Unit 2 Learning Objectives

Question 1

Know the definition of translation

Answer 1

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 synthetases
Transfer RNA
Ribosome (rRNA & ribosomal proteins)

Question 3

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

Answer 3

definition: complex structure of RNA and protein that bind mRNA and 
control translation
structure:The large subunit of the ribosome contains three binding sites for transfer RNA (tRNA)
subunits:
A (aminoacyl) site
P (peptidyl) site
E (exit) site

Question 4

Describe the properties of codons and reading frames

Answer 4

codon: group of the 3 adjacent nucleotides in an mRNA that code for an amino acid
reading the sequence of nucleotides

Question 5

Compare eukaryotic and prokaryotic ribosomes

Question 6

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

Answer 6

-Translation of the message in mRNA is carried out by tRNA molecules: 70-90 nucleotides long, each with its own self-pairing structure
-All tRNAs have CCA at their 3’ end with 3’ –OH group of the A as the attachment site for an amino acid

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
Role in Charging DNAs: A tRNA without an amino acid attached is uncharged; a tRNA with an amino acid attached is charged

Question 8

Describe the base pairing properties between codons and anti-codons

Answer 8

-The first base in the codon in mRNA (5’) pairs with the last base in the anticodon of the tRNA (3’): antiparallel
-Codons specify amino acids according to the genetic code
-The codon that initiates translation is AUG: corresponds to the amino acid methionine

Question 9

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

Answer 9

Many amino acids are specified by more than one codon: the genetic code is redundant or degenerate

Question 10

Compare translation initiation in prokaryotes vs eukaryotes

Answer 10

Prokaryotes: mRNAs lack a 5′ cap; the initiation complex forms at one or more internal sequences in the mRNA: Shine–Dalgarno sequence
Eukaryotes: initiation complex forms at the 5′ cap and scans along the mRNA until it reaches the start codon AUG

Question 11

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

Answer 11

Initiation requires Initiation Factors:
i. bind to the 5’ cap of the mRNA
ii. recruit the small subunit of the ribosome
iii. bring up a transfer RNA charged with Methionine

Question 12

Describe the process of translation elongation

Answer 12

The ribosome moves one codon farther along the mRNA:

1. tRNA in the E site is ejected
2. tRNA in the P site is moved to the E site
3. tRNA in the A site is moved to the P site
4. A site is open and available for the next tRNA

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 protein binds the A site of the ribosome: causes the bond connecting the polypeptide to the tRNA in the P site to break
-The breaking of the bond creates the carboxyl terminus of the polypeptide

Question 14

Know the structure of an amino acid

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

iii. whether they are polar or nonpolar

Question 16

Compare hydrophobic and hydrophilic amino acids to one another

Answer 16

HYDROPHOBIC:
Located in the interior of folded proteins in order to be kept away from water

HYDROPHILIC:
-Polar side chains: hydrophilic and tend to form hydrogen bonds with one another or with water molecules
-Basic and acidic amino acids are strongly polar and hydrophilic.
-Basic amino acids: positively charged
-Acidic amino acids: negatively charged
-The charged groups can form ionic bonds with one another and with other charged molecules

Question 17

Know the three special amino acids and describe the effect these amino acids have on the proteins that incorporate them

Answer 17

Glycine: R group is hydrogen: symmetric
Nonpolar and small: the hydrogen side chain allows for freer rotation around the C-N bond
Glycine increases the flexibility of the polypeptide backbone
Proline: R group is linked back to the amino group:
restricts rotation of the C-N bond
puts constraints on protein folding in proline’s vicinity
Cyestine: contains a –SH (sulfhydryl) group
Two cysteines together can form S-S disulfide bonds: bridges that can connect different parts of the same protein or different proteins

Question 18

Know the properties of peptide bond formation

Answer 18

-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 and the N-H group is an amide group
- retrieve the slide lol

Question 19

Know and compare the four levels of protein structure

Answer 19

1°: Primary structure: sequence of amino acids
2°: Secondary structure: interactions between stretches of nearby amino acids
3°: Tertiary structure: 3D shape of a protein
4°: Quaternary structure: protein subunits interacting with one another

Question 20

Describe the processes of protein denaturation and renaturation

Question 21

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

Question 22

Know and compare the cellular components of prokaryotic and eukaryotic cells.

Question 23

Know and compare protein sorting in the cytosol and protein sorting in the rough ER.

Question 24

Describe the process of transmembrane protein targeting.

Question 25

Know the structure of a phospholipid, the structures 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

Question 26

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

Question 27

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

Question 28

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

Question 29

Know and compare integral and peripheral membrane proteins

Question 30

Describe the fluid mosaic model of plasma membranes

Question 31

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

Question 32

Describe and compare the processes of diffusion, facilitated diffusion, osmosis, primary active transport, secondary active transport

Question 33

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

Question 34

Know the function of plant cell walls, turgor pressure, and vacuoles in relationship to the water content of plant cells.

Question 35

Know and compare protein sorting in the cytosol and protein sorting in the rough ER.

Question 36

Describe the process of transmembrane protein targeting.

Question 37

The Endomembrane System:

Answer 37

system of interconnected organelles

Organelles communicate with other organelles:

physically connected by membrane “bridges”
use vesicles to transport substances between them

Question 38

Typical Features of a plant cell

Answer 38

A cell wall is present in plant cells—it provides additional support to the cell.
-Vacuoles also contribute to the structure of the cell by maintaining turgor pressure.
- Chloroplasts convert the energy from sunlight into chemical energy the cell can use.

The entire contents of the cell minus the nucleus make up the cytoplasm.
The region outside the organelles but inside the plasma membrane is the cytosol

Question 39

Typical Animal Cell

Answer 39

The endoplasmic reticulum (ER) is involved in the synthesis of proteins and lipids.
The Golgi apparatus modifies proteins and lipids produced by the ER and acts as a sorting station as these molecules move to their final destinations.
Lysosomes contain enzymes that break down macromolecules such as proteins, nucleic acids, lipids, and complex carbohydrates.
Mitochondria are specialized organelles that harness energy for the cell.
The cytoskeleton is a protein scaffold that provides the cell structure

Question 40

The endomembrane system

Answer 40

This system makes two compartments within a cell: the area within these organelles and the area outside of these organelles. This separation allows specific functions to take place within the spaces defined by the membranes and also within the membrane itself.

Question 41

The Nuclear Envelope

Answer 41

-defines the boundary of the nucleus
-The nuclear membrane defines the boundary of the nucleus; it consists of two membranes (an inner and an outer).
-The nuclear membrane is perforated by protein openings called nuclear pores that allow molecules to move into and out of the nucleus. These pores are essential for the nucleus to communicate with the rest of the cell.

Question 42

The Endoplasmic Reticulum

Answer 42

-produces many of the lipids and proteins used by cells
-Network of interconnected tubules and flattened sacs that are continuous with the outer membrane of the nuclear envelope
-lumen: interior space in ER