Definitions

Independent variable: _____________________________________________________________________


Dependent variable: _______________________________________________________________________


Control group: ___________________________________________________________________________


Controlled variables: ______________________________________________________________________


Type of data? ____________________________________________________________________________


Confounding variables: ____________________________________________________________________

Experimental Errors:

  1. Know the conditions required for a controlled experiment as well as the difference between a control group & controlled variables

 

  1. Be able to describe, in detail, the components of a properly controlled experiment, beginning at an initial observation & ending with the conclusion. Include…

 

  • Observation

  • Hypothesis

  • Conclusion

  • Qualitative vs. Quantitative data

 

  1. Describe the difference between a hypothesis & a scientific theory?

 

Characteristics of Life

  1. Know all eight (8) characteristics of life in detail (from problem set/class notes & book)

  2. Useful extra terms to know (be able to describe & give examples):


DNA- Deoxyribonucleic acid


Cells - Prokaryotic, Archaebacteria, Eubacteria, Eukaryotic, Plants, Protista, Fungi, Animals


Energy- Autotroph, Heterotroph

 

Reproduction- Asexual reproduction, Binary fission, Fragmentation/budding, Sexual reproduction, Gametes (sperm/egg)


Stimulus & Response - Sensory perception, Short-term response, Long term response, Hormone


Homeostasis


Evolutionary adaptation


Organism


  1. Explain why viruses are not considered to be alive.

 

Surface Tension of Water

  1. What are polar/covalent bonds?

  2. Why is water “sticky” (Think cohesion & adhesion)

  3. What are hydrogen bonds?

  4. Autotroph (“auto” = automatically, or makes their own; “troph” = food or eating)

  5. Heterotroph (“hetero” = different; “troph” = food or eating)


CHARCTERISTICS OF LIFE

CARBS LIPIDS NUCLEIC ACIDS

Unit 2 Study Guide - Biochemistry


Chemistry

  • Be able to describe the structure of an atom & list the three (3) primary subatomic particles

  • Know the location of each of the particles in the atom

  • Know the basic differences between a covalent & an ionic bond

  • What is a polar covalent bond? What is an example of a polar molecule?

  • Know which elements form covalent bonds

  • Know the six (6) elements of life & how many bonds each of them form. 


Macromolecules

  • What are monomers, dimers, and polymers?

  • What are the four (4) major classes of biological macromolecules?

  • Know the monomer names, dimer names (if applicable, and polymer names for each major macromolecule

  • Understand how dehydration synthesis is used to link monomers together

  • Understand the function of each polymer of the major macromolecules

  • Understand how hydrolysis breaks the polymer back into individual monomers & why this is important for some polymers and not others

    • Ex:  polymers of carbohydrates store energy. To use the energy we must release the monomers by hydrolysis


Specific information

  • Be able to draw a glucose molecule completely, know it’s chemical formula,  and demonstrate how it is linked with another through dehydration synthesis

  • Be able to draw at least one (1) other monomer & recognize ALL of the major monomers & polymers if you are given a picture of one

  • Know all relevant functional groups on the molecules

    • Ex: an amino acid has an amino group, a variable (or R) group that makes each of the 20 amino acids different, and an acid (or carboxyl) group.  

  • Know examples from your notes for each of the macromolecules

    • Ex: proteins include structural proteins like keratin & collagen

  • Be able to link any of the monomers together by dehydration synthesis (or take them apart by hydrolysis) if given the molecules on paper

  • Know the structural difference between saturated & unsaturated fatty acids, where each type of fat comes from, and why these are good or bad.

  • Understand what an enzyme is, what an enzyme does, how one works, and the factors that influence an enzyme's activity.



Some terms to know

Periodic Table

Atom

Element

Molecule

Proton

Nucleus

Neutron

Ionic Bond

Covalent Bond

Electron

Hydrogen bond (in the context of water)

Monosaccharide

Disaccharide

Polysaccharide

Glucose

Fructose

Lactose

Sucrose

Cellulose (polymer of glucose, but not digestible)

Glycogen (animal starch – branched)

Starch

Peptide bond

Amino acid

Peptide

Variable (or R) group

Amino group

Acid (or Carboxyl) group

Polypeptide or protein

Essential amino acids

Enzymes

Ribosome

Glycerol

Saturated fatty acid

Unsaturated fatty acid

Trans fatty acids (hydrogenated oils)

Triglyceride (‘E’ shaped)

Phospholipid                 

Nucleotide (A,G,T,C, U)

Nucleic acid

DNA, RNA

Ribose sugar vs. deoxyribose sugar

Nitrogenous base

Phosphate group


Organelle functions

  • Organelle structure & shape - be able to identify from image or drawing

  • Know key differences between prokaryotic & eukaryotic cells

  • Know key differences between animal & plant cells



Cell Wall   

Centrioles

Chloroplast

Chromatin       

Chromosome

Microtubule

Cytoplasm

Cytoskeleton

Golgi Apparatus

Lysosome

Mitochondria

Motor Protein

Nucleolus       

Nucleus

  • Nuclear Envelope  

  • Nuclear Pores     

Cell Membrane

Ribosome     

Rough Endoplasmic Reticulum        

Secretory Pathway

Smooth Endoplasmic Reticulum

Transport Vesicle

Vacuole


Cell Membrane

  • The structure of a phospholipid

  • Hydrophilic head (phosphate group; negatively charged & polar)

  • Hydrophobic tail (fatty acids; neutral in charge & nonpolar)

  • How do the chemical properties of phospholipids influence their interaction with water?

  • Why do phospholipids in a water environment spontaneously form a bilayer?

  • Membrane = phospholipid bilayer. What does this mean?

  • The fluid mosaic model of the plasma membrane. What does this mean?

  • Selectively permeable membrane. What does this mean?


Membrane Transport


  1. Passive Transport = (does not require cellular energy) -  movement of particles from high concentration to low concentration 

    1. Diffusion (very small, uncharged molecules such as O2, CO2)

    2. Osmosis (diffusion of water across a semipermeable membrane)

    3. Facilitated Diffusion (diffusion through a protein channel); examples are glucose & amino acids


  1. Active Transport (energy requiring; uses cellular energy, ATP)

    1. Protein pumps (for charged molecules like sodium & potassium ions). Move molecules in the opposite direction as diffusion (against their concentration gradient). Why do you think that the cell creates this concentration difference?

    2. Exocytosis (‘exo’ = out).  Example:  hormones, waste, membrane proteins

    3. Endocytosis (‘endo’ = in).  engulfment by the membrane


  • Know the terms hypertonic (‘above strength’), hypotonic (‘below strength’), isotonic (‘same strength’), and what this means during osmosis.  

  • Know that solutions are mixtures of a solute (what is being dissolved) & solvent (what is doing the dissolving – usually the fluid). The cytoplasm & fluids outside of the cell are solutions of proteins, salts, sugars (solutes), vitamins, and minerals, mixed or dissolved in water (the solvent).







Experiments & Scientists Important to Discovery of DNA as the Genetic Material:

  1. Frederick Griffith – Know his experiment & what it found

  2. Oswald Avery – Know his experiment & be able to describe what happened

  3. Hershey-Chase experiment – be able to describe the results & conclusions of their experiment

  4. Structure of DNA – What ideas did the following scientists contribute?

    1. Watson & Crick

    2. Rosalind Franklin

    3. Erwin Chargaff


  1. Central Dogma of Biology

  1. Describe the relationship between DNA, mRNA, and proteins.

  2. Why is DNA essential to all organisms?

  3. Why must DNA be replicated? Relate this back to an aspect of cell theory.


  1. DNA Structure  

  1. Know the structure of a nucleotide – including the sugar, the phosphate group, and the nitrogenous base. Know the 5’ & 3’ end of a DNA strand.

  2. Can you recognize the difference between RNA & DNA?  How does RNA differ from DNA?

  3. What do RNA & DNA stand for?

  4. What is the DNA backbone composed of?

  5. What is sitting in the middle of the double helix? (the ‘rungs’ of the DNA ladder). How are they held together?

  6. Which of the three (3) functional groups of a nucleotide encodes the information for building proteins?

  7. What are the complementary base pairing rules?  

    1. Relate the size & hydrogen bonds of the four bases (A, T, C, G) to the way in which they pair, & how this contributes to the shape of the DNA molecule.

  8. What does the term antiparallel mean?

  9. How is DNA packed into a cell nucleus?

  10. What is a chromosome?  What is chromatin? When does the cell nucleus contain chromosomes?

  11. What is the relationship between chromosomes & genes?


  1. DNA replication

  1. Demonstrate using a model or diagram, the way in which DNA replicates

  2. Identify when replication happens in the cell cycle

  3. Steps in DNA replication – know the role of these enzymes & proteins

    1. Helicase

    2. DNA Polymerase

    3. DNA Ligase

  4. In which direction does DNA polymerase extend the new DNA molecule? Why does this result in leading & lagging strands? What are Okazaki fragments?

  5. Be sure to be able to apply the following terms:

    1. Replication Bubble

    2. Replication fork

  6. When & why is DNA replicated?

  7. What is the semi-conservative model of DNA replication?DNA & RNA Structure

  1. What do RNA & DNA stand for?

  2. How does RNA differ from DNA? (3 main differences)

  3. Know the structure of a nucleotide – including all 3 parts

  4. Which nucleotide is found in DNA but not RNA? Which nucleotide is found in RNA but not DNA?

  5. What is the DNA & RNA backbone made of?

  6. Which of the 3 functional groups of a nucleotide encodes the information for building proteins?

  7. What are the complementary base pairing rules for DNA & for RNA?  

  8. Be able to identify 5’ & 3’ ends of either molecule

  9. What is a chromosome? What is the relationship between chromosomes & genes?

  10. What is the difference between chromatin &. chromosomes? When does the cell nucleus contain chromosomes?

  11. What are genes instructions for?

  12. What are the 3-nucleotide sequences in mRNA that designate an amino acid called?

  13. What is the basic structure of a eukaryotic gene? (promoter, TATA box, start codon, exons, introns, stop codon).  What is the role of each of these regions?

  14. Know the basic types of mutations in DNA (point mutations (includes missense, nonsense and silent mutations), and frameshift mutations)


  1. From Gene to Protein: Transcription, RNA Processing & Translation

  1. Central Dogma - How information stored in DNA is copied into RNA and then used to build proteins: DNA → RNA → Protein

  2. What is transcription?

  1. Why does transcription occur? What is the purpose of it?

  2. Where does it occur?

  3. What enzyme does this?

  4. What is the product that is made?

  5. What part of a gene initiates transcription (where does it start)? What is a promoter?

  6. What are the parts of a gene that code for protein?

  7. What parts of a gene do not code for protein?

  8. Know how to manually transcribe a gene sequence into mRNA (if I give you a gene sequence, be able to copy it into mRNA).

  9. What happens to the mRNA after transcription, before it leaves the nucleus? What is removed? What is added?  

  1. What is translation?

    1. Where does it occur? What is the purpose of it?

    2. What organelle handles translation?

    3. Know how to draw/describe this process

    4. What role does rRNA play in translation?

    5. What are tRNAs? What role do they play in translation?

    6. What is a codon? What is an anticodon?

    7. Why do all proteins begin with the same amino acid?

    8. How does the ribosome know where to begin translation? How does the ribosome know to stop translation?

    9. How is the actual protein made? – Know the steps

    10. What type of chemical reaction does the ribosome catalyze?

    11. What do tRNAs transport?

    12. What ensures that the correct amino acid is added to the growing protein? (Hint: What is the region of a tRNA that is complementary to mRNA & allows it to interact with mRNA?)

    13. Know how to use the codon chart & manually translate a given mRNA sequence. 

    14. Be able to describe or demonstrate what would happen to a protein if the gene had a mutation.

      Promoter

      Intron

      Exon

      Terminator

      RNA Polymerase

      Uracil

      Stop codon

      Codon

      Anticodon

      Start codon

      5’ Guanosine Caps

      3” Poly A Tail

      Point mutations

      • Nonsense mutation

      • Missense mutation

      • Silent mutation

      Frameshift mutation 

      Splicing

      mRNA

      tRNA

      rRNA

      ribosome


      Tools & Techniques - You should be able to describe the following tools & techniques used in biotechnology:


    1. The source & function of restriction enzymes

      1. Restriction sites 

      2. Palindromes

    2. Recombinant DNA

      1. Sticky ends

      2. DNA ligase

    3. Gel Electrophoresis – know why DNA fragments travel through the gel & which fragments travel the fastest & farthest. 

    4. Transforming bacteria & using bacteria to clone a gene

    5. Polymerase Chain Reaction (PCR)

    6. DNA Sequencing

    7. CRISPR


    1. Applications – By combining different techniques, scientists can accomplish various goals. Understand the following applications of biotechnology:


    1. Be able to interpret the results of gel electrophoresis for forensics, paternity/maternity testing & genetic screening.

    2. Describe how genetic engineering can be used to make GMO’s, specifically transgenic organisms (organisms that contain foreign DNA)

    3. Explain how plasmids & viruses can be used as biological vectors.  

    4. Identify the organisms in which plasmids are naturally found & the role of plasmids in these organisms.

    5. Summarize the steps used to engineer a recombinant plasmid, to transform bacteria, to use the bacteria to clone the gene of interest, and possibly to produce the protein coded for by the gene. The way human insulin is now produced for sale to individuals with diabetes would be a great example of these steps.

    6. Be familiar with the applications of genetically modified organisms, including pharmaceuticals/vaccine production, transgenic crops, and transgenic animals.

    7. Identify the pros & cons of using recombinant DNA technology in different situations. 

    8. What is gene therapy?  Be able to provide an example of an attempt at gene therapy.

    9. Describe the difference between cloning gene, cloning a tissue or organ and cloning an organism (like Dolly). 

    1. Differentiate between reproductive cloning & therapeutic cloning.

    2. Both of these techniques require Somatic Cell Nuclear Transfer (SCNT).



    Words & Terms to Know:

    Blunt ends

    Gene splicing/genetic engineering

    Polymerase Chain Reaction

    Primer

    TAQ polymerase

    Nucleotides

    DNA segment you want copied

    Activities to review

    Restriction Enzyme 

    Gel Electrophoresis 

    Maternity/Paternity/Forensics

    Transforming Bacteria

    Cloning a Gene & Expressing It 

    Paper Plasmid

    Genetic Screening a case study – sickle cell

    SCNT