Exam 1: Molecules and Cells/Water, pH, and Buffers/Nucleic Acids/Nucleic Acid Structure Flashcards
hold atoms together to form molecules.
Covalent bonds
maintain biological structure and determine molecular interactions.
Noncovalent bonds (or weak chemical forces)
Types of noncovalent bonds:
- Van der Waals Interactions: result of electron cloud fluctuations that allow attractions to occur between positively charged nuclei and electrons of nearby atoms
- Hydrogen Bonds: form between a hydrogen atom, covalently bonded to an oxygen or nitrogen, and a second oxygen or nitrogen
- Ionic Interactions: result of attractive forces between oppositely charged groups, such as negative carboxyl groups and positive amino groups
- Hydrophobic Interactions: due to the strong tendency of water to exclude nonpolar groups or molecules, because water molecules prefer the stronger interactions between water molecules
Compared to similar liquids, water has a higher:
1.
2.
3.
4.
- Boiling point
- Melting point
- Heat of vaporization
- Surface tension
The unusual properties of water are due to its molecular structure:
a) Water is a polar molecule: The electronegative O atom and the two H atoms form a dipole that makes the molecule polar.
b) Hydrogen bonds are formed by interactions between the polar water molecules: H2O molecules in liquid water interact with an average of 4.4 other molecules to form a random, H-bonded network. These intermolecular attractions are responsible for the high boiling point, etc. of water.
The H bonds in ice form a rigid structure which holds the water molecules apart.
Because of its structure, it is sometimes called ice, or structure
hexagonal, open lattice
The average lifetime of an H-bond between two H2O molecules is picoseconds (1 psec = 10-12 sec).
9.5 picoseconds
Because water is a polar molecule, it is an excellent for many substances including
solvent,
ionic substances such as salts.
H2O molecules form around ions.
hydration shells
Negative partial charges on oxygen will be attracted to the positive charge of Na+, while the partial positive charges on the hydrogens will be attracted to the negative charge of Cl-.
Water Has a High Dielectric Constant
The ability of water to surround ions in dipole interactions and diminish their attraction for one another is a measure of its dielectric constant, D
water molecules form around hydrophobic solutes.
clathrate structures
Water Forms , which accounts for its excellent solvent properties.
H Bonds with Polar Solutes
Water molecules produce with molecules. Examples are fatty acids with a polar group (carboxyl group) at the end of a long nonpolar chain.
micelles
amphiphilic: means that there a two chemical natures within one molecule
two nonpolar tails instead of one results in a very different structure than amphiphilic molecules containing just one nonpolar tail – a instead of a micelle.
bilayer
the lipid bilayer helps to maintain the different concentrations of ions on the inside and outside of the membrane.
What are colligative properties?
Give examples for water
Properties that only depend on the number of solute particles per unit volume of solvent and not on the chemical nature of the solute.
EX:
- freezing point depression
- boiling point elevation
- vapor pressure lowering
osmotic pressure effects
They only depend on the amount of molecules mixed into the water.
Mixing certain starches or proteins with water can lower the freezing point of water than 32 degrees, for example. All these molecules are doing is interfering with the ability of the water molecules to form a crystal hexagonal structure, so you have to slow down the water molecules even more to get them to freeze.
Ions in solution, such as the Na+ and Cl- ions of NaCl, interact with H2O molecules to form:
a) clathrate structures
b) hexagonal ice
c) micelles
d) osmotic pressure
e) hydration shells
e) hydration shells
The structure of water in the form of normal ice can be described as “hexagonal ice”. This is because:
a) ice crystals always have six sides
b) hydration shells consist of six H2O molecules
c) the minimum number of water molecules around any closed path of H-bonded molecules is six
d) clathrate structures of water molecules are composed of six H2O molecules e) ice floats on liquid water
c) the minimum number of water molecules around any closed path of H-bonded molecules is six
If the initial pH of a solution is pH 8.0 and acid is added to increase the hydrogen ion concentration 100-fold, the final pH of the solution will be:
a) pH 8.0
b) pH 6.0
c) pH 7.0
d) pH 1.0
e) none of the above
b) pH 6.0
In the phosphate buffer system, which buffers the intracellular fluid of cells, excess acidity [H+] is neutralized to form H2PO4- by reaction with:
a) OH-
b) NaH2PO4
c) H2O
d) HPO42-
e) H2CO3
d) HPO42-
Which of the following nucleic acid bases are pyrimidines only?
a) guanine, adenine
b) cytosine, uracil, thymine
c) guanine, cytosine, adenine, thymine
d) guanine, adenine, thymine
e) guanine, cytosine, adenine, uracil
b) cytosine, uracil, thymine
Which bases are the pyrimidines commonly found in RNA?
a) guanine, cytosine
b) guanine, adenine
c) cytosine, uracil
d) adenine, uracil
e) adenine, thymine
c) cytosine, uracil
Which of the following is a nucleoside?
a) adenine
b) adenosine
c) adenosine 5’-monophosphate
d) adenylic acid
e) 3’, 5’-cyclic AMP
b) adenosine
All of the following nucleotides are substrates for the synthesis of RNA or DNA in cells except:
a) thymidine 5’-triphosphate
b) uridine 5’-triphosphate
c) deoxycytidine 5’-triphosphate
d) deoxyadenosine 5’-triphosphate
e) guanosine 5’-triphosphate
a) thymidine 5’-triphosphate
- I think this should be deoxythymidine. Thymine is only found in DNA; therefore it would have to be deoxy?
Small nuclear RNAs (snRNAs) have all of the following characteristics except:
a) involved in the processing of hnRNA into mature transcripts
b) form complexes called small nuclear ribonucleoprotein paticles (snRNPs) with specific proteins
c) have sedimentation coefficients of 16 S, 23 S, and 5 S
d) found mainly in the nucleus of eukaryotes
e) consist of 100 to 200 nucleotides
c) have sedimentation coefficients of 16 S, 23 S, and 5 S
Restriction endonucleases are used to isolate and clone DNA fragments such as genes that encode important proteins. Assuming that the four nucleotides in DNA are randomly distributed and present in equal proportions, what would be the average size in base pairs of the DNA fragments produced by a “six-cutter” restriction enzyme (one that cuts DNA molecules at a specific sequence 6 nucleotides in length)?
a) 256
b) 1024
c) 4096
d) 16384
e) 65536
c) 4096
The chain termination method of DNA sequencing is the most widely used procedure to determine the sequential order of nucleotides in DNA molecules including entire genomes. Along with the substrates for DNA polymerase (dATP, dGTP, dCTP, and dTTP), which other nucleotide must be added to the sequencing reaction mixture?
a) 3’, 5’-cyclic AMP (cAMP)
b) deoxycytidine 5’-diphosphate (dCDP)
c) 3’, 5’-cyclic GMP (cGMP)
d) 2’, 3’-dideoxynucleoside 5’-triphosphate
e) uridine 3’-monophosphate (3’-UMP)
d) 2’, 3’-dideoxynucleoside 5’-triphosphate
Which is the type of DNA that exists as a left-handed double helix and can be produced by synthetic oligonucleotides consisting of alternating pyrimidine-purine nucleotides?
a) B-DNA
b) double-helical DNA:RNA hybrids
c) A-DNA
d) Z-DNA
e) double-helical regions of RNA chains
d) Z-DNA
a) M. phlei
b) S. marcescens
c) E. coli
d) Pneumococcus
e) Yeast
e) Yeast
A=T is only a double bond, while GC forms triples bonds. This means that compounds with more A=T bonds will be easier to break, and therefore have a lower melting point.
cDNA molecules are DNA copies of mRNA transcripts, and therefore contain the protein-coding sequence of a gene uninterrupted by introns. In preparing cDNAs from purified eukaryotic mRNAs, which enzyme is used to synthesize the first cDNA strand?
a) DNA polymerase
b) reverse transcriptase
c) T4 DNA ligase
d) Taq DNA polymerase
e) SP6 RNA polymerase
b) reverse transcriptase
Which of the following would be an appropriate source of the DNA polymerase used in the PCR procedure to amplify specific DNA segments?
a) yeast
b) adenovirus
c) human
d) Thermus aquaticus
e) Escherichia coli
d) Thermus aquaticus
In PCR-based mutagenesis, which component of the PCR reaction mixture is altered to introduce a specific change (mutation) in the nucleotide sequence of a gene that is being amplified by PCR?
a) primers
b) dATP, dTTP, dGTP, dCTP
c) DNA template
d) heat-stable DNA polymerase
e) thermal cycler conditions
a) primers
Which is an example of a polar, uncharged amino acid?
a) phenylalanine
b) glutamic acid
c) lysine
d) serine
e) leucine
d) serine
Which amino acid has the single letter abbreviation “E”?
a) phenylalanine
b) glutamic acid
c) glycine
d) serine
e) leucine
b) glutamic acid
Which amino acid contains a sulfur atom?
a) methionine
b) tyrosine
c) proline
d) lysine
e) aspartic acid
a) methionine
Which amino acid contains a carboxyl group in its R side chain?
a) methionine
b) tyrosine
c) proline
d) lysine
e) aspartic acid
e) aspartic acid
Which amino acid has an R side chain covalently linked to the α-amino group?
a) methionine
b) tyrosine
c) proline
d) lysine
e) aspartic acid
c) proline
The amino acid that can form disulfide bridges (—S—S—) between side chains in the same polypeptide or different polypeptides is:
a) proline
b) hydroxylysine
c) methionine
d) γ-carboxyglutamic acid
e) cysteine
e) cysteine
The peptide Asp—Glu—Ala—Lys—Leu would have an overall net charge at pH 7.0 of:
a) +2
b) +1
c) 0
d) -1
e) -2
d) -1
What is the number of different amino acid sequences that are possible for a protein that is 100 amino acid residues in length (assuming that only the 20 common amino acids are incorporated into the protein chain)?
a) 100
b) 2000
c) 120,000
d) 2020
e) 20100
e) 20100
Conjugated proteins are proteins that:
a) are composed of several different kinds of polypeptide chains
b) have a high degree of sequence homology, such as myoglobin and alpha and beta hemoglobin
c) contain aromatic amino acids (phenylalanine, tyrosine, tryptophan) that allow spectroscopic measurements of protein concentration
d) are on the same branch of the phylogenetic tree because of their shared evolutionary relationship
e) contain various chemical constituents as an integral part of their structure
e) contain various chemical constituents as an integral part of their structure
nonpermeant solute can be like starch or protein. Water molecules will want to equalize the h20 molecule concentration on each side of the membrane, so it will diffuse through the semipermeable membrane. WATER FLOWS INTO THE TUBE IN ORDER TO EQUALIZE THE CONCENTRATION OF WATER MOLECULES ON EITHER SIDE OF THE MEMBRANE
pH equation
hydroxide ion concentration and hydrogen ion concentration are related by the equation:
- Kw = [H+][OH-] = 10 ^ -14
The Phosphate buffer system buffers
and consists of….
the intracellular fluid
Too high or too low of a pH in DNA can cause:
- high H+ concentrations in DNA, (low pH) can break down into fragments, destroying the DNA
- high pH, low H+ ion concentration, (BASIC) the two DNA strands will separate as a minimum
The Carbonate Buffer system is an important buffer system for . It consists of:
blood plasma.
bicarbonate ion [HCO3-] and carbonic acid [H2CO3]
Water molecules form hydrogen bonds with polar solutes. These include solutes containing groups.
hydroxyl (-OH)
Pyrimidines consist of:
cytosine, thymine, and uracil
Purines consist of:
adenine and guanine
Sugars include:
ribose and deoxyribose
Nucleosides consist of
a base bonded to a sugar
Ribonucleosides include:
adenosine, uridine, cytidine, guanosine
Deoxyribonucleosides include:
deoxyadenosine, deoxythymidine, deoxycytidine, deoxyguanosine
Nucleotides consist of:
1-3 phosphate groups bonded to nucleosides
Ribonucleotides (monophosphates) include:
adenosine 5’-monophosphate (AMP),
uridine 5’-monophosphate (UMP),
guanosine 5’-monophosphate (GMP),
cytidine 5’-monophosphate (CMP)
Deoxyribonucleotides (monophosphates):
dAMP, dTMP, dGMP, dCMP
Diphosphates
ADP, UDP, GDP, CDP;
dADP, dTDP, dGDP, dCDP
Triphosphates
ATP, UTP, GTP, CTP ;
dATP, dTTP, dGTP, dCTP
Nucleic acids are linear polymers of nucleotides (polynucleotides) linked 3’ to 5’ by bridges.
phosphodiester
By convention, the sequence of bases in a polynucleotide chain is read from
the free 5’ end to the free 3’ end.
Two fundamental differences between DNA and RNA:
- DNA contains deoxyribose instead of ribose.
- DNA contains thymine instead of uracil.
Messenger RNA (mRNA):
carries the “message” encoded in genes to the ribosomes, where this information is translated into polypeptide chains
Ribosomal RNA (rRNA):
major component (65%) of ribosomes, the sites of protein synthesis
Transfer RNA (tRNA):
carries amino acids to the ribosomes, where they are assembled into a polypeptide chain
Small Nuclear RNAs (snRNAs):
involved in processing of eukaryotic gene transcripts into mature messenger RNA
What is the primary structure of nucleic acids?
Linear sequence of bases along a DNA or RNA strand example: 5’-ATGAAACAAATGTTT-3’
What is the secondary structure of nucleic acids?
Formation of double helix by specific base pairing
A:T (or A:U) and G:C
Tertiary Structure
For eukaryotic cells:
For prokaryotic cells:
For eukaryotic cells: organization of DNA into chromosomes by interactions with histone proteins and nonhistone proteins
For prokaryotic cells: supercoiling of circular chromosomal DNA molecules such as:
- *E. coli chromosome
- *plasmid DNA molecules
- *mini-chromosomes of organelles including mitochondria
Tertiary Structure of DNA: Supercoils
Circular DNA or linear DNA with fixed ends can form supercoils if the two strands of the double helix are underwound (negative supercoils) or overwound (positive supercoils).
Tertiary Structure of DNA: Linking Number
The linking number is a parameter that characterizes supercoiled DNA: L = T + W where T = twist, the number of helical turns and W = writhe, the number of times that the double helix crosses over itself
Nucleotides, the building blocks of DNA and RNA, are composed of 1 , 2 , and 3 .
bases, sugars, and phosphate groups.
Nucleosides lack
phosphate groups.
DNA nucleotides consist of a base (A, T, C, or G), , and 1-3 phosphate groups. RNA nucleotides consist of a base (A, U, C, or G), , and 1-3 phosphate groups.
- deoxyribose
- ribose
The phosphodiester linkages in DNA and RNA connect the 1 carbon of one nucleotide with the 2 carbon of another.
- 3’
- 5’
A-T base pairs have 1 H-bonds, while G-C base pairs have 2 .
- two
- three
RNA molecules, particularly and , can have short double helical segments held together by A-U and G-C base pairs.
tRNA and rRNA
The percentage of total cell RNA of
mRNA is ,
while tRNA is
and rRNA is
not including the small RNAs.
- ~2%
- 16%
- 82%,
Transcription is the process of . It involves the enzyme .
- RNA synthesis from a DNA template
- RNA polymerase
In prokaryotes, a single mRNA molecule can specify several polypeptides. In contrast, eukaryotic mRNAs encode only one polypeptide. But eukaryotic mRNAs are more complex because they consist of .
protein-coding segments (exons) separated by noncoding intervening sequences (introns) that must be removed
Translation is the process of . The process involves messenger RNA, ribosomes, transfer RNA, amino acids, and other molecules.
protein synthesis at ribosomes in cells
Ribosomes are composed of and .
- ribosomal RNA
- ribosomal proteins
rRNA has a complex secondary structure due to:
many short segments of A-U and G-C intrastrand hydrogen bonds.
tRNA molecules . They also possess short hydrogen-bonded segments.
- transfer amino acids to the growing polypeptide chains.
Primary structure can be determined by the of DNA sequencing, or by newer sequencing technologies.
dideoxy or chain termination method
The dideoxy method uses:
2’,3’-dideoxynucleotides to terminate the growth of DNA chains.
The major form of the DNA double helix in cells is
B-DNA
B-DNA is a right- handed helix with about per turn of the helix. The bases are almost perpendicular to the helix axis and are stacked nm apart. The pitch, or repeat distance, along the helix is nm.
- 10 base pairs
- 0.34
- 3.4
A-DNA is formed by . DNA/RNA hybrid double helices and double helical segments of RNA also have structures like A-DNA.
- dehydrated DNA fibers
is a narrow, left-handed helix formed by synthetic oligonucleotides with an alternating pyrimidine- purine sequence (e.g. GCGCGC).
Z-DNA
Tertiary structure is long-range, three-dimensional structure that includes of circular DNA molecules in prokaryotes and packaging of DNA into chromosomes in eukaryotes.
- supercoiling
Supercoils are formed in circular DNA, or linear DNA with fixed ends, if the two strands of the double helix are . Circular bacterial chromosomes are converted to interwound supercoiled circles by .
- underwound or overwound
- DNA gyrase (topoisomerase II)
The higher-order structure of eukaryotic DNA involves the interaction of DNA with histones to produce , the coiling of nucleosomes into chromatin fibers, and the folding of chromatin fibers into DNA loops. Also, cruciform structures might be formed from palindrome (inverted repeat) sequences.
- nucleosomes
RNA molecules also have tertiary structure. The secondary structures of transfer RNA (tRNA) molecules are folded into tertiary structures. Ribosomal RNA (rRNA) molecules have many short segments of double helix which interact with numerous ribosomal proteins to form the precise 3-D structures of the small and large ribosomal subunits.
- cloverleaf
- L-shaped
- The L form is never found in DNA or RNA, so you can always just assume it is the D-Dextro form.
nucleotides are linked together by
phosphodiester bonds
RNA is stranded
single
rRNA has sedimentation coefficients of , , and
5s
16s
23s
2% of Human DNA is coding, 98% is non coding
In prokaryotes, a single mRNA molecule can contain sequences that encode for several polypeptides, while eukaryotic mRNAs can only code for polypeptide.
one polypeptide.
prokaryotic mRNAs can be translated into proteins even before transcription is completed. In eukaryotes, however, transcription occurs in the and translation in the .
- nucleus
- cytoplasm
Secondary Structure of tRNA molecule
- INTRAstrand hydrogen bonding
- 3’ end “acceptor stem” is where the new nucleotides will be added
- anticodon specifies which amino acid will be added to the acceptor stem
The Dideoxy or Chain Termination Method of DNA Sequencing
the angle of the causes the major and minor grooves
glycosidic bonds
