Unit 1 - Characteristics of Life

Bellringer

What is the difference between a theory and a hypothesis?

A theory is the concept or idea that you are testing with a hypothesis. A theory leads to a hypothesis, and a hypotheis leads to an experiment.

How would you describe the experimental group in experiments?

The experimental group is the independent variable that is acted upon to find a change or reaction. It is what is tested upon.

Notes on Experimental Design

Theory:

Statement based on multiple pieces of evidence from scientific research, it explains a phenomenon

Hypothesis:

Testable question or statement to explore one singular variable. Predicts an outcome.

Independent Variable:

What is manipulated or changed in the experiment. This is what you are controlling.

Dependent Variable:

What is measured and observed. You do not have any control over this.

Data:

Collected during observation or at a specific time.

Results:

Data in the form of graphs and charts. What you will publish/share with others

Conclusion:

Review/summary of the experiment.

Support:

• Good outcomes

• Possible future outcomes

• Peer review

• Publish

Refute:

• What went wrong

• How to fix the experiment

• Try again

Bellringer:

What are the two types of cells?

Prokaryotic and Eukaryotic

How are the two types of cells different?

Eukaryotic cells have membrane bound organelles and a nucleus. Prokaryotic cells have their DNA floating aroud in the cytoplasm.

Cell Theory Notes:

Cell Theory has 3 tenants/beliefs:

• All organisms are made of one or more cells

• The cell is the basic unit of structure and function

• All cells come from pre-existing cells

The first ever cell was called archaebacteria

Characteristics of Life Notes

Definitions:

• Multicellular - at least 2 cells, creates complex organisms

• Homeostasis - the point at which all bodily systems are stable

• Unicellular - a single cell, creates simple organisms

Notes:

Cells → Tissues → Organs → Organ Systems → Organisms

Response to Stimuli:

Organisms react to external factors in the environment

Adapt:

An organism will become familiar with its environment and will use it to its advantage.

Metabolism - sum off all life processes in an organism

Respiration - breakdown of organic material into usable energy

Transport - movement of materials through an organism

Regulation - control and coordination of all processes

Excretion - removes toxins in an organism

Growth - increases an organism’s size

Synthesis - creates larger molecules from smaller, organic materials

Reproduction - creates offspring like oneself

Nutrition - obtains and uses food for energy and survival

Growth is physical/external, Development is internal and occurs over a lifetime

Plant vs Animals Bellringer:

What are Viruses Notes

What is a Virus?

A virus is a non living particle made up of genetic material that attacks other cells

• They are considered non living because they:

  • are not cells, as they do not grow or respond

  • lack the cellular machinery to reproduce independently

    • can only reproduce if they have a host

  • have a nucleic acid core with DNA or RNA

Unit 2 - Macromolecules

Mony/Polymer Bellringer:

What is the difference between a monomer and a polymer?

Monomers are 1 molecule, polymers are 2 or more

How do molecules join together to form a compound?

Elemental molecules join together to fill the outer shell with 8 electrons to keep it balanced. Bonds hold these compounds together.

Compounds Notes:

Definitions:

Mixture:

any particles mixed together - easily seperated

Solution:

any material that a solute dissolves in - chemical combination - not easily seperated

Solvent:

the liquid that the solute dissolves in

Solute:

the particle that dissolves in the solvent

Suspension:

when materials are held in the middle of a solvent/floating

Types of Compounds:

Inorganic Compounds:

compounds that do not have Carbon (C) and Hydrogen (H) together

ex; H₂O (water), NaCl (table salt), and CO₂

Organic Compounds:

compounds that have both Carbon (C) and Hydrogen (H) together

ex; protiens, carbohydrates, nucleic acids, and lipids

The 4 Macromolecules Notes:

Nucleic Acids - CHONP

DNA:

Deoxyribonucleic Acid

RNA:

Ribonucleic Acid

• DNA is a double-stranded helix, RNA is a single-strand

• Nucleic acids are responsible for protein production and the transmission of genetics

Lipids - CHO

• commonly known as fat

• lipids do not dissolve easily, they are not soluble in water, and they can be solid or liquid at room temperature

Function of Lipids:

• provides insulation for homeostasis

• provides cushion protection for organs

• can provide long-term energy

• chemical messengers (hormones)

Where are lipids?

Cell membrane of ALL living things

Structure of Lipids

• 3 Fatty Acid molecules and 1 glycerol

• Saturated Fats are not soluble in water

• Unsaturated Fats are easiest to digest

Proteins - CHON

will have an impact on all body processes

6 Major Functions:

• storage

• transport (hemogoblin moves O₂)

• strength of movement

• regulations of hormones (adreniline; fight, fight, freeze)

• gives structure to cells and body

• enzymes (chemical reactions)

Structure of Protiens

• Built by amino acids

  • There are 20 types of amino acids

    • 12 are naturally occuring in the body, 8 come from food

      • 3 Groups that comprise protiens

        • NH₂ group

        • COOH/carboxyl group

        • R variable group/r side chain

  • Amino acids join together by peptide bonds

Carbohydrates - CHO

largest grouping of macromolecules

Functions and Characteristics of Proteins

• provides short-term energy and long-term energy

• maintains a ration of CHO ; 1:2:1

• all names end in “ose”

  • Glucose, Fructose, Sucrose

3 Types of Carbohydrates

• Monosaccharide

  • one sugar

  • simplest form of sugar

  • for glucose, the formula is C₆H₁₂O₆

  • shape - one ring structure

• Disaccharide

  • two sugars

  • for glucose, the formula is C₁₂H₂₂O₁₁

  • two hydrogens and one oxygen is lost (total of one water molecule)

• Polysaccharides

  • many sugars

  • repeating chains of sugars joined together

  • amylose is a polysaccharide, commonly called startch

Dehydration Synthesis

a chemical reaction to create larger moleculs from smaller molecules by removing water molecule(s)

Hydrolysis

a chemical reaction that breaks down larger molecules into smaller molecules by adding water molecule(s)

Enzymes Notes:

Enzymes:

• each enzyme is very specific. they will only help or break down substrates that fit into their active site.

• all enzymes end in “ase”

• enzymes will only work with their specific substrate(molecule)

• enzymes are catalysts because theyspeed chemcinal reactions up

• after an enzyme modifies a substrate, the enzyme is recycled for later use

Enzyme Malfunction:

• scientific term - denature

  • means “does not work properly”

  • denaturing will change the shape of an enzyme

  • there are two factors that can denature an enzyme

    • temperature - enzymes each work optimally at a specific emperature

    • pH level, 0-6 is acidic, 7 is neutral, 8-14 is basic

Chemical Reactions of Life:

• all chemical reactions in living orgaisms require enzymes to work

  • enyzmes speed up reactions.

    • they can speed up Dehydration Synthesis and Hydrolysis

    • they change te rate of a chemical reaction by lowering activation energy

      • activation energy is the amount of energy needed to start a chemical reaction

Enzymes:

• STRUCTURE DEERMINES FUNCTION

• enzymes are made up of proteins

  • each enyzme is named for the reaction that they help with

    • sucrase helps sucrose, protease helps protein synthesis, etc;

• enzymes are reusable, but only work with the same molecule

• the shape matters!

  • the lock and key model shows how enzymes bond

    • enzymes and substrates bond at the active site

      • the edge of an enzyme where the substrate fits perfectly

• the more enzymes there are, the faster they will work

What affects enzyme function?

• concentration

  • how much substrate there is

• temperature

  • heat can melt the enzyme, cold can freeze it

• pH

  • the level of acidicy can burn the enzyme off

Unit 3 - Cell Transport

Structure of the Cell Membrane Notes:

What is the structure of the membrane?

phospholipid bilayer

Function of Lipid:

• keep the water based environment in the cell seperate from the water based environment outside the cell

• materials cross the membrane based on size

• the tails of the bilayer is hydrophobic

  • don’t “like” water

• the head of the bilater is hydrophilic

  • “likes” water

Function of Protein:

• attached to or embedded in the membrane. help move materials in or out

Types of Proteins in the Cellular Membrane:

• peripheral

  • outside of the peripheral bilater (temporary)

• integral

  • part of the membrane’s structure (permanant)

• channel

  • helps move materials into the cell that may be larger in size

Passive Transport Notes:

Vocabulary:

Concentration:

the amount of solute in a solution

Concentration Gradient:

the graudal differencec in the concentration of solutes in a solution between the regions

Hypertonic Solution:

a solution in which there is a higher concentration of solute than there is outisde. water diffuses out, so the object shrinks. this is how grapes become raisins

Hypotonic Solution:

a solution in which there is a lower concentration of solute than there is outside. water diffuses in, so the object swells. this is similar to water balloons being filled

Isotonic Solution

a solution in which there is an equal concentration of solute and solvent. water flows equally both ways (in and out), so there is no change/always in equilibrium.

Notes:

Passive Transport:

• a process that does not require energy to move from a high to low concentration

  • diffusion: the movement of small particles across the cell membrane until homeostasis is reached

    • facilitated diffusion: requires the help of carrier and channel proteins

      • example of diffusion: air freshners - small can→big room

  • osmosis: the movement of water through a semi-permeable membrane using aquaporins

    • another form of diffusion, as it moves from high→low concentration

Active Transport Notes:

Active Transport:

• a process that requires energy to happen - cell has to work for it. active transport works against the concentration (low→high). works because of carrier proteins and ATP, which is made in the mitochondria.

Three Types of Active Transport:

• carrier protein pumps:

  • permanant part of the cellular membrane

  • create paths for the molecules

    • transports proteins that require energy to work

    • carrier proteins change shape to move different molecules

• endocytosis:

  • taking bulky material into a cell

  • phagocytosis

    • ‘cell eating’

    • cell membrane in-folds around food particles

    • this is how white blood cells ‘eat’ bacteria

• exocytosis:

  • forces material out of the cell in bulk

    • membrane surrounding the material fuses with the cell membrane

    • cell changes shape, requires energy

Unit 4 - Cell Division

Intro to Cell Division Notes:

Vocabulary

Cell Division:

the reproductive process of creating new cells

• consists of Interphase (g1, s, g2) and Mitosis (pmat)

Asexual Reproduction:

the process of reproduction which requires only one parent cells

Chromosomes:

holds specific genes for specific traits

Diploid #:

2n=46 (two sets)

Haploid #:

n=23 (one set)

Interphase Notes:

Why do Cells Divide?

• they become too large

• to make more cells for organism growth

• to replace old cells

Cells That Do Not Divide:

• brain cells

• nerve cells

• muscle cells

Things That Must Divide:

• DNA

• all organelles

• cell membrane

Interphase:

• grows cells and copies DNA

G1 (Growth 1)

• cell grows and does normal cellular activities

• Checkpoint 1: checks the size of the cell

S (Synthesis)

• DNA is copied, making two sets

• Checkpoint 2: reviews the copied DNA to make sure no mutations are present

G2 (Growth 2)

• prepares cell for division

• copies rest of the organelles

• Checkpoint 3: checks DNA consistency

Mitosis Notes:

Mitosis (M Phase)

• process in which two identical cells through asexual reproduction

Stages of Mitosis:

Prophase:

• DNA packs up into chromosomes to keep it organized

• nuclear membrane disappears and spindle fibers form our of centrioles

  

Metaphase:

• chromosomes line up in the middle of the cell

• spindle fibers attach to chromosomes and are controlled by centrioles

  

Anaphase:

• sister chromatids move apart

• chromatids are pulled to opposite ends by the spindle fibers

  

Telophase/Cytokinesis:

• two new cells start forming

Cytokinesis:

• division of cytoplasm

• Plant cells -- create a CELL PLATE here, and it becomes the cell wall.

• Animal cells divide into 2 with a cleavage furrow

• nucleus forms again

Cell Regulation and Cancer Notes:

Vocabulary

Chemical Signals:

• signals that tells a cell when to start dividing

Cyclins:

• regulates the timing of the cell cycle

Internal Regulators:

• allow the cell to proceed to the next phase of the cell cycle only when certain processes have occurred inside the cell.

Biopsy:

• procedures that tests tumor tissues by taking a small sample

What is Cancer?

• cancer is a disease of a cell where cell division is uncontrolled

  • body’s own cells lose their ability to respond to signals from regulators

  • clumps form as a result of cells dividing uncontrollably

types of tumors:

• benign tumors - remain clumped; can be removed.

• Malignant tumors: break apart (metastasize) and can form tumors in other parts of the body.

features of cancer:

• cancerous cells come from normal cells with damage to DNA.

• unusual numbers of chromosome and mutations

• can divide indefinetley

• abnormal cell surface

• don’t differentiate

• cancer cells ignore the chemical signals that start and stop the cell

causes of mutations:

• radiation

• smoking

• pollutants

• chemicals

• viruses

Unit 5 - Photosynthesis

Intro to Photosynthesis Notes:

What is Photosynthesis?

• photosynthesis is the process by which plants make sugars

  • photosynthesis directly means light-synthesis, or to make larger molecules from smaller ones using light

what is required for photosynthesis?

• carbon dioxide (CO₂), hydrogen dioxide/water (H₂O), and sunlight

what is made from photosynthesis?

• glucose (C₆H₁₂O₆) and oxygen (O₂)

what is the equation for photosynthesis?

• CO₂ + H₂O + Sunlight → C₆H₁₂O₆ + O₂

ROYGBIV and Photosynthesis:

• ROYGBIV - the color spectrum of white/visible light

• plants reflect green light (don’t grow in it)

• plants grow best in red and/or blue light

Plants:

• leaf=bottom

• two structures

  • gaurd cells and stroma (exchange)

    • these both open and close constantly

Chloroplast:

• three main structural parts:

  • stroma - protein rich liquid

  • grana - stack of thylakoid membranes

  • lamell - holds the grana together

Light Dependent vs. Independent Reactions

	light dependent reactions	light independent reaction
other names	light rx	calvin cycle, dark rx
creates	releases oxygen, high energy electrons	C6H12O6 (glucose
location	thylakoid membrane (grana)	stroma of chloroplast
products	O2 and e- (electrons)	energy and glucose
reactants	sunlight, water, carbon dioxide	electrons, atp, carbon dioxide

Factors Affecting Photosynthesis Notes:

Relationship Between the Light Dependent and Light Independent Reactions

• How does the Light Dependent Reaction work?

  • light is absorbed

  • pulls water from the roots

    • this water is then broken by light

      • the oxygen is released into the air

  • absorbs carbon dioxide from the air

  • carbon, hydrogen, and oxygen are left

  • atp and nadp are made

  • these molecules go to the stroma in the forms of:

    • atp

    • co

    • nadph

• How does the Light Independent Reaction work?

  • starts with the atp from the light dependent reaction

  • nadph drops off the hydrogen

  • co will create glucose and other carbon bi-products to help cell

    • pgal

Definitions:

ATP:

• adenosine triphosphate

  • adp + p→atp

    • the extra phosphate is energy

  • atp loses energy (phosphate) once used, goes back to adp

ADP:

• adenosine diphosphate

  • atp - p→adp

  • still very high energy

NADP⁺:

• nicotinamide andenine dinucleotide phosphate

  • helps give energy to the reactions in the Light Independent Reaction created from the Light Dependent Reaction

  • high energy electron

  • carries hydrogen

Factors Affecting Photosynthesis:

• there are 3 main factors that affect photosynthesis:

  • amount of available water

  • temperature

  • amount of available light

Unit 6 - Cellular Respiration

Cellular Respiration Notes:

Energy:

• energy for living things come from food

  • all energy in food can be traced back to the sun

• organisms that use light energy from the sun to produce food are called autotrophs

  • examples: plants and some microorganisms such as bacteria and protists

• organisms that cannot use the sun’s energy to make food are called heterotrophs

  • examples: animals and most microorganisms

• cells usable source of energy is called atp

  • atp stands for adenosine tri-phosphate

• all energy is stored in the bonds of compounds - breaking the bond releases the energy

• when the cell has energy available it can store this energy by adding a phosphate group to adp to make atp

  • adp stands for adenosine di-phosphate

• atp is converted into adp by breaking the bond between the second and third phosphate group and releasing energy for cellular proesses

Cellular Respiration:

• cellular respiration is the process by which the energy of glucose is released in the cell to be used for life processes, such as breathing, movement, and more

• cells require a constant source of energy for life processes but only keep a small amount of atp on hand. cells can regenerate atp as needed by using the energy stored in foods like glucose

• the energy stored in glucose by photosynthesis is released by cellular respiration and repackaged into the energy of atp

• respiration ccurs in all cells and can take place either with or without oxygen present

• there are two types of cellular respiration, aerobic and anaerobic

Aerobic Respiration:

• requires oxygen

• occurs in the mitochondria of the cell

• total of 36 atp produced

• basic formula: C₆H₁₂O₆ + 6O₂ → 6 CO₂ + 6H₂O + 36 ATP

• summary of aerobic respiration:

  • 3 steps:

    • glycolsis

    • kreb’s cycle

    • electron transport chain

Anaerobic Respiration:

• occurs when there is no oxygen available to the cell

• two kinds

  • alcoholic

    • occurs in bacteria and yeast

    • process used in baking and brewing, yeast produces CO₂ gas during fermentation to make dough rise and give bread its holes

  • lactic acid

    • occurs in muscle cells

    • produced in muscles during rapid excercise when the body cannot supply enough oxygen to the tissues, causes burning sensation in muscles.

• also called fermentation

• much less atp produced that aerobic respiration

Unit 7 - DNA Structure and Replication

Intro to DNA Notes:

What is DNA?

• DeoxyRibonucleic Acid

  • the buidling blocks of DNA are nucleic acids

  • dna is a polymer because it is made up of repeatig units

What is DNA made up of?

• dna is made up of repeating nucleotides. each nucleotide has:

  • phosphate group

  • 5 carbon sugar called deoxyribose

  • nitrogen base

    • these are one of 4:

      • thymine

      • guanine

      • adenine

      • cytosine

    • the nitrogen bases each pair up with one another in specific ways

      • adenine and thymine always pair together

      • guanine and cytosine always pair together

    • purines vs pyrimidines:

      • adenine and guanine are purines

      • cytosine and thymine are pyrimidines

• the backbone of dna is composed of the phosphate groups and the 5 carbon sugars from the nucleotides

DNA Discovery and Replication Notes:

How was DNA’s structure discovered?

• the shape and structure of dna was discovered in 1952

  • at this time, women were severely underrepresented in stem

    • a woman named rosalind franklin discovered dna’s shape using a method called x-ray diffraction

    • watson and crick built and published a 3d model of dna

• nitrogen basesare arranged in triplets called codon

How does DNA replicate?

• dna replication creates a copy of a dna strand. it always happens during the s phase and dna never leaves the nucleus.

  • helicase

    • enzyme

    • helps to unravel the dna strands

    • the unwound strand is called a replication fork

    • the dna then beocmes unzipped, or the h2 bonds break. it splits into the parent and templete strands

What are the main steps of replication?

1. Helicase unwinds and unzips dna, breaks h2 bonds, replication fork created

2. template strand is prepared for copying. dna primase adds an rna primer. dna then needs to add genetic code to the strands

3. dna polymerase adds complementary bases to the strands

4. dna ligase builds the new h2 bonds and backbone of the dna strand, creating the helix

Types of RNA Notes:

What is RNA?

• rna is a nucleic acid build of repeating chains of nucleotides, each of which is composed of three main groups:

  • a 5 carbon sugar called ribose

  • a phosphate group

  • a nitrogen base, either adenine, thymine, cytosine or uracil

What are the different types of RNA molecules?

• there are 3 types of rna molecules

• each type of rna has a different function in the synthesis of proteins

messenger rna (mRNA)

• carries dna’s message from the nucleus to the ribsomes

• mRNA is created by converting dna

transfer rna (tRNA)

• carries the correct amino acids to the ribosome so they can be added to the growing protein chain

ribosomal rna (rRNA)

• makes up part of the ribosome

• helps read rRNA’s message and asseble the proteins

What is the central dogma of biology?

the central dogma of molecular biology is a theory stating that genetic information flows only in one direction, from dna to rna to protein

Unit 8 - Protein Synthesis

Intro to Protein Synthesis Notes:

RNA:

• all types of rna help with protein synthesis

• there are 3 main types of rna

  • messenger rna (mRNA)

    • serves as messengers from dna/nuclues to the rest of the cell

    • copies a section/gene of dna to make single stranded rna using mRNA nucleotides

      • called transcription

    • transports the newly formed mRNA from the nucleus to the ribosomes in the cytoplasm

  • transfer rna (tRNA)

    • transfers each amino acid to the ribosome to build a protein

      • called translation

    • structure:

      • ribbon conects to anti-codon to specific amino acid

      • anti-codon matches up with mRNA codons to determine the order amino acids will connect to form a protein

  • ribosomal rna (rRNA)

    • makes up the ribosomes

      • where translation occurs

Protein Synthesis:

• proteins are long chains of amino acids/polypeptides

  • polypeptide - combination of any or all of the 20 different amino acids

• the order in which amino acids are joined together determines if the protein being made is an enzyme, hair, muscle, etc

• consists of two steps:

  • transcription

  • translation

Transcription Notes:

What is transcription?

• the first step of protein synthesis

• mRNA molecules are produced by copying a part of the nucleotide sequence of DNA (one gene, not the whole molecule) into a complementary sequence in rna nucleotides

• this works due to rna polymerase seperating one section of dna/a gene in the nucleus and using one strand of dna as a templete to assemble rna nucleotides into a strand of mRNA

Where does transcription start and end?

• there are specific nucleotide sequences that “tell” transcription where to start and stop

• the “start sequence” is called a promoter. this iniates transcription by allowing rna polymerase to bind to one side of dna

• similarly, the “stop sequence” is called a terminator. this signals the end of the gene and terminates transcription, detaching the mRNA from the dna strand

What are the phases of transcription?

1. initiation:

• promoter signals the beginning of a gene and mRNA binds to DNA to start transcription.

2. elongation:

• mRNA uses one strand of DNA as a template to match nucleotides according to Chargaff’s Rule (substituting U for T).

3. termination:

• terminator signals the end of the gene and mRNA releases from DNA, ready to leave the nucleus.

How is mRNA edited?

• before mRNA leaves the nucleus, it is modified, or processed, in several ways

  • addition of extra nucleotides to the ends; “cap” and “tail”

  • “rna splicing”- removal of introns and joining of exons

What does the transcribed mRNA tell us?

• just as in dna, mRNA nucleotides are “read” 3 at a time, as codons. each codon specifies a particular amino acid

• therefore, the order of mRNA codons determines the order of amino acids that will be linked together during the next step…

What are the steps of transcription?

1. helicase unzips DNA

2. rna polymerase base pairs – A with U, C with G

3. mRNA breaks away

4. dna rejoins

5. mRNA leaves the nucleus

Translation Notes:

What is translation?

• overview: at ribosome, mRNA “read” by tRNA, which brings amino acids to build polypeptide chain

• translation occurs at the ribosome where the codons in the mRNA produced during transcription provide instructions for the order of the amino acids, brought to the site of protein synthesis by tRNA

What is the role of tRNA in translation?

• amino acids themselves cannot recognize the codons, so they need help getting transferred to the ribosome

• each tRNA carries only one type of amino acid

• the three bases on tRNA are called the anticodon (complementary to mRNA codon)

What are the steps of translation?

1. mRNA is released from the nucleus → enters cytoplasm

2. mRNA attaches to the ribosome

3. mRNA codons move through the ribosome → anticodons on tRNA ensure correct amino acid is brought by tRNA

4. amino acids are bound together → polypeptide chain (aka protein)

Mutation Notes:

What is a mutation?

• mutation: a change in dna

  • not all mutations are harmful 

  • can happen in body cells and in gametes.

    • mutations are passed down to offspring only when they are in the gametes

What are the types of mutations?

• substitution - one nitrogen base is substituted for another

• insertion - a nitrogen base is added

• deletion - a nitrogen base is removed

What is a mutagen?

a factor in the environment that causes mutations

What is a point mutation?

•  a mutation involving one nucleotide in a gene

  • sometimes several bases are involved

• point mutations are subdivided into groups

  • substitution

    • when one base is substituted for another during replication

    • sickle cell anemia is caused by a substitution point mutation

      • the gene that codes for the hemogoblin protein on red blood cells is made incorrectly

  • silent mutation

    • a substitution where the mutated dna codes for the same amino acid as the original dna

  • deletion

    • when a single nucleotide is removed form the dna

    • causes every base after the removed one to be shifted to the left 1

    • yeilds for different amino acids since the codons change

  • insertion

    • when a single nucleotide is added to the dna

    • causes every base after the added one to be shifted to the right 1

    • also yeilds for different amino acids since the codons change

• insertions and deletions are known as frameshift mutations

  • frameshift mutation - the insertion or deletion causes a shift in the reading frame of the dna

  • deletions shift to the left

  • insertions shift to the right

  • every amino acid after the insertion or deletion is changed

  • this changes the entire polypeptide chain