human cell Flashcards
1
Q
what are the subunit and macromolecule of carbohydrates
A
Monosaccharide, poly saccharides
2
Q
what are the subunit and macromolecule of protein
A
amino acids, poly peptides
3
Q
what are the subunit and macromolecule of nucleotides
A
nucleotide, nucleic acid
4
Q
what are the subunit and macromolecule of fats
A
fatty acids, triglyceride cholesterol
5
Q
what are the two kind of secondary structures
A
beta sheets and alpha helix
6
Q
what are structure motifs
A
combinations of secondary structures
7
Q
what classification if protein domains
A
tertiary
8
Q
function of RNA polymerase
A
transcribes DNA into mRNA
9
Q
what assist in folding
A
ATP dependent chaperones
10
Q
what is the disease caused by protein misfolding
A
amyloid fibril aggregates
11
Q
what can undo protein degradation/aggregation
A
proteasomes(regulates degradation)
12
Q
what identifies proteins for proteasomes
A
identified by addition of ubiquitin to lysine residue
13
Q
what bond is carbohydrates
A
glycosidic covalent bond
14
Q
what bond is fats
A
esterification/ ester bond/ covalent bond
15
Q
what bond is nucleic acids
A
Phosphodiester bond
16
Q
what bond is proteins
A
Peptide bonds
17
Q
what are prokaryotic cells
A
Prokaryotes are uni cellars, lacking a nucleus and organelles, they are either bacteria or archaea. They tend to be small ad simple, with all their stuff clustered around the cytoplasm, they reproduce by binary fission. Features include tail-like structure called flagella, pili rode, which are used for attachment and transfer of DNA, a cell membrane, a rigid cell wall made of carbohydrates and proteins called peptidoglycans, ribosomes(small organelles that synthesize proteins), and a central nucleoid containing the genetic material
18
Q
what are Eukaryotes
A
Eukaryotes have both nuclei ad organelles enclosed by a plasma membrane, they are large and complex and reproduce via mitosis
19
Q
Cell membrane
A
Made up of phospholipids, cholesterol, and proteins. It is structured it a thin double layer of lipids. Each is one phospholipid thick. Phospholipids contain a hydrophilic head and hydrophobic tail. Adhesion proteins allow cells to bind
20
Q
Nucleus and ribosomes
A
The nucleus is surrounded by the nuclear envelope, which has two nuclear membranes the outer forms a continuous structure with the endoplasmic reticulum. All things to the nucleus pass through pores that bridge the two membranes. The nuclear envelope in supported by the nuclear lamina, a network of intermediate filament, which is in the form of a thick mesh under the inner nuclear membrane
21
Q
Chromatin, (DNA)
A
forms the chromosomes, all within the nucleus.
22
Q
ribosomes
A
The nucleolus is within the nucleus where ribosomes are made—they aid in the synthesis of protein, using m RNA as a template. these can be found in the cytoplasm or bound to the endoplasmic reticulum
23
Q
Cytoplasm
A
It includes the organelles and the cytosol, it is the main site of protein synthesis and degradation
24
Q
Cytoskeleton
A
This gives a cell it shapes. Is made of actin filaments, intermediate filaments, and microtubules. Acton filaments and microtubules provide tracks for ATP power proteins that allow cellular movement (muscle contraction) and the transport of organelles through the cytoplasm. Microtubules also play a role in cell division
25
Centrosomes and centrioles
Centrosomes is an organelle found near the nuclei. They contain two cylindrical structures called centrioles, which are made of a protein called tubulin, which also makes microtubules. Centrosomes regulate cell division through the formation of microtubule organising centres for which microtubule spindle apparatus grow (this is the structure that separates chromosomes during mitosis)
26
mitochondria
THE POWER HOSUE OF THE CELL generates ATP, it is enclosed by two lipid bilayer protein membranes infolding of the inner membranes forms tubules called cristae where enzymes that synthesize ATP are attached. The inner cavity is filled with a matric that contains soluble enzymes involved in metabolic processes
27
Endoplasmic reticulum
The ER is a network of tubular structures, which assists in processing and moving molecules to their destination, both inside and outside the cell. It is made of lipid bilayer, similar to the plasma membrane. It connects to the nuclear membrane. Attached enzymes allow the ER to synthesize and process proteins. The ER is divided in rough and smooth, rough has ribosomes attached to the outer surface, giving the granular appearance, and is a site for protein synthesis. Smooth has no ribosomes and so eh site of phospholipid synthesis. Proteins and folded in the rough ER are stored in the cisternal space (lumen). When enough protein, they are pinched off in a vesicles
28
Golgi apparatus
Found in the middle of the cell, it is made of a stack of flatted membrane-bound sacs. The Golgi receives lipids and proteins from the ER and modifies them. proteins arrive in vesicles that break off the ER. Enzymes from within the Golgi attach sugar side chains (glycosylation). Processed proteins are put back into vesicles then sent to the lysosomes or plasma membrane
29
Endosome synthesis
The endosomes synthesize at the Golgi , it delivers materials from the Golgi to lysosomes or plasma membranes. These are transported by vesicles or endosomes which are lipid membrane structures that form during protein secretion (exocytosis) or uptake of extracellular content (endocytosis)
30
vesicles
Vesicles can fuse lipid membranes of organelles, enabling transfer from on organelle to another
31
Vacuoles
Vacuoles are a type of membrane-bound structure found in plants and fungi. They are larger than vesicles and are used for storage
32
Peroxisomes
Peroxisomes contain enzymes needed for the oxidation of fatty acids and catalase that breakdown hydrogen peroxide, which is toxic by produce of oxidation. In animal cells, fatty acids are oxidized to the mitochondria. Peroxisomes participate in the synthesis of lipids (cholesterol and bile acids)
33
Lysosomes
Lysosomes are membrane bound organelles that contain enzymes which degrade old organelles and microorganism. The lumen of the lysosome has a ph. of 4.5-5. Extracellular material is delivered to the lysosomes in endocytosis and degraded. In contrast intracellular material is digested through autophagy with the lysosomes
34
binary fission
The chromosome is duplicated and then divided within the cells before it then splits in two
35
why do cells divide (mammalian)
mitosis (growth, tissue/ organ maintenance or tissue repair)
Meiosis (sex reproduction)
36
what happens during G1
duplication of organelles
cell growth
protein mas doubles
produces proteins for S phase
37
what happens during G1-S check point
checks for available materials
can only be passed with mitogens
checks for DNA damages
Checks for correct DNA replication
38
CDKs
require cyclins to phosphorylate proteins
regulate progression through cell cycle
39
S phase
DNA replication
All 46 chromosomes duplicated
40
G2 phase
general cellular growth
allows the (DNA) time to replicate (idk the word was rubbed out ) before DNA segregation
41
G2-M checkpoint
gives the cell more time to ensure all DNA replication
CDK is pivotal to move from the G2 phase
42
what are the different parts of M phase
Prophase
metaphase
anaphase
telophase
cytokinesis
43
prophase
mitotic spindle forms
nuclear envelope breaks down
centrosomes start moving towards poles
(one more thing i just can't read it)
44
Metaphase
microtubules attach to kinetochores
chromones align on spindle equator
45
Anaphase
sister chromides separates and move towards each pole
cleavage of cohesion
poles start to drift apart
46
telophase/ cytokinesis
nuclear envelope reforms
cell separation begins
chromatids de-condense
47
function of spindle checkpoint
- Check if kinetochore are orientated properly
also called metaphase-anaphase checkpoint
48
function of kinase
uses ATP to phosphorylate proteins (an enzyme that causes addition of phosphate group
49
what are the four CDK complexes ,what is their CDK, cyclin and function
G1-CDk, (Cyclin D, CDK4 and CDK6,entry to cell cycle)
G1/S-CDK (Cyclin E, CDK 2, entry to cycle/S phase)
S-CDK(cyclin A, CDK ,mitosis)
M-CDK (cyclin B, CDK1, mitosis)
50
what do mitogens tigger
- Mitogens (EDF) trigger cyclin D gene transcription and protein production
- Interacts with cyclin D binds toCDK4/6 to active downstream target
51
what destroys cyclins
- The proteosomes, ubiquitination, and ubiquitin ligases
- Two important ubiquitin ligases complex (SCF and APC/C) contribute to cyclin destruction, to maintain the forward process and promote cell cycle exit
52
basic DNA stuff
- Three components
- A five-carbon sugar molecule
- 2 Prime deoxyribose carbon is devoid of oxygen
- DNA backbone contains Phosphate groups
- Phosphate group joined by phosphodiester bonds connects 3 prime carbons of one nucleotide with the 5 prime carbons of another nucleotide
- Contains bases joined to the sugar molecule via glycosidic bone
- Purine base are adenine and guanine
- One carbon ring bases ae pyrimidine, which includes thymine and cytosine
- DNA has direction the 5 prime end attached to phosphate group
- The other end is the 3 prime end and the next nucleotide is joined there
53
Double helix shit
- Backbone is sugar and phosphate
- Twi strands are antiparallel one runs 3 to 5 the other 5-3
- Bases are on inside stacked perpendicular to fibre axis
- Pyrimidine base airs to purine base
- Adenine pairs to thymine
- Cytosine pairs to guanine
54
Chromosomes
- Longest chromosome is number 1
- Chromosomes are divided into two arms
- The short arm is p
- The long arm is q
- They are divided by a centromere
55
what is the "bubble" at the beginning of DNA division
Origin of replication(due to the break down of hydrogen bonds)
56
how many origins of replication in each eukaryotic cell
30,000-50,000
57
Origin of replication is recognized by
recognition complex (ORC) a complex of 6 proteins
- ORC binds to the origin and recruits Cdc6 (cell division cycle 6)
- This lead to the loading of the MCM2-7-Cdt1 complex (mini chromosome maintenance proteins, chromatin licensing, and DNA replication factor1)
58
what unwinds the forks and where?
- The active MCM helicase moves alone the leadings strand of the DNA at each replication fork unwinding the DNA
59
function of RPA(replication protein A)
- Replication protein A binds and coats the single-stranded DNA and prevents DNA damage activation and prevents strands from rejoining
60
what prevents supercoiling
- Topoisomerases prevent the over winding of DNA double helix ahead of replication forks
- Topoisomerases make a transient single nick in the DNA backbone to relax overwinding and then reseals the nick
61
what happens during priming
- Once DNA strands are separated the enzyme DNA primase (an RNA polymerase)synthesizes short RNA primers ( approximately 12 nucleotides) that are complementary to unwound DNA strands
- DNA primase can maker RNA from scratch (without requiring free 3Oh of an existing RNA/DNA chain)
- Once primase creates the RNA primer, DNA polymerase alpha starts to elongate the primer (from prime oh end ) with approximately 20 nucleotides
- DNA polymerase alpha primase complex contains two catalytic activities, the RNA primase activity in the smallest p48 subunit (Pri1) and the polymerase activity in the largest p180 subunit (Pol1) and two regular subunits
62
what direction is DNA synthesis
- Synthesis of primers occurs in the 5>3 direction
63
which DNA polymerases have proof reading
epsilon and delta
64
what is lagging strand synthesis parts called
Okazaki fragments
65
what removes RNA primer
Nuclease
66
which DNA polymerase is for leading and lagging
alpha- leading and lagging
epsilon- leading
delta -lagging
67
what is the sliding clamp
- Most polymerase would fall off the DNA after synthesising a short string of nucleotides
- Polymerase are clamped to DNA with homotrimer proteins PCANA (proliferating Cell nuclear antigens )
- PCNA for a large ring around DNA, binds to DNA polymerase and slides along DNA as polymerase moves on the lagging strand, each time polymerase reaches the 5 prime end of proceeding Okazaki fragment, the polymerase is released
- Three identical subunits
68
temination
- replication forks meet
DNA ligase join the DNA
(- FEN1 endonuclease- dominant pathway to remove RNA primers- by cleaving single-stranded FLAP
- RNAse H endonuclease – also contributes by removing RNA portion of RNA:DNA hybrids
- DNA ligase joins the adjacent fragments by catalyzing the formation of phosphodiester bonds between 3 prime oh and 5 prime phosphate groups of adjacent nucleotides )
69
what are DNA polymerase
- In eukaryotic cells these is alpha, delta and epsilon
- Enzymes that synthesise DNA form deoxyribonucleotides can only extend pre-existing primers, add free nucleotide to the 3prime end of the growing DNA strand, use energy from hydrolysis of free dNTP into dNMP+ pyrophosphate (dNTP =deoxynucleotides triphosphate : dNMP=deoxynucleotide monophosphate)
- High processive enzymes carry out continuous DNA synthesis without frequent dissociation
- Generally multiunit enzymes can have 3 prime exonuclease activity (exercise incorrect terminal nucleotides- useful for proof reading)
70
lagging (DNA pol)
- Polymerase delta synthesises the DNA lagging stand(when bound to PCNA has similar replication rate to pol E
- New primer is needed every 00 to 200 nucleotide to create Okazaki fragment
- Replication protein A is dislodged by Pol D
- When pol D reaches the 5 prime end of proceeding Okazaki fragment, it initiates ement synthesis ( no more than one at a time)
- Flap structure ate subsequently cleaved by FEN1 endonuclease and DNA gap sealed by DAN ligase
- Most of DNA synthesised by lower fidelity DNA polymerase alpha also replaced by polymerase delta
- Lower fidelity than polymerase E is counterbalanced by more active mismatch repairing this strand
71
leading strand ( DNA pol)
- Polymerase epsilon synthesizes the DAN leading strand
- Pol E has intrinsic 3 prime exonuclease activity to proofread its own replication errors (clips off wrong bases before resuming replication)
- 1 error per 10^5 nucleotides made during replication and with exonuclease activity only 1 error per 10^7 nucleotides
- Rate of replication approximately 50 nt/sec
- Pol E catalyse at 250 nt/sec if there was sufficient dNTP levels
72
what is transcription
making RNA from DNA
73
what is Translation
- Translation is the process where RNA directly synthesis of protein
74
basic stricture of RNA
- Sugar phosphate back bone
- Sugar connected the 3’ C of one sugar with the 5’ of another sugar connected by a phosphodiester bond
- In DNA sugar is called deoxyribose in RNA it is called ribose due to the inclusion of another OH group on the 2’ carbon
- Whilst both DNA and RNA have purine guanine and adenine, RNA has pyrimidine bases uracil and cytosine
- In RNA a-u
- The bases are bound to sugar by glycosidic bone
- 5’carbon bound to phosphate group
- 3’ carbon bound to OH group- next nucleotide is added here (transcription) 5’-3’
- RNa is single-stranded and can fold into 3D shapes
75
what is the process of of transcription and translation also called
central dogma
76
where is transcription site
+1
77
where will RNA polymerase bind
- Enzymes (RNA polymerases) will bind to 5’ site called promoter
- The promoter is -300 to -50
78
which parts are kept and which are removed
kept- exons, untranslated regions
removed- introns
79
what is the function of untranslated regions
RNA stability
80
Start codon?
AUG
81
end codon
UAA, UAG or UGA
82
what is the non coding strand
- DNA is double-stranded and only one strand serves as a template for transcription at any given time -this template stands is called noncoding strands
83
what begins transcription
RNA polymerase
84
what happens during transcription ( I'm not sure this is a correct question)
- Attach DNA and make RNA
- Add free ribonucleotides to 3’ end of growing RNA strand
- RNA synthesis occurs in 5’ to3’direction
- Use energy from hydrolysis of free rNTP into rMP +PPi
- Start RNA chain without primer
- Have modest proofreading – they make mistakes every 10^4 nucleotide
- High processivity- RNA polymerase starts and finishes transcription
- Three eukaryotic RNA polymerases catalyze the synthesis of different RNA
85
promoter bs
- TATA box located 30bp upstream of TSS
- Initiators motif overlaps with TSS- binds TAF1 more abundant than TATA
- DPE increases TFIID binding in TATA-less promoters
- BRE sequence enhances binding of TFIID to promoters
- Promoters can have single-defined or multiple, closely spaced transcription start sites
- Many promoters have regions of elevated GC content
- These CpG islands have distinct chromatin modifications and are often involved in constitutive gene expression
86
Denaturation of a protein refers to:
Denaturation (most typically via heat or pH change) results in destabilisation of the non-covalent bonds in protein 3D structures (can also affect the covalent disulfide bonds), causing them to unfold.
87
Any enzyme that adds a phosphate group to a protein is called:
kinase
88
The Km (Michaelis-Menten constant) of an enzyme represents the substrate concentration at which enzyme activity reaches half the maximal velocity (Vmax). If I had enzyme A with a Km of 6 and enzyme B with a Km of 60, for the same substrate, which of the following statements would be TRUE?
Overall, the lower the Km, the higher the affinity and faster the reaction rate reaches maximal activity (saturation of active site).
Enzyme A has a greater affinity for the substrate and the substrate concentration needed to reach Vmax will be lower than B
89
Which one of the following statements is TRUE?
a.
When soluble proteins fold in water the greater number of hydrophobic side chains will be found at the surface of the 3D structure.
b.
Amphipathic helices have both faces projecting hydrophobic residues.
c.
Proline (inherent turn) and glycine (smallest amino acid) are neutral amino acids that have good helix-forming propensities.
d.
Hydrophobic helices are most likely to be found embedded in lipid bilayer membranes.
d.
Hydrophobic helices are most likely to be found embedded in lipid bilayer membranes.
Hydrophobic helices often have 80-90% hydrophobic amino acid residues. They are not soluble in water so tend to be embedded in non-polar lipid membranes.
Amphipathic helices have polar groups on one face and non-polar (hydrophobic) groups on the other face.
Soluble proteins will have a mix of hydrophillic and hydrophobic groups - the hydrophillic groups are polar and will associate with water at the surface, the hydrophobic groups will tend to be near the centre of the protein (away from water). This allows for the lowest energy conformation of the protein; the water is not trying to repel the hydrophobic groups.
Proline having a natural kink and glycine being small means they are often used in beta turns, not in helices or beta sheets.
90
Which one of the following represents a quaternary structure?
a.
Beta sheets
b.
alpha and beta tubulin
c.
SH3 domain
d.
VLFVAKTSSAIAF
b.
alpha and beta tubulin
91
When considering various protein structural motifs, which one of the following statements is INCORRECT?
a.
Beta helices orient amino acid R groups externally.
b.
Alpha helices and beta sheets rely on hydrogen bonding for structural stability.
c.
Parallel beta sheets have only short sequence stretches connecting the end of one beta sheet to the next.
d.
The amino acid proline is more commonly found in beta turns than beta sheets.
Parallel beta sheets have LONG sequence stretches connecting the end of one beta sheet to the next because the C-terminal end of the first sheet has to attach to the N-terminal end of the next sheet. When they are parallel i.e. the C-terminal ends align and the N-terminal ends align, essentially the intervening sequence of amino acids has to stretch the length of the beta sheet. If they are anti-parallel, just a short loop is required to connect the C and N-terminal ends.
c.
Parallel beta sheets have only short sequence stretches connecting the end of one beta sheet to the next.
92
When comparing protein domains and structural motifs, which of the following statements is CORRECT?
Question 7Select one:
a.
Motifs and domains are both tertiary structures.
b.
Each protein will contain only one type of motif and one type of domain.
c.
Beta sheets are not observed in motifs or domains.
d.
Structural motifs can consist of multiple alpha helices.
d.
Structural motifs can consist of multiple alpha helices.
Motifs are considered higher order secondary structures. Several examples included coiled-coil motifs and zinc-finger motifs. Alpha helices and beta sheets are secondary structure but are not considered motifs. Motifs can be made up of multiple helices and sheets. Domains are considered tertiary structures and can include various motifs. Proteins can have multiple domains and motifs.
93
Which one of the following is able to prevent hydrophobic aggregation of polypeptide chains as they are produced by the translational machinery?
Question 8Select one:
a.
A ubiquitin ligase
b.
The 26S proteosome
c.
A chaperone
d.
A chaperonin
As polypeptides are created chaperones can bind to hydrophobic regions of the chain protecting the protein from self-aggregation of these regions. Chaperonins are macromolecular structures that can help proteins to fold collectively in their interior. The proteosome is used to degrade proteins, proteins designated for degradation are tagged with ubiquitin by ubiquitin ligases and then transported to the proteosome for peptide cleavage.
94
A protein's 3D structure is primarily determined by:
the amino acid sequence
95
