Nucleic Acids and Proteins

Question 1

Outline the structure of nucleosomes

Answer 1

a subunit of chromatin composed of DNA wrapped around the core of histone proteins.

Question 2

Describe the structure of DNA

Answer 2

-double helix with uniform width
-The small molecules that makeup DNA are called nucleotides. -Each nucleotide contains a phosphate group, a sugar molecule (called deoxyribose), and a nitrogenous base
-sugar-phosphate chains on the outside
-nitrogenous bases inside
-backbones are antiparallel

Question 3

What are the base pairings for DNA?

Answer 3

Adenine and Thymine ( 2 hydrogen bonds)
Cytosine and Guanine (3 hydrogen bonds)

Question 4

State the direction of DNA replication

Answer 4

5’ to 3’ direction (always)

Question 5

Explain the process of replication in eukaryotes

Answer 5

1. Helicase disrupts the hydrogen bonding between base pairs to separate the strands to create a replication fork
2. Primase generates primer. Primer binds to the 3’ end and serves as the starting point for replication.
3. The leading strand synthesizes continuously on in the 5’ to 3’ direction by DNA polymerase
4. The lagging strand synthesizes discontinuously. Primase synthesizes a short RNA primer which is extended by by DNA polymerase to form Okazaki fragments
5. DNA polymerase I replaces RNA primer with DNA nucleotides
6. DNA ligase links the Okazaki fragments together on the lagging strand

In the end, replication produces two DNA molecules, each with one strand from the parent molecule and one new strand.

Question 6

Explain how DNA replication is semi-conservative

Answer 6

the DNA that is created contains one strand of the original DNA and one new strand that created through replication`

Question 7

Compare the structure of DNA and RNA

Answer 7

DNA: double-stranded, contains thymine, deoxyribose sugar, longer than RNA, DNA is found in the nucleus, replicates, and stores genetic information.
RNA: single-stranded, contains uracil, ribose sugar, shorter than DNA, found in the cytoplasm, converts genetic information to a form to build proteins

Question 8

Describe the genetic code in terms of codons composed in triplets of bases

Answer 8

genetic code is a set of instructions that direct the translation of DNA into 20 amino acids Genetic code is made up of codons which are three-letter chains of nucleotides

Question 9

Explain the process of translation

Answer 9

-Initiation: Brings together mRNA, tRNA attached to first amino acid, and two ribosomal subunits
tRNA is always carrying methionine, and binds to start codon of AUG
-Elongation: mRNA codon in the A site forms hydrogen bonds with the anticodon of tRNA
Peptide bond is formed b/w polypeptide in P site and amino acid in A site
mRNA and tRNA move through ribosome together, 5’→3’ directio
-Termination codon (stop codon) = base triplet on mRNA that signals the end of translation
UAA, UAG, or UGA…do not code for amino acid

Question 10

what is degenerate and universal?

Answer 10

Degenerate = having more than one base triplet to code for one amino acid
Universal = found in all living organisms

Question 11

explain the relationship between one gene and one polypeptide.

Answer 11

Each gene will be transcribed and translated into one polypeptide sequence

Question 12

state the direction of transcription

Answer 12

5’ to 3’ direction

Question 13

Explain the process of transcription

Answer 13

Initiation: RNA polymerase binds to the DNA of the gene at the region called promoter and transcription begins
Elongation: RNA strand gets longer due to the addition of new nucleotides. RNA polymerase adds a complementary RNA nucleotide to the 3’ end of the RNA strand
Termination: RNA polymerase will keep transcribing until it gets a signal to stop.

Question 14

What are sense and anti-sense strands?

Answer 14

Sense strand = has the same base sequence as mRNA (the strand NOT being transcribed)
Antisense = the transcribed strand; it has the opposite sequence as the mRNA

Question 15

Define introns and exons

Answer 15

Introns = noncoding sequences in DNA of eukaryotes
Exons = coding sequences of a gene that are transcribed and translated

Question 16

Explain how transcriptase is used in molecular biology

Answer 16

an enzyme that catalyzes the formation of RNA from a DNA template during transcription

Question 17

direction of translation

Answer 17

5’ to 3’ direction

Question 18

Explain the four levels of protein structure

Answer 18

1. Unique sequence of amino acids in a protein
2. Regular, repeated folding, and coiling of a protein’s polypeptide backbone (alpha helix or beta-bleated sheets)
3. Three-dimensional shape of a protein; Due to bonding b/w side chains, weak bonds
4. Structure that results from the interactions b/w and among several polypeptide chains

Question 19

difference between fibrous and globular protein

Answer 19

fibrous( elongated three-dimensional shape) provides structural support; ex:insoluble: collagen and keratin

globular protein (folds up into a compact shape) : functional role; soluble, ex:hemoglobin and myoglobin

Question 20

Explain the significance of polar and non-polar amino acids

Answer 20

Nonpolar side groups (less soluble in water)
Polar side groups (soluble in water)

Question 21

states six functions of proteins,

Answer 21

Structural support
Transport (hemoglobin)
Signaling (chemical messengers)
Cellular response (receptor proteins)
Movement
Defense (antibodies)
Catalysts (enzymes)

Question 22

Define metabolic pathways

Answer 22

Metabolic pathways consist of chains and cycles of enzyme catalyzed reactions

Question 23

Describe the induced fit model

Answer 23

As substrate binds to the active site, it induces the enzyme to change its shape
Brings chemical groups into positions that enhance their interaction w/ substrate

Question 24

explain how enzymes affect the rate of reactions

Answer 24

Lower EA so the transition state can be reached at cellular temperatures.
only speeds up reaction

Question 25

Competitive vs non-competitive inhibition

Answer 25

Competitive Inhibitor = chemicals that resemble an enzyme’s normal substrate and compete with it for the active site
Noncompetitive Inhibitors = Bind to a location away from the active site, cause a change in the active site so substrate can no longer bind

Question 26

explain the role of allostery in the control of metabolic pathways by end-product inhibition

Answer 26

Allosteric site = specific receptor site on some part of the enzyme molecule other than the active site

Question 27

what are the Roles of RNA polymerase?

Answer 27

1 Separates DNA strand
2. Recognizes promoter
3. lays out RNA nucleotides and (links them)
4. recognizes termination

Question 28

6 enzymes involves in protein and their roles

Answer 28

1) helicase: unzips DNA
2) Primase - polymerizes primer
3) DNA polymerase III - links nucleotides to growing strands in 5’ to 3’ direction only
4) Nucleoside triphosphate - provides energy to synthesize strands
5) DNA Polymerase I - replaces RNA primer with DNA
6) Ligase - the glue that links Okazaki fragments together on the lagging parent strand

Question 28

codons

Answer 28

Codons = Three-nucleotide words of mRNA

Question 29

What are the 5’ and 3’ modifications?

Answer 29

5’ cap = guanine nucleotide added to 5’ end, helps ribosomes recognize attachment site
Poly (A) tail = Sequence of adenines at 3’ end of the tail, facilitates attachment, helps mRNA reach the cytoplasm

Question 30

activation energy

Answer 30

Activation energy = amount of energy that reactant molecules must absorb to start a rxn