Exam 1 Material (water, biomolecules, nucleic acids, lipids)

How many covalent bonds can Carbon have?

4

How many covalent bonds can Hydrogen have?

1

How many covalent bonds can Oxygen have?

2

How many covalent bonds can Nitrogen have?

3

How many covalent bonds can Phosphorus have?

5

How many covalent bonds can Sulfur have?

2

Name the 5 categories of biomolecules

1. Nucleic acids

2. Lipids

3. Carbohydrates

4. Amino acids and proteins

5. Vitamins, hormones, and co-factors

What are the 2 types of nucleic acids?

deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

Whats are the 4 different types of lipids?

fatty acids, triglycerides, phospholipids, and cholesterol

What are 3 properties of hydrogen bonding

1. intermolecular

2. non-covalent

3. electrostatic

What can water H-bond with?

other molecules containing oxygen, nitrogen, and other electronegative atoms

What are the 4 parts of a phospholipid

fatty acid, glycerol backbone, phosphate, and alcohol

What is this molecule

phospholipid

What do amphipathic molecules form in aqueous solution?

micelles and bilayer membranes

Why are liposomes useful for transfection?

liposomes protect genetic material from degradation and their positive charge allows for promotion of uptake with the negatively charged cell membrane via pinocytosis

What is the pH equation

pH = -log[H+]

What does a cell employ to resist pH change?

buffering

What is the definition of pKa

the pH at which an ionizable molecule is 50% deprotonated

How does acetate act as a buffer

Since the conjugate base of a strong acid will NOT take the proton back, acetate (the conjugate base of a weak acid) serves as a place holder taking the protons lost by the strong acid which prevents large changes in pH.

At what pH do buffers function best?

Their pKa

What is an equivalence point

the point where the moles of added base equals the initial moles of acid

What is the Henderson-Hasselbach equation?

pH = pKa + log([A-]/[HA]) or [A-]/[HA] = 10^pH-pKa

What in the human body requires buffering and why?

Blood since hyperventilation can cause respiratory alkalosis and hypoventilation can cause respiratory acidosis

What acts as a buffer to blood?

carbonic acid

Answer the following question

3

Answer the following question

C - be mostly deprotonated

A. Deoxyadenosine triphosphate

B. Guanosine monophosphate

C.Uracil diphosphate

D. Uracil monophosphate

E. Deoxythymidine monophosphate

F. Deoxyguanosine monophosphate

E. Deoxythymidine monophosphate

What is negentropy

the decrease of entropy, increased order

How do living things combat their thermodynamic breakdown (increase of entropy)?

extracting energy from high order states in their environment (must do this due to the second law of thermodynamics)

Why is DNA an aperiodic crystal?

their genetic information is conveyed through an irregular pattern

Is the rough strain of pneumococcus virulent or nonvirulent?

nonvirulent

Is the smooth strain of pneumococcus virulent or nonvirulent?

virulent

Why does a mouse with a mixture of the rough strain and heat-killed smooth strain die?

The DNA which contains the genetic information of the virus was not killed by the heat and was able to replicate with the rough strain

How would one be able to abolish the virulent effect in a virus?

Treat the virulent strain with a DNA specific endonuclease

What is the process of DNA being copied into RNA called?

transcription

What is the process of RNA being read by ribosomes in order to make a protein called?

translation

What is all the genetic information in a cell called?

genome

What are all the RNA molecules in a cell called?

transcriptome

What is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time called?

proteome

What is the name of the genome, transcriptome, and proteome all working together called?

metabolome

What are the 4 biochemical functions of nucleotides

1. building blocks of DNA and RNA

2. energy unit (ATP or GTP)

3. involved in biosynthesis (UDP glucose in glycogenesis)

4. signal transduction

cAMP to activate proteins, ATP provides phosphate in phosphorylation, and adenosine binds to sleep promoting adenosine receptor

What part of the nucleotide is labelled 1

the 5' carbon bonded phosphates

What part of the nucleotide is labelled 2

the 5-carbon sugar (ribose here)

What part of the nucleotide is labelled 3

the nitrogenous base (adenine here)

Name this structure

Ribose

Name this structure

Deoxyribose

Name this structure

Adenine, purine

Name this structure

Guanine, purine

Name this structure

Thymine, pyrimidine

Name this structure

Uracil, pyrimidine (mostly in RNA)

Name this structure

Cytosine, primidine

Whats the difference between adenine and adenosine?

adenine is just the base and adenosine has the base and the sugar (nucleoside)

What kind of bond is shown in this polymer?

phosphodiester bond

What direction are DNA bases written in?

5' -> 3'

What direction is the complimentary DNA strand in?

antiparallel

What is shown below

Adenine and thymine base pair

What is shown below

Guanine and cytosine base pair

What is a stronger pair?

adenine and thymine or cytosine and guanine

cytosine and guanine (3 H-bonds)

What shape is DNA

a chiral, right handed helix

What are the 3 forms of DNA?

Alpha: dehydrated

Beta: hydrated

Z: complexed with proteins

How could one reversibly melt DNA strands?

Adding base to an aqueous solution to disrupt the H-bonds

What did the Meselson-Stahl Experiment show?

That DNA replication is semi conservative

How did the Meselson-Stahl Experiment work?

Using E. coli bacteria and heavy (¹⁵N) and light (¹⁴N) nitrogen isotopes, the experiment demonstrated that after one generation, DNA molecules were a hybrid of heavy and light isotopes, confirming the semiconservative mechanism

How do eukaryotes pack so much DNA in their nucleus?

DNA is wrapped around histones which organize into nucleosomes. These form condensed chromatin which forms chromatids then chromosomes

What kind of chromatin is quiet, closed, and condensed?

heterochromatin

What kind of chromatin is loud and ready to replicate?

euchromatin

What are the ingredients for PCR?

1. DNA template

2. Primers

3. dNTPs

4. Buffer

5. Magnesium ions

What does CRISPR do?

knocks out a gene when and where you want

How many parts does CRISPR have?

2 parts:

1. cas9 nuclease

2. single guide RNA

What kind of nucleotide has a 5' cap and poly(A) tail?

mRNA (messenger)

What is this?

the amino acid attached to tRNA

What is this?

tRNA (transfer)

List the following elements from most electronegative to least: C, H, O, N, P, S

O, N, S, C, H, P

Only, Nancy, Sees, Charlie, Huff, Paint

What percent of the atmosphere is oxygen?

20.9%

What kind of hydrocarbons are fatty acids?

highly reduced aliphatic hydrocarbons

What makes an acid saturated?

When the carbon chain has no double bonds

What is a monosaturated fatty acid?

A fatty acid with one double bond

What is a polysaturated fatty acid?

A fatty acid with more than one double bond

The conjugate base of acetic acid is called....

acetate

At a physiological pH are more acids ionized or deionized

deionized

What configuration is this double bond in?

trans

What configuration is this double bond in?

cis

Which carbon do you start counting from when using the delta notation?

the ACID carbon

What is the delta notation name of this fatty acid

cis-Δ^9-octadecanoate

Which carbon do you start counting from when using the omega notation?

the END carbon

What is the common name of this fatty acid?

linoleate

What is the common name of this fatty acid?

linolenate

What is the common name of this fatty acid?

Arachidonate

What is human's main source of omega-6 and omega-3 fatty acids?

Sufficient amounts of fatty acids must be consumed through diet.

What are eicosanoids?

20+ carbon FAs

What are omega-6 and omega-3 FAs needed to synthesize?

eicosanoids and endocannabinoids

What kind of FA is essential for lipid raft formation?

omega-6 and omega-3 FAs

What kind of FA is essential for activation of transcription factors in the nucleus?

omega-6 and omega-3 FAs

What is after the last arrow?

pro-inflammatory eicosanoids

What is the COX-1 enzyme responsible for?

Converting arachidonic acid into pro-inflammatory prostaglandin D2

What does aspirin block

the action of the COX-1 enzyme

What happens if someone has too many trans-fats in their diets?

It significantly increases the risk of coronary heart disease

Answer this question

A trans-oleic acid

what does linoleic mean?

multiple double bonds

What is this?

glycerol