PROTIEN STRUCTURE

what type of bonds link amino acids together?

peptide bonds - hydrogen bonds

what bonds are in proteins? What chemicle reaction forms these bonds?

Peptide bonds are formed by condensation reaction

What is the structure of an amino acid?

central carbon with Rgroup/side chain, amino group (NH₃), carboxyl grop (COO-) & and H+ 

what important function do proteins have? 

Structural components in cells, signaling molecules, antibodies, enzymes, & transport

why are polar amino groups polar?

Because they have polar side groups like hydroxyl (OH), Amino (NH₃), & methylene (CH₂) 

charactaristics of non-polar side groups

hydropohobic → van der walls interactios

how will charged polar groups inpact the tirtiary strcuture of proteins?

• hydrophilic, in aqueous environment cause the protein to fold so they are on the outside. 

• interact w/ other charged side groups (hydrogen bonds)

what types of bonds from the tirtiary structure?

hydrogen, van der waals, ionic, disulfide bonds

what types of bonds form the secondary structure?

localized hydrogen bonds → alpha helixes & beta sheets 

what are disulfide bonds?

intramolecular covalent bond btw 2 Sulfurs in cystine groups.

• 2 cystine (SH) groups form a covelent bond btwn the Sulfur acts as a bridge and create an excess H_{2 in the process}

what are ionic bonds

complete transfer of e- from one atom to another

when dose the central dogma not hold true?

Viruses who use reverse transcriptase to go from viral RNA to DNA

How do we get from DNA → RNA?

RNA is transcribed into DNA

How do we get from DNA → protein? (simple)

The DNA is translated into Amino acid sequence, and the r group sof that sequence interact w/ each other and fold

Explain the difference btwn ionic, polar covalent, and non polar covalent bonds

Ionic: one electron transfers electrons to the other (non-covelent)

polar: Unequal sharing of electrons: the more electronegative nucleus attracts e^- more 

nonpolar: equal sharing of electrons = not charged 

what dose it mean to be more electronegative?

To have a posotive charge therfore you attract negative molecules

Covelent vs non covelent

covelent bonds include shareing of electrons in some way non covelent are wearker interaction betwn molecules

why is it important that water is a good solvent in living systems?

because it allows for nutrients to dissolve so the body can use them for other thigns: vital for the formation of macromolecules 

polarity of water gives it what properties?

Good solvent, high heat capacity, cohesion, and ice is less dense 

examples of hydrogen bonding in living systems: 

the secondary structure of Proteins 

DNA Secondary structure

Water’s cohesion

what is the lifecycle of viruses?

entry - binding or insertion 

Replication - w/ host’s material 

transcription & make capsid proteins  - uses host’s transcriptase and 

self assembly of new virus - capsid around genome

exit - phagocytosis or bursting (→ lysis) or budding 

are virusis living? why?

viruses are not living because they are unable to replicate without the use of host’s material 

what is the polarity of DNA?

5 prime end = Phosphate group, binds to the 5th carbon

3 prime end = H on the 3rd carbon of the deoxyribose (differentiates it from ribose who has an OH)

how dose polarity of DNA connect to the function of polymerase?

polymerase can only add nucleotides in the 5’→3’ direction

what type of bond holds together DNA’s secondary structure? (the nitrogenous bases) and which is stronger?

Hydrogen bonding
Bonds between Gunine and cytosine = stronger because they have 3 bonds compared to adenine & thymine’s 2 

why must the DNA strands be antiparalell?

The unifrom structure of DNA only holds true if the backbones are antiparallel to eachother

what contributes to the regular shape of DNA helix?

the pairing of purines with pyrimidines makes the width consistent

what dose “semi conservative replication” refers to?

the way DNA replicates: by splitting he dna in half, then DNA polymerase adds complimentary nucleotides in the 3 → 5 prime direction on the leading strand then on the lagging strand. this way the original dna is “semi-conserved” because it uses half in the new molecule 

Why are sugar’s polar? 

Sugar’s are highly soluble because sugars have a lot of hydroxyl groups. Since oxygen is highly  OH group and another end with an Oxygen and therefore are able to hydrogen bond with H₂O easily 

why is sugar polar?

because it has alot of polar groups with oxygen in it, since the oxygen is more electronegative it pulls torwds it’s nucleus more and

Why do alpha glycosidic linkages resist less hydrolysis than beta linkages? 

Becuase human’s dont have the right enzyme to break down beta glycidic linkages

what are the two forms that linear gklucose can convert to? which is stronger?

Alpha or beta glycidic linkages

beta linkages are stronger

what is the difference between alpha and beta glycidic linkages? 

beta glycidic linkages once of the glucoses is flipped in alpoha they both face same direction. Besides thies alpha and beta libnk on the 1 and 4 carbon

Since sugar’s are made from the same molecules what differentiates them?

the diffent monomers used & orientation of respective monomers due to beta/alpha linkages

what is glycogen? and why dose it funtion the way it dose?

a type of polysaccharide that is used to store energy in animals because it has lot of glycocidic bonds

why is glycogen water insoluble?

because the size of it means it has lots of bonds un hydrogen bonds w/in it → not alot of free OH groups for wate rto bond to 

How dose structure relate to shape and function for carbohydrates?

the type of covalent bond (beta vs alpha) gives the molecule different shapes. for example having lots of beta means the polymer is mostly unbranched and has a stronger and more uniform structure than if it were to be mostly alpha links 

 

How do the α and β forms of glucose differ?

the orintation of a Hydroxyl group

why would you not expect glycogen to be found in a cell wall?

Because glycogen has lots of Aplha linkages meanign its structure isnt uniform enough or string enough to be prefered for building a cell wall