Chemistry Exam 1

Front 1

what is signal transduction?

Back 1

the process of conversion of information into a chemical change in living cells

Front 2

what is specificity (in relation to features of a signal-transducing system)?

Back 2

signal molecule fits binding site on its complementary receptor; other signals do not fit. achieved by precise molecular complementarity between the signal and receptor molecules.

Front 3

what's a ligand?

Back 3

an activator of a receptor that's specific to that receptor

Front 4

what is PDE?

Back 4

the enzyme responsible for degrading cAMP to AMP

Front 5

steps of receptor coupled to phospholipase C (alpha1)

Back 5

(1)signal molecule binds to G-protein linked receptor (e.g., alpha1 receptor)
(2) binding of G-protein linked receptor produces activated Gq alpha subunit
(3) this activates phospholipase C (PLC)
(4) activated PLC splits PIP into IP3 and DAG
(5) DAG activates PKC and IP3 stimulates IP3-gated Ca2+ release channel to open and allow Ca2+ out of lumen of ER

Front 6

what is PKC?

Back 6

PKC (protein kinase C) is a Ca2+ activated enzyme

Front 7

Adrenergic signaling for beta receptor

Back 7

(1) epi/NE binds with receptor
(2) Gs stimulates adenylate cyclase to help ATP --> cAMP

Front 8

Adrenergic signaling for alpha 2 receptor

Back 8

(1) epi/NE binds with receptor
(2) Gi inhibits adenylate cyclase, so ATP --> cAMP is inhibited

Front 9

Adrenergic signaling for alpha 1 receptor

Back 9

(1) epi/NE binds with receptor
(2) Gq activates phospholipase C (PLC)
(3) PLC helps PIP split into IP3 and DAG and release of Ca2+

Front 10

process whereby DNA is made into RNA

Back 10

transcription

Front 11

process whereby RNA is made into protein

Back 11

translation

Front 12

what's a codon?

Back 12

three adjacent nucleotides that code for an amino acid

Front 13

common amino acid

Back 13

those amino acids for which at least one codon exists in the genetic code

Front 14

derived amino acid

Back 14

formed by enzymatic reaction on a common amino acid after that amino acid has been incorporated into a protein structure. usually one functional group is replaced with another.

Front 15

quaternary structure

Back 15

two proteins loosely linked, interact together functionally

Front 16

residue (in chemical terms)

Back 16

a building block, or functional unit. (e.g., nucleotide is residue in relation to amino acid)

Front 17

what does 'protein' refer to?

Back 17

a molecule composed of >50 amino acids

Front 18

what does 'peptide' refer to?

Back 18

a molecule composed of <50 amino acids

Front 19

four components of a common amino acid

Back 19

(1) a carboxylic acid group
(2) an amino group
(3) a hydrogen atom
(4) R group side chain
1-3 are covalently bonded and common among all common amino acids. what defines each common amino acid is the R group side chain.

Front 20

Which component defines the uniqueness of the common amino acid?

Back 20

the R group side chain

Front 21

which configuration of amino acid (enantiomer) is found in mammalian cells?

Back 21

L enantiomer

Front 22

3 facts about amino acids?

Back 22

(1) amino acids are asymmetric
(2) amino acids are enantiomeric
(3) mammalian cells have L enantiomers only

Front 23

hydrophobicity of amino acid side chain significance?

Back 23

critical for the folding of a protein to its native structure and for stability of the folded protein
hydrophobic usually buried in folded protein structure; most charged side chains occur on the surface of soluble globular proteins

Front 24

example: pKa of 6 and pH of 6. what does that mean?

Back 24

if pKa=6 and pH=6, then half of the molecules are charged and half are uncharged

Front 25

if pKa = pH, how much of an enzyme's potential activity is exhibited?

Back 25

if pKa=pH, then the enzyme exhibits 50% of its potential activity

Front 26

what is phosphorylation?

Back 26

an addition of a phosphate group from ATP to OH group on a serine, threonine, or tyrosine (by a kinase). adds negative charge to an aa, which alters structure, which then alters function

Front 27

what's the importance of the cysteine bond?

Back 27

important role in stabilizing the folded conformation of proteins

Front 28

what determines primary structure?

Back 28

dictated by the aa sequence. similar aa sequence usually means similar structure and functioning

Front 29

Name two components characteristic of RNA

Back 29

CAP a the 5' end

Poly(A) tail at the 3' end

Front 30

what is a gene?

Back 30

a section of DNA that contains the recipe for how to make a particular protein

Front 31

what composes ribosomes?

Back 31

ribosomal RNA (rRNA) and proteins

Front 32

what is the function of ribosomes?

Back 32

ribosomes function as the site of protein synthesis/they coordinate RNA synthesis

Front 33

where are ribosomes located?

Back 33

in the cytoplasm

Front 34

what do tRNAs do?

Back 34

tRNA interacts with amino acids to assist the ribosome in protein synthesis

Front 35

what is transcription?

Back 35

the process used when getting the genetic code of a gene to messenger RNA (mRNA)

Front 36

transcription is carried out by ___

Back 36

RNA polymerases

Front 37

Four characteristics of RNA polymerases?

Back 37

primer independent
DNA dependent
no proofreading ability
dependent on DNA characteristics for binding and initiation of transcription

Front 38

what does it mean to say a gene is 'turned on'?

Back 38

it is being actively transcribed

Front 39

what is a transcription complex?

Back 39

a multi-protein complex including RNA polymerase and other proteins that recognizes particular promoter sequences of the DNA that are at the beginning of the sequence to be transcribed.

Front 40

what does 'active chromatin' refer to?

Back 40

areas of DNA that are relaxed so that the RNA polymerase complex can bind to the promoter of a particular gene

Front 41

what are transcription factors?

Back 41

proteins which bind to specific sequences in the DNA of particular genes to help produce relaxation of the DNA

Front 42

what are upstream activator sequences? enhance sequences?

Back 42

the particular DNA sequences that transcription factors bind to. upstream activator sequences are upstream of the coding region, while enhancer sequences can be anywhere in relation to the coding region

Front 43

what are the two primary determinants of which genes should be transcribed in eukaryotes?

Back 43

the combination of specific transcription factors and the relaxed state of a DNA region

Front 44

what does RNA polymerase II do?

Back 44

it synthesizes mRNA in the nucleus

Front 45

which of the three types of RNA polymerase is most important? (according to our professor)

Back 45

RNA polymerase II

Front 46

what are TATA box and CAAT box examples of?

Back 46

consensus start sequences (promoters) recognized by RNA polymerase II

Front 47

what does RNA polymerase I do?

Back 47

it synthesizes ribosomal RNA (rRNA) from multiple sites on multiple chromosomes

Front 48

why are rRNA 'genes' not really genes?

Back 48

they don't direct the synthesis of proteins; they are used for a function, but not made into a protein

Front 49

What does RNA polymerase III do?

Back 49

it synthesizes tRNAs and one type of rRNA (5s)

Front 50

if two strands of DNA are written one above the other, what does the top strand represent?

Back 50

the DNA coding strand (aka 'sense' strand)

Front 51

if two strands of DNA are written one above the other, what does the bottom strand represent?

Back 51

the DNA template strand (aka anti-coding or antisense strand)

Front 52

which strand of DNA is used in mRNA synthesis

Back 52

the non-coding (aka "template") strand. It is used to make a complementary copy that is identical to the DNA coding strand.

Front 53

what causes the unwinding and rewinding of DNA?

Back 53

topoisomerases

Front 54

what is one way the cell can distinguish between the different kinds of RNA?

Back 54

the CAP tells the cell it is mRNA as opposed to tRNA or rRNA

Front 55

what are small nuclear ribonucleoproteins (snRNPs)?

Back 55

enzymes composed of both RNA and protein that recognize sequences of intron-exon junctions and splice out introns

Front 56

what is "exon shuffling"?

Back 56

when one gene can be used to form different proteins based on which exon is spliced out. Example, one gene can be used to make the protein calcitonin or the protein CGRP depending on which exon is spliced out.

Front 57

what conditions must be met before RNA can be exported from the nucleus?

Back 57

RNAs must be bound to proteins
ribosomal subunits are formed prior to export
mRNAs are exported bound to cap-binding proteins and other proteins

Front 58

in what two ways can transcription factors have an effect?

Back 58

they can promote transcription by opening up the DNA structure, or they may inhibit transcription by blocking binding of the transcription initiation complex

Front 59

what is an aminoacyl transferase?

Back 59

an enzyme that attaches a particular amino acid to its particular tRNA

Front 60

what is the significance of the following codons: TAA, TAG, TGA

Back 60

they are 'stop' codons. They tell the ribosome to stop synthesizing the protein

Front 61

what are the five steps in protein synthesis?

Back 61

1. activation of amino acids (aminoacyl-tRNA synthase)
2. initiation (assembly of the ribosomal subunits at the initiation codon)
3. elongation (addition of subsequent amino acids to the nascent protein)
4. termination and release (reaching stop codon)
5. protein folding and post-translational processing (necessary for protein function)

Front 62

what tells the ribosome to terminate translation?

Back 62

reaching a 'stop' codon.

Front 63

what can be called the 'workbench for assembling proteins'?

Back 63

the ribosome

Front 64

what does AUG represent?

Back 64

AUG is the initiation codon in most situations.

Front 65

how does elongation work?

Back 65

each tRNA brings its amino acid to the ribosome and base-pairs its anticodon with the mRNA's codon. Then the ribosome attaches the growing amino acid chain to the new amino acid
The tRNA for the next-to-newest amino acid detaches from the ribosome and it moves down to the next codon.

Front 66

what are elongation factors (EFs)?

Back 66

energy-transferring molecules used in the sliding of the ribosome down the mRNA and in the activation of the tRNA-amino acid complexes

Front 67

does the ribosome have proofreading ability?

Back 67

it has proofreading ability for base-pairing but not for amino acid sequence

Front 68

does RNA polymerase have proofreading ability?

Back 68

no.

Front 69

what creates the biggest mistake in protein synthesis?

Back 69

if the DNA has the wrong sequence, then every molecule of mRNA synthesized from that DNA will be wrong and so will every protein molecule. But, if the second copy of the gene was OK, then only half of the protein would be wrong

Front 70

what is the "wobble" position?

Back 70

the 3rd base position. it may encode the same amino acid and make no difference at all

Front 71

what is a point mutation?

Back 71

a single base change

Front 72

what is a silent mutation?

Back 72

a change in one base (a point mutation) that specifies the same amino acid. Includes change in base at the "wobble" position

Front 73

what is a missense mutation?

Back 73

a change in one base that specifies a different amino acid (e.g., CGA (Arg) --> CCA (Pro))

Front 74

what is a nonsense mutation?

Back 74

a change that produces a stop codon (e.g., CGA (Arg) changed to UGA (stop))

Front 75

what do you call people whose two genes are identical?

Back 75

homozygotes

Front 76

what happens if a homozygote has abnormal genes?

Back 76

will probably see symptoms because none of the person's protein is formed correctly (example: sickle cell disease vs. sickle cell trait)