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Biochemistry I > Biochemistry Lecture Exam 3 > Flashcards

Biochemistry Lecture Exam 3 Flashcards

1
Q

Carbohydrate

A

aldehydes or ketones with at least two hydroxyl groups, or substances that yield such compounds on hydrolysis

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2
Q

Monosaccharides

A

simple sugars, consist of a single polyhydroxy aldehyde or ketone unit

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3
Q

Oligosaccharides

A

short chains of monosaccharides units joined by glycosidic bonds

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4
Q

Disaccharides

A

oligosaccharides with two monosaccharide units

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5
Q

Polysaccharides

A

sugar polymers with 1+ monosaccharides units

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6
Q

Epimers

A

two sugars that differ only around one carbon atom

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7
Q

Pyranose

A

six membered ring compounds

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8
Q

Furanose

A

five membered ring compounds

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9
Q

What is an aldose?

A

carbonyl group is at an end of the carbon chain (in an ALDEHYDE group)

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10
Q

What is a ketose?

A

carbonyl group is at any other position but the end (in a KETONE group)

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11
Q

Which isomer (D or L) are most sugars in nature?

A

D

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12
Q

For glucose, what carbon is the carbonyl carbon?

A

Carbon 1

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13
Q

For glucose, what carbon is the anomeric carbon?

A

Carbon 1

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14
Q

What cyclical form does glucose typically take?

A

Pyranose form is most common

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15
Q

What is an aldonic acid?

A

form following oxidation of the carbonyl carbon of aldoses

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16
Q

What is an uronic acid?

A

form following oxidation at carbon 6

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17
Q

What position of the sugar is the reducing end? How can that be used to detect sugar in a solution?

A

-Reducing End: the end of a disaccharide or polysaccharide chain with a free anomeric carbon
-Produces color change when combined with different sugars (we did this in lab so I think this is right)

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18
Q

What is a homopolysaccharide?

A

contain only one single monomeric sugar species; serve as storage forms and structural elements

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19
Q

What is a heteropolysaccharide?

A

contain 2+ kinds of monomers; provide extracellular support

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20
Q

Name two biologically important homopolysaccharides?

A

starch and glycogen

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21
Q

What are some roles of polysaccharides?

A

Mainly have structural and energy storage roles

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22
Q

What is the structure of glycogen? What types of bonds occur and what types of sugar is involved?

A

-Heavily hydrated with many exposed hydroxyl groups that are available to hydrogen bond
-Most stable 3D structure is a helical structure with six residues/turns; more extensively branched and more compact than starch
-made of glucose sugar

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23
Q

What are glycosaminoglycans and what types of modifications are made to the sugars found in GAGs?

A

-Glycosaminoglycans: heteropolysaccharides found in the ECM; linear polymers composed of repeating disaccharide units; unique to animals and bacteria
-Different groups on the GAG is the modifications (amine group, sulfate added, carboxyl added)

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24
Q

Glycoconjugate

A

biologically active molecule consisting of an informational carbohydrate joined to a protein or lipid

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25
Q

Proteoglycan

A

macromolecules of the cell surface or ECM consisting of 1+ sulfated glycosaminoglycan chain(s) joined covalently to a protein or secreted protein; major component of extracellular matrices

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26
Q

Glycoprotein

A

have one or several oligosaccharides joined covalently to a protein; found on the outer surface of the plasma membrane

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27
Q

Glycolipid

A

plasma membrane components in which the hydrophilic head groups are oligosaccharides

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28
Q

What features of GAGs cause proteoglycan aggregates to form larger structures in the ECM?

A

-The 1+ sulfated glycosaminoglycan chain joins covalently to a membrane protein or secreted protein?

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29
Q

What is the difference between N and O linkages in glycoproteins?

A

-N-linked: an N-glycosyl bond joins the anomeric carbon of a sugar to the amide nitrogen of an Asn residue
-O-linked: a glycoside bond joins the anomeric carbon of a carbohydrate to the -OH of a Ser or Thr residue

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30
Q

What is a lectin and what does it do biologically?

A

-Lectin: bind carbohydrates with high specificity and with moderate to high affinity
-Functions: cell-cell recognition, signaling, adhesion, intracellular targeting of newly synthesized proteins

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31
Q

Nucleotide

A

a nucleoside phosphorylated at one of its pentose hydroxyl groups

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32
Q

Nucleoside

A

a compound consisting of a purine or pyrimidine base covalently linked to a pentose; the molecule without the phosphate group

33
Q

Gene

A

a chromosomal segment that codes for a single functional polypeptide chain or RNA molecule

34
Q

rRNA

A

components of ribosomes

35
Q

mRNA

A

intermediates in protein synthesis

36
Q

tRNA

A

adapter molecules that translate the information in mRNA into a specific amino acid sequence

37
Q

ncRNA

A

wide variety of functions (Does NOT code for proteins)

38
Q

Purine

A

a nitrogeneous heterocyclic base that is a component of nucleotides and nucleic acids; A and G

39
Q

Pyramidine

A

a nitrogenous heterocyclic base is a component of nucleotides and nucleic acids; C, T, and U

40
Q

How do pyramidine and purine structures differ? What nucleotides will base-pair using Watson-Crick pairing?

A

-Pyrimidines are planar and purines have a slight pucker
-Purines have a 2-ringed structure and pyrimidines only have one
-A base pairs with T (or U in RNA) with 2 H bonds
-G base pairs with C with 3 H bonds

41
Q

What is a phosphodiester bond? What charge does it have?

A

-Phosphodiester bond is a covalent bond that joins successive nucleotides of both DNA and RNA between the 5’ phosphate of one nucleotide and the 3’ hydroxyl of the next nucleotide
-Negative Charge

42
Q

Why is DNA inherently more stable than RNA?

A

-RNA is rapidly hydrolyzed due to the 2’ hydroxyl groups

43
Q

What wavelength of light do nucleotides absorb the most? What happens to light absorption when DNA strands denature?

A

-260 nm is the strongest absorbtion
-More light is absorb when DNA strands are denatured

44
Q

What type of double helix is found in nature?

A

-B form

45
Q

What is the difference between a nucleotide and a nucleoside?

A

-Nucleotides have 3 components: a nitrogenous base, a pentose, and a 1+ phosphate
-Nucleoside is the molecule without a phosphate group

46
Q

What are the common classes of RNA and what are their functions?

A

-rRNA: components of ribosomes
-mRNA: carries genetic information to the ribosome
-tRNA: adapter molecules that translate the information in mRNA into amino acid sequences
-ncRNCA: wide variety of functions; do not code for proteins

47
Q

What are some structural characteristics of RNA?

A

single stranded, ribose sugar, 2’ hydroxyl

48
Q

What is annealing?

A

process by which 2 strands spontaneously rewind when temperature or pH is returned to its normal range

49
Q

What type of damage is typically caused by UV light exposure?

A

pyrimidine dimers

50
Q

What nucleotide base is most subject to deamination? What does it become?

A

Cytosine turns into uracil

51
Q

Where does the chemical energy of a nucleotide come from?

A

-Hydrolysis of nucleoside triphosphates (ATP)
-Has 3 bonds between different phosphates and the breaking of those bonds creates energy

52
Q

Genome

A

the complete haploid genetic complement of an organism

53
Q

DNA Cloning

A

selective amplification of a particular gene or DNA segment so that its genetic information may be studied and utilized

54
Q

Recombinant DNA

A

composite DNA molecules comprimised of covalently linked segments from 2+ sources

55
Q

Cloning Vectors

A

small DNAs campable of autonomous replication

56
Q

Restriction Enzymes/Endonucleases

A

recognize and cleave DNA at specific sequences

57
Q

Ligase

A

joins the DNA fragments to be cloned to a suitable cloning vector

58
Q

Plasmid

A

circular DNA molecule that replicates separately from the host chromosome

59
Q

Shuttle Vectors

A

plasmids that can be propagated in cells of 2+ species

60
Q

What is cloning and how is it used to study/modify a region of DNA?

A

-DNA cloning: selective amplification of a particular gene or DNA segment so that its genetic information may be studied and utilized

61
Q

What type of sequences do restriction endonucleases target and how does that lead to the formation of sticky/ blunt ends for cloning?

A

-Restriction endonucleases target palindromic sequences and make staggered cuts which leads to blunt and sticky ends

62
Q

What is a plasmid and how can plasmids be used to bring DNA into the cell?

A

Plasmids are circular DNA molecules that replicate separately from the host chromosome that usually have a symbiotic role in the cell

62
Q

What is the difference between selectable marker and screenable marker?

A

-Selectable Marker: either permits the growth of a cell (positive selection) or kills the cell (negative selection) under defined conditions
-Screenable Marker: gene encoding a protein that causes the cell to produce a colored or fluorescent molecule

63
Q

What are some strengths and weaknesses of bacterial expression systems?

A

-Strengths: regulatory sequences are well understood, can express high levels of cloned proteins, easy to store and grow, efficient methods for transforming and extracting DNA, can be grown in huge amounts
-Weaknesses: some heterologous proteins do not fold correctly, proteins may not undergo necessary posttranslational modifications or proteolytic cleavage, some gene sequences can be difficult to express

64
Q

What are some strengths and weaknesses of yeast expression systems?

A

-Strengths: well-understood eukaryotic organism, expression of eukaryotic genes can be more efficient, proteins may be folded and modifies more accurately
-Weaknesses: heterologous proteins may not fold properly, yeast may lack the enzymes needed to modify the proteins to their active forms, certain features of the gene sequence may hinder expression of a protein

65
Q

What methods can be used to change a nucleotide sequence in order to change an amino acid sequence?

A

Oligonucleotide-Directed Mutagenesis or Site-Directed Mutagenesis

66
Q

Fusion protein

A

product of a ligated gene containing parts of two different genes

67
Q

Tag

A

peptide or protein that binds to a sample, stable ligand with high affinity and specificity

68
Q

RT-PCR

A

uses reverse transcriptase to generate a DNA strand from an RNA template, followed by the standard PCR protocols using DNA polymerase

69
Q

qPCR

A

is used to estimate relative copy numbers of particular sequences in a sample

70
Q

cDNA

A

double-stranded DNA fragments formed from mRNA templates (relies on reverse transcriptase)

71
Q

Transcriptome

A

the entire complement of transcribed RNAs present at a given moment in the cell

72
Q

Proteome

A

the entire complement of proteins present at a given moment in a cell

73
Q

How can tags be used to specifically purigy proteins or identify their location in a cell?

A

-fuse to gene encoding target protein and permits purification by affinity chromatography
-help to provide good yield and high purity and may affect the properties of attached proteins

74
Q

How are PCR and qPCR similar and how do they differ?

A

-Both amplify DNA using primers and DNA polymerase
-qPCR measures fluorescence in real time and gives a quantitative measure of the results

75
Q

How does immunoprecipitation work?

A

-Immunipreciption: process of precipitating a fusion protein (containing the gene of interest and a gene for an epitope tag) by antibodies to the epitope
-proteins that bind to the tagged protein will also precipitate

76
Q

How does tandem affinity purification work?

A

-Tandem Affinity Purification (TAP) tags: two consecutive tags that are fused to a target protein to enhance the selectivity of immunopreciption
-First tag (protein A) binds mammalian IgG
-Second tag (calmodulin-binding peptide) binds calmodulin

77
Q

What is a yeast two-hybrid experiment? What can you learn from it?

A

-technique that relies on the properties of the GaI4 protein
-two domains of GaI4p must be brought together to function correctly
-probes molecular interactions in vivo

78
Q

How does the CRISPR-Cas9 system work?

A

-The CRISPR/Cas Complex binds and the Cas9 two separate domains cleave opposite strands of DNA
-The sgRNA guide sequence can be altered to target any genomic sequence
-required to pair with the target DNA sequence and to activate the nuclease domains
-cells in which genes required to survive the treatment are inactivated or activated by teh CRISPR/Cas9 varient will die or thrive

Biochemistry I (6 decks)

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