15 and 16 - Carbohydrates and nucleic acids Flashcards
After several hours an alkaline solution of D-glucose will also contain what and why?
It will also contain D-mannose and D-fructose due to isomerizations from intramolecular shifts of a hydrogen atom and a relocation of a double bond. The intermediate formed is an enediol and the reversible transformation of glucose to fructose is an aldose-ketose interconversion. The conversion of glucose to mannose is referred to as epimerization.
What does reduction of aldehyde and ketone groups in monosaccharides yield?
The sugar alcohols additols. For example the reduction of D-glucose yields D-glucitol (aka, D-sorbitol) . Sugar alcohols are frequently used as preservatives (especially sorbitol in candy and whanot)
What are three important monosaccharides?
glucose, fructose and galactose
What is the reducing component of reducing sugars?
The anomeric C (which is not tied up) that can open to form an aldehyde. These free anomerics can form dissacharides (glucose is an example of a sugar that can do this)
Hemiacetal and hemiketals react with alcohol to form what?
The corresponding acetals and ketals, which have a glycosidic linkage and form a glycoside compound.
What are disaccharides?
Two monosaccharides linked by a glycosidic bond. Linkages can be a or b-conformation, and carbons that are connected are denoted
What is the glycosidic bond in maltose?
α(1 -> 4) between two D-glucoses, monomer of starch hydrolysis
What is the glycosidic bond in lactose?
β(1 -> 4) between galactose and glucose
What is the glycosidic bond in sucrose?
Sucrose is two glucoses connected between anomeric carbons, one α and one β. This means there is no free anomeric carbon and therefore sucrose is a non-reducing sugar
What is the max number of units in an oligosaccharide?
15
What are the two types of polysaccharides?
Homoglycans and heteroglycans. Homoglycans contain only one type of sugar monomer where heteroglycans can contain many
What is the glycosidic bond in the homoglycan polysaccharide of glucose?
What stabilizes this structural polymer?
Cellulose has glucoses attached by a β(1 ->4) bond
Found in plant cell walls and chitin
It is stabilized by interchain hydrogen bonds
Why can’t humans digest cellulose? What does this make cellulose in our diets?
Humans can’t digest β(1 -> 4) glycosidic bonds and therefore can’t breakdown cellulose. This makes cellulose fibre in our diets.
What is starch called in biochemistry? What type of glycosidic bonds and substituents does it have? How is it stored in plants? Can we break it down?
Starch is also known as α-amylose and has α(1 -> 4) bonds. We can break it down into it’s glucose monomers.
It is formed of amylose (unbranched) and amylopectin (branched)
In plant cells it can assemble into compact helical structures, (why things like potatoes are so dense).
Humans can cleave the α(1 -> 4) glycosidic bonds between glucose units with amylase, making starch a good source of glucose.
What is glycogen?
Glycogen resembles amylose (unbranched) and has the same major glycosidic bond α(1 -> 4) and similar branch pattern. But it is about twice as branched as amylopectin.
Animals produce it, it has high weight to energy ratio and is compact and easily mobilized. It is not however very efficient.
Glycogen and amylopectin are reducing sugars, why?
They have a free anomeric end, but only one, meaning that can reduce once.
What are two types of complex polysaccharides and their substituents?
Glycosaminoglycans (GAGs)
- Five classes, hyaluronic acid, chondroitin sulfate, dermatan sulfate, heparin and heparin sulfate, and keratin sulfate
- Have varying roles based on repeating unit
Glycoconjugates
- Proteoglycans
- Glycoproteins
- Glycolipids
What are glycosaminoglycans (GAGs)?
Linear polymers with a variety of disaccharide repeating units. A type of complex polysaccharide that have varying roles based on repeating units. There are five classes.
What are glycoconjugates? What are the three main types?
These result from carbohydrates being linked to proteins and lipids. A type of
complex carbohydrate, there are three main types:
Proteoglycans (main part is glycan sugar)
Glycoproteins (main part of polymer is protein). The protein is covalently linked to the glycan (N-linked or O-linked)
Glycolipids
What distinguishes proteoglycans from other glycoproteins?
By their very high carbohydrate content (95%). Proteoglycans are very hydrogen rich as well. They occur on cell surfaces or are secreted to the extracellular matrix.
What is the link between the carbohydrate and protein in N-linked glycoproteins? What is the tripeptide motifs attached to the amino acid residue attached to the carbohydrate? This template often codes for glycosylation.
A beta-glycosidic bond with the amide nitrogen of Asn. The tripeptide motif is where every third resiude from the Asn is either threonine or serine. This is like a template that results in glycosylation (though not always). A sample motif is Asn-X-Thr-Asn-X-Thr etc.
The attachment is covalent
In the O-linked form of glycoproteins what is the bond between the sugar and the amino acid residue (what residue is it?
The sugar forms a alpha-glycosidic bond with the hydroxy oxygen of Ser or Thr. Not every occurence of Ser or Thr in a protein results in glycosylation though.
Which is more common, O-glycosylation or N-glycosylation?
N-glycosylation. Even though the requirements for it in the amino acid residue sequence are more strict
How could O-linked glycoproteins play a role in cold ocean survival?
An antifreeze glycoprotein can be made. This would have repeating unit structures with free OG groups that can bind to ice.
The antifreeze is an O-linked tripeptide polymer
What type of bonds are nucleotides linked by?
3’,5’ phosphodiester bonds. These join the 3’-hydroxyl of one nucleotide to the 5’-phosphate of another
What allows the two strands of DNA to form hydrogen bonds between the nitrogenous bases?
The antiparallel nature of the two strands.
How long is one turn of double helix DNA? How many base pairs is that?
3.32 nm and 10.3 base pairs
What is the diameter of the double helix of DNA?
2.37 nm, the only length suitable for base pairing a purine with a pyrimidine.
What is the distance between adjacent base pairs in DNA?
.29 to .30 nm
How many hydrogen bonds do guanine and cytosine make? How many do thymine and adenine make?
Cytosine and guanine make 3 base pairs, adenine and thymine make two
What is the most common O-linked glycoprotein? Is the glycosidic bond alpha or beta?
An alpha linkage with N-acetylgalactosamine
What occupies most of the threonine and serine residue’s free OH group?
Many just have O-linked disaccharides linked on. Impossible to have N-linkage
How many rings do purines have?
Two rings
How many rings do pyrimidines have?
Just one ring
In nucleic acid, phosphates link riboses on what carbon with what bond?
Phosphates are linked onto ribose at the C4 carbon with phosphodiester bonds
What is at the 3’ end of DNA?
A hydroxy group on C3
What is at the 5’ end of DNA?
A phosphate Oxygen linked to C5
What noncovalent interactions contribute to DNA stability? (5)
Hydrophobic interactions - pi bonds through stacked purines and pyrimidines internal to the helix minimize interactions with water
Hydrogen bonds between CG and AT
Base stacking, planar bases are stacked above one another allowing weak Van der Waals forces between the rings
Hydration, water interacts with DNA to stabilize it
Electrostatic interactions by ions minimize destabilization due to closely spaced negative charges of the phosphates
When is A-DNA observed?
In dehydrated conditions. The base pairs are no longer horizontal but tilted and the dimensions of the double helix are distinct from the B form. This does not happen in nature but can be seen in solvent extraction.
What type of DNA sequences adopt Z-DNA structure?
Since Z-DNA structure is zigzagging and left handed helix it’s sequence usually has many G-C pairs
What is a palindromic sequence of DNA and what is its implications?
Palindromic sequences are sequences of nucleic acid that can be read the same in the 5’ to 3’ and 3’ to 5’ direction. Often bacteria make restriction enzymes that cut DNA at palindromic recognition sequences.
What is DNA denaturation in a nutshell?
The loss of H bonds between the bases leading to seperation of strands (melting) . No covalent bonds are cleaved and renaturation is possible in a sequence-specific manner.
What is renaturing melted DNA called.
Putting the two strands back together is referred to as reannealing, the reformation of H bonds between specific bases in the strand sequences.
What is underwinding of DNA?
An overly left twist in the helix, this is a type of supercoil.
What is overwinding of DNA
An overly right twist in the helix. A type of supercoiling. In a plasmid this can lead to a knot (supercoil)
Describe a prokaryotic chromosome
It has a protein core (nucleoid) with many supercoiled DNA loops and broken loops (no supercoiling) extending from it.
What are the proteins in prokaryotic chromosomes?
There is a protein core at the middle of the chromosome and palyamines, which have roles in maintaining the compressed structure of bacterial DNA.
How many histone proteins are there? What are there names? What is there charge and the consequence of that charge? What part of the histone can be covalently modified to effect gene expression?
There are 5 histones, H1 (the bar that DNA enters and leaves, to stabilize the histone), H2A, H2B, H3 and H4. They are positively charged so that they can interact with negatively charged DNA. The N-terminal histone tail can be covalently modified.
What are the components of a nucleosome?
The DNA winding around a histone core formed of H2A, H2B, H3 and H4.
What is the central dogma of genetics?
The accepted clasical flow of information from DNA (DNA to RNA to Protein).
Replication
Transcription
Translation
What is a transcript?
Each new RNA from RNA synthesis (transcription)
What is a transcriptome?
The total RNA transcripts for an organism.
What are the structural implications of palindromic sequences in DNA?
Secondary structures in the DNA
Supercoiling happens in what nature frequently in what type of organism?
Bacteria
What are rRNA molecules components of?
ribosomes
What is the proteome?
The entire set of proteins synthesized in a cell or tissue
What is gene expression?
The process by which cells control the timing of gene product synthesis in response to environmental or developmental cues.
What is a metabolome?
Refers to the sum total of low molecular weight metabolites produced by the cell
What carbon differs between RNA and DNA?
The second carbon (C2)
What are two special properties of RNA that DNA can’t do?
RNA exists as a single strand that can form complex three dimensional structures by base pairing with itself
Some RNA molecules have catalytic properties or ribozymes (eg able to cleave self or other RNA)
What is the average length of a rRNA?
About 75 bases
Why does tRNA structurally resemble a warped cloverleaf?
Due to extensive intrachain base pairing
What attaches amino acids to tRNA and to what end?
aminoacyl-tRNA synthetases attach amino acids to the end opposite the three nucleotide anticodon
What is the function of the tRNA loops?
To help facilitate interactions with the correct aminoacyl-tRNA synthetases
What is the most abundant RNA in living cells
rRNA
True or false, rRNA is a component of ribosomes in both eukaryotes and prokaryotes?
True, but eukaryotic ribosomes are larger
True or false? RNA has scaffolding and enzymatic functions.
True
What are the functions of proteins in ribosomes?
To interact with rRNA for structure and functiuon
Prokaryotic are polycistronic, and eukaryotes are usually monocistronic. What does this mean?
Polycistronic means that there are multiple genes per mRNA, and monocistronic means there is only a single gene per mRNA.
Eukaryotic mRNA requires three additional things to prokaryotic mRNA, what are they?
5’ capping
3’ tailing
splicing
What is non-coding RNA (ncRNA)?
RNAs that don’t directly code for polypeptides.
What are small nuclear RNAs (snRNA)
These combine with proteins to form small nuclear ribonucleoproteins (snRNPs) and are involved in splicing
What do small nucleolar RNAs (snoRNAs) do?
snoRNAs facilitate chemical modifications to rRNA in the nucleolus
What are the two types of RNAs involved in RNA-induced silencing complex?
Micro RNAs and small interfering RNAs. These are the shortest. Small interfering RNAs (siRNAs) are 21-23 nt dsRNA that play a crucial role in RNA interference (RNAi)
Adding more salt to a solution of DNA has what consequence?
It stabilizes the DNA and raises the melting temperature.
At what temperature does DNA unwind?
65
