Exam II Study Guide Flashcards
Know the definition of translation
Translation: the sequence of bases in mRNA specifies the order in which amino acids are added to a polypeptide chain
Know the factors required for translation
• Messenger RNA
• Initiation factors
• Elongation factors
• Release factors
• Aminoacyl tRNA synthases
• Transfer RNA (tRNA)
• Ribosome (Ribosomal RNA+ Ribosomal Proteins).
•Know the structure of the ribosome and describe the three binding sites for tRNAs
A complex structure of RNA and protein that binds mRNA and controls translation
Large Subunits (For 3 binding sites):
I. A (Aminoacyl) site
II. P (Peptidyl) site
III. E (Exit) site
•Describe the properties of codons and reading frames
Codon: group of three adjacent nucleotides in an mRNA that code for an amino acid.
The ribosome determines the correct reading frame for the codons
•Reading frame: region where the ribosome begins reading the sequence of nucleotides
Compare eukaryotic and prokaryotic ribosomes
• Eukaryotic Ribosome > Prokaryotic one in size
◦ Eukaryotic has an Extra RNA molecules ◦ Svedberg units talk about movements through a gel unit - dependent on size.
• Both are constructed out of a unique # of proteins.
•Know the structure of tRNA and describe key features of the tRNA molecule
Most important parts:
• 3’ End (CCA Sequence)
◦ All 3’ End of tRNA have the CCA sequence as the last 3 nucleotides (at the 3’ end).
◦ The CCA Sequence is the attachment site for Amino Acids
• Anticodon Loop: Reads the mRNA, sees if it can bind to it based on the anticodon sequence
◦ Interacts and binds with complementary Codon Sequences.
•Know the function of tRNA Synthetase and describe its role in charging tRNAs
Function: connect specific amino acids to specific tRNA molecules
• A tRNA without an amino acid attached is uncharged; a tRNA with an amino acid attached is charged
- Binds with uncharged tRNA and gives it a complete notary amino acid to make it a Charged tRNA molecule
•Describe the base pairing properties between codons and anti-codons
Codons and Anti-codons have anti-parallel base-pairing.
• The first base in the codon in mRNA (5’) pairs with the last base in the anticodon of the tRNA (3’): making them antiparallel
•Describe the degeneracy of the genetic code and know how to read the codon chart
The degeneracy of the genetic code refers to the fact that most codons can be specified by more than one nucleotide sequence (Think of Stop Codons as an example - There are multiple stop codons, but they have different nucleotide sequences.
Meaning: a single codon can be coded by multiple nucleotides
Compare translation initiation in prokaryotes vs eukaryotes
Eukaryotes: Initiation complex forms at the 5’cap and scans along the mRNA until it reaches the starting codon (AUG).
Initiation Complex is composed of:
• Initiator Factors (really just proteins)/ Binds to the 5’ Cap
• Small Ribosomal Subunit
• Initiator tRNA (Charged with Methionine)/ complimentary bases to AUG (Starting Codon)
Prokaryotes: mRNAs lack a 5’ cap; the initiation complex forms at one or more internal sequences in the mRNA: Shine-Dalgarno sequence.
Describe the process of translation initiation and the role of initiation factors
Translation is initiated by the Initiation Factors:
• Initiator Factors (really just proteins)/ Binds to the 5’ Cap
• Small Ribosomal Subunit
• Initiator tRNA (Charged with Methionine)/ complimentary bases to AUG (Starting Codon)
After these 3 components connect —> The entire group can start scanning the MRNA for the Start Codon.
•Describe the process of translation elongation
• The Ribosome moves one codon farther along the mRNA:
◦ I) tRNA in the E site is ejected
◦ II) tRNA in the P site is now moved to the E site
◦ III) tRNA in the A site is moved to the P site
◦ IV) A site is open and available for the next tRNA\
- Newly charged tRNA come into the A site. They then bond their amino acid with a peptide bond to make the polypeptide longer. The newly uncharged tRNA moves from the P site, into the E site and gets ejected.
The A site tRNA moves into the P site (This is the one that is “holding” the polypeptide chain”). A new tRNA comes into the A site. The (new) tRNA in the A site gives its amino acid to the poly-peptide chain, and takes it away from the tRNA in the P site. The P site tRNA moves to the E site and gets rejected, then the A site tRNA moves into the P site, and the cycle starts again.
•Describe the process of translation termination and the role of release factors
• Elongation continues until a stop codon is encountered (UAA, UAG, UGA)
• Release Factor proteins binds to the A site of the ribosome: Causes the bond connecting the polypeptide to the tRNA in the P site to break
- The Polypeptide then floats about in the cell, folds upon itself and eventually becomes a protein! YAY
• The breaking of the bond creates the carboxyl terminus of the polypeptide.
Know the structure of an amino acid
All Amino Acids have:
I) Alpha Carbon
II) Amino group
III) Carboxyl Group
IV) R Group
And a hydrogen.. I guess
•Know how amino acids are classified based on the structure and atomic makeup of their R group
Grouped based on
i. how they interact with water (hydrophillic or hydrophobic)
ii. whether they are basic or acidic
* Acidic Are Negatively Charged
* Basic are positively charged
iii. whether they are polar or nonpolar
•Compare hydrophobic and hydrophilic amino acids to one another
Hydrophilic:
Polar side chains: tend to form hydrogen bonds with one another or with water molecules
•Basic amino acids: positively charged, interacts easily through water with Hydrogen Bonding
•Acidic amino acids: negatively charged, Interacts easily through water with Hydrogen Bonding
•The charged groups can form ionic bonds with one another and with other charged molecules
Hydrophobic:
• What feature do the R-groups of the hydrophobic amino acids have in common?
◦ ANSWER: Mainly composed of Hydrocarbons (Only composed of Carbon and Hydrogen
Glycine:
Glycine:
• R group is Hydrogen: Symmetric
• Nonpolar and small: The Hydrogen side chain allows for Free Rotation around the C-N bond
• Glycine increases the flexibility of the poly-peptide backbone
Proline
Proline
• R group is linked back to the amino group:
◦ Restricts rotation around the C-N bond
◦ Puts constraints on protein folding in Proline’s Vicinity
Cysteine
Cysteine
• Contains a -SH (Sulfhydryl) group
• Two Cysteines together can form a disulfide bond (S-S): Bridges that can connect different parts of the same protein or different proteins
•Know the properties of peptide bond formation
• The Carboxyl Group of one amino acid reacts with the Amino group of another amino acid releasing a molecule of water
• The C=O Group in the peptide bond is known as a carbonyl group.
• The N-H Group is known as an Amide Group.
• The Free amino group is at the amino end of the peptide, and the carboxyl group is at the carboxyl end
Level 1 of Protein Structure, the Primary Structure, is Defined by what?
Primary Structure: The Amino Acid Sequence
• Represented by a series of three-letter or one-word abbreviations that are listed starting at the amino end and going to the carboxyl end
Level 2 of Protein Structure, the Secondary Structure, is Defined by what?
Hydrogen Bonding in the PolyPeptide Backbone
Two Types of secondary structure: Alpha helix and the beta sheet
Alpha Helix:
• Polypeptide chain is twisted in a right-handed helix with 3.6 amino acids/turn
Beta Sheet:
• The Polypeptide folds back and forth on itself, forming a pleated sheet that is stabilized by hydrogen bonds between carbonyl groups in one chain and the amide groups of another chain.
Level 3 of Protein Structure, the Tertiary Structure, is Defined by what?
Tertiary Structure: 3D Shape of a Protein
• Determined by the spatial distribution of hydrophilic and hydrophobic side chains (R Groups) along the molecule, as well as by Chemical Bonds and interactions that form between the side chains (R Groups)
Level 4 of Protein Structure, the Structure, is Defined by what?
Quaternary structure exists in proteins consisting of two or more identical or different polypeptide chains (subunits).
Describe the processes of protein denaturation and renaturation
• Proteins can be Denatured (unfolded) by chemical treatment or high temperatures and lose their function
• Renaturation: if the optimal conditions return, the protein can re-fold into its original structure - and regain its previous function(s).
Know the functional role of chaperone proteins in the folding of polypeptides
Chaperone Proteins: Aid in the folding of slow-folding proteins
• Chaperones shield hydrophobic groups to prevent aggregation until the protein attains its three-dimensional shape
• Chaperones give a protein time to find its correct shape
Know the structure of a phospholipid, the structures of phospholipids form with one another, and the role van Der Waals forces and fatty acid chain flexibility play in the composition of a plasma membrane.
All phospholipids have a polar head and non-polar tail.
- VDW forces get more flexible as they get longer
a. Large head group with one hydrophobic tail: form spheres called micelles
b. Small head group with two hydrophobic tails: form a bilayer
Compare Saturated vs unsaturated fatty acid chains and describe how each type contributes to the properties of a plasma membrane
- Saturated fatty acids lack double bonds, so it favors tight packing (gives structure to membrane)
- unsaturated fats have one or more double bonds that introduce kinks in the phospholipids, reducing the tightness of their packing. (Makes the membrane more fluid).
Know the properties of cholesterol and describe its effect on membrane fluidity at normal and cooler temperatures
Cholesterol is Amphipathic (has a region of Polar and Non-polar charges).
At room temperature, Cholesterol reduces the fluidity and mobility of the membrane.
At low temperatures, cholesterol increases membrane fluidity by preventing the phospholipids from packing tightly
Know and describe the four classes of proteins that associate with the plasma membrane
• Transporters: move ions or molecules across the membrane (Channel Transporters, and Carriers)
• Receptors: allow the cell to receive signals from the environment
• Enzymes: catalyze chemical reactions
• Anchors: attach to proteins that maintain cell structure and shape
Know and compare Integral and Peripheral Membrane Proteins
• Integral membrane proteins: permanently associated with cell membranes; span the lipid bilayer
◦ They are Ambipathic - contain layer of Hydrophobic and Hydrophilic areas - which allows for it to interact with the Aqueous environment and the Non-polar Tails of the plasma membrane
• Peripheral membrane proteins: temporarily associate with the lipid bilayer or with integral membrane proteins through weak non-covalent interactions; can be on the internal or external side of the membrane
Describe the fluid mosaic model of plasma membranes
Lipids and proteins coexist in the membrane, forming a “Mosaic:
Molecules move laterally within the membrane - so the membrane is a “fluid” space.
Describe the functions of the plasma membrane and its role as a selective barrier
The plasma membrane separates the internal contents of the cell from the environment. The membrane is also a selective barrier; it allows some molecules to move in an out freely, while other have to move in/out under certain conditions (usually through active transport).
Describe and compare the processes of Diffusion, Facilitated Difussion, Osmosis, Primary Active Transport, Secondary Active Transport.
Diffusion: Substance moving from an area of high concentration to low concentration
• Moving down their concentration gradient
Facilitated Diffusion: Molecules move through a membrane protein channel or carrier
Osmosis: The Diffusion of Water
◦ Water moves in/out of cells most efficiently by facilitated diffusion using protein channels called Aquaporins
Primary Active Transport: Movement of substances against the concentration gradient
Secondary Active Transport
◦ Active Transporters drive the transport molecules through a different transporter through the creation of an Electrochemical Gradient
Describe the effects of osmosis on cells (hypertonic/isotonic/hypotonic solutions).
Isotonic: The Water and its associated pressure are equal both within and outside of the cell (Equilibrium)
Hypertonic: The water pressure inside of the cell is greater than its environment (Water leaves the cell and goes into the environment).
Hypotonic: The water pressure inside of the cell is less than the environment (water comes inside of the cell from the environment).
Know the Function of Plant Cell walls, Turgor Pressure, and Vacuoles in relationship to the water content of plant cells.
Plant Cell Walls: Rigid structure that surrounds the plasma membrane and resists cell expansion when the cell takes in water
Turgor Pressure: Force exerted by water pressing up against the cell wal
Vacuoles: Absorb water and contribute to the Turgor pressure.
Know and Compare the cellular components for Prokaryotic and Eukaryotic Cells (Everything in the Lecture 10 slide).
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Know and Compare Protein sorting in the cytosol and protein sorting in the rough Endoplasmic Reticulum (ER)
• Proteins produced by ribosomes on the RER (essentially PUTS the proteins where the cell wants them)
◦ 1. End up within the lumen of the ER
◦ 2. Are embedded in the ER membrane
◦ 3. Are secreted out on the cell
• If the protein is destined for the lumen or to be secreted outside the cell: it is fed into the ER lumen as it is synthesized by the membrane-bound ribosome.
• If the protein is destined to be embedded in the membrane: it is inserted into the membrane as it is synthesize
Protein Sorting in the Cytosol: (essentially programs proteins where to go)
No Signal: Stays in Cytosol/Cytoplasm
Internal Signal: Moved to Nucleus
Mid-Terminal Sequence: moved to the Mitochondria/Chloroplast
Describe the process of trans membrane protein targeting
1) Proteins with signal anchor sequences are threaded through a channel in the ER membrane until the signal-anchor sequence is encountered
2) The ER Chanel releases the protein into the membrane
3) When translation is complete, the protein remains inside of the membrane (Installed and imbedded inside of the membrane!)
Know the Four Essential Elements of Cell Communication
- Signaling Cell
- Signaling Molecule
- Receptor Molecule
- Receptor Cell
Know and describe the four steps in cell signaling
Step #1: Receptor Activation
◦ The signal binds to a receptor, which is then activated
Step #2: Signal Transduction
◦ The signal is transmitted to the interior of the cell by a signal transduction pathway
Step #3: Response
◦ The cell responds, for example; by activating an enzyme or turning on transcription of a gene
Step #4: Termination
◦ The response is terminated so that new signals can be received
•Know, describe and compare the four classes of cell signaling
Endocrine Signaling
- Signaling molecules travel great distances in the body through the circulatory system
Paracrine Signaling
- Signaling molecules travels to neighboring cells, binds to their receptor (travels short distances)’
Autocrine Signaling
- Signaling and responding cell are the SAME CELL
Juxtacrine Signaling
- Signaling involves direct contact between the neighboring cells (through a transmembrane protein)
•Know and describe the interaction between a signaling molecule (ligand) and its receptor
Ligand: Signaling Molecule
Ligand-Binding Site: Location on the receptor to which the ligand binds
• Binding of a ligand to its’ binding site on a receptor causes a conformational change in the receptor that triggers chemical reactions
•Know, describe and compare polar molecules and cell-surface receptors to nonpolar molecules and intracellular receptors
Polar Molecules & Cell-Surface Receptors:
- Cannot cross the plasma membrane, and so they. Must rely on cell-surface receptors
Nonpolar molecules & Intracellular Receptors
- Can freely pass through the plasma membrane and activate cytoplasmic receptors
