Biochemistry Midterm

Front 1

What are the different types of reactions? How many are there?

Back 1

6 different types
Bond formation
Oxidation Reduction
Group Transfer
Isomerization
Nonhydrolitic Cleaving
Hydrolysis

Front 2

What goes on in the Bond Formation Reactions?

Back 2

Uses energy from ATP

Joining of two molecules. A carbocation attacks a partial positive carbon center to form a new bond b/t the molecules. Catalyzed by synthetases and ligases.

Front 3

What goes on in the Oxidation Reduction Reactions?

Back 3

involves the transfer of electrons from a molecule being oxidized (the electron donor) to a molecule being reduced (the electron acceptor)- neither oxidation nor reduction can occur without the other
-ethanol is converted to acetaldehyde, and the cofactor, NAD, is converted to NADH

Front 4

What goes on in the Group Transfer Reactions?

Back 4

transferases, move functional groups from one molecule to another

Other transferases move phosphate groups between ATP and other compounds

Occurs via a nucleophilic attack wherein an entire functional group is transferred from a donor to a recipient molecule

Front 5

What goes on in Isomerization Reactions?

Back 5

Isomerases carry out rearrangements when in in many biochemical reactions, the position of a functional group is changed within a molecule
but the molecule itself contains the same number and kind of atoms that it did in the beginning

The substrate and product are isomers and in isomerases rearrange them
Catalyzed by Mutases and isomerases

Front 6

What goes on in Hydrolysis Reactions?

Back 6

hydrolases, break single bonds by adding the elements of water

Water inserts itself and breaks bonds

Front 7

What goes on in Nonhydrolitic Cleaving Reactions?

Back 7

Molecules being split without the use of water. Enzymes called lyases catalyze these reactions and cleavage often occurs at the C-C bond.

Front 8

What are the 3steps in Transcription?

Back 8

Initiation
Termination
Elongation

Front 9

What is the Consensus Sequence?

Back 9

a group of nucleotide or amino acid sequences that show similarity but are not identical
an artificial sequence that is compiled by choosing at each position the residue that is found there most often in the sequences under study
includes the -10 region (Pribnow box) and -35 Region

Front 10

What happens in the Initiation of Translation?

Back 10

Two initiation factors (IF1 and IF3) bind to a 70S ribosome. IF3 and IF1 promote the dissociation of 70S ribosomes into free 30S and 50S subunits. mRNA and a third initiation factor (IF2) bind to a free 30S subunit. After these have all bound, the 30S initiation complex is complete.
The 50S subunit binds to the 30S initiation complex. It contains three sites for tRNA binding, called the P site (peptidyl), the A site (aminoacyl), and the E site (exit).

Front 11

What happens in the Elongation Step of Translation?

Back 11

Three tRNA binding sites on the 70S ribosome are involved in the process.
The nascent polypeptide chain is attached to a tRNA in the P site and the A and E sites are empty. Aligned with the A site is the mRNA codon corresponding to the next amino acid to be incorporated. When the appropriate charged tRNA is depositied into the A site, the GTP is hydrolyzed. Proofreading. Peptide bond formation - The polypeptide chain that was attached to the tRNA in the P site is transferred to the amino group of the amino acid carried by the A-site tRNA. Translocation - The uncharged tRNA remaining in the P site is transferred to the E site and the tRNA in a hybrid P/A state is moved to the P site. As the old tRNA is released from the E site, the empty A site accepts the aminoacyl tRNA corresponding to the next codon. The process is repeated until a termination signal is reached.

Front 12

What happens in the Termination Step of Translation?

Back 12

occurs when one of the stop codons (UAA, UAG, or UGA) appears in the A site of the ribosome.
1. RF1 or RF2 binds to the ribosome near the A site. RF3 binds elsewhere.

2. The peptidyltransferase complex transfers the C-terminal residue of the polypeptide chain from the P-site tRNA to a water molecule, releasing the polypeptide chain from the ribosome.

3. The RF factors and GDP are released.

4. The tRNA is released.

5. The 70S ribosome is now unstable in the presence of a protein called ribosome recycling factors, as well as the initiation factors IF3 and IF1. Consequently, the 70S ribosome dissociates to 50S and 30S subunits and is ready for another round of translation.

Front 13

How is the trp Operon Regulated?

Back 13

Through a CoRepressor-Mediated Negative Control Circuit

Front 14

What does the trp Operson Do?

Back 14

The trp operon encodes a leader sequence and 5 proteins (trpE through TrpA) that synthesize tryptophan
The trp operon consists of five adjacent structural genes whose transcription is controlled from a common promoter - operator regulatory region

Front 15

What does the lac Operon Constitute?

Back 15

An E. coli operon that consists of the three linked structural genes that encode enzymes of lactose utilization
The operon consists of two transcription units. In one unit, there are three structural genes, lacZ, lacY, and lacA, under control of the promoter, plac, and the operator O. In the other unit, there is a regulator gene, lacI, with its own promoter, placI.

Front 16

What is a Operator?

Back 16

A DNA site where a repressor protein binds to block the initiation of transcription from an adjacent promoter

Front 17

What is involved in the Termination of Transcription?

Back 17

Two types of transcription termination mechanisms operate in bacteria: One depends on Rho termination factor
rho is an ATP-dependent helicase
it moves along RNA transcript, finds the “transcription bubble", unwinds the DNA:RNA hybrid and releases RNA chain

Front 18

What is involved in the Elongation of Transcription?

Back 18

Unwinding and rewinding - During elongation the core enzyme moves along the duplex DNA template and simultaneously unwinds the DNA, exposing a single-strand template for base pairing with incoming nucleotides and with the nascent transcript

Front 19

What is Involved in the Initiatio nof Transcription?

Back 19

After RNA polymerase has bound to a promoter and formed an open-promoter complex, the enzyme is ready to initiate synthesis of an RNA chain.
One nucleoside triphosphate binding site on RNA polymerase is used during elongation. It binds any of the four common ribonucleoside triphosphates .

Front 20

What is Transcription Attenuation?

Back 20

Transcriptional attenuation is a regulatory mechanism that causes premature termination of transcription under certain conditions, thereby preventing the expression of the mRNA required for expression of the corresponding gene products. Attenuation typically results from mRNA folding into alternative secondary structures.
negative feedback trp operon

Front 21

What are the Three Different Types of Metabolic Pathways?

Back 21

Linear
Recyclic
spiral

Front 22

What is Cyclic Pathway

Back 22

A metabolic pathway in which a series of steps, each using different enzymes, regenerates one of the early reactants, is a cyclic pathway

Front 23

What is Spiral Pathway?

Back 23

A metabolic pathway in which a molecule is progressively built up/broken by repeated interaction with the same set of enzymes is a spiral pathway.

Front 24

What is Linear Pathway

Back 24

The biosynthesis of serine is an example of a linear metabolic pathway. The product of each step is the substrate for the next step.

Front 25

What is Metabolism?

Back 25

How cells acquire, transform store and use energy. Total sum of all chemical reactions