Nucleic Acids and Proteins Flashcards
Outline the structure of nucleosomes
a subunit of chromatin composed of DNA wrapped around the core of histone proteins.
Describe the structure of DNA
-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
What are the base pairings for DNA?
Adenine and Thymine ( 2 hydrogen bonds)
Cytosine and Guanine (3 hydrogen bonds)
State the direction of DNA replication
5’ to 3’ direction (always)
Explain the process of replication in eukaryotes
- Helicase disrupts the hydrogen bonding between base pairs to separate the strands to create a replication fork
- Primase generates primer. Primer binds to the 3’ end and serves as the starting point for replication.
- The leading strand synthesizes continuously on in the 5’ to 3’ direction by DNA polymerase
- The lagging strand synthesizes discontinuously. Primase synthesizes a short RNA primer which is extended by by DNA polymerase to form Okazaki fragments
- DNA polymerase I replaces RNA primer with DNA nucleotides
- 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.
Explain how DNA replication is semi-conservative
the DNA that is created contains one strand of the original DNA and one new strand that created through replication`
Compare the structure of DNA and RNA
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
Describe the genetic code in terms of codons composed in triplets of bases
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
Explain the process of translation
-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
what is degenerate and universal?
Degenerate = having more than one base triplet to code for one amino acid
Universal = found in all living organisms
explain the relationship between one gene and one polypeptide.
Each gene will be transcribed and translated into one polypeptide sequence
state the direction of transcription
5’ to 3’ direction
Explain the process of transcription
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.
What are sense and anti-sense strands?
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
Define introns and exons
Introns = noncoding sequences in DNA of eukaryotes
Exons = coding sequences of a gene that are transcribed and translated
Explain how transcriptase is used in molecular biology
an enzyme that catalyzes the formation of RNA from a DNA template during transcription
direction of translation
5’ to 3’ direction
Explain the four levels of protein structure
- Unique sequence of amino acids in a protein
- Regular, repeated folding, and coiling of a protein’s polypeptide backbone (alpha helix or beta-bleated sheets)
- Three-dimensional shape of a protein; Due to bonding b/w side chains, weak bonds
- Structure that results from the interactions b/w and among several polypeptide chains
difference between fibrous and globular protein
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
Explain the significance of polar and non-polar amino acids
Nonpolar side groups (less soluble in water)
Polar side groups (soluble in water)
states six functions of proteins,
Structural support
Transport (hemoglobin)
Signaling (chemical messengers)
Cellular response (receptor proteins)
Movement
Defense (antibodies)
Catalysts (enzymes)
Define metabolic pathways
Metabolic pathways consist of chains and cycles of enzyme catalyzed reactions
Describe the induced fit model
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
explain how enzymes affect the rate of reactions
Lower EA so the transition state can be reached at cellular temperatures.
only speeds up reaction
Competitive vs non-competitive inhibition
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
explain the role of allostery in the control of metabolic pathways by end-product inhibition
Allosteric site = specific receptor site on some part of the enzyme molecule other than the active site
what are the Roles of RNA polymerase?
1 Separates DNA strand
2. Recognizes promoter
3. lays out RNA nucleotides and (links them)
4. recognizes termination
6 enzymes involves in protein and their roles
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
codons
Codons = Three-nucleotide words of mRNA
What are the 5’ and 3’ modifications?
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
activation energy
Activation energy = amount of energy that reactant molecules must absorb to start a rxn
