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Molecular Genetics
DNA
173
Biochemistry
Undergraduate 3
04/30/2014

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Term
What are the monomer units of DNA and RNA polymers called?
Definition
nucleotides
Term
What are the three components of a nucleotide?
Definition
Nitrogen containing heterocyclic base, five-carbon sugar ring, phosphoryl group
Term
What are the two types of heterocyclic bases?
Definition
purine, pyrimidine
Term
What are the two types of nucleotide sugars?
Definition
ribose, deoxyribose
Term
Where are ring structures found?
Definition
base and sugar
Term
What kind of bond exists between the sugar and the phophoryl group?
Definition
covalent phosphoester
Term
What is the bond between teh base and sugar
Definition
Beta-N-glycosidic linkage
Term
What does the Beta-N-glycosidic linnkage join?
Definition
1'-carbon of the sugar and a nitrogen atom of the base
Term
What are the purine bases?
Definition
adenine, guanine
Term
What kind of structures are purines?
Definition
double ring structure
Term
What structures does the purine double ring consist of?
Definition
6 member ring fused to a 5-member ring
Term
The bases contain 1 ___ atom in the ring structure
Definition
Nitrogen
Term
Pyrimidines consist of a
Definition
single 6-membered ring
Term
How many pyrimidine bases are there?
Definition
3
Term
What are the 3 pyrimidine bases
Definition
cytosine, thymine, uracil
Term
What pyrimidine base is specific to DNA
Definition
thymine
Term
What pyrimidine base is specific to RNA
Definition
uracil
Term
How is the nitrogen base attached to the nucleic sugar?
Definition
Beta
Term
At what sugar is the carbon phosphorylated?
Definition
carbon 5'
Term
What is the organization of a nucleotide?
Definition
base, sugar, phosphoryl group
Term
How do nucleotides combine to form a chain?
Definition
series of 3' to 5' phosphodiester bonds
Term
What happens to the 5' phosphate
Definition
esterifies to the 3' OH on teh adjacent unit
Term
Which unit retains the phosphate?
Definition
terminal 5'
Term
What is the backbone of the DNA polymer?
Definition
sugar-phosphate backbone
Term
What is the pattern of the backbone?
Definition
alternating sugar and phosphoryl groups
Term
How many chains are there in DNA
Definition
2
Term
What shape does the helix take
Definition
right-handed double
Term
What are the "handrails" on the spiral "staircase"
Definition
sugar-phosphate backbones
Term
What are teh steps of the spiral staircase?
Definition
nitrogenous bases
Term
What noncovalent attraction aids in maintianing the double helix structure
Definition
hydrogen bonding
Term
Adenine forms how many H bond with Thymine?
Definition
2
Term
Cytosine forms how many bonds with Guanine?
Definition
3
Term
What is the diamater of the double helix
Definition
2.0 nm
Term
The two DNA strands are ______ strands
Definition
complementary
Term
The chains run ______
Definition
antiparallel
Term
1 complete 360 turn of the helix has how many nucleotides?
Definition
10
Term
1 complete turn is ____ nm
Definition
3.4
Term
1 nucleotide is _____ nm
Definition
.34
Term
What are prokaryotes
Definition
single chromosome
Term
Do prokaryotes have a true nucleus?
Definition
no
Term
What is a circular DNA molecule that is supercoiled?
Definition
chromosome
Term
A strand of DNA wrapped around a disk of histone proteins
Definition
nucleosome
Term
Semiconservative replication generates ___ new DNA helices
Definition
2
Term
Each helix has ___ DNA strands
Definition
2
Term
How many nucleotides in a Bacterial chromosome?
Definition
3 million
Term
Where does bacterial DNA replication begin?
Definition
replication origin
Term
Which direction does bacterial DNA replication occur
Definition
bidirectionally
Term
At what rate does bacterial DNA replication occur?
Definition
500 nucleotides per second
Term
The position where new nucleotides are added to the growing daughter strand is the ________ _______
Definition
replication fork
Term
How many replication forks are tehre during DNA synthesis?
Definition
2
Term
What is the first step in DNA replication?
Definition
strand separation
Term
What seperates DNA strands?
Definition
helicase
Term
What does helicase do to break the DNA strands?
Definition
breaks hydrogen bonds
Term
What occurs when the hydrogen bonds break?
Definition
positive supercoiling
Term
What relieves positive supercoiling?
Definition
topoisomerase
Term
What attaches to the seperated strands to keep them apart?
Definition
single-strand binding proteins
Term
What catalyzes the syntheses of a 10-12 base of RNA?
Definition
primase
Term
What is the role of primase
Definition
prime DNA replication
Term
What is the second step in DNA replication?
Definition
reading
Term
What is the role of DNA polymerase III?
Definition
reading the parental strand, catalyzing the polymerization of the daughter strand
Term
What occurs in the polymerization reaction?
Definition
pyrophosphate group is released as a phophoester bond is formed between the 5'phosphoryl group of the nucleotide being added and the previous 3'-OH of the nucleotide in teh newly synthesized daughter strand
Term
In eukaryotes, DNA replication begins at _______ replication origins and moves bidirectionally along each chromosome
Definition
many
Term
The process by which a single strand of DNA serves as a template for the syntheses of an RNA molecule?
Definition
transcription
Term
Converting the information from one language of nitrogenous bases to another of amino acids?
Definition
translation
Term
What are the 3 classes of RNA?
Definition
mRNA, rRNA, tRNA
Term
Which RNA directs teh amino acid sequence of proteins?
Definition
mRNA
Term
Which RNA is a complimemantary copy of a gene?
Definition
mRNA
Term
Which RNA has teh codon for an amino acid in a protein?
Definition
mRNA
Term
Which RNA is the structural and functional component of the ribosome?
Definition
rRNA
Term
Which RNA forms ribosomes by reacting with proteins?
Definition
rRNA
Term
How many types of rRNA are in prokaryotes?
Definition
3
Term
How many types of rRNA are in eukaryotes?
Definition
4
Term
Which RNA transfers amino acids to the site of protein synthesis?
Definition
tRNA
Term
How many tRNA are there or each amino acid to be incorporated into a protein?
Definition
at least 1
Term
How many nucleotides are in tRNA?
Definition
80
Term
What is the overall structure of tRNA?
Definition
cloverleaf
Term
Intrachain hydrogen bonding in tRNA occurs to give regions called ______ with an _____-helix
Definition
stems, alpha
Term
Intrachain hydrogen bonding in tRNA occurs to give a type of __-shaped _______ structure
Definition
L, tertiary
Term
The 3'-OH group can _________ bind the amino acid
Definition
covalent
Term
_ nucleotides at the base of the cloverleaf serve as the anticodon
Definition
3
Term
The anticodon forms hydrogen bonds to a codon on _____
Definition
mRNA
Term
What catalyzes Transcription
Definition
RNA polymerase
Term
What does transcription produce?
Definition
copy of only 1 DNA strand
Term
What are the 3 stages of transcription?
Definition
initiation, chain elongation, termination
Term
What is initiation?
Definition
binding RNA polymerase to the promoter region at teh beginning of the gene
Term
What is chain elongation?
Definition
formation of a 3'-5' phosphodiester bond, generating a complementary copy
Term
What is termination?
Definition
final step of transcription when the RNA polymerase releases the newly formed RNA molecule
Term
Prokaryotes release a mature _______ at the end of termination for translation
Definition
mRNA
Term
Eukaryote mRNA is a primary transcript which still must be processed in _______
Definition
post-transcriptional modification
Term
How many steps are in post-transcriptional modification?
Definition
3
Term
What is the 1st step of post-transcriptional modification?
Definition
a 5' cap structure is added
Term
What is the role of the 5' cap structure?
Definition
required for efficient translation of the final mRNA
Term
What is the 2nd step of post-transcriptional modification?
Definition
a 3' poly(A) tail (100-200 units) is added by poly(A) polymerase
Term
What is the role of the Poly(A) tail?
Definition
protests the 3' end of the mRNA from enzymatic digestion & prolongs the life of the mRNA
Term
What is the 3rd step of post-transcriptional modification?
Definition
RNA splicing
Term
What is RNA splicing?
Definition
removal of portions of the primary transcript that are not protein coding
Term
Are bacterial chromosomes continuous or discontinuous?
Definition
continuous
Term
What is it meant by continuous chromosomes?
Definition
all DNA sequence from the chromosome is found in the mRNA
Term
Are eukaryotic chromosomes continuos or discontinuous?
Definition
discontinuous
Term
What is meant by discontinuous chromosomes?
Definition
Presence of introns makes direct translation to synthesize proteins impossible
Term
What is another name for introns?
Definition
intervening sequences
Term
What are teh extra DNA sequences within the genes that do not encode any amino acid sequence?
Definition
introns
Term
What are exons?
Definition
coding sequences
Term
What happens during RNA splicing?
Definition
introns are cut out and exons are spliced together
Term
Degenerate
Definition
more than one three base codon can code for the same amino acid
Term
specific
Definition
each codon specifies a particular amino acid
Term
Non-overlapping and uninterrupted
Definition
none of the bases are shared between consecutive codons, no noncoding bases appear in the base sequence
Term
universal
Definition
all organisms use the same code
Term
How many codons are there?
Definition
64
Term
How many codons code for amino acids?
Definition
61
Term
How many codons are start codons?
Definition
1
Term
What is the start codon?
Definition
AUG-Methionine
Term
What are the stop Codons?
Definition
UAA, UGA, UAG
Term
If an amino acid has multiple codons for it how many bases does it tend to have in common?
Definition
2
Term
What codons code for leucine?
Definition
CUU, CUC, CUA, CUG
Term
Why are there multiple codons for one amino acid?
Definition
makes the code mutation resistant
Term
What is translation?
Definition
protein synthesis
Term
Where does translation occur?
Definition
ribosomes
Term
What are ribosomes complexes of?
Definition
rRNA, proteins
Term
Protein synthesis occurs in multiple places on one _______ at a time
Definition
mRNA
Term
mRNA plus the multiple ribosomes are called a
Definition
polysome
Term
tRNA binds a specific amino acid aided by
Definition
aminoacyl tRNA synthetase
Term
How subunits is a ribosome made up of?
Definition
2
Term
What are the subunits of a ribosome?
Definition
large and small
Term
What is the small ribosomal unit made up of?
Definition
1 rRNA and 33 proteins
Term
What is the large ribosomal subunit maide up of?
Definition
3 rRNA and 49 proteins
Term
What is the role of tRNA?
Definition
decode information on mRNA into the primary structure of the protein
Term
What are the two specific functions of tRNA?
Definition
can only bind one specific amino acid, ability to recognize appropriate codon on the mRNA for specific amino acid
Term
WHere is the binding site on the tRNA for covalent attachment of amino acid?
Definition
3' end
Term
WHat is the role of the enzyme aminoacyl tRNA synthetase?
Definition
covalent links the proper amino acid to the tRNA
Term
What is aminoacyl tRNA
Definition
covalently linked tRNA and amino acid
Term
What is the role of the anticodon?
Definition
complementary to the codon on the mRNA to recognize amino acid codon
Term
What are the 3 steps of translation?
Definition
initiation, chain elongation, termination
Term
Translation: What is initiation?
Definition
initiation factors (proteins), mRNA, initiator tRNA, small and large ribosomes come together
Term
How many sites does Ribosome have to bind tRNA?
Definition
2
Term
What are the two sites of to bind tRNA?
Definition
P-Site, A-Site
Term
What is the P-site
Definition
bind to the growing peptide
Term
What is the A site
Definition
binds to the aminoacyl site
Term
Translation: How many steps does chain elongation have?
Definition
3
Term
Translation: Chain Elongation: Step 1
Definition
Am aminoacyl tRNA bind to A-site
Term
Translation: Chain Elongation: Step 2
Definition
Peptide bond formation occurs catalyzed by peptidyl transferase
Term
Translation: Chain Elongation: Step 3
Definition
Translocation of ribosome down the mRNA chain next to codon
Term
What happens during Step 3 of chain elongation?
Definition
shifts the new peptidyl tRNA from the A-site to the P-site, requires energy
Term
What kind of energy is used during chain elongation?
Definition
GTP to GDP
Term
Translation: WHen does termination occur?
Definition
finding a "stop" codon
Term
Translation: What happens during termination?
Definition
a release factor binds the empty A-site
Term
Translation: Termination: What happens to the last amion acid and peptidyl tRNA?
Definition
bond is hydrolyzed
Term
Translation: Termination: What happens after the bond between the amino acid and peptidyl tRNA and is hydrolyzed?
Definition
the protein is released
Term
Translation: Termination: Is the released protein in its final form?
Definition
potentially no
Term
What post-translational modifications may occur before a protein is fully functional?
Definition
cleave, association with other proteins, bonding to carbohydrate or lipid groups
Term
What are mutations?
Definition
mistakes introduced into the DNA sequence of an organism
Term
What is a silent mutation?
Definition
no change in the protein
Term
WHat are the types of mutations?
Definition
point, deletion, insertion
Term
What is a point mutation?
Definition
substitution of a single nucleotide for another
Term
What is a deletion mutation?
Definition
one or more nucelotides are lost
Term
WHat is an insertion mutation?
Definition
one or more nucleotides are added
Term
WHat does UV damage cause?
Definition
covalent linkage of adjacent pyrimidine bases
Term
What is the covalent linkage of adjacent pyrimidine bases called?
Definition
pyrimidine dimer
Term
What is xeroderma pigmentosum?
Definition
genetic skin disorder; very sensitive to UV light and develop multiple skin cancers
Term
Phosphates tend to have more negative charges therefore
Definition
nucleic acids are called acids
Term
Does RNA Have a secondary structure?
Definition
no
Term
Which end has the free phosphate group?
Definition
5'
Term
WHich end has teh free hydroxyl group?
Definition
3' end
Term
What is the Watson and Creek DNA model?
Definition
double helix
Term
how many chromosomes are there?
Definition
46
Term
how many chromosome pairs are there?
Definition
23
Term
How many autosomes are there?
Definition
22
Term
How many sex chromosomes are there?
Definition
1
Term
What are okazaki fragemnts?
Definition
fragemnts of DNA on the lagging strand
Term
Where does transcription occur?
Definition
In the nucleus
Term
Where does translation occur?
Definition
cytoplasm
Term
What are the purines?
Definition
adenine and guanine
Term
What are the pyrimidines?
Definition
cytosine, thymine, uracil
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