Exam II Study Guide

Question 1

Know the definition of translation

Answer 1

Translation: the sequence of bases in mRNA specifies the order in which amino acids are added to a polypeptide chain

Question 2

Know the factors required for translation

Answer 2

• Messenger RNA
• Initiation factors
• Elongation factors
• Release factors
• Aminoacyl tRNA synthases
• Transfer RNA (tRNA)
• Ribosome (Ribosomal RNA+ Ribosomal Proteins).

Question 3

•Know the structure of the ribosome and describe the three binding sites for tRNAs

Answer 3

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

Question 4

•Describe the properties of codons and reading frames

Answer 4

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

Question 5

Compare eukaryotic and prokaryotic ribosomes

Answer 5

• 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.

Question 6

•Know the structure of tRNA and describe key features of the tRNA molecule

Answer 6

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.

Question 7

•Know the function of tRNA Synthetase and describe its role in charging tRNAs

Answer 7

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

Question 8

•Describe the base pairing properties between codons and anti-codons

Answer 8

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

Question 9

•Describe the degeneracy of the genetic code and know how to read the codon chart

Answer 9

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

Question 10

Compare translation initiation in prokaryotes vs eukaryotes

Answer 10

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.

Question 11

Describe the process of translation initiation and the role of initiation factors

Answer 11

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.

Question 12

•Describe the process of translation elongation

Answer 12

• 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.

Question 13

•Describe the process of translation termination and the role of release factors

Answer 13

• 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.

Question 14

Know the structure of an amino acid

Answer 14

All Amino Acids have:
I) Alpha Carbon
II) Amino group
III) Carboxyl Group
IV) R Group

And a hydrogen.. I guess

Question 15

•Know how amino acids are classified based on the structure and atomic makeup of their R group

Answer 15

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

Question 16

•Compare hydrophobic and hydrophilic amino acids to one another

Answer 16

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

Question 17

Glycine:

Answer 17

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

Question 18

Proline

Answer 18

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

Question 19

Cysteine

Answer 19

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

Question 20

•Know the properties of peptide bond formation

Answer 20

• 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

Question 21

Level 1 of Protein Structure, the Primary Structure, is Defined by what?

Answer 21

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

Question 22

Level 2 of Protein Structure, the Secondary Structure, is Defined by what?

Answer 22

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.

Question 23

Level 3 of Protein Structure, the Tertiary Structure, is Defined by what?

Answer 23

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)

Question 24

Level 4 of Protein Structure, the Structure, is Defined by what?

Answer 24

Quaternary structure exists in proteins consisting of two or more identical or different polypeptide chains (subunits).

Question 25

Describe the processes of protein denaturation and renaturation

Answer 25

• 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).

Question 26

Know the functional role of chaperone proteins in the folding of polypeptides

Answer 26

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

Question 27

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.

Answer 27

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

Question 28

Compare Saturated vs unsaturated fatty acid chains and describe how each type contributes to the properties of a plasma membrane

Answer 28

• 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).

Question 29

Know the properties of cholesterol and describe its effect on membrane fluidity at normal and cooler temperatures

Answer 29

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

Question 30

Know and describe the four classes of proteins that associate with the plasma membrane

Answer 30

• 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

Question 31

Know and compare Integral and Peripheral Membrane Proteins

Answer 31

• 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

Question 32

Describe the fluid mosaic model of plasma membranes

Answer 32

Lipids and proteins coexist in the membrane, forming a “Mosaic:

Molecules move laterally within the membrane - so the membrane is a “fluid” space.

Question 33

Describe the functions of the plasma membrane and its role as a selective barrier

Answer 33

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).

Question 34

Describe and compare the processes of Diffusion, Facilitated Difussion, Osmosis, Primary Active Transport, Secondary Active Transport.

Answer 34

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

Question 35

Describe the effects of osmosis on cells (hypertonic/isotonic/hypotonic solutions).

Answer 35

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).

Question 36

Know the Function of Plant Cell walls, Turgor Pressure, and Vacuoles in relationship to the water content of plant cells.

Answer 36

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.

Question 37

Know and Compare the cellular components for Prokaryotic and Eukaryotic Cells (Everything in the Lecture 10 slide).

Answer 37

K

Question 38

Know and Compare Protein sorting in the cytosol and protein sorting in the rough Endoplasmic Reticulum (ER)

Answer 38

• 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

Question 39

Describe the process of trans membrane protein targeting

Answer 39

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!)

Question 40

Know the Four Essential Elements of Cell Communication

Answer 40

1. Signaling Cell
2. Signaling Molecule
3. Receptor Molecule
4. Receptor Cell

Question 41

Know and describe the four steps in cell signaling

Answer 41

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

Question 42

•Know, describe and compare the four classes of cell signaling

Answer 42

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)

Question 43

•Know and describe the interaction between a signaling molecule (ligand) and its receptor

Answer 43

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

Question 44

•Know, describe and compare polar molecules and cell-surface receptors to nonpolar molecules and intracellular receptors

Answer 44

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