Biochem Exam 3 PLEASE

DNA and RNA

long linear polymers called nucleic acids, function as carriers of genetic info

Central dogma

flow of genetic info from DNA to RNA to proteins

NucleoTIDE

each monomer unit within the polymer, a nucleoside joined to a 1+ phosphoryl group by a ester linkage

What does each nucleotide consist of?

a sugar, phosphate, and one of four bases

Ribose

sugar in RNA where the 2’ carbon atom of sugar is linked to HYDROXYL (-OH) group

Deoxyribose

sugar in DNA where the 2’ carbon atom of sugar is linked to HYDROGEN atom

What causes DNA to be more resistant to hydrolysis than RNA?

The absence of the 2’-OH group

What do backbones of DNA and RNA consist of?

sugars that are linked by phosphodiester bridges

What are the two DNA bases that are derivatives of purines?

adenine (A) and guanine (G)

What are the two DNA bases that are derivatives of pyrimidines?

cytosine (C) and thymine (T)

What base does RNA differ from DNA?

uracil (U) instead of thymine (T)

Nucleoside

unit consisting of a base bonded to a sugar

RNA nucleosides

adenosine, guanosine, cytidine, and uridine

DNA nucleosides

deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine

E-coli genome

a single DNA molecule including 2 strands of 4.6 million nucleotides each

What is directionality of DNA chains?

polarity, one end has a free 5’-OH group or a 5’-OH group attached to a phosphoryl group. the other end has a free 3’-OH group

How are nucleic acid sequences written?

left to right in the 5’-to-3’ direction

What stabilizes the double helix?

hydrogen bonding and van der waals interactions

When G pairs with C and A pairs with T, what shape do these base pairs have?

same shape

Base pairs are held together by…

weak hydrogen bonds

What did Chargaff observe?

A:T and C:G ratios were nearly 1:1 while A:G varied

B-form

B-form = right handed double helix made from anti-parallel strands held by Watson-Crick base pairs (most DNA under physiological conditions)

A-form

A-form= similar to B but wider and shorter with tilted base pairs relative to helix axis (seen in RNA double helices and RNA-DNA hybrid)

Z-form

Z-form= left handed double helix with zigzagged phosphoryl groups (unknown biological role but have been isolated)

Why do major and minor grooves arise?

glycosidic bonds of a base pair are not directly opposite of each other, major is wider and deeper and allows for more protein info

Supercoiling

biologically important, supercoiled DNA is more compact and relaxed, may hinder or favor the capacity of double helix to unwind and interact with other molecules

Stem-loop

common structural pattern seen in nucleic acids, occurs when 2 complementary sequences within a single strand form a double helix, can include mismatched base pairs or unmatched bases

process from DNA to RNA

transcription

process from RNA to protein

translation

semiconservative replication

process where each replicated DNA molecule contains one parent strand and one newly synthesized daughter strand 

What is the Meselson and Stahl experiment and their hypothesis?

they labeled parent DNA with 15N by growing bacteria in growth media containing only 15N, then they shifted bacteria to a growth media with 14N, then performed a density-gradient equilibirum to determine distribution of 14 and 15N. their experimental question is what is the distribution of these N in the DNA molecules after successive rounds of replication?

15N isotope is heavier than 14N, density gradient centrifugation can distinguish between DNA that contains 15N and 14N

What was the outcome of Meselson and Stahl experiement?

Determined that DNA replication is semi-conservative. In E-coli DNA, after one generation, newly synthesized DNA consisted of DNA with equal parts of 15N and 14N DNA, proving their hypothesis right

How is DNA melted in the lab?

DNA strands are separated by heating a solution of DNA or adding acid (less than pH of 2.3) or alkali (more than a pH of 11.5)

What is Tm?

temperature at which half of the helical structure is lost

what is melting

dissociation of double helix

what is annealing?

renaturation of a double helix, occurs when temp is lowered below Tm

hypochromism

effect where bases stacked in double helix absorb less UV light at 260nm than bases in single stranded molecule, melting is monitored by measuring increase in absorption of 260 nm light 

What are the key characteristics of DNA synthesis?

1. the reaction requires four deoxynucleoside 5′-triphosphates and Mg 2+

2. the new DNA strand is assembled on a preexisting DNA template (the template strand)

3. DNA polymerases require a primer to begin synthesis

4. chain elongation proceeds in the 5′-to-3′ direction

5. many DNA polymerases have nuclease activity to remove mismatched nucleotides

What are retroviruses?

viruses with single stranded RNA genomes that are converted to DNA double helices by reverse transcriptase, ex. HIV-1

messenger RNA (mRNA)

template for protein synthesis

transfer RNA (tRNA)

carries amino acids in activated form to ribosome for peptide bond formation

ribosomal RNA (rRNA)

major component of ribosomes that serves as actual catalyst for protein synthesis 

What does a RNA polymerase NOT require?

a primer

What DOES a RNA polymerase require?

double or single stranded DNA template, 4 ribonucleoside triphosphates such as ATP, GTP, UTP, and CTP, and a divalent metal ion

mechanism of elongation

3’-OH at the terminus of growing chain makes a nucleophilic attack on the innermost phosphoryl group of the incoming nucleoside triphosphate

promotor sites

regions along DNA templates that specifically bind RNA polymerase and determine where transcription begins 

When does prokaryote termination occur?

when RNA polymerase synthesizes a terminator sequence or by the action of the protein rho

codon

three coding bases on the mRNA template

anticodon

three complementary bases on the tRNA

CCA terminus

region at the 3′ end tRNA sequence that contains two
cytidylates followed by an adenylate

genetic code

relationship between the sequence of bases in DNA and sequence of amino acids in proteins

ribosomes

large molecular complexes assembled from protein and ribosomal RNA

reading frame

order of the three nonoverlapping
nucleotides, established by the location of the initiator codon

exons

coding regions

introns

noncoding regions

spliceosomes

assemblies of proteins and small nuclear RNA molecules (snRNAs) that carry out splicing

exon shuffling

process by which new proteins arise by the rearrangement of exons from different genes 

alternative splicing

process where the same gene transcript can be processed differently to produce multiple proteins

carbohydrates 

carbon based molecules high in hydroxyl groups

constitutional isomers 

molecules with identical molecular formulas but are connected in different ways, ex. n-butane and isobutane

stereoisomers

molecules that differ in 3D spatial arrangement but are same in formula and connections, have either D or L configuration, can be enantiomers (mirror images of each other, think chiral centers) or
diastereoisomers (not mirror images of each other, ex. 1 chiral center differ from other), number possible = 2 n where n is the number of asymmetric carbon atoms

epimers

sugars that are diastereoisomers differing in
configuration only at a single asymmetric center

anomer 

a diastereoisomeric form of sugars that forms
when a cyclic hemiacetal is formed and an additional
asymmetric center is created

Why are pyranose rings not planar?

bc of its tetrahedral geometry of its saturated carbon atoms

What conformation dominates in beta D-glucose?

chair form bc all axial positions are held by hydrogens

blood sugar

D -glucose circulating in the blood
– only fuel used by the brain in non-starvation conditions
– only fuel used by red blood cells

what are the potential reasons why D-glucose is an important fuel?

glucose is formed from formaldehyde under prebiotic
conditions and may have been available as a fuel source
for primitive biochemical systems
– glucose is relatively inert
– the most stable ring structure is β-D-glucopyranose

Why is glycation important for diabetes?

D-glucose reacts with
hemoglobin to form glycated
hemoglobin (hemoglobin A1c,
A1C).
– has no effect on O2 binding
• In nondiabetic individuals, <6%
of the hemoglobin is glycated.
• In patients with uncontrolled
diabetes, almost 10% of the
hemoglobin is glycated.
• Only eliminated when RBC’s die
(lifespan is about 120 days)

Glycation

nonenzymatic addition of a carbohydrate to another 

example: Reducing sugars nonspecifically react with free amino
groups on proteins (often Lys or Arg) to form a stable covalent bond.

advanced glycation end products (AGEs)

products resulting from cross-linking following the primary modification
– implicated in aging, arteriosclerosis, diabetes, and other
pathological conditions

O-glycosidic linkage

covalent linkage formed between the anomeric carbon atom of a carbohydrate and the oxygen atom of an alcohol

N-glycosidic linkage

covalent linkage formed between the anomeric carbon atom of a carbohydrate and the nitrogen atom of an amine

Why is phosphorylation of sugars relevant?

it is a common modification of sugars in metabolic reactions (metabolism), purpose is to make sugars anionic to prevent crossing the lipid bilayer and interacting with transporters of unmodified sugar, blocks the formation of alternative ring conformation, creates reaction intermediates that more readily undergo metabolism

oligosaccharides

sugars that contain 2 or more monosaccharides linked by O-glycosidic bonds, have directionality bc of their reducing and non-reducing ends

reducing end

has a free anomeric carbon atom that
can form the open-chain form

nonreducing end

has an anomeric carbon in a glycosidic linkage that cannot covert to the open-chain form

α-1,4-glycosidic linkage

glycosidic linkage between the α-anomeric form of C-1 on one sugar and the hydroxyl oxygen atom on C-4 of the adjacent sugar

disaccharide

2 sugars joined by an O-glycosidic linkage, cleavage of these products can provide ATP energy

Sucrose

disaccharide of sugar cane or sugar beets that consists of glucose linked to fructose
– the anomeric carbon of glucose is linked to the anomeric carbon
of fructose
– the configuration is α for glucose and β for fructose
– not a reducing sugar
– can be cleaved by sucrase (invertase)

lactose

disaccharide of
milk that consists of a
galactose linked to a
glucose
– linked by a β-1,4-
glycosidic linkage.
– can be hydrolyzed by
lactase in human
beings and by β-
galactosidase in
bacteria
– Lack of lactase leads
to lactose intolerance

maltose

disaccharide resulting from the hydrolysis of
large oligosaccharides that consists of two linked
glucose molecules
– joined by an α-1,4-glycosidic linkage
– can be hydrolyzed to glucose by maltase (α-glucosidase )

polysaccharides (glycans)

large polymeric oligosaccharides formed by the linkage of multiple
monosaccharides
– plays roles in energy storage and structural integrity

homopolymer

polymer in which all the monosaccharide units are the same

glycogen

large branched polymer of glucose residues, most common homopolymer in animal cells, storage form of glucose linked by alpha 1-4 glycosidic linkages, branches formed by alpha 1-6 glycosidic linkages, hydrolyzed by alpha amylase

starch

homopolymer that serves as nutritional reservoir in plants

what are the 2 forms of starch?

amylose and amylopectin

amylose

unbranched type of starch made of glucose residues in alpha 1-4 linkage

amylopectin

branched type of starch with ~1 α-1,6 linkage per 30 α-1,4 linkages
– identical structure to glycogen but with a lower degree of
branching
• Amylose and amylopectin are hydrolyzed by α-amylase.

why are insoluble fibers important for humans?

because they increase digestion rate thru the large intestine, soften stools

why are soluble fibers important for humans?

because they slow the movement of food through gastrointestinal tracy, allows absorption of nutrients from diet

chitlin

homopolymer of β-1,4 linked N-acetylglucosamine
– found in fungal cell walls and
exoskeletons and shells of
arthropods
– Fibers are often crosslinked
and composited with minerals
and proteins to increase rigidity
and strength.

glycoprotein

carb group covalently attachted to a protein, makes 50% of entire human protein set

glycoproteins

the predominant molecule is a protein
– play a variety of roles, including cell adhesion

proteoglycans

the predominant molecule is a carbohydrate and the protein component is conjugated to a glycosaminoglycan
– function as structural components and lubricants

mucins (mucoproteins)

the predominant molecule is a carbohydrate and the protein components is extensively glycosylated at Ser or Thr residues, usually by N-acetylgalactosamine
– key component of mucus
– function as lubricants

N-linkage

links the sugars in glycoproteins to the amide nitrogen atom in the side chain of Asn
– Asn must be part of an Asn-X-
Ser or Asn-X-Thr sequence,
where X is any residue except
proline

O-linkage

links the sugars in glycoproteins to the oxygen atom in the side chain of Ser
or Thr

erythropoietin (EPO)

a glycoprotein secreted by the kidneys into the blood serum to stimulate production of red blood cells

GlcNAcylation

the post-translational, covalent attachment of a single N-acetylglucosamine
(GlcNAc) to Ser or Thr residues of proteins, reversible, occurs when nutrients are abundant