Week 4 Day 1 Molecular Biology

Question 1

Nonpolar Amino Acids pneumonic

Grandma

C

Always

Visits

London

In

May

Por

Tio’s

Party

Answer 1

Glycine (Gly)

Cysteine (Cys)

Alanine (Ala)

Valine (Val)

Leucine (Leu)

Isoleucine (Ile)

Methionine (Met)

Proline (Pro)

Tryptophan (Trp)

Phenylalanine (Phe)

Question 2

Acidic Amino Acids (polar)

Answer 2

Glutamic Acid (Glu)

Aspartic Acid (Asp)

Question 3

Basic Amino Acids pneumonic (polar)

Are

Liars

High

Answer 3

Arginine (Arg)

Lysine (Lys)

Histidine (His)

Question 4

Polar uncharged amino acids pneumonic

Asparagus

Gets

Sweeter

Through

Time

Answer 4

Asparagine (Asn)

Glutamine (Gln)

Serine (Ser)

Threonine (Thr)

Tyrosine (Tyr)

Question 5

What determines the identity of an amino acid?

Answer 5

it’s side chain

Question 6

Which amino acid is not chiral?

Answer 6

Glycine, it’s side chain is an H

Question 7

Which end of the zwitterion is the conjugate base of a weak acid…the carboxylate end or the ammonium-ion-end?

Answer 7

carboxylate-ion-end

Question 8

Which end of the zwitterion is the conjugate acid of a weak base…the carboxylate end or the ammonium-ion-end?

Answer 8

the ammonium-ion-end

Stated from the book:

The net electrical charge on an AA is a function of pH, and this has both critical and useful implications. At very low pH, an AA is primarily in its fully protonated form (H₂A⁺), and the net charge on an AA is positive. As pH increases, the cationionic form is gradually converted to the zwitterionic for (HA), and the net charge approaches zero. As we continue to increase the pH to strongly basic conditions, the ammonium group surrenders the second proton, converting the amino acid into its fully deprotonated form (A^-), and the net charge on an AA is negative.

Question 9

Primary structure of proteins

Answer 9

linear sequence of amino acids in a peptide chain

Question 10

Secondary structure of proteins

Answer 10

indicates local spatial arrangement of polypeptide backbone yielding alpha helical or beta pleated sheet structure

Hydrogen bonds between the ‘backbone’ amide -NH- and

-CO-

Question 11

Tertiary structure

Answer 11

how the alpha helices and beta sheet portions of a polypeptide chain are folded into a compact globular structure

Question 12

Quanternary structure

Answer 12

indicates the assemply of multiple polypeptide chains into an intact, tetrameric protein

i.e. hemoglobin

Question 13

Elements of tertiary structure of proteins

Answer 13

1. disulfide bonds (covalent bond) - strongest, but we don’t have a lot, they tend to have special/specific uses (think hair)
2. hydrogen bonds - weak, easy to break, but we have A LOT
3. salt bridges (much like an ionic bond) - stronger than hydrogen bond, less frequent
4. hydrophobic interactions

Question 14

What is the purpose of RNA polymerase?

Answer 14

Binds to the DNA strand to “unzip” or “split up” the double strand of DNA

Question 15

After the RNA copy is made in the nucleus, what are some modifications we need to do before sending it out to the cytoplasm?

Answer 15

Put a cap on the 5’ end

cut out the introns

finish with a poly A tail

Question 16

T or F: The process of making an RNA copy from DNA is called trancription.

Answer 16

True

this is called mRNA synthesis

Question 17

Where does mRNA synthesis occur?

Answer 17

The nucleus

Question 18

What is the purpose of RNAase

Answer 18

To degrade the mRNA once the mRNA is done making proteins.

Question 19

When RNAase begins degrading the protein, which end of the RNA does it start on, or does it even matter? If so, why?

Answer 19

The RNAase begins degrading the protein at the poly A tail. This is important because not all poly A tails are the same lengh. When the mRNA copy is made, the length of the poly A tail is designated by how many types of this protein will be needed. If a lot will be needed, the poly A tail will be long and this protein will take longer to degrade. If a small amount of this type of protein is needed, the poly A tail will be shorter and the poly A tail will degrade quicker.

Question 20

Another word for protein synthesis.

Answer 20

Translation

Question 21

In regards to base pairs, If the DNA has a C, G, T or A base, what will corresponding pair be for RNA

Answer 21

DNA base RNA base

C G

G C

T A

A U

Question 22

A codon has how many nucleotides?

Answer 22

3

Question 23

What is the nucleotide arrangement of the start codon and stop codon of the mRNA?

Answer 23

Start codon: AUG

Stop codon: UGA

Question 24

If the protein being synthesized is meant to remain in the cell in the cytoplasm, where will it finish translation?

Answer 24

On free ribosomes in the cytoplasm, then it will remain in the cytoplasm.

Question 25

If a protein being synthesized needs to be sent out of the cell, where will it finish synthesis and which organelle will "ship it out of the cell?"

Answer 25

Synthesis will finish on the rough ER and then the golgi will take proteins from the rough ER and either ship them to organelles within the cell or ship them out of the cell. ## Footnote \*\*Think of the golgi like the post office of the cell.\*\*

Question 26

Would unzipping of the DNA likely start at an A&T bond or C&G bond, why?

Answer 26

The DNA unzipping would likely start where there are A&T bonds becasue these are only bound by 2 hydrogen bonds whereas C&G bonds are bound by 3 hydrogen bonds. So all together the A&T bonds are weaker.

Question 27

In which direction is DNA read?

Answer 27

from the 5' end to the 3' end

Question 28

Describe a nucleic acid.

Answer 28

A nucleic acid is a polymer consisting of a 5 carbon sugar (ribose in RNA, deoxy ribose in DNA) lined together by phosphate groups. Each sugar molecules carries a nitrogenous base.

Question 29

The phosphate groups attach to which 2 carbons of the DNA's 5 carbon sugar molecule?

Answer 29

3 carbon and 5 carbon - hence, 3' and 5'

Question 30

Which carbon does the nitrogenous base of the DNA 5 carbon sugar molecule attach to?

Answer 30

Carbon 1

Question 31

We use the DNA template strand to make the RNA transcript. The RNA transcipt which will match the ____ \_\_\_\_\_\_\_ \_\_\_\_\_\_.

Answer 31

DNA coding strand.

Question 32

The RNA transcript is created from the ____ prime end to the _____ prime end. This means that the DNA template strand runs from the _____ prime end to the ______ prime end.

Answer 32

RNA transcript created from 5' to 3' DNA template strand runs from 3' to 5'

Question 33

Name 3 major ways in which RNA differs from DNA.

Answer 33

1. RNA is _single stranded_ (DNA double stranded) 2. Made of _ribose_ (not deoxyribose) 3. _Made with U's_ instead of T's

Question 34

What gives DNA the name of **_deoxy_**?

Answer 34

The 2 carbon is attached to a Hydrogen, not an oxygen. The oxygen has been removed, making it *deoxy*ribonucleic acid.

Question 35

Where are the genes for rRNA contained?

Answer 35

The nucleolous of the nucleus

Question 36

Name the two subunits of rRNA. Which is larger?

Answer 36

40S subunit, 60S subunit. 60S subunit is larger.

Question 37

What are the 40S and 60S subunits made of?

Answer 37

rRNA + "a bunch of little proteins"

Question 38

**T or F**: Multiple ribosomes can bind to an mRNA strand.

Answer 38

True

Question 39

AUG is the start codon. Which AA does AUG code for?

Answer 39

Methionine. ## Footnote \*\*This does not mean that every polypeptide chain begins with methionine. This is sometimes chopped off in post translational modification.\*\*

Question 40

UGA is the stop codon. Which AA does this code for?

Answer 40

UGA just tells the ribosome to stop. UGA does not code for any specific AA.

Question 41

5 major stages of protein synthesis.

Answer 41

**1.** Activation of tRNA **2.** Initiation **3.** Elongation **4.** Termination **5.** Folding and post-translational processing

Question 42

Which enantiomers will we focus on for AA: D or L?

Answer 42

L-Amino Acids

Question 43

Of the 20 AA acids we focus on, do they all contain a chiral carbon?

Answer 43

All but glycine, the simplest amino acid. Glycine has a side chain of H, making it not chiral because it will be bound 2 Hs. (Only 3 different side chains vs 4)

Question 44

Describe the structure of an AA.

Answer 44

Question 45

INFO CARD How do we make a peptide bond?

Answer 45