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Molecular Biology: Understanding the Role of DNA, RNA, and Proteins in Cellular Function, Study notes of Computer Science

This lecture covers the fundamental concepts of molecular biology, focusing on the roles of deoxyribonucleic acid (dna), ribonucleic acid (rna), and proteins in cellular function. Topics include the structure and composition of dna and rna, the processes of replication, transcription, and translation, and the importance of codons and amino acids in protein synthesis.

Typology: Study notes

Pre 2010

Uploaded on 07/30/2009

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CMSC 838T – Lecture 2

CMSC 838T – Lecture 2

X Premise of bioinformatics

0 Gene sequences determine biological function 0 Genomic DNA → RNA → Proteins

X This lecture

0 Try to understand biological reasons for premise 0 Review of molecular biology 0 Describe useful experimental techniques

Molecular Biology

X Living organisms (on Earth) require ability to

  1. Separate inside from outside (lipids)
  2. Build 3D machinery to perform biological functions (proteins)
  3. Store information on how to build machinery (DNA)

X Diagram of a cell

0 Lipid membranes (provide barrier) 0 Protein structures (do work) 0 DNA nucleus (store info)

CMSC 838T – Lecture 2

Molecular Biology: DNA, RNA, Protein

X DNA DNA → DNA (Replication)

X RNA DNA → RNA (Transcription / Gene Expression)

X Protein RNA → Protein (Translation)

Deoxyribonucleic Acid (DNA)

X Composition

0 Sequence of nucleotides 0 Nucleotide = deoxyribose sugar + phosphate group + base

Base

CMSC 838T – Lecture 2

Views of DNA Structure

A

T C

G

G

C

P

P P

P

P

P

CMSC 838T – Lecture 2

DNA - Denaturation, Hybridization

Denaturation

Separating DNA into single strands

Hybridization / Annealing

Forming double-stranded DNA

Heat Cool

DNA

X For bioinformatics

0 DNA can be represented as a sequence of letters (A,C,G,T) 0 5’ A T A C G T A 3’ 3’ T A T G C A T 5’ (matching strand, redundant)

X Terms

0 Base pair (bp) – one pair of DNA bases (1 letter) 0 Gene – section of DNA that produces a functional product 0 Chromosome – physical linear sequence of DNA 0 Genome – entire collection of DNA for an organism O E Coli 1 chromosome 5 x 10 6 bases (5 Mbps) O Drosophila 8 chromosomes 2 x 10 8 bases (200 Mbps) O Human 48 chromosomes 3 x 10 9 bases (3 Gbps)

CMSC 838T – Lecture 2

DNA Replication

Ribonucleic acid (RNA)

X Composition

0 Sequence of nucleotides 0 Nucleotide = ribose sugar + phosphate group + base 0 Single stranded (but may form hairpin loops) 0 Uracil (U) instead of Thymine (T)

X DNA → RNA (Transcription / Gene Expression)

0 RNA polymerase (enzyme)

  1. Finds gene initiation marker (codon) on DNA strand
  2. Reads DNA strand containing marker
  3. Builds (complementary) strand of messenger RNA (mRNA)
  4. Stops when gene end marker (codon) found 0 Resulting RNA sequence = transcript

CMSC 838T – Lecture 2

Transcription Example (Step 1)

Transcription Example (Step 2)

CMSC 838T – Lecture 2

Amino Acid

X Proteins are composed of amino acids

X Composition

0 Core + side chain (residue) 0 20 different residues → 20 unique amino acids A C D E F G H I K L M N P Q R S T V W Y

side chain (residue)

Amino acid

Amino Acid Properties

X Amino acids

have different

physical &

chemical

properties

X Different amino

acids are similar

in different ways

CMSC 838T – Lecture 2

RNA → Amino Acid

X Codon = 3-base RNA sequence

  1. Code for amino acid
  2. Signal beginning / end of protein - open reading frame (ORF)

List of Amino Acids (part 1)

Amino acid Symbol Codon

A Alanine Ala GC*

C Cysteine Cys UGU, UGC

D Aspartic Acid Asp GAU, GAC

E Glutamic Acid Glu GAA, GAG

F Phenylalanine Phe UUU, UUC

G Glycine Gly GG*

H Histidine His CAU, CAC

I Isoleucine Ile AUU, AUC, AUA

K Lysine Lys AAA, AAG

L Leucine Leu UUA, UUG, CU*

CMSC 838T – Lecture 2

Protein

X Composition

0 ~40-500+ amino acids connected in polypeptide chain 0 Sequence determines 3D shape (and function) of protein

amino end

carboxyl end

side chains (residue)

H 2 O

Amino acid

Amino acid

forms peptide bond

Protein Structure

R 2

N

H

C O

R 1

+ (^) H 3 N

C

O

N

H

R 3

C O

O - Φ ψ

X Primary structure (1D sequence)

0 Order of amino acid (residues) 0 Always begin at amino end (by convention) 0 Example (Hexokinase): A A S X D X S L V E V H X X V F I V …

amino end

residues

peptide bonds

carboxyl end

CMSC 838T – Lecture 2

Protein Structure

X Secondary structure (primary substructure)

X Alpha helix X Beta strand / pleated sheet X Coil

Alpha helix Beta strand

Protein Structure

X Tertiary structure (overall 3D structure)

X Quaternary structure (only for multi-chain structures)

Hexokinase Hemoglobin

CMSC 838T – Lecture 2

Protein Synthesis Example (Step 1)

Protein Synthesis Example (Step 2)

CMSC 838T – Lecture 2

Protein Synthesis Example (Step 3)

Protein Synthesis (In Parallel)

CMSC 838T – Lecture 2

Non-Coding Regions

Splice Sites

Complication - Mutations

X Mutations

0 Modifications during DNA replication

X Possible changes

0 Point mutation / single nucleotide polymorphism ( SNP ) 5’ A T A C G T A … 5’ A T G C G T A … 0 Duplicate sequence 0 Inverted sequence 0 Insert / delete sequence ( indel )

CMSC 838T – Lecture 2

Mutations

Mutations