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Biochem test 1 > test 1 > Flashcards

test 1 Flashcards

1
Q

What is biochemistry?

A

how we explain life at a molecular level

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2
Q

4 main characteristics of biochem

A

1) all organisms are composed of 4 macromolecules
2) energy in organisms: use, transform, storage, acquire
3) information passed generation to generation
4) Macromolecules held together (maintain structure) through weak forces

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3
Q

6 Main elements found in biological systems

A

SCHNOP

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4
Q

Ether

A

ROR

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5
Q

Ester

A

R-c=O also with C-OR

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6
Q

Cells contain which 4 major biological molecules

A

amino acids, carbohydrates, nucleotides, lipids

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7
Q

Amino Acids contain

A

an amino group (think NH3+), carboxylic acid, and side chain

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8
Q

Carbohydrates contain

A

lots of alcohol!! (think you always crave carbs when drunk)

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9
Q

Nucleotides contain

A

phosphate, nitrogenous base (think pyridine or purine), and 5 carbon sugar

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10
Q

Lipids

A

Hydrocarbon rings/ chains that primarily lack oxygen
hydrophobic
most important in human health= cholesterol

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11
Q

3 major biological polymers

A

polypeptides and proteins (amino acids), nucleic acids (nucleotides), and polysaccharides

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12
Q

Amino acid links

A

residues linked by peptide bonds (covalent)
sequences read from N terminus to C terminus

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13
Q

Functions of proteins

A

metabolic functions
structural (think collagen in cells)
energy storage (not best way)

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14
Q

Nucleotide links

A

residues link through phosphodiester bonds (covalent)
sugars are bonded through glycosidic bonds (covalent) (sounds like glucose)

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15
Q

Functions of nucleic acids

A

store info
structural (minor)
metabolic

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16
Q

Polysaccarides

A

linked sugars
Function:
info (blood cell antigen)
store energy (major)
structural

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17
Q

What types of bonds are present in DNA

A

phosphodiester and glycosidic

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18
Q

Why use hydrogen bonds in DNA

A

weak attractions= good bc requires less energy to break to use/ translate

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19
Q

Why is water a good solvent

A

high dielectric constant (water= more attracted to ions than ions to other ions)

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20
Q

Why is cellular environment fluid

A

want fluid environment for easier transport

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21
Q

Purine structure

A

4 N, hexagon + pentagon

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22
Q

Which nucleic acids are purines

A

adenine and guanine

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23
Q

Pyrimidine structure

A

2 N, hexagon

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24
Q

Which nucleic acids are pyrimidines

A

cytosine, thymine, uracil
(CUT)

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25
Q

Ribose vs Deoxyribose

A

ribose has alcohol in 2’ corner while deoxyribose has H in 2’ corner

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26
Q

Nucleoside

A

intermediate, contains nitrogenous base and 5 C sugar

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27
Q

Nucleotide vs Nucleoside

A

Nucleotide= nucleoside PLUS a phosphate group
(phosphate always has neg charge)

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28
Q

How do nucleotides link

A

via sugar in phosphodiester backbone (goes sugar phosphate sugar phosphate0
nucleotides are connected via phosphodiester binds
read bases 5’–> 3’
5’ end has free phosphate, 3’ end has free OH

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29
Q

Nucleotide base pair numbers

A

A+G=T+C (# of purines = # of pyrimidines to have consistent length)

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30
Q

DNA double helix characteristics

A

1) antiparallel
2) right handed helix
3) diameter/ turns (20A)
4) major groove and minor groove
5) Mg2+ interact with phosphate
6) bases face inward
7) bases stack (van der waals)

31
Q

RNA structure

A

single stranded
same backbone and comp pairing

32
Q

What does stability of DNA double helix depend on?

A

stacking interactions
higher % of G and C= harder to pull DNA apart (which also means higher melting temp)

33
Q

genes to proteins

A

DNA undergoes replication
DNA undergoes TRANSCRIPTION to RNA
RNA undergoes TRANSLATION to protein

34
Q

Nucleases

A

cleave phosphodiester bonds
endonucleases cleave w/in molecule
exonucleases cleave at ends (5’ or 3’)

35
Q

Replication goal

A

copy all of the DNA in cell
accomplish by separating double stranded DNA

36
Q

What do you need to accomplish replication

A

different enzymes
control temperature (especially outside the cell0
template (DNA)
dATP, dTTP, dCTP, dGTP (____ triphosphate for deoxyribose) (nucleotides)

37
Q

DNA is replicated ______

A

semiconservatively
parent with daughter (helps us minimize error)

38
Q

locomotive theory

A

OLD THEORY, enzymes/ proteins move along strand like a train

39
Q

factory theory

A

CURRENT THEORY, DNA moves through and enzymes/ proteins stay stationary

40
Q

How does replication begin?

A

replication fork opens up DNA
process of replication moves in both directions (so 2 forks)

41
Q

Proteins needed for replication

A

helicase
topoisomerase
DNA polymerase
RNA polymerase
Primase
DNA ligase

42
Q

Helicase

A

unwinds DNA
uses ATP energy source
function: protect from nucleases and prevents secondary structure from forming

43
Q

Topoisomerase

A

goal: relieve strain introduced by helices (pulling it apart adds strain and tightens up)
how? cutting DNA (phosphodiester bonds)

44
Q

Prokaryotic vs Eukaryotic unwinding

A

Pro: single stranded
Eukaryote: binding protein
eukaryote has special replication name: replication protein A (RepA)

45
Q

DNA polymerase basics

A

prokaryotic polymerases: 5 (use Roman numerals)
eukaryotic polymerases: 14 (use greek letters)
Most polymerases are processive (hang onto DNA for long periods of time)
Prokaryote most processive: pol III
Eukaryote most processive: pol E

46
Q

DNA polymerase rules

A

can only extend a preexisting chain
cannot initiate polynucleotide synthesis (work 5’–>3’ direction)

47
Q

RNA polymerase/ primase

A

10-25 nucleotides to get process started

48
Q

DNA replication- leading and lagging strand

A

lagging strand loops out

49
Q

proofreading during polymerization

A

3’–>5’ exonuclease (3’–>5’ because mistake @ 3 end and works backwards)
DNA pol 1 will remove nucleotide in prokaryotes

50
Q

completing the lagging strand

A

RNase H- removes primer in eukaryotes
ligase- repairs phosphodiester bond (gives back together)

51
Q

transcription goal

A

DNA (stored) converts to RNA (active)
selective

52
Q

what is required transcription

A

enzymes/ proteins –> Polymerase RNA (synthesize mRNA)
DNA template
nucleotide triphosphate (NTPs)

53
Q

what is a gene

A

-RNA transcript includes all info specifying sequence of amino acids
-Most RNA transcripts correspond to a single functional unit (exception: pro operon)
-RNA transcripts undergo processing- addition, removal, and modification of nucleotides before becoming fully functional
-transcription may depend on not transcribed DNA that help position RNA polymerase at start site or are involved in gene expression regulation

54
Q

Types of RNA

A

mRNA- transcription
tRNA translation
noncoding RNA- regulation
in cell

55
Q

DNA packaging and transcription

A

ADD PICTURE LATER

56
Q

Transcription initiation

A

Promoter- DNA sequence, helps recruit machinery needed for transcription =, NOT A PROTEIN but sequence in DNA
Recognition:
Specific proteins- recognize promoter sequence
RNA polymerase- recruit

57
Q

E Coli Promoter

A

-35 region: TATA box promoter region
-10 region: promoter region
#= how many nucleotides from start site (neg= upstream (5’), pos= upstream (3’))
prokaryotic

58
Q

Sigma factor

A

Core enzyme + Sigma factor–> Holoenzyme
core enzyme: required for polymerization activity, 1 RNA pol in prokaryotes
Sigma factor: only possible variable factor, role= recognizer promoter, 7 different sigma factors
Holoenzyme: required for correct initiation of transcription: binding to promoter

59
Q

Eukaryotic start size

A

NOT predictable, hard to find

60
Q

Transcription factor II (TFII)

A

A, B, D, E, F, H
works with helicase
Due to RNA polymerase II, transcribes mRNA
recognizes promoter

61
Q

Eukaryotic regulation

A

enhancer
w/o an activator nothing occurs!
Silencer (DNA sequence)
Repressor (protein)
Mediator

62
Q

Enhancer

A

DNA sequence–> enhance transcription of certain gene

63
Q

Mediator

A

multiple proteins that will connect activator w/ transcription machinery to start process (gives physical connection)

64
Q

Repressor

A

protein
physically turn on/ off based on need
gets in the way of transcription occurring

65
Q

Prokaryotic regulation

A

operons allow coordinated gene expression
gene that makes repressor–> promoter–> operator–> operon (2-4 genes that work together)

66
Q

Initiation summary

A

Prokaryotes: promoters, RNA polymerase, regulation
Eukaryotes: same as prokaryotes PLUS general transcription factors

67
Q

RNA transcription

A

doesn’t need starting point/ primer for RNA polymerase

68
Q

3 Eukaryotic polymerases:

A

RNA Polymerase I: rRNA
RNA Polymerase II: mRNA
RNA Polymerase III: tRNA/ other small RNAs

69
Q

Transcription initiation to elongation

A

transcription machinery is firmly with promoter
DNA scrunching (prokaryotes)- sigma factor is released
Phosphorylation of C-terminal end of large subunit

70
Q

Difference between coding strand and mRNA

A

T to U, otherwise the exact same
template/ noncoding/ antisense strand= what you translate

71
Q

Transcription termination mechanisms (prokaryotes)

A

a couple of factors to end: rho factor dependent and independent
idea= destabilize DNA RNA hybrid

72
Q

Eukaryotic termination

A

same idea as prokaryotes
RNA polymerase slows/ pauses (during splicing/ following polyadenylation signal)
during pausing - proteins may bind to phosphorylated C-terminal domain and trigger termination
after mRNA has been cut an exonuclease may “eat away” the tail of the RNA until it catches up with polymerase and nudges it away from the template

73
Q

RNA processing

A

Eukaryotes only!!!
mRNA 5’ cap to protect end of transcript from exonucleases
addition of poly A tail (3’ end)
AAUAAA= signal for poly A tail, makes it slow down and get ready for termination

74
Q

5’ cap

A
  1. triphosphatase removes phosphate
  2. transferase transferes GMP (guanine monophosphate)
  3. addition of methyl groups

Biochem test 1 (2 decks)

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