity, and energy storage.

What is a monosaccharide?

A “one-sugar” molecule; the monomer of carbohydrates.

What is an oligosaccharide?

A “few-sugars” molecule; a small carbohydrate polymer.

What is a polysaccharide?

A “many-sugars” molecule; a large carbohydrate polymer.

What are carbohydrates made of?

• They are made of carbon, hydrogen, and oxygen.

• The number of “sugar units” can be small (3) or very big (over 1000).

• They have a carbonyl group (C=O) and lots of C-H bonds.

• Not everything with C, H, and carbonyl is a carbohydrate (like formaldehyde).

Why are sugars important in cells?

• Provide energy for cells

• Serve as building blocks for bigger molecules

How did monosaccharides play a role in chemical evolution?

• Monosaccharides like ribose were needed to make nucleotides, the building blocks of RNA and DNA

How do monosaccharides differ from each other?

• Carbonyl group location:

  • End → aldose

  • Middle → ketose

• Number of carbons:

  • 3 → triose

  • 5 → pentose

  • 6 → hexose

• Spatial arrangement of atoms:

  • Different arrangement of hydroxyl (–OH) groups

• Shape in water:

  • Sugars usually form ring structures instead of straight chains

How are complex sugars (polysaccharides) made and broken?

• Polysaccharides = lots of single sugars (monosaccharides) linked together

• 2 sugars together = disaccharide

• Sugars stick together by losing water → makes a glycosidic bond

• You can break them apart by adding water (hydrolysis)

What are glycosidic linkages and how do they differ?

• Glycosidic linkages can form between any two hydroxyl groups of sugars

• Two common types: α-1,4 glycosidic linkage, β-1,4 glycosidic linkage

• Both connect the C-1 carbon of one sugar to the C-4 carbon of the next sugar

• Difference: the hydroxyl on C-1 can be up or down, which changes the shape of the sugar chain

Starch

• sugar storage in plants

• Made of many glucose monomers

Composed of:

• Forms a helix shape

• Amylose = unbranched chains of starch with only 4-glycosidic linkages

• Amylopectin = branched chains of starch with mostly 4-glycosidic linkages and some 6-glycosidic linkages

  • Branches happen about once every 30 glucose monomers

Glycogen

• sugar storage in animals

• Stored in liver and muscle cells

• Can be broken into glucose monomers for energy

• Highly branched alpha-glucose polymer, very similar to starch

  • Branches happen about once every 10 glucose monomers

Cellulose

• structural polysaccharide

• Major part of the protective layer around the plant cell wall

• Made of glucose monomers joined by 4-glycosidic linkages

• Every other glucose is flipped, so it:

  • Makes a straight (linear) molecule instead of a helix

  • Allows hydrogen bonds to form between parallel strands

Chitin

• Structural polysaccharide

• Found in cell walls of fungi and exoskeletons of insects and crustaceans

• Monomer = N-acetylglucosamine (NAG)

• Structure is similar to cellulose:

  • 4-glycosidic linkages with every other monomer flipped

  • Forms linear strands with hydrogen bonds between them

Peptidoglycan

• Structural sugar polymer in bacterial cell walls

• Made of long backbones of alternating monosaccharides joined by 4-glycosidic linkages

• Short amino acid chains connect the backbones with peptide bonds, giving strength

Functions of carbohydrates

• Act as building blocks to make other molecules (like nucleotides and amino acids)

• Provide structural materials (like fibers in cell walls)

• Indicate cell identity (help cells recognize each other)

• Store chemical energy for the cell

What are glycoproteins and glycolipids?

• Glycoproteins: proteins with attached carbohydrates

• Glycolipids: lipids with attached carbohydrates

• They are involved in:

  • Cell–cell recognition (identify cells as “self”)

  • Cell–cell signaling (cell communication)

Why do carbohydrates store a lot of energy?

The electrons in carbohydrate bonds are held less tightly, giving them higher potential energy.

• Tightly held electrons → low potential energy

• Weakly held electrons → high potential energy

How are starch and glycogen broken down to release glucose?

They are hydrolyzed (broken down) by enzymes because they have α-glycosidic linkages.

Which enzyme breaks down glycogen, and where is it found?

• Phosphorylase

• Many animal cells have phosphorylase to break down glycogen into glucose.

Which enzyme breaks down starch, and what is its role?

• Amylase enzymes

• plays a key role in carbohydrate digestion.

Plasma membrane (cell membrane)

• Separates living cells from nonliving surroundings

• Acts as a selective barrier

  • Lets needed materials into the cell

  • Keeps harmful substances out

• Helps life’s chemical reactions happen by holding the right chemicals in the right place

Lipids

• Molecules made mostly of carbon

• Do not dissolve in water

• This is because they have nonpolar bonds (C–C and C–H) that don’t mix with water

Hydrocarbons

• Nonpolar molecules made of only carbon and hydrogen

• Hydrophobic (repel water)

• Electrons are shared equally in C–H bonds, so there’s no charge