Week 6 (part 1 - ch. 3) Flashcards
Define DNA
A linear polymer of four subunits; the information archive in all organisms.
Define double helix
The structure formed by two strands of complementary nucleotides that coil around each other.
What are the two major biological functions of DNA?
DNA stores information
DNA transmits genetic information from one generation to the next
Defien genetic information
Information carried in DNA, organized in the form of genes
Define genes
The unit of heredity; the stretch of DNA that affects one or more traits in an organism, usually through an encoded protein or noncoding RNA
Define gene expression
The production of a functional gene product.
Define gene regulation
The various ways in which cells control gene expression
What causes differences in genes?
the order of the individual sub units (bases) in the DNA
Define nucleotides
A constituent of nucleic acids, consisting of a 5-carbon sugar, a nitrogen-containing base, and one or more phosphate groups.
What does the elegant shape of the twisting strands rely on?
the structure of the DNA’s subunits aka nucleotides
What do nucleotides consist of (3 things)
- a 5 carbon sugar
- a base
- one or more phosphate groups
Define sugar
The simplest carbohydrate molecule; also called a saccharide
Define base
A nitrogen-containing compound that makes up part of a nucleotide.
Define phosphate group
A chemical group consisting of a phosphorus atom bonded to four oxygen atoms.
What are the roles of the phosphate group and 5 carbon sugar in the DNA structure?
They form the backbone. Each sugar is linked to the phosphate group of the neighboring nucleotide
What is the role of the bases sticking out of the sugar on nucleotides?
They give the nucleotide its chemical identity
By convention, which direction are the carbon atoms on the sugar ring in DNA/RNA numbered?
clockwise
Define deoxyribose
The sugar in DNA.
Where is the base attached on the carbon ring in DNA/RNA?
it is attached to the 1’ carbon
Define purine
In nucleic acids, either of the bases adenine and gunanine, which have a double-ring structure
Define adenine (A)
A purine base.
define Guanine (G)
A purine base.
Define pyrimidine
In nucleic acids, any of the bases thymine, cytosine, and uracil, which have a single-ring structure.
Define thymine (T)
A pyrimidine base.
Define cytosine (C)
A pyrimidine base.
Define nucleoside
A molecule consisting of a 5-carbon sugar and a base.
a nucleoside with one or more phosphate groups constitutes a _____.
nucleotide
Why are nucleoside triphosphates particularly inmportant?
because they are the molecules that are used to form nucleotide polymers: DNA and RNA.
What other functions do nucleoside triphosphates do besides make up DNA and RNA?
They are carriers of chemical energy in the form of ATP and GTP
Define phosphodiester bond
A bond that forms when a phosphate group in one nucleotide is covalently joined to the sugar unit in another nucleotide.
_____ _____ are relatively stable and form the backbone of a DNA strand
Phosophodiester bonds
What is the name of the C-O-P-O-C linkage?
Phosophodiester bond
What gives DNA strands their polarity?
the phosphodiester linkage
Define 5’ end
The end of a nucleic acid strand containing a free 5′ phosphate group.
Define 3’ end
The end of a nucleic acid strand that carries a free 3′ hydroxyl.
When a base sequence is stated without specifying the 5′ end, by convention the end at the left is the __ end
5’
How would you specify a strand of DNA with the sequence TCGA with the T being nearest the hydroxyl group and the A being nearest the phosphate group?
5′-AGCT-3′ or equivalently 3′-TCGA-5′.
How many base pairs are there per complete turn in the the double helix?
10
What is the diameter or DNA?
2 nm
Define major groove
The larger of two uneven grooves on the outside of a DNA duplex.
Define minor groove
The smaller of two unequal grooves on the outside of a DNA duplex.
What is the importance of minor and major groove in DNA?
proteins that interact with DNA often recognize a particular sequence of bases by making contact with the bases via the major or minor groove or both.
Define antiparallel
Oriented in opposite directions; the strands in a DNA duplex are antiparallel.
What does A pair with?
T
What does G pair with?
C
What does T pair with?
A
What does C pair with?
G
Each base pair contains a ____ and a _____
purine
pyrimidine
Why does the precise pairing of bases maintain the structure of the double helix?
because pairing two purines would cause the backbones to bulge and pairing two pyrimidines would cause them to narrow
Define complementary
Describes the relationship of purine and pyrimidine bases, in which the base A pairs only with T and G pairs only with C
Because they form specific pairs, the bases A and T are said to be _____, as are the bases G and C
complementary
The specificity of base pairing is brought about by ____ _____ that form between A and T and between G and C
hydrogen bonds
How many hydrogen bonds do A and T share?
two
How many hydrogen bonds do G and C share?
Three
What two things can disrupt hydrogen bonding?
high pH or high temperatures
Define base stacking
Stabilizing hydrophobic interactions between bases in the same strand of DNA.
What is one of the most important features of DNA structure?
There is no restriction on the sequence of bases along a DNA strand
What do the base pairing rules imply?
%A = %T and %G = %C
and that the percentage of purines equals the percentage of pyrimidines
Many of the double-stranded DNA molecules in prokaryotic cells are ___ and form _____
circular
supercoils
Define supercoils
A coil of coils; a circular molecule of DNA can coil upon itself to form a supercoil.
Supercoiling is caused by enzymes called _____ that cleave, partially unwind, and reattach a DNA strand, which puts ____ on the DNA double helix.
topoisomerases
strain
Define topoisomerases
Any one of a class of enzymes that regulates the supercoiling of DNA by cleaving one or both strands of the DNA double helix, and later repairing the break.
Supercoils relieve the ___ and help to preserve the 10 base pairs per turn in the double helix.
strain
n eukaryotic cells, most DNA molecules in the nucleus are _____, and each individual molecule forms one _____
linear
chromosome
Define chromosome
In eukaryotes, the physical structure in which DNA in the nucleus is packaged; used more loosely to refer to the DNA in bacterial cells or archaeons.
Double-stranded DNA molecules in eukaryotes are usually packaged with proteins called ______, and others, to form a complex of DNA and proteins referred to as ______
histones
chromatin
Define chromatin
A complex of DNA, RNA, and proteins that gives chromosomes their structure; chromatin fibers are either 30 nm in diameter or, in a relaxed state, 10 nm.
What are the main differences between RNA and DNA
- the sugar in RNA is ribose whereas the sugar in DNA is deoxyribose (which is why RNA is less stable than DNA)
- RNA is less stable than DNA
- in RNA the base uracil replaces thymine
- while the 5′ end of a DNA strand is typically a monophosphate, the 5′ end of an RNA molecule is typically a triphosphate
- RNA is usually a shorter strand than DNA
- RNA is usually single stranded
Why is a deoxyribose called a 2’-deoxyribose?
Because the oxygen is missing of the 2’ carbon atom
What is the covalent bond which links monomers together?
a phosphodiester bond
What is the difference between structural polarity and bond polarity
structural: difference in EN of two ends of a molecule
Bond: difference in EN between two atoms bonded together
What is the name of the enzyme that forms at the start of transcription?
A. RNA polymerase B. DNA polymerase C. DNA gyrase D. RNA helicase
A. RNA polymerase
What genetic material is made during the process of transcription?
A. mRNA B. tRNA C. rRNA D. All of the above
D. All of the above
If the first nucleotide after the promoter on the top DNA strand is changed from G to T, what would the resulting nucleotide be on the mRNA?
A. C B. A C. G D. T
B. A
If you made a change in the promoter sequence in the DNA, what would happen at the RNA level?
A. The RNA polymerase would not be able to recognize and bind the DNA, so no RNA would be made. B. The DNA helicase would not be able to recognize and bind the DNA, so the RNA would not be made. C. The mutation of the DNA would be carrier through to the RNA sequence. D. Nothing, the RNA would be made as usual.
A. The RNA polymerase would not be able to recognize and bind the DNA, so no RNA would be made.
If the first nucleotide after the promoter on the bottom DNA strand is changed from C to T, what would the resulting nucleotide be on the mRNA?
A. A B. U C. C D. T
A. A
