Nucleic Acids and Proteins- Structure and Function

Question 1

What is genetics?

Answer 1

A branch of biology that deals with the heredity and variety of organisms

Question 2

What is heredity?

Answer 2

The transfer of traits from one generation to the next (why you may look similar to your parents)

Question 3

What is variation?

Answer 3

The difference between cells, organisms, or groups of organisms caused by either genetic differences or by the effect of environmental factors

Question 4

What is X-ray diffraction?

Answer 4

A pure crystal is bombarded with x-rays and the diffraction pattern is cast on a film- which is then studied.

Question 5

How was x-ray diffraction used in the discovery of the structure of DNA?

Answer 5

Scientists had been trying to capture a quality image of DNA for years. Eventually Rosalind Franklin was able to capture an image that revealed to double helix structure.

Question 6

What’s the story of Franklin, Watson, and Crick?

Answer 6

The owner of the lab Franklin worked at showed her research to Watson and Crick w/o her permission. From it, they were able to determine the double helix structure, and published their research w/o crediting her. The owner, Watson, and Crick won the Nobel Prize for their “discovery” in 1962, 4 years after Franklin died of ovarian cancer.

Question 7

What are organic molecules?

Answer 7

Molecules that contain carbon and hydrogen atoms bonded to other atoms

Question 8

What are macromolecules?

Answer 8

Large organic molecules which consist of repeating units of smaller molecules linked together

Question 9

What are the four types of macromolecules?

Answer 9

Carbohyrates- “sugars”
Lipids- “fats and oils”
Proteins
Nucleic acids

Question 10

What is a monomer?

Answer 10

a molecule that can be bonded to other identical molecules

Question 11

What is a polymer?

Answer 11

A chain of monomers that come together to form organic molecules

Question 12

How does the composition of monomers help define the structure and function of the polymer?

Answer 12

The polymer is comprised of monomers– the composition of the monomers will effect which IMFs the polymer can utilize, and where, which will effect how the polymers folds itself– which determines the function.

Question 13

What are nucleic acids? What is the name of the monomers that comprise nucleic acids?

Answer 13

Nucleic acids are a class of macromolecules which are comprised of monomers called nucleotides.

Question 14

What are the two main classes of nucleic acids? What unique component of their structure gives them their name?

Answer 14

Deoxyribonucleic acid (DNA)- uses deoxyribose-containing nucleotides 
Ribonucleic acid (RNA)- uses ribose-containing nucleotides

Question 15

What are the three primary components of nucleotides?

Answer 15

Pentose sugar group- group consisting of 5 sugars number 1’-5’, 2’ differs b/w DNA (no OH group) and RNA (has OH group)

Phosphate group- forms bonds b/w nucleotides (5’ and 3’)

Nitrogenous bases- basis for the genetic code and links strands together; 5 types

Question 16

What is typically attached or is unique at the 1’, 2’, 3’, and 5’ carbon positions of the pentose sugar?

Answer 16

1’- links to the nitrogenous base
2’- nitrogenous base attachment point
3’, 5’- location of phosphodiester linkage
5’- also the location of the phosphate group

Question 17

What are the four nitrogenous bases used in DNA and the four nitrogenous bases used in RNA? Which base is unique to each class of nucleic acid?

Answer 17

DNA- guanine, cytosine. adenine, thymine*

RNA- guanine, cytosine, adenine, uracil*

Question 18

Which bases are considered purines and which bases are considered pyrimidines?

Answer 18

Purines have two sugar rings- adenine and guanine

Pyrimidines have one sugar ring- cytosine, thymine, and uracil

Question 19

What occurs during a dehydration reaction and a hydrolysis reaction? Which is used to link monomers together and which is used to break apart monomers?

Answer 19

Dehydration- removal of water to link two monomers together

Hydrolysis- addition of water to break two monomers together

Question 20

What is the name of the unique linkage or bond used to link nucleotides in DNA? Which carbon positions on the pentose sugar facilitate this linkage?

Answer 20

Phosphodiester linkage- the 3’ and 5’ carbon positions on the sugar ring link nucleotides together following a dehydration reaction

Question 21

What charge does DNA have? Why? What specific component of the DNA molecule provides the overall charge?

Answer 21

DNA is negatively charged due to the phosphate charges in the backbone

Question 22

How do you identify the directionality of a DNA strand?

Answer 22

5’ –> 3’

5’ end has a phosphate attached 3’ end doesn’t

Question 23

How is the double helix of DNA formed? Specifically, what is unique about the orientation of the two strands and what type of force/bond is used to hold the strands together? What is meant by the term antiparallel?

Answer 23

Antiparallel- one strand runs is the 5’-3’ direction, the other runs in the 3’-5’ direction– this allows the purines to bond with pyrimidines via h-bonds so the the helical strand is more stable

Question 24

What are Chargaff’s rules?

Answer 24

the ratios of adenine to thymine and cytosine to guanine are consistently 1:1– therefore adenine must bond with thymine and guanine must bond with cytosine

Question 25

What is annealing?

Answer 25

binding

Question 26

How many hydrogen bonds are present between each nucleotide pair?

Answer 26

Adenine and thymine share 2

Cytosine and guanine share 3

Question 27

What are the three conformations of DNA? Which is most common? Which is most likely to be found under dehydration conditions?

Answer 27

A form- squished, less common, occurs under dehydrated conditions

B form- most common form. occurs in normal physiological conditions

Z form- has a left handed twist and may form under some unique cell conditions

Question 28

Be able to compare and contrast the structures of DNA and RNA. Which is generally single-stranded and which is double-stranded? Which is more stable? Why?

Answer 28

DNA is two-stranded and RNA is one-stranded. DNA is more stable because it can form hydrogen bonds between strands

Question 29

What is the central dogma of biology?

Answer 29

DNA makes RNA which makes protein; the order cannot reverse

Question 30

What is translation and transcription?

Answer 30

Translation- RNA –> protein

Transcription- DNA –> RNA

Question 31

What is a gene?

Answer 31

A specific region of DNA which encodes the sequence used to produce one or more proteins

Question 32

What type of macromolecule is a gene?

Answer 32

Nucleic acid

Question 33

What is the name of the monomer which comprises proteins?

Answer 33

Amino acids

Question 34

What are the 4 groups which are attached the central carbon in an amino acid?

Answer 34

Central (alpha) carbon
Amino group
Carboxylic acid
Variable side chain (R)

Question 35

Which group differs between amino acids? How many different types of amino acids are there?

Answer 35

All amino acids are identical except for their R group– there are 20 different types of amino acids

Question 36

Amino acids are linked to form polypeptides by what kind of unique bond? What two groups of the amino acid are responsible for forming this bond? What type of reaction occurs?

Answer 36

Polypeptides are formed by peptide bonds via a dehydration reaction b/w amino and carboxyl groups of adjacent amino acids

Question 37

Nonpolar amino acids

Answer 37

hydrophobic; interacts exclusively in hydrophobic or van der Waals interaction

Question 38

Polar amino acids

Answer 38

hydrophilic; can form polar or h-bonds

Question 39

Electrically charged amino acids

Answer 39

sub group of polar amino acids which have a fixed charge- capable of ion-dipole interactions

Question 40

What is the primary structure of a protein?

Answer 40

a chain of peptide bond interactions b/w amino acids

Question 41

What is the secondary structure of a protein?

Answer 41

the backbone amino and carboxyl groups form h-bonds and fold into either an alpha helix or a beta pleated sheet based on the size of the R groups

Question 42

What is the amino terminus and carboxy terminus

Answer 42

Amino terminus- the group with a free amino group; usually the first one

Carboxyl terminus- the group with the free carboxyl group; usually the last one

Question 43

What is the tertiary structure of a protein?

Answer 43

The level structure where the R groups begin to interact with each other; one peptide chain; can be a functional preotein at this level
Hydrophobic
Disulfide bridges– sulfur-sulfur bonds that function essentially like h-bonds
Ionic-bonds

Question 44

What is the quaternary structure of a protein?

Answer 44

The highest level of protein structure; interactions b/w R groups of 2+ polypeptide chains
The basis for protein-protein interactions

Question 45

What is denaturation? Why are protein so susceptible to denaturation?

Answer 45

Denaturation– the process by which a protein loses its structure or function
Proteins go through a very complex process to form and have to complete many molecular interactions– therefore there are many environmental or chemical conditions that may disrupt key interactions

Question 46

What forces may denature a protein? How does each type of force affect protein structural stability?

Answer 46

pH– changes in acid or base conditions can affect availability of charge states on the protein

Temperature– increases in temperature=increased molecular motion which can disrupt weaker IMFs

Ions– similar effect as pH; can disrupt charge and polar interactions

Question 47

In general terms, what is the role of a protein in a cell? name at least 3

Answer 47

Proteins are the primary workers of the cell-- they drive nearly all biological processes:
Enzyme action
Defense 
Transport
Support
Motion
Regulation
Storage