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Bio 151 > protein structure, transcription, and translation > Flashcards

protein structure, transcription, and translation Flashcards

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1
Q

protein structure

A

made up of amino acids, linked by peptide bonds
different levels of protein structure

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2
Q

what is the general structure of amino acids?

A

central carbon atom, amino group, carboxyl group, variable R group (side chain that determines the properties of the amino acid)

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3
Q

proteins function

A
  • catalyzing biochemical reactions
  • providing structural support
  • facilitating movement within cells
  • movement, such as muscle contraction and cellular mobility
  • antibodies in the immune system
  • signaling molecules. facilitating communication between cells
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4
Q

what are the levels of protein structure

A

primary, secondary, tertiary, quaternary

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5
Q

what is primary structure

A

the sequence of amino acids in a polypeptide chain, determined by genetic information encoded in DNA

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6
Q

what is secondary structure

A

local folding of the polypeptide chain into structures such as a-helices and b-pleated sheets, stabilized by h-bonds

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7
Q

what is tertiary structure

A

the overall 3d shape of a protein, resulting from interaction among r-groups, including hydrophobic interactions, ionic bonds, and disulfide bridges

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8
Q

what is quaternary structure

A

the assembly of multiple polypeptide chains into a single functional protein, with interactions between the chains

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9
Q

what is denaturation of proteins

A

the process where proteins lose their native structure due to external stressors (heat or pH changes) which can make them nonfunctional

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10
Q

structure of nucleic acids

A

they’re polymers made up of nucleotide monomers,

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11
Q

what do nucleotide monomers consist of

A

phophate group, pentose sugar, and nitrogenous base

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12
Q

what kind of sugar does DNA contain

A

deoxyribose

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13
Q

what kind of sugar does rna contain

A

ribose

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14
Q

what are the nitrogenous bases

A

a, t, c, g, u

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15
Q

what are the purine nitrogenous bases

A

adenine and guanine

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16
Q

what are the pyrimidine nitrogenous bases

A

cytosine, thymine, and uracil

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17
Q

what links nucleotides?

A

phosphodiester bonds, which from the backbone of the nucleic acid strand

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18
Q

functions of nucleic acids

A
  • storage and expression of genetic information
  • dna is the genetic blueprint, rna plays a part in translating that information into proteins
  • rna can leave the nucleus, dna stays in the nucleus
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19
Q

what is transcription?

A
  • the first step in gene expression, where dna sequence is transcribed into an RNA molecule
  • the process consists of 3 main stages: initiation, elongation, and termination
  • rna polymerase 2 is the enzyme responsible for synthesizing rna and dna template
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20
Q

steps of transcription and their descriptions

A

initiation - rna polymerase 2 binds to the promoter region of the gene, aided by activator proteins and transcription factors
elongation - rna polymerase 2 reads the template strand of DNA and synthesizes a complementary RNA strand in the 5’ to 3’ directions
termination - the transcription process ends when RNA polymerase 2 reaches a terminator sequence, releasing the newly formed RNA transcript

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21
Q

what is the importance of post-transcriptional mRNA processing?

A

-eukaryotic mRNA undergoes post-transcriptional modifications, including the addition of a 5’ cap and a poly-A-tail, which protect the mRNA from degradation
- pre-mRNA splicing removes introns (non-coding regions) and joins exons (coding regions) to produce a mature mRNA transcript ready for translation

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22
Q

overview of translation and ribosome structure - tRNA and Amino acids

A
  • tRNA molecules are responsible for bringing specific amino acids to the ribosome based on their anticodon sequences, which are complimentary to the mRNA codons
  • each tRNA molecule has a unique anticodon that pairs with a corresponding codon on the mRNA strand, ensuring the correct amino acid is added to the growing polypeptide chain
  • the process of translation occurs in three main sites of the ribosome: A, P, and E
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23
Q

what are the sites where translation occurs on the ribsome? What are they called and what do they do

A

A, Aminoacyl - where the tRNA carrying the next amino acid enter
P, peptidyl - holds the tRNA with the growing polypeptide chain
E, Exit - where the empty tRNA exits the ribosome after its amino acid has been added

24
Q

overview of translation and ribosome structure - ribosome functionality

A
  • the ribosome is a complex molecular machine made of ribosomal RNA (rRNA) and proteins, crucial for translating mRNA into proteins
  • the ribosomes structure allows it to move along the mRNA strand, reading codons and facilitating the binding of tRNA molecules
  • peptide bonds are formed in the p sie, where amino acids from the tRNA in the A site is transferred to the growing polypeptide chain
  • the ribosome continues the process until it encounters a stop codon on the mRNA, signaling the end of translation
  • the release factor then binds to the ribosome, prompting the release of the newly synthesized polypeptide chain and the disassembly of the ribosome complex.
  • this process is essential for protein synthesis, which is vital for cellular function and structure
25
Q

summary of translation process

A
  • begins in the initiation phase, where the small ribosomal subunit binds to the mRNA and the first tRNA attaches to the start codon (AUG)
  • during elongation, tRNA molecules continue to bring amino acids to the ribosome, and peptide bonds are formed between them, extending the polypeptide chain
  • the termination phase occurs when a stop codon is reached, leading to the release of the polypeptide and the disassembly of the ribosome
  • the entire process is highly regulated and involves various factors that ensure accuracy and efficiency in protein synthesis
  • the final polypeptide undergoes folding and modifications to become a functional protein
  • understanding translation is crucial for grasping how genetic information is expressed in living organisms
26
Q

structure of dna

A

DNA (deoxyribonucleic acid) is a macromolecule composed of nucleotides, which are the building blocks of nucleic acids.
- each nucleotide consists of three components: a pentose sugar, phsophate group, and a nitrogenous base
- the structure of dna is a double helix, with two strands running in opposite directions (antiparallel) and held together by h-bonds between complementary base pairs
-

27
Q

what is chargaff’s rule

A

that in a double-stranded DNA molecule, the amount of a=t, and the amount of g=c. maintaining a 1:1 ratio

28
Q

what is the direction of dna synthesis

A

5’ to 3’

29
Q

what is dna replication

A

process by which DNA makes a copy of itself before cell division, ensuring that each daughter cell receives an identical set of genetic information

30
Q

DNA replicaion and transcription overview

A
  • the enzyme DNA polymerase plays a big role in synthesizing new dna strands by adding nucleotides complementary to the template strand
  • transcription is the first step in gene expression, where a specific segment of DNA is copied into mRNA by RNA polymerase
31
Q

what are the three steps in dna transcription

A

initiation, elongation and termination (like translation)

32
Q

what happens in the elongation phase of transcription

A

rna polymerase synthesizes the mRNA strand by reading the template DNA strand and incorporating complementary RNA nucelotides (U instead of T)

33
Q

what happens in post-transcriptional modifications of mRNA?

A

addition of a 5’ cap and a poly-A tail, and splicing out introns

34
Q

overview of the endomembrane system

A
  • the endomembrane system is a network of membranes within eukaryotic cells that work together to synthesize, modify, and transport proteins and other macromolecules
  • key components include: the nucleus, er, golgi apparatus, and vesicles
    the nucleus: has the DNA and is the site of transcription, where mRNA is synthesized from the DNA template
    the rough er: has ribosomes, where translation occurs, and polypeptides are synthesized and folded into functional proteins
    the smooth er: involved in lipid synthesis and detoxiication processes, lacking ribosomes
    vesicles: transport proteins and lipids between organelles and to the cell membrane for secretion
35
Q

golgi apparatus functions

A
  • functions as s post office, tagging and sorting proteins and lipids for their final destination
  • proteins synthesized in the RER are packaged into vesicles and sent to the golgi for further modification, such as glycosylation
  • the golgi works for the proper funcitoning of proteins, ensuring they reach their correct cellular or extracellular locations
  • after processing, molecules can be directed to lysosomes, the plasma membrane, or secreted outside the cell
  • the golgi’s structure consists of flattened membrane-bound sacs called cisternae, which facilitate the sorting process
36
Q

what happens during splicing?

A

introns, non-coding regions, are spliced out of the pre-mRNA, leaving only exons, which code for proteins

37
Q

what facilitates splicing process?

A

spliceosome, which recognizes splice sites and excises introns accurately

38
Q

DNA replication process

A
  • it involves helicase, dna polymerase, ligase
  • the leading strand is synthesized continuously, while the lagging strand is synthesized in short segments call Okazaki fragments due to it’s 3’ to 5’ orientation
  • primase synthesizes RNA primers necessary for DNA polymerase to initiate replication
  • the replication fork is the area where the DNA double helix is unwound, allowing for the synthesis of new strands
  • topoisomerase alleviates strain on the DNA molecule during unwinding, preventing supercoiling
  • exonuclease removed rna primers after replication, ensuring the final dna strand is composed entirely of DNA nucelotides
39
Q

where does dna replication begin

A

origin of replication, where helicase unwinds the dna strands, creating a replication fork

40
Q

helicase

A

unzips the dna by breaking h-bonds between bases, allowing access for replication

41
Q

dna polymerase 3

A

synthesizes the new dna strand in a 5’ to 3’ direction, continuously on the leading strand and in fragments on the lagging strand

42
Q

ligase

A

joins the okazaki fragments on the lagging strand to create a continuous dna strand

43
Q

primase

A

synthesizes RNA primers necessary for DNA polymerase to initiate synthesis on both strands (lagging and leading)

44
Q

How dna repairs itself

A
  • mismatch repair involves DNA polymerase 1 and 3 proofreading newly synthesized DNA to correct errors
  • nucleotide excision repair removes damaged DNA segments, such as those caused by UV light, and replaces them using the intact strand as a template
45
Q

what is telomeres

A
46
Q

what is telomerase

A

an enzyme that extends telomeres, allowing cells to divide without losing important DNA sequences, which is crucial for germ cells

47
Q

what does the cell cycle consists of (what phases)

A

G1 - cell growth (dna transcription and translation)
S - dna synthesis (dna replication happens here)
G2 - preparation for mitosis
M - mitosis and cytokinesis

48
Q

what is the purpose of checkpoints in the cell cycle

A

to ensure the integrity of the cell cycle

49
Q

what does checkpoint G1 do?

A

check for DNA integrity

50
Q

what does checkpoint G2 do?

A

checks for proper chromosome duplication

51
Q

what does checkpoint metaphase do

A

checks for spindle attachment

52
Q

what happens if there is failure at checkpoints?

A

apoptosis

53
Q

what does p53 do?

A

it regulates the cell cycle and initiates apoptosis when DNA damage is detected

54
Q

what are the types of mutations and give definitions

A

substitution - involve replacing one nucleotide with another, potentially altering the resulting protein
Deletion - remove nucleotides from the sequence, which can lead to frameshifts if not in multiples of three

55
Q

consequences of mutations

A

missense - result in a different amino acid being incorporated into the protein, which can affect protein function
nonsense - create premature stop codons, leading to truncated proteins that are often nonfunctional

56
Q

frameshift mutations

A

occur during insertions or deletions that are not in multiples of three, shifting the reading frame and altering the downstream amino acid sequence
- these mutations can lead to consequences on protein structure and function, often resulting in loss of activity

Bio 151 (15 decks)

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