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Foundations 110 > Lecture 1 > Flashcards

Lecture 1 Flashcards

1
Q

plasma membrane

A

communication with environment

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2
Q

cytoplasm

A

protein synthesis, metabolic pathways

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3
Q

nucleus

A

DNA synthesis, transcription, splicing

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4
Q

mitochondria

A

energy production, metabolic pathways

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5
Q

lysosomes

A

protein and carbohydrate degradation

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6
Q

peroxisomes

A

disposal of peroxide, fatty acid metabolism and other metabolic pathway

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7
Q

secretory and endocytic organelles

A

protein transport out of and into cells

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8
Q

Multicellular organisms are made of – that are organized to carry out specialized functions

A

different types of cells

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9
Q

odontoblast –

A

dentine production

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10
Q

ameloblast

A

enamel production

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11
Q

The specialized cells all derive from a common – cell (the fertilized egg) through the process of development, which is a complex series of events involving both cell division and differentiation into particular cell types

A

progenitor

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12
Q

stem cells they have the ability to divide to produce more stem cells called –

A

self-renewal

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13
Q

stem cells can – into specialized cell types

A

differentiate

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14
Q

– cells can give rise to all embryonic tissues including germ cells (e.g. embryonic stem cells)

A

Pluripotent stem

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15
Q

– can give rise to all cell types in a tissue (e.g. hematopoietic stem cells

A

Multipotent stem cells

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16
Q

Manipulation of – (embryonic or adult stem cells) offers great potential for therapeutic organ replacement, e.g. teeth.

A

stem cell differentiation

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17
Q

– are the most versatile components of cell

A

Proteins

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18
Q

act as –to synthesize or degrade cellular components

A

enzymes

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19
Q

proteins act as – to provide shape, organization and stability to cells

A

structural components

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20
Q

T/F: proteins act as carriers and motors to move molecules within and between cells, regulators of different cellular processes,

A

true

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21
Q

Proteins are encoded in DNA as genes that contain information for the – of each protein

A

structure and expression

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22
Q

in addition to mRNA, DNA also encodes – used in protein synthesis and a variety of other non-coding RNAs

A

ribosomal and transfer RNAs

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23
Q

decoding of the DNA into proteins involves – RNA

A

messenger

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24
Q

Synthesis of RNA from DNA occurs by the process of –

A

transcription.

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25
Q

Regulation of transcription determines what genes are expressed –, at what time, and at what amounts

A

in what cells

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26
Q

transcription dictates cell –

A

type and function.

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27
Q

In eukaryotic cells, newly transcribed RNA must be – to the cytoplasm in order to be decoded into protein by ribosomes and tRNA.

A

processed and exported

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28
Q

central dogma of molecular biology

A

DNA –> RNA –> protein

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29
Q

Proteins are linear polymers of –

A

20 different amino acids

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30
Q

An individual cell contains thousands of different proteins, each with a – of amino acids

A

unique sequence

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31
Q

each of these proteins has a distinct three-dimensional structure that specifies its function, and the 3D structure is determined by the –.

A

linear sequence of amino acids

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32
Q

amino acid is an – bonded to an amino group, a carboxyl group, a hydrogen, and one of twenty different side chains (R)

A

alpha carbon

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33
Q

determines the properties of the amino acid.

A

side chain

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34
Q

Hydrophilic amino acids (acidic, basic and uncharged) are generally found at –

A

the surface of water-soluble proteins or protein domains.

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35
Q

Hydrophobic amino acids (linear, branched and aromatic) are generally found in the – or in lipid-associated regions of membrane proteins.

A

interior of water-soluble proteins

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36
Q

The sulfhydryl group (SH) of a cysteine can form a – with the SH group of another cysteine.

A

covalent disulfide bond

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37
Q

T/F: Disulfide bonds can occur within a protein or between proteins

A

true

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38
Q

its R group is a hydrogen making it the smallest amino acid

A

glycine

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39
Q

Glycine causes little – and allows structural flexibility

A

steric hindrance

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40
Q

in proline, the amino group is –, forming a ring structure that makes proline rigid

A

covalently joined to the side chain

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41
Q

Amino acids are covalently joined together in a protein by a – involving the carboxyl group of one amino acid and the amino group of the next.

A

peptide bond

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42
Q

By convention peptides are written

A

N –> C

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43
Q

peptide bonds have – character and thus is rigid and planar.

A

partial double bond

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44
Q

The carbonyl oxygen and the amide hydrogen on either side of a peptide bond are usually in a –

A

trans configuration (opposite sides of peptide bond)

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45
Q

Free rotation around – (except proline) allows high degree of conformational flexibility.

A

C-Calpha and Calpha-N bonds

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46
Q

Proteins fold into the thermodynamically most stable conformation called –

A

native conformation

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47
Q

Native conformation is determined by interactions between –

A

amino acid residues.

48
Q

linear sequence of amino acids.

A

primary

49
Q

localized organization of aa usually close to each other in sequence

A

secondary

50
Q

secondary structure mostly stabilized by –

A

H bonds

51
Q

alpha helix is a regular coil structure stabilized by hydrogen bonds between the peptide bond carbonyl group and the peptide bond –

A

amide four residues towards the carboxy-terminus

52
Q

R groups of alpha helix

A

project outwards

53
Q

– interrupts alpha helix

A

proline

54
Q

beta strands are – of amino acids.

A

linear, extended stretches

55
Q

Lateral (side-by-side) association of beta strands form –

A

beta sheets

56
Q

Beta sheets strands are joined by H bonds between

A

carbonyl groups on one strand and amide groups on other

57
Q

strands of beta sheets are –

A

parallel or antiparallel

58
Q

R groups of beta strands

A

project up or down

59
Q

beta turns: – stabilized by hydrogen bonds between carbonyl group of first residue and amide group of last residue

A

3-4 aa U-shaped turn

60
Q

– are combinations of 2° structures

A

Structural motifs

61
Q

protein’s overall 3D conformation

A

tertiary

62
Q

– can involve interactions between amino acids as far away from each other in primary sequence

A

tertiary structures

63
Q

tertiary interactions

A

Stabilized by non-covalent interactions – H-bonding, electrostatic (binding of oppositely-charged side chains), hydrophobic interactions (in interior of globular protein), van der Waals forces due to close packing of atoms, sometimes S-S

64
Q

oxygen storing molecule in muscle

A

myoglobin

65
Q

myoglobin’s amino acids are complexed with an iron-containing heme group that is necessary for –

A

oxygen binding

66
Q

3D structure of protein made up of multiple subunits

A

quarternary

67
Q

T/F: Quaternary held together by same forces as 3D structure

A

true

68
Q

Each subunit of hemoglobin has a structure very similar to myoglobin, even though the – are quite distinct

A

primary sequences

69
Q

The quaternary structure of hemoglobin allows – which makes hemoglobin more suited for oxygen delivery to tissues than myoblobin

A

cooperative binding and dissociation of oxygen

70
Q

This type of effect on substrate (oxygen) binding by an interaction at another site (binding to another hemoglobin chain) is known as –

A

allosteric effect

71
Q

Many proteins larger than 150 amino acids are organized into –.

A

structurally distinct domains

72
Q

These domains are usually 100-150 amino acids in length and are folded into –

A

distinct 3D structures

73
Q

Domains in proteins are linked by – of the polypeptide chain.

A

intervening segments

74
Q

For example, transcriptional activators are often organized into –

A

DNA-binding and transcriptional activation domains.

75
Q

Many – are associated with the lipid bilayer of cellular membranes

A

proteins

76
Q

embedded (pass through) the lipid bilayer

A

integral membrane proteins

77
Q

The region of the protein that spans the membrane (membrane-spanning domain) is usually an –

A

alpha helix composed of hydrophobic amino acids

78
Q

The protein regions on either side of the membrane use the same organizing principals as –

A

soluble proteins

79
Q

Integral membrane proteins are often – on the lumenal (non-cytoplasmic) domains

A

glycosylated

80
Q

Sugar chains are covalently linked to the NH2 of –(“N-linked”)

A

asparagine

81
Q

Sugar chains are covalently linked to the OH groups of –(“O-linked”).

A

serine and/or threonine

82
Q

Some integral membrane proteins do not have hydrophobic transmembrane domains but instead have covalently attached lipids that – and act as anchors.

A

insert into the bilayer

83
Q

–are associated with the surface of membranes but do not extend into the hydrophobic core of the bilayer.

A

Peripheral membrane proteins

84
Q

Association of peripheral membrane proteins usually involves interaction with a transmembrane protein and/or with the –

A

hydrophilic head groups of the membrane lipids.

85
Q

Genes are the basic unit of –

A

inheritance (Mendel, 1860)

86
Q

Genes are arranged into – that are distributed to daughter cells during mitosis and segregated into gametes during meiosis

A

chromosomes

87
Q

Heritable variations between individuals in a species are due to changes in the genes, called – in the DNA sequence of the gene

A

mutations

88
Q

If the mutation occurs in the – then it can be passed on to offspring

A

germ-line

89
Q

If the mutation occurs in cells other than the germ-line then it is not passed on to offspring but it is passed on to progeny of the mutant cell in the individual as the cell divides.

A

somatic mutation

90
Q

Somatic mutations that affect – can lead to cancer

A

cell growth control

91
Q

Many common congenital malformations (such as cleft lip/palate) and common adult diseases such as diabetes, heart disease and cancer are due to the combined effects of mutations in multiple genes (polygenic), often combined with environmental factors.

A

multifactorial

92
Q

different forms of a gene.

A

alleles

93
Q

The normal allele of a gene is often referred to as the

A

wildtype allele

94
Q

One copy of each chromosome (1N).

A

haploid

95
Q

Humans are formed by the union of a – and 22 other chromosomes (autosomes) with a haploid egg carrying an X chromosome and 22 autosomes

A

haploid sperm carrying 1 sex chromosome (X or Y)

96
Q

If an individual has the same allele on both chromosomes then the individual is

A

homozygous

97
Q

Human males have only one copy of alleles on the Y chromosome and this is referred to as

A

hemizygous

98
Q

different alleles on the two chromosomes.

A

heterozygous

99
Q

the entire set of an organism’s genes

A

genotype

100
Q

But in practice genotype is often used to refer to –

A

a single gene.

101
Q

the function and physical appearance of an organism

A

phenotype

102
Q

In practice phenotype is often used to refer to the – of a single gene

A

physical and functional consequences

103
Q

both alleles have to be mutant in order to see a mutant phenotype.

A

recessive mutation

104
Q

Recessive mutations normally cause inactivation or elimination of a gene/protein.

A

loss of function

105
Q

mutant phenotype is present in heterozygous individual.

A

dominant mutation

106
Q

haplo-insufficiency: If – does not produce enough protein to prevent disease then an individual with one normal allele and one inactivated allele would develop disease and the mutation would be designated as dominant

A

one normal copy of a gene

107
Q

dominant negative: If the mutant allele produces a form of the protein that interferes with the function of the normal protein, often by –, then this could cause disease in a heterozygote.

A

binding to the normal protein

108
Q

If the mutant allele produces a protein with new, or increased levels, of function , then this could cause disease in a heterozygote.

A

dominant-positive or gain-of function

109
Q

mitochondrial DNA encodes genes for some proteins involved in oxidative phosphorylation and –

A

protein synthesis in the mitochondrion

110
Q

Mutations in mitochondrial DNA can cause – called mitochondrial disorders

A

inherited disease

111
Q

Prions are infectious agents, consisting only of protein, that have the ability to –

A

reproduce within cells

112
Q

prions represent an amazing exception to the dogma that infectious agents (like viruses, bacteria, etc) require – for reproduction

A

nucleic acids

113
Q

Prions are abnormally folded forms of – and convert the endogenous form into the abnormal form

A

endogenous protein that can form aggregates

114
Q

The abnormal form of prions is in a mostly – while the normal form is mostly a helical.

A

b -sheet conformation

115
Q

The normal and abnormal prions forms have exactly the same –, but different –

A

same amino acid sequence and different secondary and tertiary structures.

Foundations 110 (10 decks)

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