AP Bio

Unit 1 and Enzyme (3.1-3.4) TEST Review:  AP Biology

Multiple Choice Topics:

  1. How different factors (temperature, pH, substrate concentration, enzyme concentration, inhibitors, cofactors, coenzymes, and salinity) affect enzyme activity.



  1. Differences between competitive inhibitors, noncompetitive inhibitors, and allosteric enzymes.  Competitive inhibitors bind to the active site of an enzyme and block the normal substrate from binding.  This decreases the reaction rate of an enzyme.  Non:  Bind to another location on the enzyme slightly changing the shape of the active site making the enzyme non-finctional until the noncomp inhibitor leaves.  Allosteric enzymes are fancy and regulate how much of an end product is produced.  They have an active site and an allosteric site where a non competitive inhibitor binds. 

  2. How do mutations affect the levels of protein structure?  Mutations will change the sequence of amino acids which will then change the shape and function of the protein.

  3. How and when proteins are denatured.  Proteins denature when exposed to high or low pH’s as well as high temperatures.  These things unravel the hydrogen bonds in the quat, tert, and secondary levels thus rendering the protein unusable.  Usually this is NOT a reversible reaction.

  4. What organisms eat to obtain the necessary elements to build all four macromolecules. (CHO, CHO(p), CHONS, CHONP)  Organisms eat glucose (which is produced in photosynthesis).  Glucose contains CHO and then plants gain the S, N, and P from minerals in the ground.  We eat carbs and lipids to get CHO, and proteins to get N and S and Nucleic acids to get N and P.  The CHO in glucose can be used to build the CHO in all macromolecules.  

  5. Properties of water:

    1. Polarity:  Water is polar which means there is uneven sharing of electrons between the H and O in one water molecule.  This makes the H slightly positive and the O slightly negative.  

    2. Hydrogen bonding (cohesion, adhesion, surface tension):  Because water is polar, hydrogen bonds form between the positive H of one water molecule and the electronegative O of another water molecule.  

    3. Expansion upon freezing:  The hydrogen bonds in solid ice space the water molecule further apart making ice less dense. 

    4. Moderation of temperature:  Water has a high specific heat which means it takes a lot of energy that needs to be gained or lost to change the temperature of water.  

  6. Types of reactions (hydrolysis and dehydration synthesis)  How many water molecules are added or taken away.  Dehydration builds with the removal of one water and hydrolysis breaks with the addition of one water molecule.  If a protein had 110 amino acids, 109 waters would be added to fully break it apart and 109 waters would be taken away to build it. ON FRQ

  7. Formation of a dipeptide This is a carb and shows dehydration synthesis, ON FRQ

  1. DNA and RNA similarities and differences RNA:  single stranded, uracil, ribose    DNA;  double stranded, thymine, deoxyribose

  2. Experimental design:  positive and negative controls negative controls do not contain the independent variable (many times water is used instead of the thing that is being tested)  The positive control shows what effect the thing has on the situation.

  3. Types of fatty acids (differences and structure)  Saturated:  derived from animals, no double bonds, solid at room temperature, not healthy (butter). Unsat:  Derived from plants, double bonds present, liquid at room temperature, healthier (olive oil).  Lipids are for long term energy because they have more bonds.  

  4. Hydrogen bonding and polarity in water:  Water is polar so this is what causes hydrogen bonds to form between two water molecules. 

  5. Positions of hydrophobic and hydrophilic amino acids in a protein:  The hydrophobic one is located within the interior of the protein and the hydrophilic ones are on the exterior of a protein. 

  6. ATP formation and negative feedback:  ATP is a product in a negative feedback reaction.  It is the noncompetitive inhibitor for the allosteric reaction at the very beginning of cell respiration.  If there is enough ATP then the reaction needs to be shut down and when more ATP is needed then ATP will be kicked out of the allosteric site the the allosteric enzyme will return to a functional state. 

  7. Pictures:  amino acid, fatty acids (saturated and unsaturated), DNA, dipeptide, disaccharide, monosaccharide, triglyceride  See macromolecule ID sheet

  8. Levels of protiein structure:  Primary, secondary, tertiary, and quaternary  See protein POGIL

  1. Lipids and carbohydrates:  (Reactions:  dehydration synthesis and hydrolysis)RNA DNA structures

    RNA &DNA hold heritable information

    DNA is genetic material

    Livine S = capsule - mouse died

    Livine R = no capsule - mouse lived

    Transformation - assimilation of foreign DNA into a cell

    Kill S keep R alive, cell DNA transfers from S to R and R transforms into S

    Plasmid = good for bacteria, no good for human (unless we want them to make things)

    A to T C to G

    STRUCTURE OF DNA

    Bases in the middle connected by hydrogen bonds

    Y = Thymine and Cytosene = Pymidine

    Adenine and Gonene = Puridine

    Procariotes = one chromosome (circular)

    Eurcaryotic = multiple chromosomes wrapped around histone proteins (stretch and condense DNA)

    DNA replication is DEMI CONSERVATIVE

    Centromere connects sister chromatids into X

    DNA          to          RNA(mRNA)        to           proteins

             Transcription                      Translation                     (alphabetical)

    Genotype - genetic makeup

    Phenotype - what proteins produce (what we see)

    The process of transcription and translation forms protein synthesis. 


    Prokaryotes - Transcription and translation happens in cytoplasm

    Eukaryotes - Transcription in the nucleus, Translation in the cytoplasm


    mRNA grows 5’ to 3’

    5’ - 3’ = nontemplate strand

    3’ - 5’ = template strand

    U = RNA T = DNA

    Codon = every group of 3

    Codes for amino acids

    Genetic code is redundant = multiple codons can code the same amino acid


    RNA Polymerase - makes RNA

    Promoter tells Polymerate to transcribe a gene

    Polymerase can detach and the genes will reconnect and so it can be used over and over again

    Bind to promoter - understand where to transcribe - separate strand - use template strand - at end of gene it detaches with the 2 original, and the 1 new. 2 original rebind, 1 new is used


    Pre mRNA is processed to mature RNA

    Caps and tails are added to protect mRNA

    Introns - eukaryotes only, they need to be removed as non-coding regions (intruders, need to be removed)

    Exons - expressed

    Length shrinks, but becomes Mature

    Prokaryotic mRNA is shorter life


    Translation - tRNA (transfer RNA)

    Codon connects to anticodon of tRNA

    Complimentary base pairs

    Carries amino acids 

    Even if something is not a protein, a protein made it


    Prokaryotes

    Changes in replication, environmental factors, ect. 

    Operons forms proteins

    Point mutation, a change in a single nucleotide

    Swapping out base or nucleotide = same thing

    Substitution, or frameshift - insertion or deletion of nucleotides

    Silence: no change to amino acid (3rd base)

    Missense: swapping one amino acid for another (change phenotype)

    Nonsense: premature stop codon

    Insertion: a DNA piece is added, which changes all amino acids after that because they shift

    Silent, missense, nonsense = substitution

    Frameshift = insertion or deletion


    Mutation adaptive value = positive, negative, neutral

    Nondysjunction = uneven split of chromosomes in meiosis

    Meiosis 1 = 2 with one extra, 2 with one less

    Meiosis 2 = 1 with one extra, 1 with one less, 2 normal


    Gene expression in Eukaryotes

    Blue = chromosome

    Orange = transcription

    Purple = translation

    Genes in highly packed heterochromatin = not expressed                                                 OFF

    Acetalated (all stretched out) DNA has access to gene and can made RNA                     ON

    DNA undergoes methylation = condensing = no gene expression (think of a knot in hair)

    ^ Add methyl group to certain DNA bases

    Cells differentiate due to methylation

    Epigenetics - how to environment affects genetics

    Chemicals, eat, sleep, exercise, stress, ect

    Gene expression leads to protein (transcription factor) which triggers other genes to be turned on and other proteins to be made ect

    Causes other proteins to clamp down RNA polymerase to cause RNA synthesis

    Activators = transcription factors

    Switches = sites transcription factors bind to

    Lense cell uses crystalline (crystal clear)

    mRNA that looks fishy can be cut up by RNAi


    Artificial selection is basic genetic engineering


    Cells split unevenly if they don't pass the S stage

    Cyclin does not accumulate until after G checkpoint

    Cycling makes things GO

    Cyclin becomes EDF to start mitosis

    This then undergoes hydrolysis to keep the egg stable

    External proteins/factors

    Growth factors (ligands): proteins

    These bind to receptors in membranes (Lock and key fit)

    EPO: stimulates the division of red blood cells 

    Benign tumor: forms from the overwhelm of cell growth in one space

    Metastisizing 

    Malignant tumor: invades cells around them, then spreads between separate cells and into cell movement WITH FRIENDS which allows it to keep growing 

    Cancer in genes

    Proto-oncogene: codes for growth or suppression

    MUTATION

    Oncogene: cancer causing genes (oncologist) 

    Two strike theory: your allowed one cancerous gene (heterozygous) YOUR OKAY get a second one? It has friends (homozygous) and CAN (not necessarily will) continue to grow and reproduce

    Born with a cancerous mutation from a parent? One strike. 

    Genes code for proteins

    P53 gene codes for P53 protein which inhibits the cell cycle of a cancerous cell until it can either fix it or apoptosis (kill)

    HeLa cells: cells without division limits to divide indefinitely 

    Excretory: when growth factors bind it triggers a protein that stimulates the cell cycle, making the production of extra cells to heal a wound

    Ras gene: codes for a growth factor that when mutated can code for cell growth on its own. 



    Cells need to talk to each other

    Gat junctions/plasma dismoder (small holes to allow proteins to cross)

    Neurons don't have to touch, but the electricity can bind to receptors on another cell (like teleporting)

    Hormone traveling bloodstream (like a flight)

    Signal transduction pathway - how a cell that's been targeted works

    Ligand = a signaling molecule that bonds to the receptor

    This process is reception

    Cells only have receptors for what they need

    Reception - transduction - response

    Polar bind to receptors IN the membrane

    Nonpolar bind to intracellular receptors (in the cytoplasm)

    Ligands have to be the right shape for the receptor

    Transduction: all the stuff in between 😀

    Response = the new protein formed 

    RNA is made during transcription

    In a polar ligand you have 3 options

    GPCR, Ion channel, Protein kinase


    GPCR: GTP and GDP - guanine

    ATP - Adenine

    GTP replaces GDP

    P is removed when the ligand is removed

    GDP is recreated

    Gate is closed

    Ligand forms the gate to open, and ions rush in (changes electro gradient)

    A cellular response forms


    Protein Kinase:

    A ligand binds

    This amplifies a signal in a multistep pathway

    One person is quieter than multiple

    More proteins = bigger cellular response

    When kinase and inactive to active, the active protein gains a phosphate from an ATP (its phosphorylated), which changes shape, and gives it energy

    C.A.M.P. MOST COMMON SECOND MESSENGER

    Responces can be in nucleus or cytoplasm

    Nucleus = transduction

    Cytoplasm = regulation instead of synthesis

    Epinephrine = adrenaline

    When it binds, it forms transduction to promote glycogen breakdown to form glucose to allow cellular respiration


    Apoptosis = programmed cell death

    It can be triggered by a death signaling ligand

    Negative feeback is normal and helps maintain homeostasis

    Intracellular receptors = steroids


    How do photosynthesis and cell respiration form a cycle

Photosynthesis forms glucose/oxygen for cell respiration, which forms CO2 and water for photosynthesis.

Light is taking in photosynthesis so it is endergonic

Cell respiration forms ATP and heat so its exergonic

  1. Locations of all steps for both photosynthesis and cell respiration

Photo: Light dependent: thylakoid Calvin: Stroma

CR: Glycolysis: cytoplasm/cytosol Pyruvate Oxidation/Krebs: Matrix ETC: inner membrane Fermentation: cytoplasm/cytosol

  1. Overall equations for photosynthesis and cell respiration and how radioactive 

isotopes can trace molecules through the processes of both photosynthesis and cell respiration

Radioactive isotope/tracer is like airtagging an item You tell location and pathway

PHOTO: CO2 + H2O + Light ---> C6H12O6 + O2

CR: C6H12O6 + O2 ---> CO2 + H2O + ATP

  1. What reactants and products are oxidized and reduced in photosynthesis and cell respiration

OILRIG

Oxidation is losing, reduction is gaining (electrons)

Photo is oxidizing water to allow reduction of the glucose

CR is oxidizing sugar to allow reduction of water

  1. How do electrons help to form a concentration gradient (proton gradient) to aid in the formation of ATP in both the light reactions of photosynthesis and the ETC of cell respiration

Photo: 2e provides energy to pump H from Stroma (low) to Thylacloid membrane (high) which forms a gradient. This momentum from H forms energy to combine ADP & P to form ATP

CR: 2e provides energy to pump H from matrix to inner membrane space. Momentum of H+ does ATP Synthase 

SPACE IS ALWAYS High H

  1. How do the light reactions help the Calvin cycle work

It produces ATP and NADPH for the Calvin Cycle to use

  1. Purpose of coenzymes in both cell respiration and photosynthesis

Coenzymes: NADPH(photo), NADH, FADH3(cr) Ubers carrying electrons 

  1. Purpose of brown adipose tissue (BAT)

A leaky proton gradient/innermembrane - No gradient = no ATP movement which means you generate heat not energy. You'll burn more calories as your body needs more ATP because your making heat with the calories

  1. Purpose of oxygen in the ETC of cell respiration

Final electron acceptor

  1. Purpose of a double membrane in cell respiration

The double membrane forms a proton gradient to form ATP

  1. Aerobic versus anaerobic respiration

Aerobic is better because it produces more ATP (Pyruvate oxidation) (ALOT)

Anaerobic is worse and is through fermentation (A lil)

  1. What is the evolutionary significance of fermentation (both types)

Fermentation happens to recycle NAD+ back to glycolysis. If you run out of NAD+ you can't make ATP and your donzo

It oxydizes NADH to take away electrons

Lactic acid helps humans exercise - Alcohol and yeast makes CO2

  1. How ATP synthase works

The momentum of H moving from low to high helped push ADP to P together (passive)

  1. pH of locations in the chloroplast and mitochondria and how this contributes to the amount of H+ (protons) in each location

High H is in thylakoid (Basic, high PH), Low H is in Stoma (Acidic, low PH)

H+ = acidity which lowers the PH

  1. How is oxygen produced in photosynthesis?

The splitting of H2O

  1. Glycolysis and how it suggests a universal common ancestor.

Since ALL organisms start with glycolysis, they must be related

  1. What is the purpose of the Calvin Cycle

It makes Sugar (G3P) to allow it to grow and increase biomass (dry weight)

Essays:

  1. Substrate versus oxidative phosphorylation

Substrate = glycolysis in krebs (only makes 4 atp)

Oxidative includes ETC and makes ALOT of atp

  1. Cyclic versus noncyclic photophosphorylation

                              v---------^

H2O ---> PII ---> ETC ---> PI ---> NADPH

           Cyclic is used to generate more ATP by creating a higher concentration gradient 

E moving back to the ETC gives energy to pump electrons longer

Pigments are found in photosystems in order to absorb light (what you see is what is reflected)

Rubisco grabs CO2 (sometimes grabs O2) in Calvin Cycle

When you transfer a phosphate group is changes its shape 

Oxygen is the final electron acceptor 


Active versus passive transport (be able to look at diagrams as well as scenarios)

  1. Differences and similarities between prokaryotes versus eukaryotes

ALL CELLS HAVE Plasma membrane (cell membrane), cytosomes, DNA, ribosomes

Pro: No nucleus, no membrane bound organelles, HAVE A NUCLEOID REGION (on test) Circular DNA - Bacteria (looks like a tampon)

Euk: Nucleus, Membrane bound organelles, linear DNA - Animals, Plants, Protists, Fungi

  1. Function of aquaporins and also the fact that water can use both simple diffusion and facilitated diffusion

Aquaporins: protein that moves water, water can get through SLOWLY, but it would rather facilitated

  1. Things that can fit through the plasma membrane via simple diffusion versus facilitated diffusion and WHY (polar, nonpolar, ions)

Simple: Non polar, CO2, O2

Facilitated: Polar, Ions

  1. Surface area to volume ratio (cells want to have a high surface area to volume ratio:  that is why cells are typically small)

The smallest = The highest surface ratio

Which of these 3 cells have the highest SA to V ratio? 1

V:      1     2      3

SA:   5    2.3   1.2

  1. Types of endocytosis 

Membrane wraps around whatever it wants

Phagocytosis - taking in a solid

When white blood cell engulfs bacteria

  1. Jobs of organelles 

    1. Endomembrane system:  

Lysosome - Recycle, digest, apoptosis

rough ER - studded with ribosomes, makes proteins for secretion or cell membrane. 

smooth ER - stores calcium ions, detoxifies, synthesizes(makes) lipids

Golgi apparatus - packaging and distribution center

Nucleus - control center of cell, surrounded by nuclear envelope


  1. Mitochondria - cell respiratory (makes ATP)

Chloroplast - Photosynthesis

  1. Movement (cilia (tiny hairs) and flagella (sperm)) - Movement, 9+2 of microtubules

  2. Plant (Cell wall, chloroplast, central vacuole) versus animal cell (Lysosome, centriole) - 

  3. ER to Golgi to Cell membrane

  1. Osmosis (hypertonic, isotonic, hypotonic) and movement of water

Water goes Hypo to Hyper 

Low to high solute

High to low H2O

  1. Water potential (no calculations but which direction water will move)

  2. Structure of the plasma membrane 

    1. Phospholipids - hydrophobic tails and hydrophilic heads

    2. Types of proteins - Transport - “channel” “carrier” moves Polar or Ions - Enzymes, Receptors

    3. Cholesterol in animal cells - to maintain membrane fluidity (ability to let things in and out)

    4. Glycoproteins - to ID your cell as yours and not anyone elses

  3. Differences between the rough ER and free ribosomes in the types of protein they make

Free ribosome: proteins for the inside of the cell (citoskeleton, lysosome, john (the motor protein)

Rough ER: secretion or plasma membrane

FRQ’s

  1. Water potential (movement of water: no calculations)

High to low

  1. Jobs of organelles and parts of the plasma membrane in the cell including the endomembrane system

  2. Organelles and what diseases can be caused by too many or not enough

No contractile vacuoles: Lyse

No lysosomes: Bad cells

No mitochondria: tired

ect

  1. Contractile vacuolesa

Contractile vacuole (what protists have to pump water out) 

Having to push water out is based on the gradient, easy if it naturally leaves, harder if the gradient (difference) is higher and into the cell

  1. Experimental set-up (independent, dependent variables, controls, error bars)

Error bars overlap = no difference

  1. Active versus passive transport

Passive: no energy needed, high to low concentration - simple and factor diff, osmosis

Active: low to high concentration, ups the concentration gradually - ion pumps, endo/exo cytosis (bulk transport)

  1. What can enter and leave the cell 

  2. Macromolecule components of the plasma membrane


Convolution = folds. Think intestines, more area for vitamins to escape

More convolution the better

Transport lets things in and out, motor (john) moves thing inside

Letter size = higher concentration