Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIO130 > Test 1 > Flashcards

Test 1 Flashcards

1
Q

Endosymbiont model

A
  • Bacterial endosymbiont engulfed by archael membrane fusions
  • Archael membrane fusion protrusions expanded to fully engulf
    (precursor to aerobic eukaryote)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

E3 model / common features of both models

A

Entangle, engulf, endogenize

An ancient anaerobic archael cell, an ancient aerobic bacterium, and over evolutionary time, a symbiotic relationship between the two

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Evidence of endosymbiant hypothesis

A
  1. Mitochondria / chloroplasts still have remnants of their own genomes and their genetic systems resemble that of modern-day prokaryotes
  2. Mitochondria and chloroplasts have kept some of their own protein and DNA synthesis components and these also resemble prokaryotes
  3. Membranes in mitochondria and chloroplasts often similar to those in prokaryotes and appear to have been derived from engulfed bacterial ancestor
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Info flow in the cell: the central dogma

A

DNA - transcription - RNA - translation - PROTEIN

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Genome

A

All DNA in the cell (includes mitochondrial and chloroplast DNA)
- doesn’t change

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Transcriptome

A

All RNA in the cell at a particular point in time
- changes constantly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Proteome

A

Protein in a cell at a point in time
- changing constantly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Interactome

A

Set of protein-protein interactions happening in a cell at a point in time

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Metabolome

A

Set of metabolites found in a cell at a point in time (smaller than proteins ex. sugars, ATP, vitamins)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Phenome

A

Whole collection of -omes together with some characteristic (way to connect -omes with physical traits)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are nucleic acids

A

The genetic material in a cell: organism’s blueprints
- DNA, RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

3 parts of a nucleotide

A
  1. Pentose sugar
  2. Nitrogenous base
    - attached to 1’C
    - gives nucleotide its identity
  3. Phosphate group (1, 2, or 3)
    - gives DNA its overall negative charge
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Nucleoside, deoxyadenosine

A

Just a base and a sugar, no phosphate
(Nucleoside monophosphate, diphosphate, triphosphate)

Deoxyribose sugar instead of ribose sugar with adenosine nitrogenous base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Nucleic acid chain synthesis and linkages

A

DNA is synthesized from deoxyribonucleic triphosphates, otherwise known as dNTPs

RNA is synthesized from ribonucleoside triphosphates or NTPs

Nucleotides are linked by phosphodiester bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Three forces that keep DNA strands together

A

H bonds, hydrophobic interactions, van der Waals attractions (temporary dipole interactions becomes important in great numbers such as crowded DNA arrangements)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

DNA structure

A

Energetically favourable conformation

Protein can recognize and bind to sequences in major and minor grooves

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Two ends of DNA strands

A

5’ Phosphate group
3’ OH group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Protein structure: hierarchal organization

A

Primary (sequence)

Secondary (local folding)

Tertiary (long-range folding)

Quarternary (multimeric organization)

Multi protein complexes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Amino acid structure / major categories of amino acids

A

R group determines type of amino acid
R group, amino group, alpha carbon, carboxyl group

Basic, acidic, nonpolar, uncharged polar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Roles of amino acid types

A

POLAR
Negatively/positively charged: enzymatic function, shape
Uncharged: on the outside of proteins to interact with water (cell is full of water)

NONPOLAR
Often form inner core of proteins since they are hydrophobic, associated with lipid bilayer in proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Cysteine: disulphide bonds

A

Oxidizing conditions can create bond between cysteines in two polypeptide chains (interchain) or within a single peptide (intradisulfide bond)

  • very strong covalent bond
  • important for proteins undergoing chemical/mechanical stress
  • in cytosol, less needs for these bonds as reducing conditions are favoured
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Peptide bond formation

A

Reaction between carboxyl group of one amino acid and amino group of another amino acid

Hydrolysis releases water (peptide bond formed by a condensation reaction)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Primary protein structure

A

Amino acid has a carbonyl, no longer carboxyl, peptide bond to N of adjacent amino acid

N terminus and C terminus

NCC backbone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Once an amino acid has been joined by a peptide bond, it is called a …

A

Residue, due to the effect of the loss of the water molecule

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Alpha helix structure

A

R groups not involved

Bonds form 4 residues apart between carbonyl oxygen and amide hydrogen parallel to axis of helix

3 amino acids per turn, begin to see helix after 2 bonds form

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Alpha helix vs DNA double helix

A

ALPHA HELIX
- single stranded
- R-groups face out

DNA DOUBLE HELIX
- usually double-stranded
- bases face out

Both have polarity, but of different types

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Beta sheet

A

H-bonding between carbonyl oxygen and amide hydrogen of amino acid in a neighbouring polypeptide strand

R groups not involved, but alternately point up and down

Typically contain 4-5 strands but can have 10+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Two types of beta sheets

A

Anti-parallel

Parallel
- longer due to extra looping to connect strands

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

H-bonding in secondary structures summary

A

Which atoms H-bond?
Carbonyl oxygen, amide hydrogen in peptide backbone

Alpha helices
4 amino acids apart within the same segment of the polypeptide chain

Beta sheet
Between amino acids in different segments or strands of polypeptide chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Coiled coil

A

Two helices wrap around each other to minimize exposure of hydrophobic amino acid side chains to aqueous environment (hydrophobic R groups get pushed into the middle)

Strong structure: found in alpha-keratin of skin, hair, motor proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Amphipathic (type of alpha helix)

A

Means it has hydrophobic and hydrophilic areas, coiled coil is an example of an amphipathic alpha helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Tertiary structure

A

3D overall structure of a protein held together by:
- hydrophobic interactions
- non-convalent bonds
- covalent disulfide bonds (“atomic staple” which really helps hold together tertiary structure)

Proteins generally fold into the most energetically favourable conformation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Proteins fold into the shape dictated by …

A

Their amino acid sequences.

But chaperone proteins help make the process more efficient and reliable in living cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Protein domains

A

Specialized for different functions

Portion of a protein that has its own tertiary structure, often functioning in semi-independent manner

Connected by intrinsically disordered sequences

(Whole protein and all domains still made up of one continuous polypeptide)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Protein families

A
  • similar amino acid and tertiary sequences
  • members have evolved to have different functions
  • most proteins belong to families with similar structural domains
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Quarternary structure

A

Only in proteins with more than one polypeptide chain, held together by covalent bonds
- each subunit in separate polypeptide

Ex. Hemoglobin has 2a and 2b subunit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Multi protein complexes and molecular machines

A
  1. Can be many identical subunits (ex. actin filaments)
  2. Mixture of different proteins and DNA/RNA (ex. viruses and ribosomes)
  3. Very dynamic assemblies of proteins to form molecular machines (ex. for DNA replication initiation or transcription)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Scaffold proteins

A

Get interacting proteins close together so they can interact more quickly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

How are proteins studied

A
  • purify protein (separate from other cell material)
  • determine amino acid sequence (can be by mass spectrometry)
  • discover precise 3D structure (NMR, crystallography, AI)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Proteomics

A

Large scale study of proteins, researchers use a range of approaches to collect data on the set of proteins in a sample including
- identity and structure
- protein-protein interactions
- adbundance and turnover
- location in cell or tissue

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

1 kb

A

1000 base pairs (one kilo base pair)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Bacterial genome shape

A

Circular

43
Q

Organelles genomes

A

Circular
- support for endosymbiant theory

Much smaller than bacterial genome
- because some genetic info has revolved to be in nuclear genome instead

44
Q

Human genome

A
  • 3 billion base pairs (haploid set)
  • 6 billion base pairs per cell (one set from each parent)
  • 20000 protein-coding genes spread across 23 pairs of chromosomes per cell
  • 2n aka diploid
45
Q

Genome size is correlated with number of genes / organism complexity

A

False, not always

46
Q

Repeated sequences: mobile genetic element (human genome)

A

Less than 14 bp repeated over and over

Half of human genome

Most no longer move, evolutionary fossil

47
Q

Unique sequences (human genome)

A

Nonrepetitive DNA that is neither introns nor exons (things like promoter sequences, regulatory sequences), introns, exons
- other half of human genome together with repeated sequences

48
Q

Prokaryotic DNA packaging

A

DNA is condensed through folding and twisting about 1000 times and complexed with proteins to form prokaryotic nucleoid, where condensed DNA and non-histone proteins are found (not membrane-bound)

49
Q

Chromosomes in prokaryotes vs eukaryotes

A

Prokaryotes: circular

Eukaryotes: linear

50
Q

Eukaryotic DNA packaging

A

Chromosomes
- 23 pairs
- each chromosome contains a single long linear DNA molecule called chromatin
- DNA must remain accessible and tightly packed

51
Q

Chromatin

A
  • single, long, linear DNA molecule which folds into a chromosome
  • dynamic, changes throughout life of a cell
52
Q

Chromatin levels of organization

A
  1. DNA double helix
  2. Beads on a string
  3. Chromatin fiber of packed nucleosomes
  4. Fiber folded into loops
  5. Entire mitotic chromosome (10000 fold shorter than extended length)
53
Q

Nucleosome (beads in the beads on a string)

A
  1. Core particle
  2. Double stranded DNA wrapped around
  3. Linker DNA to link to other core particles

DNA wraps twice around each nucleosome
Each has 200 nucleotides

54
Q

Histones

A

Small proteins rich in arginine and lysine

Positive charge so DNA doesn’t repel itself

Four core histone proteins with N-terminal tail which can be modified and one linker histone

55
Q

Packaging of nucleosomes

A

Sequence-specific clamp proteins bind to DNA and cohesins form chromatin loops

As cell enters mitosis, condensins replace cohesins to form double loops of chromatin for more compaction

Result is metaphase chromosome

56
Q

Heterochromatin vs Euchromatin

A

Heterochromtin
- highly condensed
- regions of interphase chromosomes where gene expression is suppressed

Euchromatin
- non-condensed chromatin
- areas where genes tend to be expressed

Fluid movement between states at any given time

57
Q

DNA replication

A

Semiconservative

5’ to 3’
- nucleotides added on 3’ end

Starts at specific origins of replication in a chromosome

58
Q

DNA replication procedure

A
  1. Separate strands
  2. Synthesized new strands
  3. Proofread new strands
59
Q

6 Ingredients for DNA synthesis

A
  • original of replication
  • primers
  • dNTPs (nucleotides)
  • ATP
  • DNA polymerase
  • accessory proteins
60
Q

How many origins of replication in bacterial and linear chromosomes

A

Bacterial: 1
Linear: 2

61
Q

Initiator proteins

A

Recognize and bind to origin of replication

62
Q

Helicase

A

Unwinds DNA double helix
- predominant type moves 5’ to 3’ along the lagging strand template
- requires ATP

63
Q

SSBPs

A

Keep helix separated and untangled (prevents reannealing)

64
Q

RNA primers

A

Made by primase

Makes RNA primer for DNA polymerase to start synthesizing DNA

65
Q

DNA polymerase

A

Adds nucleotides onto 3’ OH

66
Q

Sliding clamps

A

Hold polymerase onto DNA so it doesn’t fall off

Allows it to proceed more quickly

Needs ATP and clamp loader to be loaded onto template strand

67
Q

DNA ligase

A
  • Seals nicks in 5’ to 3’ fragments (between Okazaki fragments)
  • Removes RNA primer sequences and replaces the gaps with DNA
68
Q

Origin of replication contains

A

AT rich sequence (only 2 H bonds so it is easier to break)

69
Q

Binding of initiator proteins requires energy to…

A

Regulate replication

70
Q

In order to begin, DNA polymerase requires…

A
  1. Bound primer
  2. Template
  3. 3’ OH to add nucleotide onto (provided by primer)
71
Q

Primase main purpose and direction

A

Synthesize RNA primer in 3’ to 5’ direction along template strand

72
Q

How does DNA polymerase add new nucleotides

A

Clips off 2 phosphate groups for energy and to allow formation of phosphodiester bonds

73
Q

Nucleases

A

General term for enzyme that digests nucleic acid

74
Q

Replisome

A

Example of a molecular machine used in bacterial DNA replication

75
Q

Topoisomerases

A

Create transient single-strand break to alleviate tension and strain in DNA as it is unwound by helicase

76
Q

Which strand has a gap that remains unreplicated at the end? Why is this a potential problem?

A

Lagging strand (no 3’ OH gap)

Loss of genetic information over time

77
Q

Telomerase

A

Enzyme that adds nucleotides to telomeres without needing a primer

78
Q

Telomere replication generates

A

G-rich ends

79
Q

Telomeres are abundant in…

A

Stem and germ cells, not in somatic cells

80
Q

Telomeres and cancer

A

Cancer cells produce high levels of telomerase, with high replication levels contributing to instability of cancer cells

81
Q

DNA or RNA polymerase more accurate?

A

DNA polymerase

82
Q

Two mechanisms of DNA proofreading and repair

A
  1. 3’ to 5’ exonuclease occurs during synthesis
  2. Strand-directed mismatch repair occurs just after synthesis
83
Q

3’ to 5’ exonuclease activity

A

Removes misincorporated nucleotide; DNA polymerase moves backwards one spot and clips off one nucleotide (only happens on end of strand)

84
Q

DNA polymerase two domains

A
  1. Polymerizing
  2. Editing
85
Q

Strand-directed mismatch repair

A
  • MutS recognizes and locks on to mismatch
  • MutS recruits MutL and scans DNA
  • strand with error is removed
  • gap filled in by polymerase sigma
86
Q

Pyrimidine dimer

A

2 covalent bonds with a strand of DNA (TT/CC/CT)
- DNA polymerase can’t move through, either skips area or makes a mistake

87
Q

2 mechanisms of DNA repair

A
  1. Base excision repair
    - one nucleotide is fixed
  2. Nucleotide excision repair
    - bigger section cut out
    - needs helicase
88
Q

2 types of repair of double-stranded breaks

A

Nonhomologous end joining
- break repaired with some loss of nucleotides

Homologous recombination
- break repaired with no loss of nucleotides

89
Q

Molecular definition of a gene, two types of genes

A

The entire nucleic acid sequence necessary for the synthesis of a protein or RNA

RNA encodes a protein or RNA that functions as RNA

90
Q

RNA transcript

A
  • only one template strand, ssDNA
  • RNA polymerase doesn’t need a primer
91
Q

Transcription steps in prokaryotes

A
  1. Sigma factor binds to RNAP and finds promoter (several failed attempts)
  2. Unwinding
  3. Elongation
  4. Termination
92
Q

Promoter sequence is __________ from the +1 site

A

Upstream (more negative number)

93
Q

RNA Terminator Sequences

A

GC rich area which forms hairpin followed by AT rich area
- disrupt H-bonding of new mRNA to help dissociate RNA transcript from polymerase

94
Q

Transcription factors (eukaryotes only)

A

Proteins that help position eukaryotic RNAPs at the promoter (similar to sigma submit of bacterial RNAPs)

95
Q

How is RNA polymerase ll activated?

A

Phosphorylation inducing conformational change to shed general transcription factors

96
Q

Eukaryotic mRNA processing

A
  • addition of 5’ cap to protect RNA from exonucleases
  • removal of introns by rRNA splicing introns into lariats, requires snRNPs
  • processing and polyadenylation of 3’ tail
97
Q

Alternative RNA splicing

A

Increases the number of gene products

98
Q

Where is mRNA translated

A

Cytoplasm, site of protein synthesis

99
Q

Redundancy

A

Multiple codons for most amino acids (third nucleotide most flexible)

100
Q

Types of mutation

A

Silent
- same amino acid due to redundancy

Missense
- different amino acid

Nonsense
- premature stop codon

101
Q

Two steps in ensuring fidelity, error correction

A
  1. Aminoacyl tRNA synthetases
  2. Base pairing

Hydrolysis editing

102
Q

tRNA structure

A

Aminoacyl site
Peptidyl site
Exit site

Clover leaf shape

103
Q

Shine-Dalgarno sequences and polycistronic mRNA occurs in…

A

Prokaryotes only

104
Q

Translation release factor

A

Protein, not RNA

BIO130 (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions