Exam 1 Study Guide Flashcards
Explain the Central Dogma:
. The central dogma of molecular biology is a theory stating that genetic information flows only in one direction, transcribed from DNA, to RNA. Then, translated from RNA to protein, or RNA directly to protein.
Describe the 4 characteristics of living things
- Living organisms are complex
- Ability to reproduce
- Able to change in response to environment
- Have the capacity to evolve
Define a Cell:
The simplest self-replicating entity that can exist as an independent unit of life.
•Describe the three essential features of all cells:
- Store and Transmit Information
- Plasma Membrane that separates cell membrane from the environment.
- Harness Energy from the environment — Converts energy from sugar into ATP.
Define matter and element
Matter: Anything that takes up Space and Has Mass
Element: An element is a substance that cannot be broken down into simpler components by chemical Reactions
•Know the four most abundant elements in the human body
Oxygen, Carbon, Nitrogen, and Hydrogen
•Know the structure of an atom and the function of its 3 subatomic particles (protons, neutrons, electrons)
Structure: Electrons exist in the Orbitals surrounding the Nucleus, Protons and Neutrons exist in the Nucleus
Functions:
• Electrons: Provide a Negative Charge
• Protons: Provide a Positive Charge, and Mass
• Neutrons: Provide mass
Differentiate between an atom’s atomic number and atomic mass
An Atom’s Atomic Number is based on the # of Protons (This is what gives an atom its “elemental identity”).
An Atom’s Atomic Mass is determined by the # of Protons and Neutrons (Just measuring mass)
- Electrons also contribute mass, but its a negligible amount so we usually don’t include them.
Define an isotope and an ion and differentiate between the two
Isotope: two or more forms of the same element that contain equal numbers of protons but different numbers of neutrons in their nuclei, and hence differ in relative atomic mass but not in chemical properties
Example: Carbon-12 and Carbon-14.
Ion: an atom or molecule with a net electric charge (+/-) due to the loss or gain of one or more electrons:
Example: Na^(+) or Cl^(-).
•Explain electron orbitals
Electron Orbitals: regions of space where an electron spends most of is time, only 2 electrons can exist in any orbital at one time. Atoms with more than two electrons have multiple orbitals that differ in size, shape, and distance from the nucleus.
•Describe the 4 types of chemical bonds used to make molecules
- Covalent Bonds: Atoms equally share their valance electrons.
- Polar Covalent Bonds: Atoms in-equally share their valance electrons.
- Hydrogen Bonding: Hydrogen bonding is a special type of dipole-dipole attraction between extremely electronegative molecules. Occurs between (H-O), (H-F), (H-N). The attraction is possible because of the Partial Positive/Negative charges.
- Ionic Bonds: Bonding formed between two oppositely charged ions in a chemical compound; like
(Na^+) — (Cl^-)
Describe the properties of water that make it indispensable to life on earth:
• Water is Polar
• Water has a Neutral pH (pH=7)
• Water is an amazing solvent (Dissolving agent).
•Describe the interaction between the atoms of a single molecule of water, and among water molecules
• A single Water Molecule has Polar Covalent Bonds between the (O-H) bonds.
• However, from one water molecule to another, they interact through Hydrogen bonds. This allows the Partial Positive charge on one Hydrogen to be attracted to the Parital Negative charge on another water molecule’s Oxygen!
•Correlate water’s high specific heat with its ability to stabilize temperature fluctuations
Water’s ability to stabilize temperature stems from its high ‘specific heat’
-water changes its temperature less when it absorbs or releases a given amount of heat. Water’s high specific heat is a result of its hydrogen bonding.
Define solution, solute, solvent, aqueous solution
• A solution is a liquid that is a homogeneous mixture of substances
• A solvent is the dissolving agent of a solution
• The solute is the substance that is dissolved
Aqueous Solution: A solution in which water is the solvent is called an aqueous solution.
•Differentiate between hydrophilic and hydrophobic substances
• Hydrophilic Substances are those that are Water-Loving (Polar)
• Hydrophobic Substances are those that are Water-hating (Non-Polar).
Correlate changes in hydrogen ion concentration (H+) with pH
• As the Concentration of Hydrogen Ions increases [H+], pH will go down. (More Acidic Substance)
• Likewise, As the Concentration of Hydrogen Ions DECREASE, the pH will Increase (More Basic Substance).
•Describe the bonding properties of Carbon that relate to its structural diversity
• Carbon atoms form non-polar covalent bonds. It also prefers to bond to 4 others atoms (Forming a tetrahedral Molecular Geometry). Carbon atoms link with one another to form long Carbon “chains;” which can be branched or a ring structure (Cyclical).
•Define an isomer
Isomers: Molecules with the same chemical formula, but arranged differently
• Different Structures
• Different Functions
Describe the basic structure of an amino acid
• Amino Acids have an Amino Group, An Alpha Carbon, a Carboxyl group, and an “R” Group
◦ The “R” Group will change depending on the Amino Acid
•Describe how amino acids link together via peptide bonds to form proteins
• Amnio Acids connect by linking the Carboxyl Group (C=O, C-OH) of Amino Acid #1, to the Nitrogen of the Amino group (NH2) of the Adjacent amino acid (Amino Acid #2); forming a Peptide Bond
◦ This formation produces a Water Molecule
•Identify and Define the three components of a single nucleotide
- The 5-Carbon Containing Sugar (Ribose or Deoxyribose)
- Base Containing Nitrogen
- One or More Phosphate Groups
•Describe the difference between a deoxyribonucleotide and a ribonucleotide
• The main difference between a Deoxyribonucleotide and a Ribonucleotide is the existence of another Hydroxyl group on the 2’ Carbon. This particular (O-H) bond is present in Ribose, but not Deoxyribonucleotide.
•Identify the five nitrogen-containing bases of nucleic acids and differentiate between the two classes (purines and pyrimidines)
The Pyrimidine Bases only have one Cyclical Structure: Thymine (T), Cytosine (C), and Uracil (U).
The Purine Bases have two cyclical structures: Adenine (A), and Guanine (G).
•Describe the process of nucleotide joining
• Nucleotides are joined by Phosphodiester bonds.
◦ These bonds form from the 5’ Phosphate group of one nucleotide, to the 3’OH group on the sugar of another nucleotide.
◦ This bond formation results in the loss of a water molecule
Describe the Structure of DNA
• DNA exists in two strands of nucleotides twisted around each other to form a “Double-helix”
◦ Sugar Phosphate Backbones wrap around the outside
◦ The Inside has Complementary Base-Pairing (A-T), (C-G)
•Define a carbohydrate and identify/describe the two main classes of sugars
• Carbohydrates: Macronutrient used for energy, composed of Carbon, Hydrogen, and Oxygen
◦ Cabohydrates are separated into different classes dependent on the groups attached to them. Aldehyde groups make it an Aldose Sugar; Ketone groups make it a Ketose Sugar.
•Define Mono- Di- and Poly- saccharides
• Monosaccharides: One Sugar
• Disaccharides: Two Sugars linked together
• Polysaccharides: Many Sugars Linked Together.
Describe the cyclization process of ketose and aldose sugars
In Those sugars, usually a OH group will curve up and attatched to the Carbonxyl group (C=0) of itself. Making the structure cyclical
•Describe the process of glyosidic bond formation
• Glycosidic Bonds form on the end of one cyclical sugar, and connects it to the adjacent sugar. This formation also results in the loss of a water molecule. (Two Hydoxyl groups coming together — Releases water when combined).
•Identify the major difference between lipids and the other three classes of biomolecules
• Lipids are NOT defined by Chemical Structure, But they are instead defined by their hydrophobic nature.
•Describe and compare the three types of lipids
- Fatty Acids (Triacylglycerol): Long Carbon Chains attached to a carboxyl group
- Steroids: Lots of Carbon Rings
- Phospholipids: Glycerol Backbone + 2 Fatty Acid Chains, and a Phosphate Head Group.
* Has a polar head
* has a non-polar tail (1 is Saturated, 1 is Unsaturated)
•Compare saturated vs unsaturated fats
• Saturated fats do not contain C=C bonds, and are completely saturated with Hydrogen Atoms. (Solid at Room Temp
• Unsaturated fats DO contain C=C Bonds, and have lower melting temperatures, and do not have molecular Packing (Very long structures), Liquid at Room Temp
•Define Van der Waals forces and describe their role in lipid structure.
• Van Der Waals forces are the result of constant motion of electrons around a molecule. This constant movement means that there are moments where regions will have slight charges (both negative and positive). This allows for attraction/Repulsion to occur between other molecules. Many Van Der Waals forces will act together to stabilize the molecule
• The longer the Hydrocarbon (or any compound for that matter), the greater the Van Der Waals force
•Describe the structure and function of a phospholipid
• Phospholipids have a Hydropphilic Head (Polar, Water-Loving)
• Phospholipids have a Hydrophobic Tail (Non-Polar, Water-Fearing)
• Phospholipids are the main component of a cell membrane. They allow for the Cell to selectively allow passage of substances into and out of the cell. (Think of this as the “Border-Control” of the cell).
Describe Frederick Griffith’s groundbreaking experiment
• In Griffith’s experiment, Griffith found that the DNA from dead organism could change the living cells of another organism. Meaning that - DNA from dead organisms can be absorbed into living cells of a new organism —> Which can then corrupt the living cells, so that they become like the “Originally dead organism.”
•Describe the Avery, MacLeod, McCarty experiment and explain how it proved that DNA is the genetic material
Avery and McCarty observed that RNase - enzymes that degrade RNA - did not destroy the transforming principle. Neither did Protease - enzymes that digest proteins. They found that DNase - enzyme that digests DNA - successfully destroyed the transforming principle.
This proved that DNA was the genetic material.
•Relate the regulation of transcription and translation to the formation of different cell types in the body (at a very basic level)
Transcription and translation are tightly regulated: can be turned on or off according to the needs of a cell.
The diversity of cell types in the body arises from differences in transcription and translation
◦ While our cells share the Same DNA, they are all unique - because the regulations allowed us to make unique cells for unique purposes/functions
Know and compare where transcription and translation takes place in eukaryotes and prokaryotes.
•Prokaryotic cells: transcription and translation both occur in the cytoplasm
Eukaryotic cells: transcription occurs in the nucleus and translation occurs in the cytoplasm
Know the components of a nucleotide and relate the negative charge of DNA to the presence of phosphate groups
Chemical Composition of DNA
1) Phosphate Group
2) 5-Carbon Sugar
3) Nitrogen-Containing Base
Describe the polarity of DNA with respect to its 5’ and 3’ ends
The Phosphate group is connected to the 5’ Carbon. And a Hydroxyl group (OH) is connected to The 3’ Carbon. This gives DNA it’s polarity.
DNA has polarity: one end differs from the other; free 5’ phosphate group and a free 3’ hydroxyl group
Know the properties of the double helix
two strands of DNA wrap around each other to form a helix that coils to the right
•sugar-phosphate backbones wind around the outside of the molecule and the bases point inward
•outside contours form the major and minor grooves; sites of protein contact
•the two strands are antiparallel: they run in opposite directions.
Chargaff’s Rule
All bases and their corrsesponding part exist in 1:1 ratios. If an organism has 20% Adenine, it must have 20% Thymine.
Likewise, if it has 30% Guinean, it must have 30% Cytosine
Describe hydrogen bonding and base stacking
Hydrogen bonds are weak but contribute to the stability of the DNA double helix
•Base stacking: nonpolar surfaces of the bases stack tightly and repel water; contributes to the stability of DNA
Know the basic structure of chromatin and the function of histone proteins
Histone proteins: rich in positively charged amino acids; form ionic bonds with the negatively charged sugar-phosphate backbone of the DNA
True or False? We assume that DNA goes from 5’ to 3’
TRUE!
Describe the RNA world hypothesis and the reasons why RNA is thought to be the original information storage molecule
RNA World Hypothesis
RNA was the information storage molecule in early life forms
●Evidence:
•RNA is used in replication, transcription, translation
•RNA has been shown to evolve over time
•RNA can act as a catalyst
Know the similarities and differences between RNA and DNA
RNA has an additional Hydroxyl (O-H) group on the 2’ Carbon, which makes RNA very unstable.
Otherwise, they both have Phosphate-Sugar Backbones and Nitrogenous base Pairing
•Describe template and nontemplate strands of DNA
•As a region of DNA unwinds, one strand is used as the template for RNA transcription, we refer to this strand as the “Template DNA Strand”
- The other strand is the non template DNA Strand
•Know the key features of transcription
RNA Polymerase: enzyme used for RNA synthesis
•The new RNA strand grows in the 5’ —> 3’ direction: the template DNA strand is in the 3’ —> 5’ direction
•Uracil containing nucleotides are inserted in RNA when there is an Adenine in the template strand
•Describe the process of transcription initiation including all factors involved
•RNA polymerase and associated proteins bind DNA at promoter sequences
•Eukaryotic promoters contain a sequence similar to TATAAA: TATA box
•The first nucleotide to be transcribed is positioned ~25 base pairs from the TATA box.
•Describe the process of transcription termination and all factors involved
RNA polymerase moves along the template strand until it encounters a terminator sequence
•Know and compare promoter recognition in prokaryotes and eukaryotes
Prokaryotic Promoter Recognition
•Promoter recognition is mediated by a Sigma factor protein
i.associates with RNA polymerase
ii.facilitates binding of RNA Polymerase to promoters to initiate transcription
Eukaryotic Promoter Recognition •General Transcription Factor proteins recruit RNA polymerase II (Pol II) to the Promoter •Proteins bound to an Enhancer sequence recruit a Mediator complex that interacts with the Pol II complex to initiate transcription
•Describe the functions of RNA Polymerase during transcription
RNA Polymerase II Adds Nucleotides to the 3’ End of a Growing RNA strand
•Transcription takes place in a ‘transcription bubble’ that is ~14 base pairs in length
•The RNA-DNA duplex in the bubble is ~8 base pairs in length
•Describe the RNA polymerization reaction
Incoming Nucleotides (joining the chain) are accepted if they have a complimentary Nitrogenous Base. When accepted, the OH group on the 2’ carbon attacks the phosphate group of the new Nucleotide.
The phosphate group binds with the hydroxyl group, and the rest of the phosphate group gets released as “Pyrophosphate”
Know and compare the RNA processing events that occur in prokaryotes and eukaryotes
Prokaryotes:
In prokaryotes:
•the primary transcript is the mRNA
•transcription and translation both occur in the cytoplasm
•primary transcripts contain the information for more than one gene: polycistronic mRNA
Eukaryotes:
Nuclear membrane: barrier between transcription and translation
•RNA processing: the primary transcript undergoes chemical modifications
•3 types of chemical modifications occur before an mRNA is translated by the ribosome
i.5’ Cap addition
ii.3’ Poly A tail addition
iii.Splicing
•Describe the process of RNA splicing
III. RNA Splicing:
Excision of introns and joining together of exons
•Spliceosome: protein complex that catalyzes intron removal
•Splicing: binding of Spliceosome to sequences at the ends of introns and subsequent cutting of one end of the intron to form a loop (Lariat)
•The exon on one end of the intron is joined to the exon at the other end and the intron (lariat) is released and broken down
True or False?
If the RNA Builds in the 5’ —> 3’ direction, then the Template strand must be in the 3’ —-> 5’ direction
True
Glycosidic Bond formation
Carboxyl groups splits apart and bonds to the neighboring carbon of a separate sugar - releases a water molecule and connects multiple sugars together
