BIOL130 > module 5 > Flashcards

module 5 Flashcards

protein structure, function and synthesis (70 cards)

Study These Flashcards
1
Q

what are proteins

A

mediate cellular activities/reactions involved in cellular function

linear polymers of a combo of 20 amino acids

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

what are the 3 models of protein structure

A

ball and stikc model

ribbon model

space filling model

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

what are amino acids

A

building blocks of protein, key as proteins function is related to structure

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

what are the 4 parts of an amino acid

A

identical for all amino acids:
1. carboxyl
2. amino grp
3, hydrogen
* at physiological pH amino and carboxyl grps are charged

different for all amino acids:
4. r group

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

what are all of the components of an amino acid attached to

A

alpha carbon

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

what is the role of the r group in amino acids

A

make each amino acid unique

responsible for chemical and physical properties of each amino acid monomer

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

how are amino acids classifed

A

hydrophilic or hydrophobic
basic or acidic
polar or nonpolar

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

what are properties of hydrophobic amino acids

A

tend to be buried in interior of folded proteins

hydrophobic r groups aggregate together away from water

weak van der waals forces help with stability - causes hydrophobic r grps to be attracted to each other

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

what are properties of hydrophilic amino acids

A

polar molecules contain electronegative elements (O, N)

unequal charge -> allows R grps to interact with each other or with H2O via H bonding

charged grps (basic/acidic amino acids) can form ionic bonds with one another and other charged molecules

typically found on “outer” surface of proteins

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

what chemical groups do polar R group side chains contain

A

carboxylic acid

amine hydroxyl

sulfur

amide group

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

what chemical group do basic R groups contain

A

amine group

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

what chemical group do acidic R groups contain

A

carboxylic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what are the 3 special amino acids and why are they special

A

special for how they affect protein structure

glycine -> R grp is hydrogen

proline -> R grp links back to the amino grp

cysteine -> R grp contains a SH grp

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

what is the structural significance of glycine

A

R grp is hydrogen

alpha carbon is bonded to 2 H atoms -> not asymmetric

small and non polar, allows for free rotation around C-N bond

increases flexibility of polypeptide backbone

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

what is the structural significance of proline

A

R grp links back to amino grp

linkage restricts rotation of C-N bond, limits amnt of protein folding around proline

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

what is the structural significance of cysteine

A

R grp contains a SH grp

allows 2 cysteines to form a S-S disulfide bond - cross bridge

cross bridges can connect diff parts of the same protein/diff proteins together

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

what bond are adjacent amino acids joined by

A

peptide bond

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

what reaction occurs when amino acids link

A

dehydration rxn where carboxyl grp of one amino acid reacts with the amino grp of another amino acid

releases a molecule of H2O

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

what does the free amino grp at the amino end of the peptide form

A

N-terminus

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

what does the carboxyl grp at the carboxyl end form

A

C-terminus

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

what is a polypeptide

A

synonymously protein

polymer of amino acids connected by peptide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

what are the 4 levels of protein structure organization

A

primary (1°)
secondary (2°)
tertiary (3°)
quaternary (2°)

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

what is protein conformation

A

3d structure of a protein

described by 2°, 3°, 4°

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

what is the primary structure of a protein and how is it denoted

A

specific linear sequence of amino acids that make up the polypeptide chain (amino to carboxyl end)

sequence of 3 letter/1 letter abbreviations
ex. Val-Gly-Ala or V-G-A

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
what structure determines 2°, 3° and 4° of a protein
primary structure
26
where are R grps positioned in polypeptides
alternate position on either side of the chain of amino acids affects protein folding and interaction of R grps
26
what is the secondary strutcure of a protein
conformation of portions fo polypeptide chain
27
what are the 2 types of secondary stru ture
alpha helices and beta sheets
27
how does secondary structure occur
hydrogen bonding bewteen neighbouring amino acids of the polypeptide backbone -> between functional grps R grps are uninvolved fixed configuration of polypeptide backbone
28
what is the alpha helix
type of secondary strutcure stable struture righthandded helices-> let molecules not nearby in main structure interact with one another
28
what are right handed helices adn why do they form
alpha helices is an example let molecules not nearby in main structure to interact with one another form due to H bonds to the 4th amino acid neightbour above and below in the spiral -> the carboxyl grp of one amino acid and the amide grp of 4th amino acid
29
what is a beta sheet
type of secojdary strutcure segment of polypeptide lying side by side -> assumes a pleated/folding conformation can be antiparallel or parallel stabilized by H bonds between carbonyl grps in one chain and amide grps in the other chain within the same polypeptide
30
what is tertiary structure
describes confromation of entire protein -> single polypeptide chain folded into 3° structure how 2° confromations are oriented results in functional form -> unless part of protien with multiple subunits
31
what is tertiary structure determined by
spatial distribution of hydrophillic and hydrophobic R grps chemical bonds and interactions that form between R grps - H-bonds, hydrophob bonds and ionic bonds - disulfide bonds -> covalent bond between 2 cysteine residues
32
what may the overall shape (3° strutcure) of a functional protein result in?
areas of the protein that form active sites for enzymes exterior R grps that may impact how a protein interacts with other molecules/proteins
33
what is the quaternary structure of a protein
spatial arrangement of subunits many proteins are made up of a multiple polypeptide chains (subunits) arise due to the same bonds found in 3° strutcure
34
what is a homodimer
protein containing 2 identical subunits
35
what is a heterodimer
protein containing 2 non idendtical subunits
36
what do each of the 4 structures within a protein do, on a high level?
primary -> sequence of amino acids secondary -> results from interactions of nearby amino acids (alpha helices/beta sheets) tertiary -> 3D shape of a polypeptide quaternary -> results from interactions of polypeptide subunits
37
what are the components required for translation?
mRNA ribosome tRNAs aminoacyl tRNA synthases initiation factors, elongation factors, release factors
38
what are ribosomes?
protein factories - where trnaslation takes place complex structure of RNA and protein consist of a small subunit and l;arge subunit
39
are eukaryotic or prokaryotic ribosomes larger?
eukaryotic
40
how do mRNA and the small/large ribosomes interact
mRNA is bound by large and small ribosomal subunits, then moved thru centre of ribosome ribosome moves down mRNA from 5' to 3' and reads individual codons to incorporate appropriate amino acids
41
what is a codon
nucleotide combination that specifies the placement of an amino acid, codes fro amino acid placement grp of 3 nucleotides
42
what si the reading frame
where ribosome begins reading sequence of nucleotides
43
where does translation begin
with a start codon - AUG codes for methionine
44
what are the 3 fucntional sites within the large ribosome
A site - where aminoacyl tRNA is accepted in P site - where peptide bond formation happens E site - where tRNA exits ribosome
45
what are tRNA
small molecules with 70-90 nucleotides each bonds with itself to form base pairs cloverleaf structure
46
what are the 3 important sites on each tRNA
3' hydroxyl site on 5'-CCA-3' end of tRNA -> where specific amino acid attaches 3 bases in anticodon loop make up anticodon
47
hwo are aminio acids attached to tRNA
specific amjino acids area connected to specific tRNA moelcules by enzymes called amino acyl tRNA synthetases
48
what is an uncharged tRNA
tRNA without an amino acid attached
49
what is a charged tRNA
tRNA with an amino acid attached
50
how do tRNAs pair with mRNA during translation
anticodon of tRNA base pairs with codon on mRNA anticodon of tRNAs base pair in antiparallel fashion
51
how many amino acids does the genetic code have
20, specified by 64 codons many amino acids are specified by more than 1 codon, making genetic code redundant/degenerate
52
how are mRNA read using the standrad genetic code
bases are read 5'-3'
53
what are the 3 stages of translation on a high level
1. initiation - AUG codon, Met is first amino acid 2. elongation - each successive amino acid is added to growing polypeptide chain 3. termination - adding amino acids stops and chain is released from ribosome
54
what end in the codon pairs with what end in the anticodon
first base in codon (5' end) pairs with last base (3' end) in anticodon
55
what happens in eukaryotic translation initiation
initaiton complex forms at 5; cap of mRNA small ribosome and initiation factors then scan mRNA for AUG once start codon is reached, large ribosome then recruited and translation starts initation factors are released
56
what happens in translation elongation
after ribosome is assembled, new tRNA enters A site, allowing peptide bond to form amino acid on tRNA in P site transfers to tRNA in A site reaction is catalysed by rRNA molecule in large ribosome ribosome then shifts 1 codon right moves uncharged tRNA to E site peptide bearing tRNA move to P site frees A site for next charged tRNA in line
57
what happens in translation termination
process continues until one of 3 codons are reached: UAA, UAG or UGA -> stop codons protein release factor binds to A site of ribosome at stop codon cuases bond that is connected to polypeptide of tRNA to break creates carboxyl terminus of polypeptide -> compeltes chain
58
what occurs in prokaryotic trnaslation initiation
mRNA moleucles have no 5' cap in prokaryotes initiation complex is formed at 1+ internal sequences present in mRNA -> Shine-Dalgarno sequence elongation and termination are similar to eukaryotic processes
59
high level, what is the difference in trnalsation initiation between prokaryotes and eukaryotes
eukaryotes: ribosome binds 5' cap, with translation beginning at AUG codon prokaryote: ribosome binds to any Shine-Dalgarno sequence, with translation beginning at first downstream AUG start codon so one mRNA can code for several polypeptides
60
what are levels of regulation in the cell
DNA accessibility transcription factors rna processing post-translational modifications
61
what is dna accessibility
special peoteins are req to displace other DNA binding proteins and make it accessible to transcriptional machinery
62
what is transcription
transcrip factors gain access to protein coding gene and transcribe an RNA strand with complementary sequence
63
what is RNA processing
rna transcript is mod in nucleus by various types of processing and then transported to cytoplasm for trnaslation into protein
64
what is post translational modification
many proteins are produced in an inavtyive form and must be activated by cleavage or other types of posttranslational modification
65
what happens to a protein after translation?
depends on how it will be sorted - specific signal sequences no signal - stay in cytosol amino terminal signal - to chloroplast/mitochondria internal signal - to nucleus
66
what proteins are transported to the ER
specific amino terminal signal sequence for transport to ER bound by signal recognition particle (SRP) ribosome with associated mRNA and newly formed polypeptide are transported to ER
67
where can proteins prod by ribosomes on the rough ER be found?
embedded in ER membrane -> inserted as it was synthesized within lumen of endomembrane system secreted out of cell
BIOL130
flashcards
Decks in class (11)
# Cards
Brainscape helps you reach your goals faster, through stronger study habits.
© 2026 Bold Learning Solutions. Terms and Conditions