Exam 2

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  • Uracil
  • pyrimidine
  • nucleoside name uridine 

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  • thymine
  • pyrimidine
  • nucleoside name thymidine 

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  • cytosine
  • pyrimidine
  • nucleoside name  cytodine

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  • Adenine
  • purine
  • nucleoside name adenosine

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  • guanine
  • purine
  • nucleoside name guanosine

example of a primary protein structure
a polypeptide chain
example of a secondary protein structure

the helix

the pleated sheet

an example of a tertiary protein structure
myoglobin with heme
which bonds are broken during protein hydrolysis
amide bonds
Which bonds and/or attractions are affected by denaturation

hydrogen bonds

ionic attractions

hydrophobic interactions

disulfide bridges

What is true about denaturation?

  • a denatured protein has a different tertiary structure than its native state
  • egg white meringue contains denatured proteins
  • soakin fish in lime juice to make ceviche denatures the proteins 
  • digestive enzymes hydrolyze proteins

What are the characteristics of enzymes?

  • an enzyme yields a specific product, whereas a nonbiological catalyst may produce more than one product, and side reactions may occur
  • a sustrate must bind to the active site before a reaction occurs
  • an enzyme is specific for a substrate
  • reactions occure at the active site, which usually consists of a crevice on the surface of the enzyme

Describe lock-and-key model of an enzyme.

  • enzyme atcive site has a rigid structure complementary to that of the substrate 

describe the induced-fit model of an enzyme.
enzyme conformation changes when it binds the substrate so the active site fits the substrate
what happens to an amino acid at pH<isoelctric pH (pI)?

the carboxylate anion picks up a proton (COO- becomes COOH)

 

what are nucleic acids?

  • unbranched polymers composed of repeating monomers called nuleotides
  • DNA and RNA are nucleic acids

 

What are some common characteristics of induced-fit and lock-and-key models of enzymes?

  • substrate binds to the enzyme at the active site, forming an enzyme-substrate complex
  • substrate binds to the enzyme through noncovalent interactions 

describe competitive inhibitor

  • inhibitor structure resembles substrate structure
  • inhibitor does not alter the maximum reaction rate

describe a non-competitive inhibitor

  • inhibitor distorts the shape of the enzyme
  • inhibitor binds noncovalently at other than active site 

What is the role of mRNA
messenger RNA carries the information from DNA to the ribosome
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  • the monosaccharide present in DNA
  • beta-furanose form 

What are the structural features of a purine?

  • contain two heterocyclic rings
  • contain four ting nitrogens 

what are the structural features of a pyrimidine?

  • contains one heterocyclic ring
  • contains only two ring nitrogens

What is a phosphoester bond?

P—O—C

 

what is a phosphoanhydride bond?
P—O—P
What is a phosphoanhydride bond?
P—O—P
Replication

  • both DNA strands are duplicated
  • semi-conservative
  • uses DNA polymerase

transcription
single DNA strand is used to produce mRNA
translation

  • amino acids added to peptide chain
  • requires tRNA
  • ribosomes 
  • RNA to protien

In which dirction does replication occur?
3′ end to the;5′ end
tRNA

  • anticodon
  • smallest RNA molecule
  • transports amino acids 

mRNA

  • carries genetic information from nucleus to cytoplasm 
  • contains the sequence of codons that determines the order of amino acids in the protein
  • initiation begins with mRNA bindind to the ribosome

rRNA
combines with protein to form ribosomes

Describe silent mutation and give examples

  • the new codon codes for the same amino acid
    • substitution of one base: a codon is changed from UAU to UAC
    • a base substitution does not have any noticeable effects 

Describe a missense mutation and give examples.

  • the new codon codes for a different amino acid
    • substitution of one base: a codon is changed from GAG to GUG
    • substitution of one base: a codon is changed from CAC to CGC
    • a person makes a protein of normal length but with altered function 

describe a nonsense mutation and give examples

  • the new codon is a stop codon
    • subtitution of UGA for a codon
    • a person makes a truncated, nonfunctional protein 

Name the basic amino acids

 

  • Arginine – Arg – R – essential
  • Histidine – His – H – essential
  • Lysine – Lys – K – essential

Name the acidic amino acids

  • Aspartic acid – Asp – D
  • Glutamic acid – Glu – E 

What are the essential amino acids?

  • Isoleucine
  • leucine
  • methionine
  • phenylalanine
  • threonine
  • tryptophan
  • valine
  • arginine
  • histidine
  • lysine 

Myoglobin
stores oxygen in the tissues
myosin
controls muscle contractions
What is the role of rRNA?
ribosomal RNA provides the site where polypeptides are assembled during protein synthesis
simplest amino acid
glycine
What determines an L- or D-amino acid?
If the amide group is on the left then it is an L-amino acid
What is the charge of an amino acid at a pH equal to its pI?
neutral
what is the charge of an amino acid ant a pH below its pI?
positive
What is the charge on an amino acid at a pH above its pI?
negative
What is the strongest type of interaction between two cysteine amino acids in a protein?
disulfide bond
What is the strongest type of interaction between an isoleucine amino acid and a phenylalanine amino acid?
london dispersion forces (all carbons)
What is the process of altering the shape of a protein without breaking the amide bonds that form the primary structure?
denaturation
what is a zymogen
an inactive form of an enzyme that can be converted to the active form when needed
What is the three-dimensional arragement of localized regions of a protein into α-helices and β-pleated sheets called?
secondary structure of protein
What are some characteristics of an α-helix?

  • the N—H and the C=O bonds point along the axis of teh helix in opposite directions
  • there are 3.6 amino acids  in each turn of the helix
  • the C=O group of one amino acid is hydrogen bonded to an N—H group four amino acid residues farther along the chain  

examples of globular proteins

hemoglobin

myglobin

alpha-keratins

  • found in hair, hooves, nails skin, and wool
  • nonpolar amino acids exten outwrd from the helix
  • insoluble in water
  • super coil or superhelix

collagen

  • most abundant protein
  • connective tissues
  • glycine and proline are are large fraction of its amino acid residues
  • left-handed helis
  • right-handed super-helix or triple-helix 

What happens when the pH>isoelectric pH of an amino acid?

The ammonium cation loses a proton and the amino acid has a net negative charge

(NH3+ becomes NH2)

What is denaturation?
te process of altering the shape of a protein without breaking the amide bonds that form the primary structure.
What is a co-factor?
a metal ion or an organic molecule needed for an enzyme-catalyzed reaction to occur.
What is teh role of tRNA?

  • transfer RNA brings specific amino acids to the ribosomes for protein synthesis
  • is drawn as a cloverleaf shape

What happens during transcription?

  • is the synthesis of mRNA from DNA
  • DNA splits and the template strand used to make RNA
  • proceeds from the 3′ end to the 5′ end
  • U replaces T on the mRNA strand

Where are new phosphodiester bonds formed?
between the 5′ -phosphate of the nucleoside triphosphate and the 3′ -OH group of the new DNA strand
What is elongation?
elongation proceeds as the next tRNA molecule delivers the next amino  acid, and a peptide bond forms between teh two amino acids
What is a mutation?
a change in the nucleotide sequence in a molecule of DNA
What is a point mutation?
the substitution of one nucleotide for another
What is a deletion mutation?
when one or more nuclotides is?are lost from a DNA molecule
What is an insertion mutation?
when one or more nucleotides is/are added to a DNA molecule
What is a silent mutation?
when the resulting mutation codes for an amino acid that is identical