LM Week 1 Flashcards

Question

What is RNA

Answer 1

The polymer of ribonucleotides Plays many roles in the expression of genetic information

Answer 2

Base+sugar

Answer 3

Purine Adenine Guanine Two heterocyclic rings Only adenine and guanine are commonly found in nucleic acids = found in both DNA and RNA

Answer 4

Pyrimidine Cytosine Uracil Thymine Single rings

Answer 5

DNA = cytosine and thymine RNA = cytosine and uracil

Answer 6

Ribose+base=ribonucleoside Bases are always attached to the 1’ carbon on the sugar OH in the 2’ position

Answer 7

2’deoxyribose+base = deoxyribonucleoside Bases are always attached to the 1’ carbon on the sugar H at the 2’ position instead of the OH in ribose

Answer 8

``` Base = adenine Side = adenosine Tide = adenosine monophosphate (AMP) ```

Answer 9

``` Base= guanine Side = guanosine Tide = guanosine monophosphate (GMP) ```

Answer 10

``` Base = cytosine Side = cytidine Tide = cytidine monophosphate (CMP) ```

Answer 11

``` Base = uracil Side = uridine Tide = uridine monophosphate (UMP) ```

Answer 12

``` Base = adenine Side = deoxyadenosine Tide = deoxyadenosine monophosphate (dAMP) ```

Answer 13

``` Base = guanine Side = deoxyguanosine Tide = deoxyguanosine monophosphate ```

Answer 14

``` Base = cytosine Side = deoxycytidine Tide = deoxycytidine monophosphate (dCMP) ```

Answer 15

``` Base = thymine Side = thymidine Tide = thymidine monophosphate (TMP) ``` Deoxyribonucleosides are named by specifying the deoxy form. An exception is made for thymidine since thymidine is almost always in the deoxy form, the deoxy designation is omitted - so thymidine monophosphate is called TMP even though it contains deoxyribose

Answer 16

G-C A-T So the % of G always equals the % of C and same with A and T = Chargaff rules

Answer 17

The % of G is always equal to C and the % of A is always equal to that of T in DNA base pairing

Answer 18

Phosphodiester bonds

Answer 19

5’—>3’ direction Phosphoester bonds are made by adding nucleotides to the 3’ hydroxyl end of the chain Phosphates are in the 3’ and 5’ position of the sugars

Answer 20

Sugar-phosphate backbone!! The sugar-phosphate backbones have opposite polarities in the two strands

Answer 21

The are lined by potential hydrogen bond donors and acceptors that can interact with proteins and other molecules (not directly involved in base-pairing) DNA binding proteins can recognize specific sequences and bind to them in the groovesz

Answer 22

Two right handed hélices Strands can’t be separated without unwinding the duplex The two strands are anti parallel and complementary in sequences and have opposite polarities

Answer 23

The use of uracil instead of thymine and the use of ribose instead of deoxyribose Made single-stranded and forms complex secondary structures due to formation of double stranded regions (rRNA and tRNA) RNA forms more diverse structures

Answer 24

Hydrolysis The 2’ hydroxyl in the ribose of RNA makes is susceptible of hydrolysis in basic solutions OH- will take the H from the hydroxyl group to make water and leave a negatively charged oxygen on the ribose **DNA is much more stable and suitable for long term storage of genetic information

Answer 25

The double helical structure formed by complementary strands explains the DNA properties of melting and renaturation (hybridization)

Answer 26

DNA —> transcription —> RNA —> translation —> protein *can also have reverse transcription **all these processes depend upon formation of complementary base pairing

Answer 27

Double stranded DNA

Answer 28

An old strand serves as template for the new strand and the old strand remains paired with the new strand at the end Template strand is read 3’-5’ and RNA is synthesized 5’-3’

Answer 29

DsDNA unwinds to allow copying by RNA polymerase of one of the strands into a complementary RNA strand

Answer 30

Complementary antiparallel binding of he anticodon for methionyl-tRNA (CAU)to the mRNA codon for methionine (AUG, the initiation codon for translation) An essential step is recognition of the codon in the mRNA by the anticodon of the corresponding tRNA A complementary strand is NOT synthesized, just recognized

Answer 31

1. Double-stranded linear 2. Double-stranded circular 3. Single-stranded linear 4. Single stranded circular

Answer 32

Chromosomal and some viral DNA

Answer 33

Mitochondrial, bacterial and some viral DNA

Answer 34

Some viral DNA

Answer 35

Some viral DNA

Answer 36

Single stranded DNA

Answer 37

It’s based on the % of G-C base pairs High GC content = higher buoyant density Denatured DNA forms a less extended structures packs together better, and is more dense than dsDNA Used for analysis and purification

Answer 38

Standard way to separate DNA based on density using cesium chloride (CsCl2) gradient DNA mixed with CsCl2 and centrifuged for many hours so that a gradient of cesium chloride salt is established and then the DNA migrates to its corresponding density in the salt gradient DNA will separate based on different portages of AT and GC bases This can be used to separate DNA from other cellular components like RNA and proteins because they have very different densities than DNA

Answer 39

G-C content!! The more G-C pairs the more dense!

Answer 40

Heat Extremes of pH Urea Formamide They disrupt hydrogen bonds between the bases **these same things unfold proteins!!

Answer 41

Hybridization = renaturation Heat the DNA to separate the strands then slowly cool to re-form dsDNA or hybridize DNA (re-annealing)

Answer 42

Time and concentration After denaturation, DNA is incubated at a temperature below the melting temperature Next, in the nucleation step (second order), short complementary regions form double strands Then in the second step (first order), if the short regions are within a region of extended complementary sequences, the dsDNA zips up rapidly

Answer 43

Hyperchromic effect = melted single stranded DNA absorbs more light at 260 nm than dsDNA Absorbance at 260 nm decreases as single strand anneal to form dsDNA The change in absorbance can be used to measure the degree of melting of the nucleic acids (Nucleic acids have an absorbance maximum around 260 no)

Answer 44

Tm = temperature at which half of the DNA is single stranded

Answer 45

Depends on base composition: High GC content results in higher Tm - linear relationship Depends on ionic strength: high concentration of mono/divalent cations stabilize the duplex DNA (because DNA is negatively charged)

Answer 46

20 C below the estimated melting temperature

Answer 47

Southern blots and PCR (polymerase chain reaction) Southern blot = hybridization of a labeled DNA probe with DNA immobilized to a filter PCR = method to amplify DNA using alternate cycles of hybridization, polymerization and melting - the GC content of the DNA primers is needed to calculate the hybridization temperature

Answer 48

1. Single-copy genes (unique sequence) 2. Middle repetitive genes 3. Highly repetitive DNA

Answer 49

Protein coding genes

Answer 50

- tRNA and rRNA coding genes (these coding genes products must be made in large amounts for protein translation) - pseudogenes Most are tandemly duplicated

Answer 51

Simple-sequence DNA (ex. Satellite DNA = ATATAT) Dispersed repetitive DNA = most abundant and derived from mobile genetic elements - arise from endogenous retroviruses which transpose via an RNA intermediate More than 30% of human DNA consists of sequences repeated at least 20 times

Answer 52

Simple repeat sequence like ATATAT Called this because they have a base composition and buoyant density different from bulk DNA - they’re lighter!! After gradient centrifugation, satellite DNA Is a lighter density and shows up as separate bands from the main band

Answer 53

- ensures transmission of genetic information - errors in replication can give rise to mutations - mutations in somatic cells can lead to cancer (any cell other than reproductive) - enzymes of DNA replication are also involved in DNA recombination and repair - replication provides a target for antimicrobial and chemotherapeutic agents

Answer 54

DNA polymerase makes DNA by binding nucleotides together! Substrates = dNTPs and the 3’ end of the growing new DNA chain Nucleophilic attack by the 3’-OH on the alpha phosphate of the incoming dNTP which forms a phosphoester bond —> the hydrolysis of the pyrophosphate drives the reaction in the forward direction PP is the leaving group!

Answer 55

You need: - all four deoxynucleoside 5’-triphosphates and Mg+2 - a primer (RNA or DNA) with a free 3’OH end - a template of single-stranded or dsDNA Synthesis of the new DNA chain is always in the 5’—>3’ direction

Answer 56

1. 5’—>3’ exonuclease activity which hydrolysis the RNA primers 2. 3’—>5’ exonuclease activity removes mismatches bases (proofreading) 3. Required for DNA repair and removal of RNA primers in DNA replication 4. DNA polymerase First known DNA polymerase from E. Coli and composed of a single polypeptide chain

Answer 57

The major polymerase for DNA replication in E. Coli An aggregate of 7 different polypeptides 2 enzymatic activities: - DNA polymerase - 3’—>5’ exonuclease activity removes mismatched bases (proofreading)

Answer 58

New bases are added to the 3’ end of the growing strand If a wrong base is incorporated, that’s detected and this region of the strand moves to the exonuclease site where the misincorporated base is removed Then the strand returns to the polymerase site and synthesis resumes The strand gets proof read from 3’—>5’

Answer 59

1. Only nucleotides that can base pair with the template are incorporated 2. The 3’—>5’ exonuclease activity removes mismatched bases = proofreading 3. Mismatched bases can also be repaired immediately after replication by mismatched repair

Answer 60

Has activity in both the 3-5 direction (proofreading) and in the 5-3 direction to remove RNA primers DNA Polymerase III lacks the 5-3 activity

Answer 61

A special RNA polymerase called primase copies a region of DNA into a complementary RNA strand After a tiny stretch of RNA is made, DNA polymerase takes over and synthesized DNA (This is DNA polymerase III in e. Coli) Then to join together then RNA-DNA pieces, DNA polymerase I in e. Coli uses its 5’-3’ exonuclease activity to digest the RNA primer Then DNA polymerase I synthesized DNA to fill the gap - this leaves a nick in the new strand which gets sealed by a DNA ligase (does this via a phosphoester bond)

Answer 62

Since DNA can only be synthesized in the 5’-3’ direction, the orientation of synthesis on one of the strands will be in the opposite direction of movement of the replication fork The solution is to copy one strand continuously (leading strand) and the other strand discontinuously (lagging strand)

Answer 63

Short DNA fragments from the lagging strand that are briefly present in the vicinity of the replication fork Gaps between Okazaki fragments are filled by DNA polymerase I I would look at slide 66 in LM 1.1-2.1 or khan academy to make sure you get this

Answer 64

Relieves supercooling ahead of the replication fork

Answer 65

Enzymes that unwind DNA to make single strands accessible Energy for this reaction comes from hydrolysis of ATP to ADP Required for DNA replication, transcription and repair

Answer 66

It causes supercoiling which has to be relieved by topoisomerase Think about pulling apart two wound up strings, it’ll cause a big knot at the other end

Answer 67

Small circular DNA molecules

Answer 68

Type I: cuts one strand of the duplex and relieves supercoiling Type II: cuts both strands of the DNA duplex and induces ATP dependent negative supercoiling Both types form tyrosyl DNA-protein covalent intermediates Both types are targets for anti cancer drugs and antibiotics that stabilize the DNA-protein covalent intermediate inducing double strand breaks

Answer 69

They inhibit DNA gyrase (a bacterial topoisomerase II)

Answer 70

Require energy from hydrolysis of ATP (type I does NOT) Cleaves both strands of duplex so that another duplex can pass through (unlike type I that just nicks the DNA on one strand and then reseals the nick) Removes positive supercoiling formed ahead of the replication fork Introduces negative supercoiling into relaxed DNA

Answer 71

Type II topoisomerase inhibited by quinolone drugs DNA gyrase is a bacterial type II topoisomerase that is required for DNA replication. The bacterial enzyme is more sensitive to quinolones than the corresponding eukaryotic enzymes.

Answer 72

helicase to separate strands single stranded DNA binding proteins primase-RNA polymerase DNA polymerase 5’-exonuclease to hydrolyze RNA primer 3’-exonuclease “Editor” ligase to join DNA fragments topoisomerase to relieve torsional stress generated from replication fork

Answer 73

Mostly due to transcription and translation Regulation of expression is required for development, differentiation, and adaptation Different cell types due to differential expression Steroid hormone response mediated by gene expression Cancer arises from dysregulation of gene expression

Answer 74

The process of making an RNA strand complementary to one of the DNA strands RNA polymerase incorporates nucleotides that can base pair and are complementary to the template strand (antisense strand) The other DNA stand that is not the template strand has a sequence that is identical to the copied RNA except for having T instead of U so it’s called the sense strand

Answer 75

Sense strand = not the template strand, has an identical sequence to copied RNA Antisense = template strand

Answer 76

Catalyze the initiation and elongation of RNA chains Direction of synthesis is in the 5’-3’ direction Eukaryotes use different RNA polymerase for each class of RNA (mRNA, tRNA, rRNA) ``` RNA polymerase requires energy! ATP —>AMP GTP—>GMP CTP—>CMP + PPi UTP —>UMP ```

Answer 77

5’-3’ direction Just like DNA!

Answer 78

During transcription the DNA region being copied unwinds to make a single strand accesible The region of “melted” DNA is referred to as the transcription bubble and moves down the DNA along with the RNA polymerase When transcription is over, RNA disassociates from the DNA which resumes its double-stranded structure

Answer 79

DNA elements that control the start site for transcription

Answer 80

Eukaryotes: TATA box Prokaryotes: Pribnow box There are always multiple binding sites for different transcription factors

Answer 81

A sequence (DNA or RNA) specifically recognized by a binding protein Some variation allowed, represented by a consensus sequence = represents the most common base at each position Variations = TATAAT< TTATAT< TATTAT

Answer 82

In bacteria, the genes that encode the enzymes for tryptophan in e. Coli are clustered together in an operon The operon is transcribed into one long mRNA The different genes in this mRNA are translated separately to produce distinct proteins This mRNA encoding multiple proteins is called polycistronic ***eukaryotic mRNA are almost always moncistronic and express a single protein!! Each mRNA sequence produces ONE protein

Answer 83

Chromosomes are in the nucleus which means that mature mRNA must be transported through the nuclear membrane for translation in the cytoplasm All these steps allow for regulation (: In prokaryotic cells the chromosomes aren’t in the nucleus so translation of mRNA can start even before the whole transcript is made

Answer 84

Ribosomal (rRNA) = most abundant!! Messenger (mRNA) Transfer (tRNA) = 2nd abundant Small nuclear (snRNA) Micro (miRNA)

Answer 85

RNA polymerase I - rRNA precursor, in the nucleolus RNA polymerase II - mRNA, miRNA, most snRNA, in the nucleoplasm RNA polymerase III - tRNA, rRNA< some snRNA, in the nucleoplasm mtRNA polymerase - all types of RNA in the mitochondria

Answer 86

Rifampicin: binds to beta subunit of bacterial RNA polymerase, used to treat tuberculosis Actinomycin D: Inhibits prokaryotic and eukaryotic transcription by intercalating in DNA and blocking RNA polymerase progression Alpha-amanitin: Synthesized by the poisonous mushroom, inhibits both eukaryotic RNA polymerase II and III

Answer 87

Can act as antibiotics!

Answer 88

Rifampicin: binds to beta subunit of bacterial RNA polymerase, used to treat tuberculosis Inhibits bacterial RNA polymerase which blocks transcription

Answer 89

Intercalating agent that inserts between the bases in DNA distorting its structure It can inhibit transcription in any cell type The first antibiotic to have anti cancer activity!

Answer 90

Mushroom toxin Inhibits RNA polymerase II and III

Answer 91

N-terminal to C-terminal

Answer 92

Rifampicin, alpha-amanitin, actinomycin D

Answer 93

Nucleotides added to the 3’ hydroxyl Requirement for Mg+2 ion Substrates are a type of nucleoside triphosphate Direction of synthesis is 5-3 **difference: RNA polymerase doesn’t need a primer

Answer 94

Proteins that regulate transcription! They activate or repress transcription (Activators or repressors) May bind to specific DNA sequences in the regulatory sites that control specific genes May act as adaptor molecules to mediate communication between other factors and RNA polymerase (co-activators and co-repressors)

Answer 95

Trans-acting factors The DNA elements that they bind are cis-elements since they regulate genes nearby on the same chromosomal region

Answer 96

Upstream of the transcription start site They are binding sites for transcription factors

Answer 97

They contain binding sites for multiple transcription factors They can be quite a distance from the target gene

Answer 98

RNA polymerase II can’t start transcription by itself, it needs a lot of accessory factors called TFIIs Each TFII is a complex of proteins The assembly of the pre-initiation complex is usually initiated by binding of the TFIID complex to the TATA box —> TBP is the TATA binding protein and is a subunit of TFIID that directly binds to the TATA box

Answer 99

The TATA binding protein that is a component of the TFIID complex TBP binds to the minor groove of DNA causing the DNA to bend The binding of TBP as part of TFIID to the TATA box forms a platform for binding. Of the other TFIIs and RNA polymerase

Answer 100

Formed by a step-wise assembly of the different general transcription factors (FTIIs) 1. TBP in TFIID binds to the TATA box 2. Other TFIIs bind 3. RNA polymerase binds THEN the initiation of transcription involves melting DNA in the initiation region followed by RNA polymerase moving away from the initiation site to transcribe the first segment of RNA - the TFIIs disassociate and CDT is phosphorylated as RNA polymerase begins to move Slide 22 in LM 2.1

Answer 101

1. TFIIS disassociate 2. Phosphorylation of the CDT, a repetitive domain at the C-terminus of the largest subunit of RNA polymerase II - CTD needs to be phosphorylated for RNA polymerase to leave the promoter

Answer 102

Transcription factors! They have discrete DNA binding and activation domains - they recognize specific short DNA sequences

Answer 103

They are next to the DNA binding domain They recruit general transcription factors such as TFIID

Answer 104

They are DNA regulatory sequences (cis elements) that are not part of the basal promoter They can function close to a promoter (binding sites for transcription factors) or at a distance or even from within an intron They bind transcription factors (activators or repressors) that are usually cell specific Activators bind to enhancers and repressors bind to silencers

Answer 105

Site specific DNA-binding factors interacting with cis elements in the proximal promoter region and stabilizing the recruitment of transcriptional machinery through direct interaction of the site-specific factor and the general factors Promoter activity can be further stimulated to higher levels by site-specific factors binding to enhancers Enhancer factors can stimulate transcription by recruiting a histone-modifying enzyme to create a more favorable chromatin environment for transcription

Answer 106

Histone acetylation Recruitment of a kinase to phosphorylate the carboxy-terminal domain of RNA polymerase II and stimulate elongation

Answer 107

Anywhere with respect to the promoter - upstream, downstream, even within the target gene itself

Answer 108

RNA polymerase I and III

Answer 109

RNA polymerase III

Answer 110

RNA polymerase II

Answer 111

In the mitochondria!! Made and translated in the mitochondria

Answer 112

Triplets of bases They are read by the translational apparatus as amino acids!! ``` TTT = Phe GGT = Gly ```

Answer 113

It takes us from the 4 letter nucleotide alphabet to the 20 letter amino acid table! Each sequence of three nucleotides specifies an amino acid 64 possible triplets are called the genetic code! Most amino acids are encoded by more than one codon = degenerate

Answer 114

AUG Codes for Met which is ALWAYS the first amino acid in the protein

Answer 115

UGA UAA UAG U go away, U are annoying, U are gross

Answer 116

Changes in the third position in a codon are the least likely to change the encoded amino acid

Answer 117

Orf A stretch of consecutive amino acid codons undisrupted by a termination codon

Answer 118

One nucleotide is switched for another (ex. G substituted in place of C) This changes the codon from AGG to AGC which changes the AA from Arg to Ser The end result is an AA substitution = missense mutation

Answer 119

a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid AGG —> AGC Arg —> Ser

Answer 120

Deletion of a single nucleotide This causes a shift in the reading frame = frameshift mutation

Answer 121

Deletion or addition of a nucleotide that makes the sequence nondivisible by 3 and shifts the reading frame AUC-aGG-GUA_AGC Delete a AUC-GGG-UAA Now downstream of the frame shift are codons for incorrect amino acids and stop codons

Answer 122

Mutation in the HBB gene that encodes the hemoglobin beta chain normal: GAG = Glu mutant: GTG = Val

Answer 123

Completely eliminates the function of the gene

Answer 124

Change involving a single base pair

Answer 125

Change in codon that results in substitution of one amino acid for another

Answer 126

Any change in DNA that results in a termination codon replacing an amino acid codon

Answer 127

Deletion or insertion of bases that alters reading frame

Answer 128

- proteins are assembled on the surface of ribosomes - they’re composed of two dissimilar ribonucleoprotein subunits - each rRNA species is found only once per ribosome subunit - they are drawn from a free pool to be used again after their release from mRNA

Answer 129

A single mRNA molecule being translated by multiple ribosome If they’re free in the cytoplasm they synthesize cytoplasmic or organelle proteins If they’re attached to the ER then they synthesize secreted or plasma membrane proteins

Answer 130

A minute particle consisting of RNA and associated proteins found in large numbers in the cytoplasm of living cells They bind messenger RNA and transfer RNA to synthesize polypeptides and proteins.

Answer 131

described in terms of their approximate sedimentation in a centrifuge the higher the S value the greater the rate of sedimentation and the larger the size of the ribosome

Answer 132

A large and a small ribosomal subunit Each subunit is made of specific ribosomal RNA and ribosomal proteins

Answer 133

On ribosomes in the cytosol

Answer 134

On ribosomes associated with the Endoplasmic reticulum

Answer 135

Transfer-RNA Adaptors that bring the correct AA to the corresponding codon There are separate tRNA for the different amino acids! AA are attached to the 3’ end at the CCA terminus Serve as an adaptor between mRNA and the growing polypeptide chain - the anticodon sequence interacts(base-pairs) with the mRNA codons

Answer 136

AA are attached to the 3’ end at the CCA terminus All tRNA have the same general structure: - about 50% of the bases are paired - unpaired regions form loops Contain modified nucleosides

Answer 137

mRNA, tRNA and rRNA

Answer 138

Nucleotide sequence encodes the order of AA a ribosome assembles into polypeptide chain

Answer 139

Each AA type is covalently bound to a subset of tRNAs containing a specific three-nucleotide anticodon sequence Each anticodon basepairs with its complementary mRNA codon to position the encoded amino acid in the ribosome A site where it is covalently linked to the C-terminus of the growing peptide Codon: GGG (mRNA) Anticodon: CCC (tRNA)

Answer 140

Ribosomes are made of many proteins and three (bacterial) or four (eukaryotic) rRNA molecules The largest rRNA has a catalytic function in the formation of the peptide bond between incoming AA-tRNA amino group and the carbohydrates terminus of the growing protein chain

Answer 141

Charging of tRNA = attachment of AA to tRNA Aminoacyl tRNA synthetases catalyze these processes - there’s at least one aminoacyl tRNA synthetase for each AA Each synthetase recognized its own AA and appropriate tRNA = aminoacyl tRNA synthetases are the molecules that actually translate the genetic code because they have to attach the correct AA to the correct tRNA!

Answer 142

1. The enzyme couples a specific AA via a high energy ester bond (which actives the AA) to either the 2’ or 3’ hydroxyl of the terminal adenosine in the tRNA that has the proper anticodon for that AA 2. The energy of the ester bond subsequently drives the formation of the peptide bonds linking adjacent AA in a growing polypeptide chain in the ribosome 3. The anticodon three base sequence in the tRNA base-pairs with a complementary codon in the mRNA specifying the attached AA (so on one side of the tRNA is the AA and on the other it base pairs to the mRNA)

Answer 143

Anticodon loops Different AA are always encoded by different codons and therefore anticodon

Answer 144

1. Initiation 2. Elongation 3. Termination Each step is facilitated by specific factors IFs - initiation factors EFs - elongation factors RFs - release factors

Answer 145

Assembly of components *major differences between prokaryotes and eukaryotes

Answer 146

Synthesis of the protein chain Translocation of tRNAs between the sites on the ribosome

Answer 147

Release of the completed protein chain from the ribosome

Answer 148

In prokaryotes the start site for translation is specified by a sequence directly upstream of the coding sequence called the shine-dalgarno sequence at the 5’ end of the mRNA The complementary rRNA binds to it which positions the small ribosomal subunit for initiation of translation

Answer 149

The preinitiation complex slides down the RNA until the first initiation codon for translation is detected If the codon is surrounded by an optimal arrangement of nucleotides then translation will be initiated This ideal arrangement is called the Kozak consensus

Answer 150

In prokaryotes the ribosome binding side is recognized by 16s rRNA which allows translation of multiple proteins from polycistronic messages - translation can initiate at internal sites in the mRNA In eukaryotes the preinitiation complex scans for translation initiation side from the 5’ end of the mRNA which allows for translation of monocistronic mRNAs - normally only the first translation initiation site is recognized

Answer 151

A (aminoacyl) P (peptidyl) E (Exit) These are binding sites for tRNA

Answer 152

A charged tRNA corresponding to the second codon is recruited to the A site on the ribosome The AA attached to the tRNA in the P site (first codon) is then transferred to the AA in the A site by formation of a peptide bond - this reaction is catalyze by peptidyl transferase Then the ribosome moves down the mRNA one codon so that the tRNA bearing the peptide chain is in the P site and the uncharged tRNA is in the E site from which it exits the ribosome E P A tRNA(Met) tRNA(Val) ``` E P A tRNA tRNA(Val)(Met) ``` ``` E P A tRNA tRNA(Val)(Met) tRNA(Phe) ```

Answer 153

Formed by peptidyl transferase Involves a nnucleophilic attack of the carbonyl carbon in the P site amino acid by the amino nitrogen of the amino acid in the A site The growing peptide chain is attached to the tRNA in the A site to form peptidyl tRNA - the peptidyl tRNA then translocates to the P site

Answer 154

Transfer of an amino acid from its aminoacyl-tRNA to the amino end of the growing peptide chain

Answer 155

When a stop codon is in the A site of the ribosome There is no tRNA to recognize stop codons - the stop codon is recognized by proteins called release factors which then fit into the A site Binding of the release factors to the A site promotes cleavage of the peptide chain from the tRNA in the P site

Answer 156

1. Initiation - Binding of mRNA 5’ cap by cap-binding protein - initiator Met-tRNA binds to 40S subunit to form pre-initiation complex - mRNA binds to form initiation complex - 60S subunit binds to form active 80S initiation complex: Met-tRNA is in P site of ribosomes 2. Elongation - AAtRNA binds to A site of ribosome - peptide bond forms - translocation of growing peptide from the A site to the P site 3. Termination - stop codon in A site is recognized by eRF - hydrolysis of peptide-tRNA bond - peptide released from ribosome - ribosome disassociates into 60S and 40S subunits

Answer 157

The first two bases of the codon hydrogen bond with the last two base pairs of the anticodon - these base pairings follow GC AU rules The third anticodon will recognize more than one codon base - base-pairing rules in the third position of the codon are relaxed Separate tRNA is not required for every codon because of wobble tRNA anticodon: 3’AAG5’ mRNA codon: 5’UUU3’ tRNA anticodon: 3’AAG5’ mRNA codon: 5’UUC3’ UUU and UUC both code for Phe

Answer 158

If A or G are the third codon base then the anticodon U will recognize both of them If U or C are the codon base in mRNA then the tRNA anticodon G will recognize both of them If U,C or A are the codon base in mRNA then the tRNA anticodon I will recognize them tRNA G < U or C 3’ mRNA tRNA U < A or G 3’ mRNA tRNA I < U, C or A 3’ mRNA

Answer 159

Inhibition of mitochondrial protein synthesis Inhibition of mitochondrial protein synthesis. Erythromycin inhibits translation in bacteria. The translational machinery in mitochondria are derived from bacteria, and are sensitive to some antibiotics targeting bacteria

Answer 160

Covalent bonds

Answer 161

Equal sharing of electrons within the outer shell between two atoms AA are linked together to form proteins using covalent bonds!!

Answer 162

Much weaker than covalent ~6 kJ/mol Involve transfer of an electron between one atom to another Depend on the electronic charge of the atoms interacting Coulomb’s law: E = kq1q2/Dr (Don’t need to know)

Answer 163

Via electrostatic/ionic interactions

Answer 164

Weak electrostatic bonds! E = 4-13 kJ/mol Because the interaction between NH or OH for example, is polar, H can still interact weakly and at a greater distance with another molecule that becomes the hydrogen bond acceptor

Answer 165

Amino terminal and carbohydrates terminal as well as many polar R groups in proteins have NH or OH groups where the hydrogen is paired more closely with an N or O acting as the hydrogen bond donor Because the interaction between NH or OH for example, is polar, H can still interact weakly and at a greater distance with another molecule that becomes the hydrogen bond acceptor N-H - - - - - - - - N donor. acceptor

Answer 166

The point at which the two atoms exhibit the greatest attraction for each other It’s that graph you’ve seen tons in chemistry!

Answer 167

Similar in strength to electrostatic interactions but are what over in hydrophobic environments like in the core of a protein Depend on the distance between the 2 atoms and the non symmetrical charge distribution around each of them

Answer 168

They are greatly diminished int he very polar environment of water Covalent interactions have much closer bonding lengths = stronger AND their strength is undiminished in water as compared to a vacuum

Answer 169

It competes for electrostatic interactions between other polar molecules like Na+ and Cl- Has a high D, dielectric constant so slats and alcohols are completely dispersed in water

Answer 170

Free energy is released by water when it does not have to surround individual nonpolar molecules in ordered complexes This causes nonpolar molecules to aggregate in aqueous environments If water has to surround individual nonpolar molecules more water has to be in ordered complexes surrounding each molecule but when they aggregate then some of the water molecules are released = higher entropy!! This is why lipid membranes are formed!!!

Answer 171

Hydrophobic AA that are nonpolar will be located in the interior of protein molecules away from the aqueous environment

Answer 172

Decrease pH Increase PaCO2 Normal HCO3-

Answer 173

Increase pH Decrease PaCO2 Normal HCO3-

Answer 174

Decrease pH Normal PaCO2 Decrease HCO3-

Answer 175

Increase pH Normal PaCO2 Increase HCO3-

Answer 176

Donates an H+ Accepts an H+ Water can act as either a weak acid or a weak base!! Weak acid has a strong conjugate base

Answer 177

pH = log(1/[H+] = -log[H+] Normal water: [H]=[OH]=1x10-7 M

Answer 178

A weak acid produces a strong conjugate base Strong conjugate bases produce a great pH buffering capacity when the ionization equilibrium (Ka) for the acid is reached When the Ka of a weak aid is reached, then the addition of extra free H+ doesn’t change the pH because instead it reacts with the conjugate base

Answer 179

pH at which [acid]=[conjugate base] This is when resistance to pH change is the greatest = highest buffering capacity!! S shaped graph (inflection point is the pKa) pKa: [HA]=[A-] Ka=[H+][A-]/[HA]

Answer 180

pH = pKa + log[A-]/[HA] When [A-]=[HA] the pH=pKa

Answer 181

Increased H+ in blood due to hypoventilzation and build up of CO2 - pulmonday problems - head injury - drugs - brain tumors H+ HCO3- H2CO3 H2O + CO2

Answer 182

Hyperventilation Releases too much CO2 and drives the equation to the right which decreases [H+] H+ HCO3- H2CO3 H2O + CO2

Answer 183

HCO3- is mainly regulated by the kidney can be effected by loses of bases through stool, ingestion of acids/bases, decreased excretion of acids

Answer 184

The lungs PCO2 effected by changes in production of volatile acids, pulmonary ventilation or composition of inspired air

Answer 185

20 used by bacteria and humans!

Answer 186

the central carbon is linked to the following in these specific positions: 1. amino group (NH3+) 2. Carboxylic group (COO-) 3. distinctive R group side chain 4. a hydrogen atom they are CHIRAL with mirror images called the L-isomer and the D-isomer (rare)

Answer 187

constituents of human proteins and have a counter-clockwise direction of arrow from highest to lowest priority substituents

Answer 188

glycine its R group is an H

Answer 189

by their R group side chain ``` they give AA: size shape charge hydrogen binding capacity hydrophobic character chemical reactivity ```

Answer 190

how you usually draw AA with charges - this charge changes with pH carboxyl group loses a hydrogen to become negatively charged COO- (weak acid) amine group accepts a hydrogen to become positively charged NH3+ (weak base)

Answer 191

isoelectric point the pH at which total net charge is 0 of an AA pI of each AA is the total combination of all three pKa's of that AA

Answer 192

non polar R groups don't have a pKa the R groups that have a pKa are what facilitate chemical reactions and form ionic bonds!

Answer 193

histidine the side chain pKa is 6.0 which is very close to physiological pH and so it's really reactive in the body

Answer 194

low pKa = more acidic

Answer 195

it's the one with the pentagon structure! its R group is bonded to both the nitrogen of the nitro group and the alpha carbon

Answer 196

hydrophobic

Answer 197

hydrophobic!! glycine, alanine, proline, valide, leucine, isoleucine, methionine *methionine barely fits into this group because it has a S in the side chain forming a thither sulfur bond but it's not charged = polar-uncharged

Answer 198

phenylalanine, tyrosine, tryptophan

Answer 199

both! they are aromatic rings = phobic tyrosine has an OH and tryptophan has an NH = philic used for their unique absorption spectra at 280 nm (trp absorbs better and they're 4.6% of all protein mixtures)

Answer 200

serine, threonine, cysteine, asparagine, glutamine

Answer 201

has an SH group at the end two cysteines together would undergo oxidation to form an S-S covalent disulfide bridge! cysteine + cysteine = cystine

Answer 202

lysine, arginine and histidine all have positively charged R groups at physiological pH because the amino molecules in the R group at H+ acceptors lysine and arginine are H+ acceptors at neutral pH histidine is reactive at a neutral pH

Answer 203

aspartate and glutamate negatively charged at physiological pH because they are H+ donors COO- groups

Answer 204

histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine your body can't produce them so you have to incorporate them into your diet!

Answer 205

the carboxyl group of one AA is covalently linked to the amino group of another AA by a peptide bond and H2O is released O=C-NH input of free energy is required two AA linked together = peptide bond more than two AA = polypeptide chain

Answer 206

backbone always contains: a carbonyl group (C=O): hydrogen bond acceptor an amino group (NH): hydrogen bond donor backbones can interact with each other and with side chains

Answer 207

they're planar because of the partial double bond characteristics between the C=N peptide bond O=C-NH-CH this bond can only be cis or trans

Answer 208

the two R groups are on opposite sides of the peptide bond

Answer 209

ALL polypeptide chains are polar the amino "N" terminal is always the beginning and the carboxy "C" terminal is always at the end

Answer 210

the spatial organization of amino acids within a short distance of each other within a single polypeptide sequence determined by: - rigidity of the peptide bond between each AA - restricted set of allowed angles

Answer 211

alpha helix beta sheets

Answer 212

tightly coiled backbone that's right-handed side chains extend outward this secondary structure is stable because of hydrogen bonding between NH and CO groups in the backbone that are FOUR residues apart ALL backbone NH and CO groups are hydrogen bonded

Answer 213

- keratin (actually a superhelix because it's alpha helices coiled around each other) - ferritin: an iron storage protein that's a bundle of helices

Answer 214

parallel and antiparallel

Answer 215

the one beta strand amino head is directly across from the other beta strand carboxy tail so they line up perfectly! this is a shorter and stronger hydrogen bond between the C=O and NH in the backbones of adjacent strands

Answer 216

both amino head groups are lined up across from each other so that the C=O and NH hydrogen bond between the two backbones is staggered

Answer 217

twisted more structurally diverse than alpha helices

Answer 218

protein chains have unique distribution of alpha helices, B strands and reverse turns along their AA length secondary structure can be kind of predicted based on the relative frequencies of each AA because certain AA are more likely to be found in a certain secondary structure

Answer 219

primary = AA seuqnece secondary = substructures (a helices, beta sheets) tertiary = 3D structure quaternary = complex of protein molecules

Answer 220

spatial arrangement of amino acid residues within the polypeptide chain that are far apart in sequence includes disulfide bonds

Answer 221

1. thermodynamic stability: the least amount of energy expended to achieve tertiary shape is the better route to take 2. the contribution of each portion of the folding into tertiary shape is important to the overall mechanism of folding

Answer 222

covalent bond resulting in cross-linking within (intrachain) and between (interchain) proteins by the R groups of cysteines oxidizing the SH side groups of a pair of cysteine residues to S-S forms one cystine

Answer 223

the backbone C=O group of amino acid i hydrogen bonds with the backbone NH group of amino acid i+3 in the primary amino acid sequence which creates a sharp turn this is how you form compact globular proteins whether the other secondary structures are alpha helices, beta strands or mixture

Answer 224

porins they're found in hydrophobic lipid membrane and are used as aqueous channels within the membrane to allow polar molecules through the membrane

Answer 225

when alpha helices bind together using hydrophobic van der waals bonding by putting all the hydrophobic side chains in the center

Answer 226

compact globular protein regions of a single protein chain connected by flexible segments of polypeptide chains each globular region is a different domain of the same individual protein

Answer 227

the spatial arrangement of proteins containing more than one protein chain or subunit and the nature of subunit interactions ex. dimer that consists of two identical subunits ex. hemoglobin has 4 subunits: two alpha, two beta

Answer 228

most proteins are only marginally stable because the energy difference between the folded and unfolded amino acid chain is very small but this is good!! because a lot of enzymes have to undergo conformation changes to induce the fit or release of a substrate this allows a single protein to perform multiple different tasks

Answer 229

calculated versus actual time for a protein to fold correctly with all the combinations of amino acids it should take 100 AA 1.6x10ˆ27 years to find the right conformation through a random search but it only takes 5 seconds in e. coli

Answer 230

- maintains structural integrity - determines how a cell interacts with its environment - maintains the charge differential across the membrane (cytoplasm inside cell is negatively charged) - compartmentalization: of the cell from other cells and environment and also compartmentalization of regions of the cell from each other which allows for specialized functions each individual intracellular organelle also has a membrane

Answer 231

Na+, Cl- and HCO3- more basic than ICF

Answer 232

K+, Mg+2 anions are proteins and organic phosphates more acidic than the ECF

Answer 233

higher in the ECF

Answer 234

higher in the ICF

Answer 235

higher in ECF

Answer 236

higher in ICF

Answer 237

higher in ECF

Answer 238

higher in ICF

Answer 239

higher in ECF

Answer 240

closed sheet-like structures 2 molecules thick mostly lipids and proteins (lipid bilayer) able to spontaneously form closed bimolecular sheets in aqueous media due to amphipathic nature fluid structures = fluid mosaic due to asymmetry asymmetric electrically polarized, cytosolic side is negative

Answer 241

both the lipid and some protein components of the membrane are laterally mobile and can move across the plane of the membrane

Answer 242

polar head and two fatty acyl chains (tail)

Answer 243

eh not really proteins can differ greatly between different membranes

Answer 244

regulates nutrient and ion transport into the cell regulates transport of waste out of the cell maintains correct chemical concentrations in the cell

Answer 245

provide a site for lipid-based chemical reactions interacts with other cells or the ECM detects and transducer signals from environment to the cell = signal transduction (ex. ligands binding to cell surface receptors)

Answer 246

1. water insoluble 2. great variety of structure 3. some function in field and energy storage (triglycerides) 4. some function in signaling mechanisms

Answer 247

1. phospholipids 2. glycolipids 3. cholesterol

Answer 248

carry out most membrane processes and greatly vary between cells each cell type has a unique set of membrane proteins involved in transport of molecules across the membrane to allow for selective membrane permeability also function in energy uptake, signal transduction, etc.

Answer 249

favorable: - gases (CO2, N2,O2,NO) - small uncharged polar molecules (ethanol) pass through by diffusion without transport protein unfavorable: - large uncharged polar molecules (glucose) - all ions - charged polar molecules (AA) usually need transmembrane proteins like transporters, channels, pumps to get through

Answer 250

these are all energetically favorable non-covalent interactions!!! you don't need ATP or covalent bonds to make a membrane (: 1. electrostatic and hydrogen bonds between the polar heads and water 2. van der walls forces between the hydrocarbon acyl tails of the phospholipids 3. hydrophobic interactions between the fatty acyl tails that exclude water

Answer 251

must be amphipathic aka have a hydrophilic and hydrophobic part ``` philic = head phobic = tails ```

Answer 252

glycerol is usually the backbone of phospholipids it's a simple alcohol with three carbons in membrane phospholipids the C1 and C2 positions of the glycerol backbone are each attached to a fatty acid hydrocarbon side chain

Answer 253

fatty acid - glycerol - phosphate head group/alchol

Answer 254

fatty acid - glycerol - sugar group glucose or galactose could be the sugar and they're be the polar part of the molecule

Answer 255

fatty acid - sphingosine - sugar group

Answer 256

saturated = all single bonds unsaturated = double or triple bonds

Answer 257

on the exoplasmic leaflet of the membrane usually, not always though!!

Answer 258

cytoplasmic leaflet of the membrane usually, not always though!!

Answer 259

phosphatidylserine in healthy cells a high % of phosphatidylserine in the membrane is in the cytoplasmic leaflet under certain conditions, this distribution is altered so that there's an increased presence of phosphatidyl serine in the exoplasmic leaflet when phosphatidyl serine is externalized it signals for platelet activation & aggregation, recognition and removal of old cells, apoptosis, etc.

Answer 260

glycerol backbone phosphate group at C3 position acyl chains in C1 and C2 positions - they can be saturated, unsaturated or a mix of both most simple phospholipid

Answer 261

- influences arraignment of proteins and lipids - altering fluidity can alter membrane and/or cell fnx - foster assembly/disassembly of protein signaling complex - changes membrane permeability - excessive fluidity leads to membrane destruction - biological membranes have mechanisms to maintain stable, proper levels of fluidity

Answer 262

longer acyl tails have more hydrophobic interactions than shorter chains so they're more stable = need more energy to melt them = higher Tm unsaturated side chains have kinks which means the packing and hydrophobic interactions of the tails won't be as good so it'll take less energy to break them up = lower Tm

Answer 263

cholesterol as temperature falls, cholesterol increases membrane fluidity as temperature rises cholesterol decreases membrane fluidity this is why animal membranes don't have a melting temperatures!

Answer 264

steroids, cortisol, vitamin D, etc.

Answer 265

micro-domains of enhanced membrane fluidity that aid rapid movement of lipids and proteins in signaling processes increased amount of cholesterol and glycosphingolipids in these areas **they have no impact on the overall membrane fluidity!!

Answer 266

real time alterations of acyl side chain length and/or saturation of membrane phospholipids depending on changes in their environment

Answer 267

class of antibiotics one type of ionophore is polyene antifungals: they work by selectively disrupting cell membranes of bacteria or yeast without affecting cell membranes in humans/animals (ex. nystatin)

Answer 268

Fungal membranes don't contain cholesterol, they have ergosterol so nystatin specifically binds to ergosterol and increases the fluidity of the cell membrane which opens it up to ion flow and the electrochemical gradient is lost and kills the cell

Answer 269

single layer of phospholipids forming a spherical structure

Answer 270

small spherical structure of a phospholipid bilayer the center is composed of a polar environment the exterior and interior of the liposome are the phospholipid heads facing either the aqueous outer environment or the aqueous interior

Answer 271

the phospholipid structure protects drugs from degradation polar drugs can be placed in the aqueous center of the liposome and non polar drugs can be embedded in the lipid core of the bilayer because the bilayer structure of liposomes mimics that of the plasma membrane, the liposome can fuse with cell membranes to deliver the drugs to the cell interior extended release drugs like morphine!

Answer 272

give strength, flexibility and function to the membrane they carry out most processes occurring at the cell membrane!

Answer 273

1. peripheral: more loosely associated with the membrane (sitting on top of it) 2. integral: rightly associated with the membrane (embedded) --> removal requires lipid bilayer destruction

Answer 274

completely extend through the lipid bilayer all transmembrane proteins are integral but not all integral membrane proteins are transmembrane because if you're integral just part of the protein has to be in the lipid core

Answer 275

alpha helical the R side groups of the individual AA of the alpha helix membrane-spanning region are hydrophobic and/or non polar BUT the AA at the beginning and end of the helix are polar so they can interact with the polar heads for the most part, these membrane spanning alpha helices don't have amino acids whose R groups are polar or charged but sometimes there are polar groups as long as it's overall hydrophobic groups all of these are non-covalent interactions!

Answer 276

hydrocarbon chains that allow their anchored proteins to be very tightly associated with the membrane usually this insertion into the lipid core of the membrane makes the resulting protein integral can also be a short alpha-helix portion

Answer 277

they usually have multiple alpha helical structures passing through the membrane ex. ligand activated ion channels: when a ligand binds to the protein, the channel subunits turn to a different conformation - initially hydrophobic leucine lined the channel interior but after the conformation change, now small polar amino acids line the channel interior which allows ions to pass through

Answer 278

CO2! only small uncharged molecules can pass through without help a. glucose is large and polar b. Cl- is a charged ion c. ATP is polar d. arginine is polar

Answer 279

- small proteins are more mobile - dependent on interactions it has/doesn't have with surrounding membrane proteins or proteins of the cytoplasm/extracellular matrix - increase temperature increases mobility - increased mobility within lipid rafts YOU CAN'T PREDICT PROTEIN MOBILITY FROM SECONDARY STRUCTURE!! MUST BE DONE EXPERIMENTALLY

Answer 280

proteins with a complex sugar group added on signals within the primary structure of a membrane protein would indicate to the cell machinery if glycosylation is to occur on a certain AA of a certain protein only present on the extracellular region of the protein

Answer 281

refers to how many times they span the membrane or otherwise associate with it also which end of the protein, the amino terminus or carboxyl terminus, is extending extracellularly or intracellularly proteins don't flip flop in membranes because their topology is stable! if they did then polar regions of the protein would have to pass through the membrane

Answer 282

cell alters its type of membrane proteins for growth factor receptors to attain a higher degree of proliferation then to metastasis, the interaction of the cell with its environment has to be disrupted for the cancer cell to spread and then re-establish in new places

Answer 283

- cancer - diabetes type II - heart disease

Answer 284

defective insulin signaling through the insulin receptor which is a transmembrane plasma membrane protein expressed on specific tissues like adipose and muscle

Answer 285

connexins these proteins form the gap junctions that syncytial cells such as cardiac muscle use to rapidly communicate directly to each adjacent cardiac muscle defects in connexins lead to inherited cardiac arrhythmias

Answer 286

because many membrane proteins and membrane transporters in particular have a region of their structure facing outward from the cell membrane to the extracellular environment that way the drug itself wouldn't need to cross the cell membrane to exert its action

Answer 287

prilosec targets gastric transporter that pumps HCl from parietal cells of the stomach into the stomach lumen transporter: H+/K+ ATPase proton pump

Answer 288

farxiga targets kidney sodium/glucose cotransporter SGLT2 that reabsorbs glucose helps the kidney reabsorb glucose

Answer 289

procardia targets calcium channels in the heart and blocks calcium channels

Answer 290

prozac targets transporter involved in serotonin reuptake in the brain - inhibits the SSR (selective serotonin reuptake) transporter in the brain

Answer 291

Change in free energy Energy available to do work Approaches zero as reaction proceeds to equilibrium Predicts whether a reaction is favorable The maximum amount of energy that can be obtained from a reaction at constant temperature and pressure! kJ/mol or kcal/mol

Answer 292

Change in enthalpy Heat released or absorbed during a reaction Does not predict whether a reaction is favorable

Answer 293

Change in entropy Measure of randomness Dos not predict whether a reaction is favorable

Answer 294

ΔG ＝ ΔH - T ΔS

Answer 295

ΔG < 0 = forward reaction ΔG > 0 = reverse reaction ΔG = 0 equal rate If ΔG is negative it means there’s a net loss of energy so the reaction proceeds spontaneously in that direction

Answer 296

The free energy of the forward reaction is always equal in magnitude of the reverse reaction but opposite in sign If ΔG for A —> B = -5 kcal/mol Then ΔG for B —> A = +5 kcal/mol

Answer 297

When a reaction with a large + ΔG is coupled with a second process with a larger ΔG so that the + ΔG process can occur because the net ΔG will still be negative Ex. Moving ions against a concentration gradient is favored by coupling it to reactions with a huge negative ΔG like hydrolysis of ATP

Answer 298

Adenosine triphosphate Purine base adenine Give carbon sugar ribose 3 phosphate groups The two phosphoanhydride linkages are high-energy bonds and their hydrolysis yields large negative change in free energy

Answer 299

Chemical reactions proceed spontaneously only if ΔG is negative Hydrolysis of ATP has a huge -ΔG and it occurs spontaneously without any energy requirement Coupling with ATP hydrolysis helps to bring the ΔG of unfavorable reactions to a net negative value

Answer 300

Catabolism Anabolism

Answer 301

The chemical reactions that harvest energy from the degradation of energy rich molecules Degradation of molecules to salvage components Energy is stored in the form of ATP Carbs, fats, proteins —> CO2, H2O, NH3

Answer 302

Chemical reactions that require energy (usually in the form of hydrolysis of ATP) Biosynthesis of molecules from simple components Often involves reducing chemical reactions involving electron donors like NADH AA, sugars, fatty acids, nitrogenous bases —> proteins, polysaccharides, lipids, nucleic acids

Answer 303

Catabolic reactions capture chemical energy in the form of ATP from the degradation of energy rich molecules in 3 steps: 1. Hydrolysis of complex molecules to simple building blocks 2. Conversion of building blocks to simple intermediates like acetyl CoA 3. Oxidation of acetyl CoA (oxidative phosphorylation) NADH can be used to synthesize ATP

Answer 304

Regulatory signals that arise from within the cell such as availability of substrates, inhibition by products, or alternations in the levels of allosteric inhibitors/activators Affects the rate of the metabolic pathway

Answer 305

Regulatory signals between cells that provide for long range integration of metabolism and usually results in a response slower than intracellular signals Ex. Chemical signaling between cells by blood borne hormones, neurotransmitters or even by direct communication between cells through surface contacts or through gap junctions

Answer 306

1. Synaptic signaling Nerve cell, neurotransmitter, target cell 2. Endocrine signaling Hormone, blood vessel, target cell 3. Direct contact Signaling cell, gap junction, target cell For energy metabolism, the most important route of communication is chemical signaling between cells by blood borne hormones or by neurotransmitters

Answer 307

Small intracellular molecules that mediate the effects of first messengers (neurotransmitters and hormones) They intervene between the original extracellular messenger and the ultimate intracellular effect They’re part of a cascade of events that convert ligand binding into responses

Answer 308

Ligands like hormones or neurotransmitters They bind to cell surface receptors and initiate a series of reactions involving these second messenger molecules

Answer 309

Calcium phosphatidyl inositol system Adenylyl (adenylate) cyclase system

Answer 310

According to the number of carbon atoms of carbons

Answer 311

Carbohydrates with an aldehyde group Have the suffix -ose like y lose, ribose and glucose

Answer 312

Carbohydrates with a keto group Have the suffix -ulose attached like xylulose

Answer 313

By the number of carbon atoms - three = triose: glyceraldehyde, dihydroxyacetone - four = tetrose: erythrose - five = pentose: ribose, ribulose, xylose, xylulose, deoxyribose - six = hexose: glucose, mannose, galactose, fructose, fucose - seven = heptose: sedoheptulose - Eight = octose: none in human bio - nine = nonose: neuraminic acid

Answer 314

Compounds with same chemical formula but different structures Ex. Fructose, glucose, galactose and mannose ar wall C6H12O6

Answer 315

Isomers that differ in the configuration of only one carbon (except the carbonyl CHO) Carbon atoms are numbered beginning at the end which contains the carbonyl carbon (C1)

Answer 316

Special type of isomer pairs of structure that are mirror images of each other The two members of the pair are designated as D and L forms

Answer 317

D isomer!! In the D-isomer the OH group on the asymmetric C atom farthest from the carbonyl group is on the right and for the L-isoform it’s on the left So in D isomer of a carbohydrate, the the C1 carbon is HC=O and on the other end is CH2OH — the carbon next to CH2OH that’s still chiral and in the backbone, if the OH is on the right then it’s the D isomer, if it’s on the left it’s the L isomer

Answer 318

Enzymes that can interconvert two enantiomers like D to L

Answer 319

Carbon linked to four different groups

Answer 320

Most monosaccharides with more than 5 carbon atoms are in a cyclic form Cyclization happens with the reaction of the aldehyde or keto group with the hydroxyl group of the same sugar to form a hemiacetal Cyclization creates a new asymmetric center at C1 for Aldo se and at C2 for ketose (anomeric carbon)

Answer 321

R-C-R || O

Answer 322

The asymmetric carbon made from monosaccharide cyclization

Answer 323

When glucose turns cyclic, a new pair of isomers is formed = α-D-glucopyranose and B-D-glycopyranose α = OH group on the anomeric carbon is on the same side as the ring or trans to the CH2OH group B = OH group on the anomeric carbon is on the opposite side as the ring or cis to the CH2OH Preferred conformation is the B anaomer because then the OH groups on C1 and C2 are opposite each other Slide 18 LM 7.2

Answer 324

Bonds that link sugars Formed between hemiacetal carbon of one sugar and a hydroxyl group of another sugar by enzymes called glycosyltransferases The bonds are blamed according to the numbers of the connected carbons and with regard to the position of the anomeric OH group of the first sugar α-1,4-glycosidic bond

Answer 325

Lactose = galactose + glucose Sucrose = glucose + fructose Maltose = glucose + glucose

Answer 326

Glycogen: Heavily branched, animal sources Starch Moderately branched, plant sources Cellulose Unbranched, plant sources All are polymers of glucose

Answer 327

Present in most of our tissues, mostly in muscle and liver Large branched polymer of glucose Main linkages are α,1-4 glycosidic bonds but branches are made of α,1-6 glycosidic bonds

Answer 328

Nutritional reservoir in plants Branched and unbranched forms More than half of the carbs ingested by humans is starch! Ex. Rice, potatoes, wheat

Answer 329

Found in plants Serves as a structural rather than nutritional role Important components of cell wall Unbranched polymer formed by B,1-4 linkages (starch and glycogen are α linkages)

Answer 330

If the OH group on the anomeric carbon of a cyclized sugar is not involved in a glycosidic bond then the ring can open - these sugars act as reducing agents and can react with chromogenic reagents The aldehyde (RCH=O) group gets oxidized to carboxyl group (RCOH=O) and the reagent is reduced to form a colored compound - used to detect presence of a reducing sugar in urine Fructose has a keto group but is also a reducing sugar since it can be isomerized to an Aldo se like glucose or galactose All monosaccharides are reducing sugars!!

Answer 331

It’s an energy-conversion pathway Takes place in the cytoplasm of eukaryotes and converts one molecules of glucose to 2 molecules of pyruvate with the generation of 2 molecules of ATP

Answer 332

- thought to be available for primitive biochemical systems because can form under prebiotic conditions - the most stable hexose so it has a low tendency to nonenzymatically glycosylate proteins

Answer 333

anaerobic glycolysis: pyruvate can undergo fermentation in the absence of oxygen to produce NAD+ aerobic glycolysis: pyruvate gets converted into acetyl CoA which then enters the TCA cycle to produce more reducing equivalents

Answer 334

stage 1: traps glucose in the cell and modifies it so that i can be cleaved into a pair of phosphorylated 3-carbon compounds step 2: oxidizes the 3-carbon compounds to pyruvate while generating 2 ATP

Answer 335

glucose + ATP -----------> glucose 6-phosphate (G-6P) catalyst: hexokinase cofactor: Mg+2 or Mn+2 hexokinase traps glucose in the cell and begins glycolysis. irreversible. G6P can't penetrate the cell membrane due to lack of cell surface receptors and because they are too polar to diffuse through membrane

Answer 336

G6P open chain G6P open chain fructose 6-phosphate fructose 6-phosphate catalyst: phosphoglucose isomerase catalyzes G6P to F6P in the open chain form (aldose to ketose) glucose 6-phosphate is converted into fructose 6-phosphate

Answer 337

F6P + ATP ---------> F1,6-BP + ADP + H+ catalyst: phosphofructokinase (PFK) fructose 1,6-bisphosphate is generated from fructose 6-phosphate ****this is the most important control point and rate limiting and committed step in glycolysis!!!**** IRREVERSIBLE

Answer 338

F1,6-BP DHAP + GAP catalyst: aldolase fructose 1,6-bisphosphate is cleaved into two 3 carbon compounds, dihydroxyacetone phosphate and glyceraldehyde 3-phosphate end of phase 1 of glycolysis, not regulated

Answer 339

DHAP GAP catalyst: triode phosphate isomerase DHAP converted to GAP so that it can enter into glycolysis so now you have to GAP molecules and each one will make a pyruvate so TWO pyruvate molecules are generated during a single glycolytic reaction

Answer 340

DHAP is used for synthesis of triglycerides

Answer 341

GAP + NAD+ + Pi 1,3-BPG + NADH + H+ catalyst: glyceraldehyde 3-phosphate dehydrogenase 1,3-bisphosphoglycerate is generated from the oxidation of GAP 1,3-BPG has high phosphoryl transfer potential the NAD+ used must be regenerated!! this is the first oxidation-reduction reaction takes two steps actually but just know it's done by coupling an energetically unfavorable reaction with a favorable one

Answer 342

1,3-BPG + ADP + H+ 3-phosphoglycerate + ATP catalyst: phosphoglycerate kinase ATP is formed by transfer of phosphate group from 1,3-bisphosphoglycerate since you made 2 GAP molecules, this process happens twice and you get 2 ATP!

Answer 343

3-phosphoglycerate 2-phophoglycerate phosphenolpyruvate + ADP + H+ ------> pyruvate + ATP catalyst 1: phosphoglycerate mutase catalyst 2: enolase catalyst 3: pyruvate kinase additional ATP is generated with the formation of pyruvate you get 2 more ATP here because you had two GAP molecules which made two 1,3-BPG which made two 3-phosphoglycerate

Answer 344

glucose + 2Pi + 2ADP + 2NAD+ --> 2pyruvate + 2 ATP + 2NADH + 2H + 2H2O

Answer 345

galactose and fructose galactose --> glucose-6P (G-6P) fructose --> fructose-6P (F-6P) in adipose tissue** fructose (liver) --> DHAP GAP

Answer 346

so that fructose can enter into glycolysis fructose + fructokinase --> fructose 1-phosphate THEN F1P + F1P-aldolase --> glyceraldehyde + *DHAP* THEN glyceraldehyde + ATP + triose kinase --> GAP + ADP DHAP + triode phosphate isomerase --> glyceraldehyde 3-phosphate

Answer 347

used to convert galactose to glucose so that it can enter glycolysis don't need to know the intermediates but just included it so stuff makes sense

Answer 348

regeneration of NAD+ is CRUCIAL for continuation of glycolysis ANAEROBIC 1. pyruvate + NADH --> lactate + NAD+ 2. P --> acetaldehyde + CO2 +NADH --> ethanol + NAD+ AEROBIC 3. P --> acetyl CoA + CO2 --> oxidative phosphorylation

Answer 349

formation of ethanol and lactate from pyruvate ethanol fermentation is carried out by yeast and bacteria - used to make bread, wine, biofuels lactic acid fermentation is carried out by bacteria in yogurt and your muscles under certain conditions

Answer 350

pyruvate + NADH + H+ lactate + NAD+ catalyst: lactate dehydrogenase net: glucose + 2Pi + 2ADP --> 2lactate + 2ATP + 2H2O anaerobic glycolysis in eukaryotes in poorly vascularized tissues like lenses and cornea of the eye or medulla of the kidney lactic acid fermentation also happens in RBC because they lack mitochondria lactate production also happens in tissues when oxygen is limited like during exercise

Answer 351

NADH production exceeds the oxidative capacity of the electron transport chain so now it's favorable for pyruvate to be reduced to lactate so during exercise lactate accumulates in the muscle which leads to a drop in intracellular pH and causes cramps eventually the lactate diffuses into the blood stream and is used by the liver to make glucose

Answer 352

the combustion of fuels into CO2 and water to generate ATP requires oxygen and takes place inside the double membrane of mitochondria has two parts: 1. TCA cycle 2. oxidative phosphorylation

Answer 353

acetyl CoA

Answer 354

serves as a bridge between carbohydrates and the TCA cycle the complex is made of 3 enzymes: 1. pyruvate dehydrogenase (E1 or PDH) 2. dihydrolipoyl transacetylase (E2 or DLTA) 3. dihydrolipoyl dehydrogenase (E3 or DLDH) two regulatory enzymes too that are also part of the complex: pyruvate dehydrogenase kinase and pyruvate dehydrogenase phosphatase

Answer 355

pyruvate + NAD+ + CoA-SH --> acetyl CoA + NADH + H + CO2

Answer 356

cofactors: lipoamide flavin adenine dinucleotide (FAD) thiamine pyrophosphate (TPP) enzymes: E1, E2, E3

Answer 357

oxidation of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate

Answer 358

3-phosphoglycerate phosphoglycerate kinase transfers phosphoryl group from 1,3-bisphosphoglyverate to ADP to form ATP and 3-phosphoglycerate

Answer 359

zero!! it's anaerobic

Answer 360

catalyzes the conversion of 2-phosphoglycerate to phosphoenol pyruvate

Answer 361

synthesis of glucose from noncarbohydrate precursors especially important during fasting or starvation because glucose is the primary fuel for the brain and the only field for RBC

Answer 362

liver can also occur in kidney during a prolonged fast

Answer 363

lactate, AA, and glycerol - pyruvate is made in the liver from muscle-derived lactate through lactate dehydrogenase - carbon skeleton of AA can be turned into pyruvate or oxaloacetate - glycerol is from the hydrolysis of triacylglycerols and can be converted into dihydroxyacetone phosphate

Answer 364

glucose + ATP --> G-6P + ADP fructose 6P + ATP --> fructose 1,6-bisphosphate + ADP phosphoenolpyruvate + ADP --> pyruvate + ATP all have -ΔG which means gluconeogenesis is NOT a complete reversal of glycolysis because these steps have to be bypassed also enzymes for glujconeogeneis are in the cytoplasm except for pyruvate carboxylase in the mitochondria and glucose 6-phosphatase which is membrane bound in the ER

Answer 365

need two enzymes in the mitochondria: pyruvate + CO2 + ATP + H2O oxaloacetate + ADP + Pi + 2H (enzyme = pyruvate carboxylase) now we need to go to the cytoplasm where everything else is so oxaloacetate is reduced to malate in the mitochondria. then the malate is exported to the cytoplasm and reduced back into oxaloacetate THEN oxaloacetate + GTP phosphoenolpyruvate (enzyme = phosphoenolpyruvate carboxylase)

Answer 366

glycerol + ATP + glycerol kinase --> glycerol phosphate + ADP glycerol phosphate + glycerol phosphate dehydrogenase + NAD+ --> dihydroxyacetone phosphate + NADH DHAP can go through gluceneogenesis or glycolysis depending on needs of the body two enzymes: glycerol kinase and glycerol phosphate dehydrogenase

Answer 367

F 1,6-BP + H2O + fructose bisphosphatase --> F-6P HIGHLY REGULATED STEP

Answer 368

1. occurs essentially only in the liver is the final step in gluconeogenesis 2. G-6P is transported into the lumen of the ER 3. glucose 6-phosphatase is an integral membrane enzyme on the inner surface of the ER, catalyzes the formation of glucose from glucose 6-phosphate

Answer 369

no they're regulated so that one is relatively inactive while the other is highly active

Answer 370

pyruvate carboxylase and phosphoenol pyruvate carboxylase

Answer 371

2 one ATP and one GTP used in the formation of oxaloacetate to glucose also one NADH is used

Answer 372

1. defects in specific enzymes cause inherited metabolic diseases - phenylketonuria - phenylalanine hydroxylase deficiency which produces abnormal AA metabolism - hemolytic anemia - glucose 6P dehydrogenase deficiency 2. enzymes are targets for many drugs 3. enzymes are useful as diagnostic markers and in the evaluation of organ function

Answer 373

1. proteins that facilitate catalysis 2. enhance reaction rate relative to uncatalyzed reacton 3. often stereospecific, distinguish between R and S isomers

Answer 374

proteins!! a small number of RNA has catalytic activity also prosthetic groups attached to proteins are usually required for enzyme activity

Answer 375

maximum velocity of an enzyme the number of substrate molecules converted to product per unit time under optimal conditions mcat is the turnover number = Vmax/# of active sites

Answer 376

1. oxidoreductases 2. transferases 3. hydrolases 4. lyases 5. isomerases 6. ligases

Answer 377

enzymes that catalyze oxidation/reduction reactions ex. dehydrogenases oxidize a substrate by a reduction reaction that transfers one or more hydrides to an electron acceptor like NAD or NADP ex. lactate + NAD+ pyruvate + NADH via lactate dehydrogenase

Answer 378

enzymes that catalyze transfer of C,N or P containing groups ex. amino, glycosyl, methyl or phosphoryl groups ex. glycogen synthase, kinases ex. serine + THF glycine + THF-CH2 via serine hydroxy-metal transferase

Answer 379

enzymes that catalyze hydrolysis ex. cleavage of C-C, C-O or C-N bonds ex. proteases, nucleases ex. special case of group transfer where h2o is acceptor ex. urea + H2O --> CO2 + 2NH3 via urease

Answer 380

enzymes that catalyze atom elimination often generating a double bond ex. cleavage of C-C or C-N bonds ex. non hydrolytic, nonoxidative ex. pyruvate decarboxylase ex. pyruvate --> acetaldehyde + CO2 via pyruvate decarboxylase

Answer 381

enzymes that catalyze geometric or structural changes within a molecules ex. phosphohexose isomerase, triode phosphate isomerase ex. methylmalonyl CoA succinylcholine CoA via methylmalonyl CoA mutase

Answer 382

enzymes that catalyze joining two reactants coupled to the hydrolysis of ATP - catalyze formation of bonds between carbon and O, S, and N coupled to hydrolysis of high energy phosphates like ATP many are caked syntheses ex. glutamine synthetase, glutathione synthetase, DNA ligase ex. pyruvate + CO2 + ATP --> oxaloacetate + ADP + Pi