Biochemistry Final Exam

Thermal noise

Random movement of molecules. Increases with increasing temperature.

What makes water a good solvent for biochemical molecules?

Thermal noise: water molecules "bump" other molecules.

Why are nonpolar solutes driven together in water?

Not primarily because they have a high affinity for each other, but because clumping together allows water molecules to be free and disordered. If nonpolar solutes are separate, water has to form cages around them and water molecules are not free to be spontaneous. In short, when they associate, water molecules are released.

What powers membrane formation?

The hydrophobic effect. Membranes are made of amphipathic molecules.

Amphipathic molecules

Have hydrophobic group and hydrophilic group. Ex: hydrophobic tails and hydrophilic heads.

What powers protein folding?

Hydrophobic effect

Auto

ionization

What is the relationship between H+ and pH

Larger H+ concentration means lower pH

What is max buffering capacity?

pH = pKa

Buffering range

pKa +/

What are the four types of biological molecules?

Nucleic acids, amino acids, carbohydrates, and lipids.

Nucleoside

Nitrogenous base and 5C sugar but NO phosphate group.

Nucleotide

Nitrogenous base, 5C sugar, and at least 1 phosphate group.

How do ribose and deoxyribose differ?

Ribose has 2

Pyrimidine

1 member ring: C and T.

Purine

2 member ring: A and G.

Diphosphate

2 phosphates linked to each other.

Biphosphate

2 phosphates not directly linked to each other.

DNA bases

ATCG

RNA

AUCG

Enol

Alcohol group next to a double bond

Keto

N

How can change in H

bonding introduce mutations in DNA and RNA strand?

How are nucleotides joined?

Phosophodiester bonds

What end of DNA is free phosphate connected to?

5' C on sugar

What end of DNA is free

OH group connected to?

What makes up a phosphodiester bond?

Phosphate esterfied to two ribosome units.

Compare nucleotide to a nucleotide residue

Nucleotide is a sequence that contains information, individual resides do not

How many H--bonds between A and T?

2

How many H-bonds are between C and G?

3

Chargaff's rule

A=T and C=G, only applies to double stranded DNA

Watson and Crick bps

A

Major groove

Place for protein to fit and bind.

What factors contribute to helix stability?

Hydrophobic effect, charge repulsion, H

Diploid

Half set of DNA from both parents

How do Eukaryotes package DNA?

Chromosomes

What makes up chromatin (histones)?

DNA + protein

Is there more RNA or DNA?

RNA

What are the three major types of RNA?

Ribosomal, messenger, and transfer

Ribosomal RNA

Most abundant, associates with ribosomes (enzyme that is not a protein)

Messenger RNA

Carries transient message for protein synthesis from DNA to ribosomes. Each molecule of mRNA encodes a single gene (one type of polypeptide product).

Transfer RNA

Smallest nucleic acids. Form ester bonds with specific amino acids for protein synthesis.

Is RNA single or double stranded?

Single

How are stem loops formed?

Bases pair with themselves (in same strand)

What is the difference between thymine and uracil?

2

Why is rRNA short-lived?

Less stable because very reactive because of hydroxyl group (compared to DNA).

Can multiple tRNA's correspond to each anti-codon (AA)?

Yes

What does a scissile do?

Cuts!

Central dogma of molecular biology

DNA (replication)

Okazaki fragments

On one strand of DNA, it is difficult because it cannot add to the 3' end. SO.. must replicate in fragments (once DNA is unwound).

What is the link between DNA and Enzymes?

RNA

Wobble rule

Multiple codons code for the same AA (3rd position only). This helps make up for mistakes. If strand is slightly flawed, same AA can be coded for.

What is the overall sequence strategy for nucleic acid sequencing?

Break nucleic acids into smaller pieces (w/ restriction enzymes), determine the sequence of each, figure out the order of the pieces based on overlap.

What are some examples of portions of genes that do not get transcribed into RNA?

Promoter and enhancer regions and regions between DNA

What is the function of restriction endonuclease?

Cleave DNA at a specific sequence

What are "blunt ends"?

Sequences with no bps hanging off

What are palindromic sequences?

Read same front to back. Restriction enzyme targets these sequences.

What is the purpose of "sticky ends"?

Sticky ends make things easier when inserting a gene. Cutting smaller sections is easier to sequence and sticky ends can bp to each other and get connected by ligase.

Why can electrophoresis determine size?

Size is a controlled variable. Charge density, shape, and diameter are uniform and consistent between DNA. The only difference between bands is size!

How can you tell DNA size through electrophoresis?

The heavier (bigger) DNA moves slower through the gel, so is closer to the top. The lighter (smaller) DNA moves faster through the gel, so is closer to the bottom.

How do electrophoresis bands help you determine amount of bps in DNA?

Use a marker that you already know base pairs for to compare other bands to.

What is first way DNA was sequenced?

Sanger method

What enzyme does the Sanger method use to make complementary copies of a single stranded DNA?

E. coli DNA polymerase I

What are dideoxynucleosidetriphosphates used for in the Sanger methods?

They are used for different versions of the genes. "Special nucleotides"

In the Sanger method, what does peak tell you?

Nucleoside

In the Sanger method, what does color tell you?

Base

Is Sanger method good for large sequences?

No, only good for ~1,000 nucleosides

What method of next-gen sequencing is best for around 1,000,000 nucleotides?

Pyrosequencing

What method of next

gen sequencing is best for around 200 nucleotides?

What percentage of the human genome is various repeated sequences?

~50%

What percentage of human genome is transcribed into RNA?

80%

What percentage of human genome encodes for proteins?

1.2%

How many nucleotides out of 1000, does the average two people differ in?

1

Point mutation

Single nucleotide error caused by errors in replication, chemicals, radiation

Recombination

Exchange of DNA between chromosomes

Transposition

Movement of genes with or between chromosomes

Phenotype

Physical characteristics

Are most diseases caused by 1 gene or multiple genes?

Multiple

What accounts for most of the difference between human genomes?

Single Nucleotide Polymorphism

What does recombinant DNA technology allow us to study?

Specific DNA sequences

How do we obtain (amplify) DNA?

Fragment of DNA of appropriate size is generated by a restriction enzyme by PCR or chemical synthesis, fragment is incorporated into a vector (another DNA molecule), and cell containing desired DNA are selected.

Vector

Circular DNA that contains gene of interest

How to use antibiotic resistance vectors to test whether desired DNA is present?

Put vectors in antibiotic and whichever ones grows are the ones with the gene of interest because survived antibiotics.

Plasmids

Circular DNA molecules found in bacteria or yeast

Why are plasmids used for lab?

Small, replicate easily, carry genes for antibiotic resistance, and have many recognition sequences for restriction enzymes.

How to use the lac promoter to test whether desired DNA is present?

Grow colonies on plate (blue before you insert gene), if you insert a gene it will disrupt enzyme and will be colorless.

PCR

Makes tons of copies of gene of interest

Steps of PCR

Heat to separate strands, cool so primers can bind to complementary sequences, heat a little so DNA polymerase (usually Tac polymerase) will make copies, repeat x30.

Amino acids

Subunit of proteins

How many amino acids are incorporated into proteins?

20

How do amino acids differ?

R

Physiological pH

7.4

Are amino acids chiral or achiral?

Chiral

Chiral

Central C has four different groups, cannot be superimposed

Which amino acid is not chiral?

Glycine because H is side chain

Do enzymes in body use D or L configuration?

L

"L"

Most important group on left

"D"

Most important group on right

Are L&D and R&S related?

Nope

What is the only R amino acid?

Cystine because side chain has higher priority than COO