AP Bio Midterm Review (૭ ｡•̀ ᵕ •́｡ )૭

Independent Variable

the variable that is being manipulated or changed

Dependent Variable

the variable that is being measured

Controlled Experiment

the experiment that serves as a comparison to the actual experiment to see if the independent and dependent variable truly have a relationship

Alternate Hypothesis

a testable prediction that states that the independent variable DOES have an effect on the dependent variable

Null Hypothesis

a testable prediction that states that the independent variable DOES NOT have an effect on the dependent variable

Negative Control

• a control where there are no expected results expected to happen

• can remove independent variable entirely with this control

Positive Control

a control where there are expected/standard or well understood results

Standard Error of the Mean

• measures how close the sample mean is to the population mean

• the larger the range of data, the larger the standard error of the mean will be

Error Bars

• graphical representation of the variability of data

• add by 2 SEM on the graph to show error bars

• when error bars overlap in the data shows that the data isn’t statistically significant

• how to: plot your mean data points, and for each point, draw a vertical line (the bar) extending up and down by a value of twice the SEM

Elements

• substances that cannot be broken down any further by chemical reactions

• matter is made up by these

• In this unit, Carbon, Hydrogen, Oxygen are the most important. Nitrogen, Phosphorus, and Sulfur are semi-important

• Hydrogen is positively charged

• Oxygen is negatively charged

• H+O covalently bond to each other.

• Can form hydrogen bonds (H2O)

Polar

• when two or more elements bonded together have an uneven charge of electrons (partially negative, partially positive)

• H2O is polar meaning that whatever else is polar will dissolve in water → like dissolves like

• Hydrophilic → water loving

  → → lipids have hydrophilic heads

• Acids and Bases will be attracted to polar molecules

    Nonpolar - when two or more elements bonded together have an equal amount of charge of electrons.

• Nonpolar substances dissolve nonpolar substances

• Hydrophobic → water fearing

  → → lipids have hydrophobic tails

Hydrogen Bonding

• when H and O bond together

• weak attraction

• can form and break easily

• but when there are many bonds of H → very strong

• found in DNA, H2O and proteins

Van der Waals Interactions

• transient connections resulting from asymmetrical distributior of electrons within a molecule

• very weak bonds

• lizards feet sticking to wall

Cohesion

• the linking of similar (properties) molecules

• water sticking to water

• high surface tension

• hydrogen bonds between the oxygen atom and hydrogen atom of two different water molecules

Adhesion

• water sticking to other polar molecules

• meniscus

Transpiration

water travels against gravity from roots to leaves in plants due to cohesion and adhesion

Moderation of Temperature

• water has high specific heat

• must absorb/give off a lot of energy before temp increases/decreases

• allows animals and plants to live in large bodies of water since the temp is stable

Insulation of bodies of water by floating ice

• ice is less dense than water

• prevents water from freezing solid (fish can survive)

• enables a moderation of temperature

Universal Solvent

• hydrophilic/polar substances are soluble in water and can dissolve

• hydrophobic/nonpolar substances aren’t soluble in water and repels water (fats and oils)

Heat of Vaporization

• the amount of heat energy a liquid must absorb to change from a liquid to a gas state at a constant temperature.

• Water has a high heat of vaporization due to hydrogen bonds,which require significant energy to break

• - making evaporative cooling in organisms and climate moderation by large bodies of water important biological functions. → sweating

pH scale

• scale is 0-14. Measures how acidic or basic a substance is

    -- Acids - 0-6 on pH scale.

• H+ donors

• excess H+ → the lower on the scale you go the higher amount of H+ you will have

• H+ increases by 10x each level

• OH- acceptors

    --Bases - 8-14 on pH scale.

• H+ acceptors

• excess OH-

--Pure Water - 7 on the pH scale, neutral

Buffers

• real life example of homeostasis

• our bodies try to regulate our pH and keep it normal

• Formula: H2O+CO2 ←→ H2CO3 ←→ HCO3 +H+

• If the human body became slightly more acidic the equation would shift left

• If the human body became slightly more basic the equation would shift right

Organic Compounds

• compounds that contain carbon and hydrogen and are the molecules of life

    Isomers - compounds with the same number of atoms but different strucuture → different properties

        Hydroxyl - -OH

        Methyl - CH3

        Carboxyl - COH (double bonded)

        Carbonyl   - COOH or CO2H

        Amino/Amine - NH2

• in amino acids (monomers of proteins) alongside carboxyl

        Phosphate - PO4

• in lipids specifically phospholipids and nucleotides

        Sulfhydryl - -SH

• can be called a disulfide bridge which is a covalent bond that plays a crucial role in stabilizing the three-dimensional structure of proteins. 

Polymers

• long molecules made of many similar building blocks (monomers) linked by covalent bonds

• Polysaccharide (carb)

• Lipids

• Proteins

• Nucleic Acids

Monomers

• small building blocks to polymers

• monosaccharide

• no monomer for lipids

• amino acids

• nucleotides

Condensation Reaction (Dehydration Synthesis)

• removing water in order to combine monomers together

• covalent bonding

• water is formed

Hydrolysis Reaction

• adding water in order to break down polymers

• digestion

• water is added

Carbohydrates

• most abundant molecules for life, on display, lines connect monomers

• Carbon Hydrogen and Oxygen

 Simple Sugar

• monosaccharides (one unit of sugar)

• C:H:O → 1:2:1 ratio

• -ose ending

• carbonyl and -OH group included

Polysaccharides

• complex carbs that have thousands of sugar monomers

• glycogen - long term energy for animals

• starch - long term energy for plants

• cellulose - structure in plants

• chitin - structure in coach roaches, and fungui

Oligosaccharides

• short chain of 2 (disaccharide) or more sugar monomers

• 2-10 monomers long

• lactose, sucrose, maltose

Lipids

• Carbon, Hydrogen, Oxygen, (Phosphorus), (Nitrogen), (Sulfur), on display, they are stitched together

• no true monomer

--Triglycerides - typical fats in foods

• CHO

• long term energy storage

• shock absorber for organs

• insulation

• One glycerol and 3 fatty acids=TRIglyceride

    --Phospholipids - has a hydrophilic head and hydrophobic tail

• Phospholipid Bilayer - forms the fundamental structure of the cell membrane

• Helps cell permeability

• Makes up cell membrane

• saturated fatty acids = tighter packing

Steroids

• used for signaling the body

• can be a component of the cell membrane

• 4 fused rings

• Cholesterol

Fatty Acid

• a hydrocarbon chain with a carboxyl group at one end

• can be saturated or unsaturated

    --Saturated - animal fats

• packed tightly together

• only contain one single bond of carbon

• chains are straight

• solid at room temp

• higher risk of heart disease

• less reactive than unsaturated

    --Unsaturated - plant fats

• one or more double bonds

• chains are straight until it removes hydrogen

• liquid at room temp

• many double bonds of carbon

• healthier than saturated fats

Proteins

• Growth and repair, signaling between cells, defense against invaders, catalyzing chemical reactions (enzymes)

• Sulfur, Oxygen, Nitrogen, Carbon, Hydrogen

• all enzymes are proteins

Amino Acids

• monomers of protein

• 20 different ones

• can be hydrophobic, hydrophilic, acid/bases, or have charges

• Carboxyl group attached to central C and variable R with side chain (amine)

• when combining amino acids dehydration synthesis occurs

Protein Structure

• 4 levels that are responsible for protein’s unique structure/conformation

   --Primary - the protein has no particular shape and just linked together

• linear

• covalent bonded

    --Secondary - the protein is in a spiral/coil (alpha-helix)

• hydrogen bonded

• beta strand if folded

    --Tertiary - the protein is raveled all together

• hydrogen bonded

• ionic

    --Quaternary - the protein combines with other proteins

• two or more polypeptide chains attach together

Denaturation

• enzymes losing shape due to pH, temperature, or salt changes.

• Enzymes lose their function and can never return

• the active site of the enzyme changed

Fibrous protein

• structure is in strands or sheets

• water insoluble → hydrophobic

• strong

Globular proteins

• folded in compact rounded shapes

• water soluble

• tertiary structure

Peptide bond

• proteins are held together by peptide bonds

• covalently bonded

• eventually makes polypeptide chains

Polypeptides

• polymers of peptide bonds can help make bigger proteins

• covalently and hydrogen bonded

Nucleic Acids

polymer of nucleotides

Nucleotides

• the monomers of nucleic acids

• 5-C sugar (ribose or deoxyribose) → backbone

• Nitrogen base → in the interior

• ATGCU → hydrogen bonded

• phosphate group → backbone

Purines

• Adenine and Guanine

• two rings

• must match with pyrimidines

Pyrimidines

• Thymine and Cytosine

• one ring

• must match purines

DNA

• stores genetic information

• deoxyribose sugar

• A+T (2 h-bonds) G+C (3 h-bonds)

• left to right → 5’3’

RNA

• translated code from DNA to make proteins

• ribose sugar

• A+U (2 h-bonds) T+A (2 h-bonds) G+C (3 h-bonds)

• left to right → 5’3’

Polarity

• hydrocarbons are nonpolar

• oxygen and nitrogen tend to make molecules polar

Plasma Membrane

• selective permeable phospholipid bilayer

• regulates the passageway of substances in and out of the cell

Cytosol

• the fluid part of the cytoplasm

• facilitates the movement of substances

Chromosomes

• inside the nucleus

• made up by DNA

• carries genetic information

Eukaryotic Cell

• have internal membrane systems, nucleus, and are much larger than prokaryotes

• are efficient, specialized, more complex and protection, and more surface area

• animal, plant, fungi, protist

Prokaryotic Cell

• lack membrane bound organelle,

• no nucleus

• rapid growth, adaptable, low energy demands, simpler regulation

• are smaller than eukaryotes

Surface Area to Volume

• a higher surface area to volume ratio means that it is more efficient at transporting

• most plant cells are between 1-100 micrometers in diameter (100 being the smallest)

• cells want a high surface area to volume ratio so they create folds or projections

• higher surface area to volume ratio = smaller cell

Nucleus

• the control center

• contains the nuclear envelope, pores, nucleolus, chromosomes, and ribosomes

Pores

• protein-lined channel

• located in nuclear envelope

• regulates the transport of molecules between the nucleus and cytoplasm

Nucleolus

• responsible for the synthesis and assembly of ribosomes

    Chromosomes/Chromatin

• chromatin is the complex of DNA and proteins (histones) that forms chromosomes

• within the nucleus of eukaryotic cells.

• chromosomes are the highly condensed

Ribosomes

• free in cytosol

• bound to E.R

• small spheres that synthesize proteins by translating into mRNA into polypeptide chain

• ribosomes make proteins

 Free Ribosomes

• unattached ribosomes floating in the cytoplasm

• synthesize protein used in the cell itself → enzymes and structural proteins

    Bound Ribosomes

• attached to the outer surface of the rough ER

• are responsible for synthesizing proteins destined for secretion from the cell or for insertion into membranes.

• are part of the endomembrane system facilitating the protein's entry into the ER lumen for further modification and transport. 

Endomembrane system

• a group of membranes and organelles in eukaryotic cells that work together to modify, package, and transport proteins and lipids.

• Golgi apparatus, lysosomes, vacuoles, vesicles, nuclear envelope, and plasma membrane.

• essential for synthesizing, processing, and sorting these molecules for use within the cell or secretion outside of it.  

Vesicles

• a small, membrane-bound sac that transports, stores, or digests cellular substances.

• act as "bubbles" that move materials within the cell or between organelles and the plasma membrane

• playing a vital role in processes like secretion, endocytosis, and the endomembrane system.  

   Transport vesicles

• small, membrane-bound sacs that bud off from organelles like the endoplasmic reticulum or Golgi apparatus

• moves materials such as proteins and lipids to other locations within the cell or to the outside of the cell.

• also known as vesicular transport, is a form of active transport that requires energy and is essential for functions like secretion and moving cargo along cytoskeletal tracks. 

Endoplasmic Reticulum

• creates, modifies, and transports proteins to different areas in the cell

• sends proteins to the Golgi Appartus

 Rough ER

• Studded with ribosomes, which are the sites of protein synthesis, giving it a "rough" appearance.

• Plays a crucial role in the folding and processing of newly made proteins, helping them achieve their functional forms.

• are tubules

    Smooth ER

• lacks ribosomes

• lipid synthesis

• are tubules

Golgi Apparatus

• flattened sacs that modifies, sorts, and packages proteins/lipids from the ER into vesicles for delivery to their final destination in or out of the cell

Lysosomes

• breaks down substances

• digestion enzymes

• fuses with food vacuoles/vesicles containing damaged organelles to break them down

Phagocytosis

• a process in cell biology where a cell engulfs and digests large particles, such as bacteria, dead cells, or debris.

• It is a crucial part of the immune system and plays a role in clearing infections and removing cellular waste. 

Vacuoles

• membrane-bound sacs that are used for storage and transport within the cell

• can contain nutrients, waste products, or enzymes essential for digestion.

 Food

• formed by phagocytosis

    Contractile    

• pumps excess water out of the cell

• maintains homeostasis 

• some protists have this

    Central

• becomes large

• absorbs water in plant cells

Endosymbiotic theory

• theory that eukaryotes stemmed/evolved from prokaryotes

Endosymbiotic evidence

• double membrane

• inner membranes have enzymes and transport systems

• replicates the same and has circular DNA

• both have ribosomes (similar structure)

• ribosomes make proteins

• mitochondria have circular DNA like prokaryotes

• chloroplasts replicate through a splitting process like prokaryotes 

Mitochondria

• powerhouse of the cell

• uses glucose and oxygen

Cristae

• the folded inner membranes of the mitochondria that dramatically increase the surface area for ATP production.

• This increased surface area is crucial for housing the electron transport chain and ATP synthase

Matrix

• The gel-like fluid within the mitochondria that contains enzymes and other molecules necessary for the Krebs cycle and other metabolic processes.

Chloroplast

• uses photosynthesis

• converts light energy to glucose

Thylakoids

• a flattened, membrane-bound sac inside a chloroplast where the light-dependent reactions of photosynthesis occur

• contain chlorophyll and other pigments that capture light energy

• their membranes house the photosystems, electron transport chains, and ATP synthase.

• Stacks of thylakoids are called grana.  

• membrane contain chlorophyll, electron transport chains, light dependent reactions, which convert light energy into chemical energy (ATP and NADPH)

• located in the stroma

 Granum

• a stack of thylakoid discs within the chloroplast

  Stroma

• the fluid-filled space inside a chloroplast, surrounding the grana (stacks of thylakoids)

• located where light-independent reactions of photosynthesis (the Calvin cycle) occur.

• It is rich in enzymes, ribosomes, and the chloroplast's own DNA

• provides the necessary environment for carbon fixation to create sugar.  

• surrounding the thylakoiuds

• contains enzymes, ribosomes, chloroplast DNA

• the light independent reactions of photosynthesis (calvin cycle) occurs here, converting CO2 into sugars

Cytoskeleton

• the structure of a cell

• a network of protein filaments that extend through the cytoplasm

• composed of three types of molecular structures: microtubules, microfilaments, intermediate filaments

  Microtubules

• largest of the three

• tracks for motor proteins to move vesicles and organells

• make up spindle fibers to move chromosomes during cell division

• cilia and flagella

• globular protein

• polar

Microfilaments

• smallest of the three

• muscle contraction 

• changes a lot → rebuilds then debuilds

• polar

• cell movement

• cell divison

• shape support and transport 

• globular proteins

Intermediate Filaments

• medium size

• located in some vertebrates

• permanent unlike the other two cytoskeletal elements, which can be disassembled and reassembled as needed.

• nonpolar

• provides strength, structure, cell adhesion

Centrosomes and centrioles

• microtubules based cylinders

• 2 centrioles that organize microtubules

• form spindle fibers that pull chromosomes apart

• helps form cilia and flagella

Cilia

• hair-like structures on cell that aid cell movement

• sensory receptors

• cell signaling 

Flagella

• long hair like appendages 

• allow cell movement

• microtubules

Cell Wall

• present in plant cells and not animal cells

• with plant cells it is able to maintain structure and provide protection

• prevents plant cells from bursting or shriveling too much (tugor, placcid)

Extracellular Matrix

• interconnected fibrous proteins

• provide strucutral support

• cell signaling

• communication

Plasmodesmata

• microscopic channels that create a cytoplasmic bridge between nearby cells

• facilitates the transport of water, proteins and RNA

Tight Junctions

• protein

• cell to cell connections that form a semiperable barrier between cells to control what passes between them

• make tissues water tight (skin)

Desmosomes

• protein

• cell junction that act as strong anchors

• connects filaments of nearby cells to maintain tissue integrity and strength

• cell signaling 

• forms them in strong sheets that can stretch (skin, bladder, muscles)

Gap Junction

• protein

• channels between cells that facilitate direct exchange of ions

• cellular communication function

• regulates cell growth 

• heart cells beat as one, embryonic development, plasmodesmata in plants move water and small solutes

Fluid Mosaic Model

• contains components that can move throughout the membrane → flexible

• composed of lipids, proteins, carbs → not just one macromolecule

• unsaturated, not truly bonded

Phospholipid

• hydrophobic, nonpolar tail

• hydrophilic, polar head

• phospholipid bilayer: usually nonpolar substances can travel through the membrane freely → selective permeability 

• creates fluidity and structure in the cell

Cholesterol

• a lipid → nonpolar

• adding more cholesterol would cause the cell membrane to be less flexible and more stable

• acts as a fluidity buffer

• prevents tight packing at low temp 

• restricts movement at high temp

• provides less structural flexibility

• reduces permeability for some molecules

Glycolipid

• molecules on the outer surface of cell membrane (lipids and carbs)

• cell recognition and adhesion

• differentiates self from non-self

• involved in the formation of tissue/organs

• forms H-bonds

Integral membrane proteins

• permanently embedded within cell membrane’s phospholipid bilayer

• has both hydrophobic regions that interact with polar parts that are exposed to liquid environment 

• example: glycoproteins, ion channels, EPCR

Peripheral proteins

• loosely bound to cell’s surface either to heads of phospholipids or integral proteins

• maintains cell shape

• cell signaling pathways and receptor protein on cell surface

• example: spectrin, ankyrin

Selective permeability

• membrane’s ability to control which substance can pass through it → allows essential in and restricts others

• are semi-peremable due to phospholipid bilayer → mostly nonpolar/hydrophobic so lets those types of molecules in (water in exception)

Functions of proteins in the membrane

• Transport

• Enzymatic activity

• Signal transduction

• Cell to cell recognition

• Intercellular joining

• Attachment to the cytoskeleton and extracellular matrix (ECM)