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UD / Biology / BIOL 401 / What are living organisms?

What are living organisms?

What are living organisms?


School: University of Delaware
Department: Biology
Course: Molecular Biology of the Cell
Professor: Salil lachke
Term: Fall 2016
Tags: Biology, molecularbiology, and cellandmolecularbio
Cost: 50
Name: Exam 1 Study guide
Description: This is the study guide for exam 1. Good luck!
Uploaded: 09/20/2016
17 Pages 6 Views 5 Unlocks

Exam 1 Study guide  

What are living organisms?

Lecture 1

1. Living Organisms

- Living cells are bounded by membranes 

o Phospholipids

 Head – hydrophilic

 Tail – hydrophobic  

- Water, inorganic ions and a wide array of relatively small molecules  make up for 75% to 80% of living matter by weight  

2. Life is classified into how many groups?

 - Three 

o Bacteria

o Archaea  

o Eukaryota  

3. List the two types of cells  

- Prokaryotic  

o Lack defined nucleus  

o Nucleoid, cytoplasm, inner membrane, cell wall, periplasmic  space, and outer membrane

Life is classified into how many groups?

o Simple internal organization  

- Eukaryotic

o Enclosed system  

o Key parts

o 1. Nucleus 

 Site of DNA replication and the synthesis of ribosomal RNA, mRNA and a large variety of noncoding RNA

o 2. Cytoskeleton 

 Gives cell strength and rigidity  

 Maintains cell shape  

 Three types  

∙ Microtubules  

∙ Intermediate filament  If you want to learn more check out alan shabel

∙ Microfilament  

 o Endoplasmic Reticulum  

 Two types  

∙ Smooth ER

o Lacks ribosome  

What are the the two types of cells?

∙ Rough ER  Don't forget about the age old question of utep identity guide

o Ribosomes present  

Lecture 2

1. What happens when you remove Pax6 from a fly?  - Absence of eyes

Exam 1 Study guide  

- Pax6 is a protein encoded by Pax6 gene. Important in eye and brain development, although, it does not fully control the development of the eye

2. What some of the sophisticated tools used by molecular  biologist?

- 2D gel electrophoresis; Used in the separation of proteins - Gene array technology; Used in the study of nucleic acid like DNA 3. Chemistry of life  

- There are four key concepts  

o Molecular complementarity  

o Chemical Building blocks  

o Chemical equilibrium  

o Chemical bond energy  

4. Weak vs strong interactions  

- Weak  

o Non covalent bonds  If you want to learn more check out intermeasured
Don't forget about the age old question of What are the types of data?

o Constantly being formed and broken in room temperature  o What are the four types of noncovalent bonds?

 Ionic interactions  

∙ Attraction between positively charged ion (a cation)  

and a negatively charged ion (an anion)

∙ Ionic interactions do not have a fixed geometry

orientation. True or false?

o True. No fixed or specific geometry  


∙ The electrostatic field around an ion is uniform in all  


 Hydrogen bonds  

∙ Hydrogen bonds allow uncharged molecules to  

dissolve in water

 Van de Waals forces  

∙ Results due to formation of transient dipole when two We also discuss several other topics like tulane bms

atoms are close

 Hydrophobic effect  Don't forget about the age old question of cfd sdsu

∙ Water molecules can’t form hydrogen bonds with  

nonpolar substances so they form “cages” of  

relatively rigid hydrogen bonded pentagons and  

hexagons around nonpolar molecules  

- Strong  

o Covalent bonds  

 Two atoms share a single pair of electrons  

 Stable in room temperature and body temperature  

 Double bonds require more energy to break than single  bonds

Exam 1 Study guide  

5. what are the most fundamental molecules?

Most fundamental elements in biological molecule  


Number of covalent bonds that can  be formed










3 or 4


2, 4, or 6

6. Why is phosphorus important?  

- backbone of nucleic acid

- used in the regulating protein activity  

- Helps in the phosphorylation of amino acid  

- Amino acids  

o Serine  

o Threonine

o Tyrosine  

7. Double bonds cannot move freely. True or false  

- True. Only single bonds can rotate freely

8. The stereoisomer of a molecule has the same functions. True or  false  

- False. Different stereoisomers of a molecule have different functions  9. Electronegativity  

- The ability of an atom to attract electron

- O-H bond possess an electric dipole 

o The dipole moment in water permanent

o The dipole moment allows water to form electrostatic,  

noncovalent interactions 

10. Is radiant energy a form of potential energy? Yes, or No - No. it is a form of kinetic energy  

- Kinetic energy – energy of movement  

o Types  

 Thermal energy - Heat  

 Radiant energy - Kinetic energy of photons or waves of  light. Can be converted to thermal energy  

 Mechanical energy - Results from the conversion of stored  chemical energy  

 Electric energy - The energy of moving electrons or other  changed particles  

- Potential energy - Stored energy

Exam 1 Study guide  

o Types  

 Chemical potential energy - The energy stored in the bonds connecting atoms in molecules  

 Concentration gradient potential energy - Generates ATP   Electric potential - Energy of charge separation

11. Gibb’s law  

- System change to minimize free energy  

- ΔG = Gproduct – Greactant  

- If ΔG is negative, the forward reaction is spontaneous (it does not  mean it will occur spontaneously)

o Energy will be released as the reaction takes place

o Exergonic reaction  

o Thermodynamically favorable

- If ΔG is positive, the forward reaction is not spontaneous  o Energy is needed to force the reactants to become products o Endergonic reaction  

- If ΔG is zero, both forward and reverse reactions will occur at equal  rates  

o The system is at equilibrium 

12. Activation energy  

- Energy needed to excite reactants to a higher energy stable  - Catalysts, like enzymes, lower the activation energy required to start  the reaction  

13. What are the components of a typical cell?

- Water; 70%

- Macromolecules; 26%

- Sugar; 1%

- Fatty acids; 1%

- Amino acid; 0.4%

- Nucleotides; 0.4%

Exam 1 Study guide  

Lecture 3

1. Amino Acids

- There are 20 types of amino acids  

- What are the Hydrophobic amino acids?  

o Aliphatic – no ring

 Alanine, Valine, Isoleucine, Leucine, Methionine,  

o Aromatic  

 Phenylalanine, Tyrosine, Tryptophan

- What are the Hydrophilic amino acids?  

o Basic – Lysine, Cysteine, Arginine, Histidine

o Acidic – Aspartate, Glutamate,  

o Polar – Serine, Threonine, Asparagine, Glutamine

o Special – Cysteine, Glycine, Proline  

o Why are special amino acids called special?

 Cysteine – form disulfide bonds

 Glycine – small, flexible  

 Proline – rigid  

- An amino acid is bonded to four different chemical groups  o An amino (-NH2) group

o A carboxyl or carboxylic acid (-COOH) group

o A hydrogen (H) group

o One variable group called a side chain or R group  

- The α-carbon in all amino acids except glycine is asymmetric - Amino acids can be classified into several broad categories based on o Size, Shape, Charge, Hydrophobicity (measure of water  solubility), Chemical reactivity of their side chain  

- Humans and other mammals can synthesis 11 of the 20 amino acids  o The rest are essential amino acids (9) 

 Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine,  Methionine, Leucine, Lysine, Histidine

2. Chemically Modified Amino Acids  

- They have important biological roles  

- Phosphorylation: Serine, Threonine, Tyrosine  

- Glycosylation: Asparagine, Serine, Threonine  

- Methylation: Arginine, Histidine

- Acetylation: Lysine, other amino acids (Most common)  - Hydroxylation: Proline, Lysine (Collagen protein)  

3. Some functions of protein  

o Determine the shapes of cells and their extracellular  


o Bind two or more proteins together to perform specific functions o Catalyze chemical reactions

o Allow the flow of ions and molecules across cellular membranes

Exam 1 Study guide  

o Act as signals, sensors, and switches to control the activities of  cells by altering the functions of other proteins and genes

o Move other proteins, organelle, cell

- A polypeptide’s primary structure determines the secondary structure - What are the levels of protein structure?  

o Primary

 Sequence of amino acids in a polypeptide  

 Bonds: covalent  

o Secondary

 Structural motifs in a polypeptide

 Bonds: Hydrogen bonds (between NH and CO groups in  the backbone of the polypeptide

 The principal secondary structures are

∙ The alpha (α) helix

∙ The beta (β) sheet

∙ The short U-shaped beta (β) turn  

o Tertiary  

 Folding up a single polypeptide chain

 Bonds: various bonds; covalent (disulfide bond) hydrogen  bonds, ionic, van de Waals, hydrophobic  

 Not rigidly fixed because the stabilizing interactions are  often weak

o Quaternary

 Association of multiple folded protein subunits into a larger multimeric protein

 Bonds: various bonds

4. Peptide bonds  

- Amino acids are joined by peptide bonds  

- Protein structure is limited by the flexibility of the peptide backbone  o Double bond character of C-N bond prevents rotation around the  peptide bond itself

o Electrons are distributed between C-O and C-N bonds

5. Protein Shape and Function

 - Fibrous Protein 

o Long strands or sheet

o Collagen: α-helix conformation. Fibroin: β-sheet conformation   - Globular Protein 

o Water soluble. Usually have both α-helices and β-sheet

o For example, myoglobin, hemoglobin, most enzymes and soluble  proteins in the cell

6. Secondary Structure: The α-Helix

Exam 1 Study guide  

- Within an α-helix, all the backbone amino and carboxyl groups are  hydrogen bonded to one another except at the very beginning and end of the helix  

- Side chains face out (away) from the helix

- The α-helix is a semi-rigid structure  

- What amino acids are found in α-helix?

o Leucine, Methionine, Glutamate  

- Hydrophilic helixes - outside the surfaces and Hydrophobic helices -  within the core of the folded protein  

7. Hair curls are due to?

o shape of the hair follicle; the presence of disulfide bonds  between R groups found on individual amino acids in the keratin  protein

Exam 1 Study guide  

Lecture 4

1. Secondary Structure – The Beta (β) Sheet

- Consists of literally packed β strands; Pleated structure  - Each β strand is a short (5-8 residues) polypeptide segment - Hydrogen bonds in the β sheet occur between backbone atoms in  separate.

- They are oriented perpendicularly to the chains of backbone atoms - Beta-sheets can form structural motifs called as Beta barrels o Beta-barrels are found in membrane-spanning proteins. o The interior of the barrel is hydrophilic while the exterior is  hydrophobic.  

- What are the amino acids found in β-sheet?

o Isoleucine, Valine, Phenylalanine  

2. β-Turn

- Composed of four residues  

- Stabilized by a hydrogen bond between their end residues - Help long polypeptides fold into highly compact structures 3. Proline and Glycine are found in β-turns

 - Type I 

o Proline reside is at position n+1 

o The type I turn is stabilized by a hydrogen bond between the  carbonyl oxygen of the first N-terminal residue (Phenylalanine) and the amide hydrogen of the fourth residue (Glycine) 

- Type II

o Glycine residue is at position n+2 

o The type II turn is stabilized by a hydrogen bond between the  carbonyl oxygen of the N-terminal residue (Valine) and the amide hydrogen of the fourth residue (Asparagine) 

4. Tertiary structure  

- Three-dimensional arrangement of all the atoms in a protein - Not rigidly fixed because the stabilizing interactions are often weak  - Primary forces that stabilize protein 3D structure 

o Sequestration of hydrophobic amino acids away from water (e.g.  in the interior of water-soluble proteins)

o Maximizing van der Waals contacts in the interior of proteins  (minimizing open space)

o Maximizing hydrogen bonds (e.g. in α helices or ß sheets) o Ion pairing between oppositely charged amino acids (e.g.  Arginine and Glutamate)  

5. Quaternary Structure  

- Quaternary structure of a protein is the level of organization concerned with subunit interactions and assembly

6. What are the types of globin?  

- Alpha and Beta

Exam 1 Study guide  

- Hemoglobin  

o 2 alpha globin subunits and 2 beta globin subunits

7. Explain Structural Motif  

- A combination of two or more secondary structures that forms a  distinct three dimensional structure

- List and explain the types of structure motif  

o Coiled coil

 The coiled coil is a structure composed of two or more  alpha helices interacting with one another

 Amino acids: valine and leucine

o EFhand/helix-loop-helix

 Binding of Ca2+ changes protein conformation and alters  its activity 

o Zinc-finger motif

 Contains an α-helix and two β strands with an antiparallel  orientation  

 Forms a finger link bundle held together by a zinc ion

 Help regulate transcription 

8. Domains with Proteins

- distinct region of protein structure made with combinations of several motifs.

- What are the types of domains?  

- Functional domain – exhibits a particular activity, even in isolation - Structural domain – >40 a.a. in length, stable distinct structure; E.g.  Epidermal growth factor (EGF)EGF is a small peptide hormone that  binds to cells and causes them to divide

- Topological domain – regions of proteins that have distinctive spatial  relationship to the rest of the protein  

- Immunoglobulin molecules consist of 4 chains, each having several  domains

o 2 identical light chains and 2 identical heavy chains

o Linked by disulfide bonds

9. Proteins  

- Different proteins have different shapes and sizes

- Native state of a molecule  

o most stably folded form of the molecule that allows it to be  functional

- Chaperone proteins facilitate proper folding of nascent proteins o For example, Hsp70 

 Interaction of a non-properly folded protein with Hsp70  allows it to be correctly folded.

 Hsp70 function involves ATP hydrolysis

o List two co-chaperone accessory proteins

 DnaJ/Hsp40

Exam 1 Study guide  

 GrpE/BAG1

Lecture 5

1. The molecule in which a protein binds is called its ligand 2. The two properties of a protein that characterize how it binds to a Ligand   a. Specificity  

o Ability of a protein to bind to molecules or a very small group of  molecules in preference to all other molecules  

 b. Affinity  

o Refers to the tightness/strength of binding

3. What are enzymes?  

- Proteins that catalyze chemical reactions

- The ligands of enzyme are called substrates 

- Like all catalysts, enzymes increase the rate of a reaction, but they do  not affect the extent of a reaction

4. Active Site  

- 1. Substrate-binding site 

o Recognizes and binds the substrate(s)  

o Responsible for the remarkable specificity of enzymes

o Alteration of the structure of an enzyme’s substrate can result in  a variant molecule that is no longer a substrate of the enzyme  - 2. Catalytic site 

o Carries out the chemical reaction once the substrate has bound  - In some enzymes, the catalytic and substrate-binding sites overlap; in  others, the two region are structurally distinct  

5. How a Substrate Polypeptide Binds to the Substrate-binding site  in the active site of Trypsin?

- 1. The substrate and enzyme form hydrogen bonds that resemble  those of a β-sheet  

- 2. A Key side chain of the substrate that determines which peptide in  the substrate is to be cleaved extends into the enzyme’s side-chain specificity binding pocket, at the bottom of which resides the  negatively charged side chai of trypsin’s Asp-189

6. Allostery  

- Refers to any change in a protein’s tertiary or quaternary structure, or  in both, induced by the noncovalent bonding of a ligand

- Ligand – allosteric effector/factor 

- Site A or site of ligand binding = allosteric binding site 

- The protein is called allosteric protein (target)

7. Cooperativity  

- Often used synonymously with allostery 

- Refers to the influence that the binding of a ligand at one site has on  the binding of another molecule of the same type of ligand at a  different site

- For example, hemoglobin, an example of positive cooperative binding

Exam 1 Study guide  

o Binding of oxygen increases the affinity of hemoglobin for the  next oxygen molecule  

o Four subunits in hemoglobin contains one heme molecule  Heme groups are the oxygen binding components of  


8. Noncovalent Binding of Calcium (Widely used as allosteric)  - The concentration of free Ca2+ in the cytosol is kept very low (≈10-7M) - Many Ca2+- binding proteins bind Ca2+ using the EF hand/helix-looping helix structural motif  

9. Calmodulin  

- Very sensitive to Ca2+ concentrations and changes in structure and  function in response to Ca2+ levels >10-7M. Contains four Ca2+- binding  EF hands  

- The binding of Ca2+ to calmodulin causes a conformational change that permits Ca2+/calmodulin to bind to conserved sequences in various  target proteins.  

10. Noncovalent Binding of GTP  

- Used as allosteric switches to control protein activity  

- They are enzymes – GTPases – that can hydrolyze GTP (guanosine  triphosphate) to GTP (guanosine diphosphate). The GTP is obtained  from the cytosol 

- Include the monomeric Ras protein. Both Ras and Gα can bind to the  plasma membrane  

 - Functions  

o Cell signaling  

o Cell proliferation and differentiation  

o Protein synthesis  

o Transport of proteins between the nucleus and the cytoplasm o Vesicles

- Exist in two forms

o 1. Active (on) form with bound GTP 

 Influence the activity of specific target proteins to which  they bind

 Intrinsic activity of GTPase is low

 The switch is turned on when a GTP molecule replaces a  bound GDP in the inactive form  

o 2. Inactive (off) form with bound GDP 

 The switch is turned off when the relatively slow GTPase  activity of the protein hydrolyzes bound GTP, converting it  to GDP and leading the conformation to change to the  

inactive form  

- GTPase-activating proteins (GAPs) increases the rate of GTPase activity, thus reducing the time the GTPase is in the active form

Exam 1 Study guide  

o Activation of GTPase activity results in GTP conversion to GDP.  GDP-associated Ras is now inactive

- Guanine nucleotide exchange factors (GEFs) 

o Proteins whose function is to regulate the conversion of inactive  GTPases to active ones

o Mediates exchange of GDP for GTP

11. Phosphorylation 

- The reversible addition of phosphate groups into hydroxyl groups on  the side chains of serine, threonine and tyrosine residues  12. Phosphoproteins 

- Phosphorylated proteins

13. Which enzymes catalyze phosphorylation?

o Kinases  

14. Dephosphorylation is catalyzed by what?

o Phosphatases  

o Removal of phosphates  

15. Phosphorylation/dephosphorylation

o Can influence the location of a protein within the cells

o Its intrinsic activity  

o Its ability to bind to other molecules

o Its ability to undergo further covalently modification  

o Its stability  

16. Phosphorylation sites can be masked by NAG (N-acetyl glucosamine) 17. In human genome there are about 500 human proteins kinases

Exam 1 Study guide  

Lecture 6

1. ES (enzyme-substrate) complex

- Enzyme kinetics suggest that enzymes (E) bind substrate molecules (S) at a fixed and limited number of sites – the enzymes’ active site o The bound species is known as an enzyme-substrate (ES)  complex 

- Intermediate structures, such as ES and EX* form at the active site of  the enzyme and require the participation of key amino acid residues - Enzymes catalyze the conversion of substrates to products by dividing  the process into multiple, discrete chemical reactions that involve  multiple, discrete enzyme substrate complexes

2. Optimizing Enzyme Activity  

- Products from one reaction can move by diffusion to the next enzyme  in the metabolic pathway

- Why is diffusion not preferred?

o It can be slow, relatively inefficient process for moving molecules between enzymes  

- Cells evolved mechanisms for bringing enzymes in a common pathway  into close proximity  

- Close association of polypeptides with different catalytic activities  cluster closely as subunits of a multimeric enzyme or on a protein  scaffold, which makes coupled reactions much more efficient.

- Enzymes that have several catalytic domains within the same  polypeptide and therefore can catalyze several enzymatic reactions are the pinnacle of efficiency 

3. Nucleotides

- The monomers from which DNA and RNA polymers are built  - What are some of the functions of Nucleic acid: DNA and RNA? o Information storage “devices”

 Genomes (DNA or RNA) contain all the information required to make a new member of a species.

o Enzymatic and biosynthetic roles

 RNA can function as a catalytic enzyme (Self-splicing) and  it plays a major role in the synthesis of proteins (rRNA and  tRNA)

o Regulate expression of genes

 Small RNA mediated control of gene expression

- Which bases are found in both DNA and RNA?

o Adenine (A), Guanine (G), Cytosine (C)

- Which base found in DNA alone?

o Thymine (T)

- Which base found in RNA alone?

o Uracil (U)

Exam 1 Study guide  

 - Adenine and Guanine  

o Are purines; both contain a pair of fused rings 

 - Thymine and Uracil  

o Pyrimidines; both contain a single ring 

- What causes the acidic character of nucleotides?

- The phosphate group 

- Nucleosides 

o Combinations of a base and a sugar without a phosphate  4. DNA – Deoxyribonucleic acid  

- Informational molecule that contains in the sequence of its nucleotides  the information required to build all the proteins and RNAs of an  organism  

- 109 nucleotides long; 3 x 109 base pairs in the human genome  - Proteins are largely responsible for regulating gene expression - The process whereby the information encoded in DNA is decoded into  

proteins in the correct cells at the correct times in development  - Nucleic acids function as the “brains and central nervous system” of  the cell.  

5. Central dogma?  

- DNA -> RNA -> Proteins  

6. DNA and RNA

- All nucleotide consists of an organic base linked to a five carbon sugar  that has a phosphate group attached to the 5’ carbon

o In RNA, the sugar is ribose 

o In DNA, the sugar is deoxyribose 

- A single nucleic acid strand has a backbone composed of repeating  pentose-phosphate units from which the purine and pyrimidine bases  extend as side groups  

- Like a polypeptide, a nucleic acid strand has an end to end chemical  orientation: the 5’ end has a hydroxyl or phosphate group on the 5’  carbon of its terminal sugar; the 3’ end usually has a hydroxyl group on the 3’ carbon of its terminal sugar

o Polynucleotide sequences are written and read in the 5’-> 3’ direction (from left to right)  

- What is a phosphodiester bond?

o The chemical linkage between adjacent nucleotides.

- Polynucleotide can twist and fold into three-dimensional conformations stabilized by noncovalent bond  

- The three-dimensional conformation of DNA and RNA are different 

7. Structure and Properties of DNA

- DNA consists of two associated polynucleotide strands that wind  together to form a double helix

- The two sugar-phosphate backbones are on the outside of the double  helix and the bases project into the interior

Exam 1 Study guide  

o The orientation of the two strands is antiparallel; that is their 5’- > 3’ directions are opposite. Bases are flat, perpendicular to axis  of helix  

o A is paired with T through 2 hydrogen bonds 

o G is paired with C through 3 hydrogen bonds 

- The presence of thousands of hydrogen bonds in a DNA molecule  contributes greatly to the stability of the double helix  

o Hydrophobic and van der Waals interaction between the stacked  adjacent base pairs further stabilize the double-helical structure  - Most DNA in cells take the form of a right-handed helix 

- The stacked bases are regularly spaced 0.34nm apart along the helix  axis

- The helix makes a complete turn every 3.4-3.6nm, about 10-10.5 base  pairs per turn

- What is B-form of DNA?

o Normal form present in most DNA stretches in cells

- On the outside of the helix, the space between the intertwined strands  form two helical grooves of different widths, described as the major  groove (22 Å) and the minor groove (12 Å)  

- The double helix is flexible about its long axis

- Unlike the α helix in proteins, it has no hydrogen bonds parallel to the  axis of the helix

- This property allows DNA to bend when complexed with a DNA-binding  protein, such as the transcription factor TBP

o The conserved C-terminal domain of the TATA box-binding protein (TBP) binds to the minor grove of specific DNA sequence rich in A and T, untwisting and sharply bending the double helix

o Transcription of most eukaryotic genes require participation of  TBP  

- Why did DNA, rather than RNA, evolve to be the carrier of  genetic information in cell?

o The hydrogen at the 2’ position in the deoxyribose of DNA makes it a far more stable molecule than RNA, which instead has a  hydroxyl group at the 2’ position of ribose 

o The 2’ hydroxyl groups in RNA participate in the slow, OH catalyzed hydrolysis of phosphodiester bonds at neutral pH o The presence of deoxyribose in DNA makes it a more stable molecule  

o A characteristic that is critical to its function in the long term  storage of genetic information  

8. DNA Can Undergo Reversible Strand Separation

Exam 1 Study guide  

- The unwinding and separation of DNA strands, referred to as  denaturation or melting, can be induced experimentally by increasing  the temperature of a solution of DNA

- As the thermal energy increases, the resulting increase in molecular  motion eventually breaks the hydrogen bonds and other forces that  stabilize the double helix

- What is hyperchromicity?  

o A phenomenon useful for monitoring DNA denaturation - The stacked base pairs in duplex DNA absorb less ultraviolet (UV) light  than the unstacked bases in single-stranded DNA

- The temperature at which DNA denatures increases with the proportion of G•C pairs  

- Melting of double-stranded DNA can be monitored by its absorption of  UV light at 260nm 

- As regions of double-stranded DNA unpair, the absorption of light by  those regions increases almost two fold.  

- Light absorption by single-stranded DNA changes much less as the  temperature is increased  

9. GC content of DNA affects its melting temperature

- Tm = Temperature required to denature (separate) half the number of  nucleotides in DNA molecule

- Molecules that contain a greater proportion of G•C pairs require higher temperatures to denature because the three hydrogen bonds in G•C  pairs make these base pairs more stable than A•T pairs, which have  only two hydrogen bonds

- Agents that destabilize hydrogen bonds, such as formamide or urea  also lower the Tm

- Lowering the temperature, increasing the ionic concentration, or  neutralizing the pH causes two complementary strands to re-associate  into a perfect double helix  

- Two DNA strands that are not related in sequence will remain as  random coils and will not renature 

- Denaturation and renaturation of DNA are the basis of nucleic acid  hybridization 

o A powerful technique used to study the relatedness of two DNA  samples and to detect and isolate specific DNA molecules in a  mixture containing numerous different DNA sequence  

10. Common Forms of DNA in the Lab

- Small circular DNA without protein can have supercoils

- Localized unwinding of DNA can cause supercoils in other parts of the  molecule

Exam 1 Study guide  

- Topoisomerase enzyme can relieve this torsional stress by breaking a  phosphodiester linkage to enable loss of supercoils, and then rejoins  the broken ends

11. RNA Forms Higher Ordered Structures based on H-bonding - Like DNA, RNA is a long polynucleotide that can be double-stranded or  single-stranded, linear or circular  

- RNA molecules are like proteins in that they have structured domains  connected by less structured, flexible stretches

- Hairpins, stem-loop, and other secondary structures can form by base  pairing between distant complementary segments of an RNA molecule - In stem-loops, the single-stranded loop between the base-paired helical stem may be hundreds or even thousands of nucleotides long, whereas in hairpins, the short may contain as few as four nucleotides  - Pseudoknots are forms by interactions of loop through base pairing  between complementary bases.  

12. Use of DNA hybridization 8-37

- Fluorescent in situ hybridization (or FISH) is a technique that allows  scientists to visualize the chromosomes that hybridize with fluorescent  DNA probes specific to sequences within that chromosome.

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