Nucleic Acids and Proteins- Structure and Function Flashcards
What is genetics?
A branch of biology that deals with the heredity and variety of organisms
What is heredity?
The transfer of traits from one generation to the next (why you may look similar to your parents)
What is variation?
The difference between cells, organisms, or groups of organisms caused by either genetic differences or by the effect of environmental factors
What is X-ray diffraction?
A pure crystal is bombarded with x-rays and the diffraction pattern is cast on a film- which is then studied.
How was x-ray diffraction used in the discovery of the structure of DNA?
Scientists had been trying to capture a quality image of DNA for years. Eventually Rosalind Franklin was able to capture an image that revealed to double helix structure.
What’s the story of Franklin, Watson, and Crick?
The owner of the lab Franklin worked at showed her research to Watson and Crick w/o her permission. From it, they were able to determine the double helix structure, and published their research w/o crediting her. The owner, Watson, and Crick won the Nobel Prize for their “discovery” in 1962, 4 years after Franklin died of ovarian cancer.
What are organic molecules?
Molecules that contain carbon and hydrogen atoms bonded to other atoms
What are macromolecules?
Large organic molecules which consist of repeating units of smaller molecules linked together
What are the four types of macromolecules?
Carbohyrates- “sugars”
Lipids- “fats and oils”
Proteins
Nucleic acids
What is a monomer?
a molecule that can be bonded to other identical molecules
What is a polymer?
A chain of monomers that come together to form organic molecules
How does the composition of monomers help define the structure and function of the polymer?
The polymer is comprised of monomers– the composition of the monomers will effect which IMFs the polymer can utilize, and where, which will effect how the polymers folds itself– which determines the function.
What are nucleic acids? What is the name of the monomers that comprise nucleic acids?
Nucleic acids are a class of macromolecules which are comprised of monomers called nucleotides.
What are the two main classes of nucleic acids? What unique component of their structure gives them their name?
Deoxyribonucleic acid (DNA)- uses deoxyribose-containing nucleotides Ribonucleic acid (RNA)- uses ribose-containing nucleotides
What are the three primary components of nucleotides?
Pentose sugar group- group consisting of 5 sugars number 1’-5’, 2’ differs b/w DNA (no OH group) and RNA (has OH group)
Phosphate group- forms bonds b/w nucleotides (5’ and 3’)
Nitrogenous bases- basis for the genetic code and links strands together; 5 types
What is typically attached or is unique at the 1’, 2’, 3’, and 5’ carbon positions of the pentose sugar?
1’- links to the nitrogenous base
2’- nitrogenous base attachment point
3’, 5’- location of phosphodiester linkage
5’- also the location of the phosphate group
What are the four nitrogenous bases used in DNA and the four nitrogenous bases used in RNA? Which base is unique to each class of nucleic acid?
DNA- guanine, cytosine. adenine, thymine*
RNA- guanine, cytosine, adenine, uracil*
Which bases are considered purines and which bases are considered pyrimidines?
Purines have two sugar rings- adenine and guanine
Pyrimidines have one sugar ring- cytosine, thymine, and uracil
What occurs during a dehydration reaction and a hydrolysis reaction? Which is used to link monomers together and which is used to break apart monomers?
Dehydration- removal of water to link two monomers together
Hydrolysis- addition of water to break two monomers together
What is the name of the unique linkage or bond used to link nucleotides in DNA? Which carbon positions on the pentose sugar facilitate this linkage?
Phosphodiester linkage- the 3’ and 5’ carbon positions on the sugar ring link nucleotides together following a dehydration reaction
What charge does DNA have? Why? What specific component of the DNA molecule provides the overall charge?
DNA is negatively charged due to the phosphate charges in the backbone
How do you identify the directionality of a DNA strand?
5’ –> 3’
5’ end has a phosphate attached 3’ end doesn’t
How is the double helix of DNA formed? Specifically, what is unique about the orientation of the two strands and what type of force/bond is used to hold the strands together? What is meant by the term antiparallel?
Antiparallel- one strand runs is the 5’-3’ direction, the other runs in the 3’-5’ direction– this allows the purines to bond with pyrimidines via h-bonds so the the helical strand is more stable
What are Chargaff’s rules?
the ratios of adenine to thymine and cytosine to guanine are consistently 1:1– therefore adenine must bond with thymine and guanine must bond with cytosine
What is annealing?
binding
How many hydrogen bonds are present between each nucleotide pair?
Adenine and thymine share 2
Cytosine and guanine share 3
What are the three conformations of DNA? Which is most common? Which is most likely to be found under dehydration conditions?
A form- squished, less common, occurs under dehydrated conditions
B form- most common form. occurs in normal physiological conditions
Z form- has a left handed twist and may form under some unique cell conditions
Be able to compare and contrast the structures of DNA and RNA. Which is generally single-stranded and which is double-stranded? Which is more stable? Why?
DNA is two-stranded and RNA is one-stranded. DNA is more stable because it can form hydrogen bonds between strands
What is the central dogma of biology?
DNA makes RNA which makes protein; the order cannot reverse
What is translation and transcription?
Translation- RNA –> protein
Transcription- DNA –> RNA
What is a gene?
A specific region of DNA which encodes the sequence used to produce one or more proteins
What type of macromolecule is a gene?
Nucleic acid
What is the name of the monomer which comprises proteins?
Amino acids
What are the 4 groups which are attached the central carbon in an amino acid?
Central (alpha) carbon
Amino group
Carboxylic acid
Variable side chain (R)
Which group differs between amino acids? How many different types of amino acids are there?
All amino acids are identical except for their R group– there are 20 different types of amino acids
Amino acids are linked to form polypeptides by what kind of unique bond? What two groups of the amino acid are responsible for forming this bond? What type of reaction occurs?
Polypeptides are formed by peptide bonds via a dehydration reaction b/w amino and carboxyl groups of adjacent amino acids
Nonpolar amino acids
hydrophobic; interacts exclusively in hydrophobic or van der Waals interaction
Polar amino acids
hydrophilic; can form polar or h-bonds
Electrically charged amino acids
sub group of polar amino acids which have a fixed charge- capable of ion-dipole interactions
What is the primary structure of a protein?
a chain of peptide bond interactions b/w amino acids
What is the secondary structure of a protein?
the backbone amino and carboxyl groups form h-bonds and fold into either an alpha helix or a beta pleated sheet based on the size of the R groups
What is the amino terminus and carboxy terminus
Amino terminus- the group with a free amino group; usually the first one
Carboxyl terminus- the group with the free carboxyl group; usually the last one
What is the tertiary structure of a protein?
The level structure where the R groups begin to interact with each other; one peptide chain; can be a functional preotein at this level
Hydrophobic
Disulfide bridges– sulfur-sulfur bonds that function essentially like h-bonds
Ionic-bonds
What is the quaternary structure of a protein?
The highest level of protein structure; interactions b/w R groups of 2+ polypeptide chains
The basis for protein-protein interactions
What is denaturation? Why are protein so susceptible to denaturation?
Denaturation– the process by which a protein loses its structure or function
Proteins go through a very complex process to form and have to complete many molecular interactions– therefore there are many environmental or chemical conditions that may disrupt key interactions
What forces may denature a protein? How does each type of force affect protein structural stability?
pH– changes in acid or base conditions can affect availability of charge states on the protein
Temperature– increases in temperature=increased molecular motion which can disrupt weaker IMFs
Ions– similar effect as pH; can disrupt charge and polar interactions
In general terms, what is the role of a protein in a cell? name at least 3
Proteins are the primary workers of the cell-- they drive nearly all biological processes: Enzyme action Defense Transport Support Motion Regulation Storage
