Study Guide / TA Exam Review

The anomeric carbon of one sugar to the carbon bearing the OH group of another sugar

In a glycosidic linkage, which carbons are joined?

Proteoglycans primarily consist of glycosaminoglycans (long, unbranched polysaccharide chains)

Glycoproteins consist mainly of short, branched oligosaccharide chains

What’s the difference between glycoproteins and proteoglycans?

N-linked or O-linked

What are the two ways that sugars attach to proteins?

Asn side chain and the reducing end of the sugar molecule

In an N-linked glycoprotein, what two things are attached?

Ser or Thr side chain and the reducing end of the sugar molecule

In an O-linked glycoprotein, what two things are attached?

They have a negative charge that attracts a lot of water to make give them the gel-like, shock-absorbing properties

What gives glycosaminoglycans their properties in the matrix?

a carboxyl head group with a long hydrocarbon tail

What is the structure of a fatty acid?

one glycerol backbone attached to three fatty acid tails via ester bonds

What is the structure of a triacylglyercol?

less fluidity / higher boiling point

What is the effect of a fatty acid having a long chain on the amount of fluidity and the boiling point?

more fluidity / lower boiling point

What is the effect of a fatty acid having a short chain on the amount of fluidity and the boiling point?

They store energy without extra water weight because they are hydrophobic, as compared to glycogen.

Their structure allows them to pack tightly in adipose cells

Why do triacylglyercols store energy so well?

a phosphate head with a hydrocarbon (fatty acid) tail

What is the structure of a phospholipid?

a glycerol backbone connected to a phosphate head group and two fatty acyl groups

What is the structure of a glycerophospholipid?

sphingosine backbone connected to a head group and one fatty acyl group

What is the structure of a sphingolipid?

a sphingosine but with an extra fatty acid chain joined by an amide linkage

What is the structure of a ceramide?

ceramides with one or more sugars in beta-glycosidic linkage at 1-hydroxyl-group

What is the structure of glyosphingolipids?

glycosphingolipids with one sugar residue

What is the structure of cerebrosides?

sialic acid + other sugars

What is the structure of gangliosides?

isoprene units (isoprene is 2-methyl-1,3-butadiene)

What is the unit that builds terpenes?

terpenes

What is the unit that builds cholesterol?

D-glucose

What monosaccharide is this? (Include D or L in your answer)

D-fructose

What monosaccharide is this? (Include D or L in your answer)

D-galactose

What monosaccharide is this? (include D or L in your answer)

micelle

Will a cone-shaped lipid form a bilayer or micelle?

bilayer

Will a cylinder-shaped lipid form a bilayer or a micelle?

It allows the membrane to have different properties on its two sides.

Why is lipid asymmetry between leaflets important?

Loosely; high salt concentrations or mild detergent treatment

Are peripheral proteins loosely or strongly associated to the membrane? Because of this, what can be used to extract them from the membrane?

Strongly; organic solvents or strong detergents

Are integral proteins loosely or strongly associated to the membrane? Because of this, what can be used to extract them from the membrane?

simple diffusion

a type of passive transport where small, nonpolar molecules just pass right through the membrane

facilitated diffusion

a type of passive transport where large, polar, or charged molecules pass through either a transporter (open on one end, then closed entirely, then opens on the other end) or a channel (open both ends always)

primary active transport

transport against a solute’s concentration that requires energy directly from ATP hydrolysis

secondary active transport

transport against a solute’s concentration that needs energy, but uses the energy from another solute going down it’s concentration gradient; uses a coupled transporter

yes, because if you add enough solute, eventually all of the channel / carrier proteins will be full

Does facilitated diffusion saturate?

yes, because if you add enough solute, eventually all of the channel / carrier proteins will be full

Does primary active transport saturate?

yes, because if you add enough solute, eventually all of the channel / carrier proteins will be full

Does secondary active transport saturate?

no

Does simple diffusion saturate?

pumps 2 K+ in and 3 Na+ out so that they naturally want to move the opposite way they are pumped. This gradient has stored potential energy

How does the Na+ / K+ ATPase build a gradient?

Example: Glucose is able to enter a cell against ITS concentration gradient because Na+ also enters that same cell going with ITS concentration gradient

How does a symporter spend the energy stored in a gradient?

Sodium Potassium pump is not able to maintain low intracellular Na+, and then glucose is not able to enter the cell via symport with Na+

What happens if the pump is blocked?

cytidine

What is the name for a cytosine nucleoside on ribose?

deoxycytidine

What is the name for a cytosine nucleoside on deoxyribose?

uridine

What is the name for a uracil nucleoside on ribose?

thymidine

What is the name for a thymine nucleoside?

adenosine

What is the name for an adenine nucleoside on ribose?

deoxyadenosine

What is the name for an adenine nucleoside on deoxyribose?

guanosine

What is the name for a guanine nucleoside?

inosine

What is the name for a hypoxanthine nucleoside?

Nucleotide has phosphate group, sugar, and nitrogenous base

Nucleoside doesn’t have a phosphate

What’s the structural difference between a nucleoside and nucleotide?

5’ to 3’

In what direction does nucleic acid synthesis proceed (from what prime to what prime?)

the 3’ OH of one sugar connects to the 5’ phosphate of the next nucleotide

Between what two parts of nucleotides is the phosphodiester bond?

260 nm

At about what wavelength do bases strongly absorb UV light?

they have aromatic structures, and aromatics can absorb UV light

How are nitrogenous bases able to strongly absorb UV light?

They allow proteins to read DNA sequence without opening the helix

Why are major and minor grooves in DNA’s double helix important?

topoisomerases

What are enzymes that temporarily break DNA strands and then reseal them to introduce or remove supercoils?

type 1 topoisomerase

type of topoisomerase that cuts 1 strand and doesn’t require ATP

type 2 topoisomerase

type of topoisomerase that cuts 2 strands and requires ATP

DNA gyrase in bacteria that adds negative supercoils

What is an example of type 2 topoisomerase?

sticky ends

What does EcoR1 produce?

restriction enzymes

enzymes that cut DNA at a specific recognition site?

3

How many carbons must an aldose have for it to have a chiral center?

4

How many carbons must a ketose have for it to have a chiral center?

diastereomers

What category do epimers and anomers fall under?

On a fischer projection, it’s the carbon that contains the OH that you look at when determining D or L configuration

What is the penultimate carbon?

ketose

Is fructose a ketose or aldose?

aldose

Is glucose a ketose or aldose?

aldose

Is galactose a ketose or aldose?

Look at C5 (ring carbon to the left of the oxygen); if the CH2OH group is up, it’s D; if the CH2OH group is down, it’s L

How do you know if a monosacharide is D or L if it’s in a Haworth projection?

beta-glucose

What are the subunits found in cellulose?

alpha-glucose

What are the subunits found in amylose?

alpha-glucose

What are the subunits found in amylopectin?

alpha-glucose

What are the subunits found in glycogen?

1-4

What are the bonds in cellulose?

1-4

What are the bonds in amylose?

1-4 and 1-6

What are the bonds in amylopectin?

1-4 and 1-6

What are the bonds in glycogen?

amide linkage

What type of bond connects a fatty acid to a sphingosine in a ceramide?

An example of a terpene that is an antioxidant and a red pigment in foods like tomatoes

What is lycopene?

an example of a terpene that is a precursor to cholesterol

What is lanosterol?

inner; functions as an “eat me” apoptotic signal

Is phosphatidylserine found in the inner or outer leaflet? What are its functions?

outer; builds cell membranes, support liver / brain / gut function

Is phosphatidylcholine found in the inner or outer leaflet? What are its functions?

The 2’ OH group on RNA promotes alkaline hydrolysis; DNA, however, doesn’t have this OH group (because it’s DEoxy) so it’s more stable in basic conditions

Why is RNA less stable than DNA in basic conditions?

alpha is the phosphate right next to the sugar, beta is the next one to the right, and gamma is the one furthest to the left.

In dNTP, which phosphates are the alpha, beta, and gamma?

Because of their aromatic character

Why are purines and pyrimidines insoluble on their own?

They become incorporated into a hydrophilic, charged sugar-phosphate backbone

How do purines and pyrimidines become soluble with DNA or RNA?

260 nm

What wavelength absorbs DNA best?

280 nm

What wavelength absorbs proteins best?

tryptophan and tyrosine

Which amino acids in proteins is largely responsible for their ability to absorb wavelength?

supercoiled state

the state that DNA may be in if it has more or less than 10 base pairs per turn

positive supercoiling

When DNA is overwound

negative supercoiling

When DNA is underwound

11

How many base pairs per turn is A-form DNA?

10

How many base pairs per turn is B-form DNA?

12

How many base pairs per turn is Z-form DNA?

right

Is A-form DNA right or left handed?

right

Is B-form DNA right or left handed?

left

Is Z-form DNA right or left-handed?

snRNA

What type of RNA functions in various nuclear processes?

snoRNA

What type of RNA facilitates chemical modifications of RNAs?

miRNA and IncRNA

What type of RNA regulates gene expression?

siRNA

What type of RNA silences gene expression